spec: add {install_status} format attribute

`{install_status}` is handled in a funny way in `Spec.tree()`, and it can't be used in
other useful places like `Spec.format()`.

- [x] Make `{install_status}` a format attribute like most other things we want to print
      about specs.

- [x] Refactor whitespace handling in `Spec.format()` to only strip whitespace that wasn't
      in the original format string (i.e. that was added by our own attributes)

.github/pull_request_template.md

@@ -0,0 +1,6 @@
+<!--  
+Remember that `spackbot` can help with your PR in multiple ways:
+- `@spackbot help` shows all the commands that are currently available
+- `@spackbot fix style` tries to push a commit to fix style issues in this PR
+- `@spackbot re-run pipeline` runs the pipelines again, if you have write access to the repository 
+-->

.github/workflows/audit.yaml

@@ -43,7 +43,7 @@ jobs:
           . share/spack/setup-env.sh
           $(which spack) audit packages
           $(which spack) audit externals
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # @v2.1.0
       if: ${{ inputs.with_coverage == 'true' }}
       with:
         flags: unittests,audits

.github/workflows/build-containers.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
 
-      - uses: docker/metadata-action@dbef88086f6cef02e264edb7dbf63250c17cef6c
+      - uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
         id: docker_meta
         with:
           images: |
@@ -118,7 +118,5 @@ jobs:
           context: dockerfiles/${{ matrix.dockerfile[0] }}
           platforms: ${{ matrix.dockerfile[1] }}
           push: ${{ github.event_name != 'pull_request' }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
           tags: ${{ steps.docker_meta.outputs.tags }}
           labels: ${{ steps.docker_meta.outputs.labels }}

.github/workflows/ci.yaml

@@ -40,7 +40,7 @@ jobs:
         with:
           fetch-depth: 0
             # For pull requests it's not necessary to checkout the code
-      - uses: dorny/paths-filter@4512585405083f25c027a35db413c2b3b9006d50
+      - uses: dorny/paths-filter@ebc4d7e9ebcb0b1eb21480bb8f43113e996ac77a
         id: filter
         with:
           # See https://github.com/dorny/paths-filter/issues/56 for the syntax used below

.github/workflows/style/requirements.txt

@@ -1,5 +1,5 @@
-black==23.12.1
-clingo==5.6.2
+black==24.2.0
+clingo==5.7.1
 flake8==7.0.0
 isort==5.13.2
 mypy==1.8.0

.github/workflows/unit_tests.yaml

@@ -91,7 +91,7 @@ jobs:
           UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044
       with:
         flags: unittests,linux,${{ matrix.concretizer }}
   # Test shell integration
@@ -122,7 +122,7 @@ jobs:
           COVERAGE: true
       run: |
           share/spack/qa/run-shell-tests
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044
       with:
         flags: shelltests,linux
 
@@ -181,7 +181,7 @@ jobs:
           SPACK_TEST_SOLVER: clingo
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # @v2.1.0
       with:
         flags: unittests,linux,clingo
   # Run unit tests on MacOS
@@ -216,6 +216,6 @@ jobs:
         $(which spack) solve zlib
         common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
         $(which spack) unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044
       with:
         flags: unittests,macos

.github/workflows/windows_python.yml

@@ -33,7 +33,7 @@ jobs:
         ./share/spack/qa/validate_last_exit.ps1
         coverage combine -a
         coverage xml
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044
       with:
         flags: unittests,windows
   unit-tests-cmd:
@@ -57,7 +57,7 @@ jobs:
         ./share/spack/qa/validate_last_exit.ps1
         coverage combine -a
         coverage xml
-    - uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
+    - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044
       with:
         flags: unittests,windows
   build-abseil:

lib/spack/docs/basic_usage.rst

@@ -1130,6 +1130,10 @@ A version specifier can also be a list of ranges and specific versions,
 separated by commas.  For example, ``@1.0:1.5,=1.7.1`` matches any version
 in the range ``1.0:1.5`` and the specific version ``1.7.1``.
 
+^^^^^^^^^^^^
+Git versions
+^^^^^^^^^^^^
+
 For packages with a ``git`` attribute, ``git`` references
 may be specified instead of a numerical version i.e. branches, tags
 and commits. Spack will stage and build based off the ``git``

lib/spack/docs/conf.py

@@ -199,6 +199,7 @@ def setup(sphinx):
     ("py:class", "contextlib.contextmanager"),
     ("py:class", "module"),
     ("py:class", "_io.BufferedReader"),
+    ("py:class", "_io.BytesIO"),
     ("py:class", "unittest.case.TestCase"),
     ("py:class", "_frozen_importlib_external.SourceFileLoader"),
     ("py:class", "clingo.Control"),

lib/spack/docs/developer_guide.rst

@@ -357,91 +357,23 @@ If there is a hook that you would like and is missing, you can propose to add a
 ``pre_install(spec)``
 """""""""""""""""""""
 
-A ``pre_install`` hook is run within an install subprocess, directly before
-the install starts. It expects a single argument of a spec, and is run in
-a multiprocessing subprocess. Note that if you see ``pre_install`` functions associated with packages these are not hooks
-as we have defined them here, but rather callback functions associated with
-a package install.
+A ``pre_install`` hook is run within the install subprocess, directly before the install starts.
+It expects a single argument of a spec.
 
 
-""""""""""""""""""""""
-``post_install(spec)``
-""""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""
+``post_install(spec, explicit=None)``
+"""""""""""""""""""""""""""""""""""""
 
-A ``post_install`` hook is run within an install subprocess, directly after
-the install finishes, but before the build stage is removed. If you
-write one of these hooks, you should expect it to accept a spec as the only
-argument. This is run in a multiprocessing subprocess. This ``post_install`` is
-also seen in packages, but in this context not related to the hooks described
-here.
+A ``post_install`` hook is run within the install subprocess, directly after the install finishes,
+but before the build stage is removed and the spec is registered in the database. It expects two
+arguments: spec and an optional boolean indicating whether this spec is being installed explicitly.
 
+""""""""""""""""""""""""""""""""""""""""""""""""""""
+``pre_uninstall(spec)`` and ``post_uninstall(spec)``
+""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-""""""""""""""""""""""""""
-``on_install_start(spec)``
-""""""""""""""""""""""""""
-
-This hook is run at the beginning of ``lib/spack/spack/installer.py``,
-in the install function of a ``PackageInstaller``,
-and importantly is not part of a build process, but before it. This is when
-we have just newly grabbed the task, and are preparing to install. If you
-write a hook of this type, you should provide the spec to it.
-
-.. code-block:: python
-
-    def on_install_start(spec):
-        """On start of an install, we want to...
-        """
-        print('on_install_start')
-
-
-""""""""""""""""""""""""""""
-``on_install_success(spec)``
-""""""""""""""""""""""""""""
-
-This hook is run on a successful install, and is also run inside the build
-process, akin to ``post_install``. The main difference is that this hook
-is run outside of the context of the stage directory, meaning after the
-build stage has been removed and the user is alerted that the install was
-successful. If you need to write a hook that is run on success of a particular
-phase, you should use ``on_phase_success``.
-
-""""""""""""""""""""""""""""
-``on_install_failure(spec)``
-""""""""""""""""""""""""""""
-
-This hook is run given an install failure that happens outside of the build
-subprocess, but somewhere in ``installer.py`` when something else goes wrong.
-If you need to write a hook that is relevant to a failure within a build
-process, you would want to instead use ``on_phase_failure``.
-
-
-"""""""""""""""""""""""""""
-``on_install_cancel(spec)``
-"""""""""""""""""""""""""""
-
-The same, but triggered if a spec install is cancelled for any reason.
-
-
-"""""""""""""""""""""""""""""""""""""""""""""""
-``on_phase_success(pkg, phase_name, log_file)``
-"""""""""""""""""""""""""""""""""""""""""""""""
-
-This hook is run within the install subprocess, and specifically when a phase
-successfully finishes. Since we are interested in the package, the name of
-the phase, and any output from it, we require:
-
- - **pkg**: the package variable, which also has the attached spec at ``pkg.spec``
- - **phase_name**: the name of the phase that was successful (e.g., configure)
- - **log_file**: the path to the file with output, in case you need to inspect or otherwise interact with it.
-
-"""""""""""""""""""""""""""""""""""""""""""""
-``on_phase_error(pkg, phase_name, log_file)``
-"""""""""""""""""""""""""""""""""""""""""""""
-
-In the case of an error during a phase, we might want to trigger some event
-with a hook, and this is the purpose of this particular hook. Akin to
-``on_phase_success`` we require the same variables - the package that failed,
-the name of the phase, and the log file where we might find errors.
+These hooks are currently used for cleaning up module files after uninstall.
 
 
 ^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/environments.rst

@@ -416,6 +416,23 @@ that git clone if ``foo`` is in the environment.
 Further development on ``foo`` can be tested by reinstalling the environment,
 and eventually committed and pushed to the upstream git repo.
 
+If the package being developed supports out-of-source builds then users can use the
+``--build_directory`` flag to control the location and name of the build directory. 
+This is a shortcut to set the ``package_attributes:build_directory`` in the
+``packages`` configuration (see :ref:`assigning-package-attributes`).
+The supplied location will become the build-directory for that package in all future builds.
+
+.. warning::
+   Potential pitfalls of setting the build directory
+    Spack does not check for out-of-source build compatibility with the packages and
+    so the onerous of making sure the package supports out-of-source builds is on
+    the user.
+    For example, most ``autotool`` and ``makefile`` packages do not support out-of-source builds
+    while all ``CMake`` packages do.
+    Understanding these nuances are on the software developers and we strongly encourage
+    developers to only redirect the build directory if they understand their package's
+    build-system.
+
 ^^^^^^^
 Loading
 ^^^^^^^
@@ -472,11 +489,11 @@ a ``packages.yaml`` file) could contain:
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      packages:
        all:
          compiler: [intel]
-     ...
+     # ...
 
 This configuration sets the default compiler for all packages to
 ``intel``.
@@ -822,7 +839,7 @@ directories.
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      view:
        mpis:
          root: /path/to/view
@@ -866,7 +883,7 @@ automatically named ``default``, so that
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      view: True
 
 is equivalent to
@@ -874,7 +891,7 @@ is equivalent to
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      view:
        default:
          root: .spack-env/view
@@ -884,7 +901,7 @@ and
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      view: /path/to/view
 
 is equivalent to
@@ -892,7 +909,7 @@ is equivalent to
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      view:
        default:
          root: /path/to/view

lib/spack/docs/getting_started.rst

@@ -623,7 +623,7 @@ Fortran.
 
       compilers:
       - compiler:
-        ...
+        # ...
         paths:
           cc: /usr/bin/clang
           cxx: /usr/bin/clang++

lib/spack/docs/module_file_support.rst

@@ -10,7 +10,7 @@ Modules (modules.yaml)
 ======================
 
 The use of module systems to manage user environment in a controlled way
-is a common practice at HPC centers that is often embraced also by
+is a common practice at HPC centers that is sometimes embraced also by
 individual programmers on their development machines. To support this
 common practice Spack integrates with `Environment Modules
 <http://modules.sourceforge.net/>`_ and `Lmod
@@ -21,14 +21,38 @@ Modules are one of several ways you can use Spack packages. For other
 options that may fit your use case better, you should also look at
 :ref:`spack load <spack-load>` and :ref:`environments <environments>`.
 
-----------------------------
-Using module files via Spack
-----------------------------
+-----------
+Quick start
+-----------
 
-If you have installed a supported module system you should be able to
-run ``module avail`` to see what module
-files have been installed. Here is sample output of those programs,
-showing lots of installed packages:
+In the current version of Spack, module files are not generated by default. To get started, you
+can generate module files for all currently installed packages by running either
+
+.. code-block:: console
+
+   $ spack module tcl refresh
+
+or
+
+.. code-block:: console
+
+   $ spack module lmod refresh
+
+Spack can also generate module files for all future installations automatically through the
+following configuration:
+
+.. code-block:: console
+
+   $ spack config add modules:default:enable:[tcl]
+
+or
+
+.. code-block:: console
+
+   $ spack config add modules:default:enable:[lmod]
+
+Assuming you have a module system installed, you should now be able to use the ``module`` command
+to interact with them:
 
 .. code-block:: console
 
@@ -65,33 +89,17 @@ scheme used at your site.
 Module file customization
 -------------------------
 
-Module files are generated by post-install hooks after the successful
-installation of a package.
-
-.. note::
-
-   Spack only generates modulefiles when a package is installed. If
-   you attempt to install a package and it is already installed, Spack
-   will not regenerate modulefiles for the package. This may lead to
-   inconsistent modulefiles if the Spack module configuration has
-   changed since the package was installed, either by editing a file
-   or changing scopes or environments.
-
-   Later in this section there is a subsection on :ref:`regenerating
-   modules <cmd-spack-module-refresh>` that will allow you to bring
-   your modules to a consistent state.
-
 The table below summarizes the essential information associated with
 the different file formats that can be generated by Spack:
 
 
-  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
-  |                             | **Hook name**      |  **Default root directory**   | **Default template file**                    | **Compatible tools** |
-  +=============================+====================+===============================+==============================================+======================+
-  |  **Tcl - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | share/spack/templates/modules/modulefile.tcl | Env. Modules/Lmod    |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
-  |  **Lua - Hierarchical**     | ``lmod``           |  share/spack/lmod             | share/spack/templates/modules/modulefile.lua | Lmod                 |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
+  +-----------+--------------+------------------------------+----------------------------------------------+----------------------+
+  |           | Hierarchical |  **Default root directory**  | **Default template file**                    | **Compatible tools** |
+  +===========+==============+==============================+==============================================+======================+
+  |  ``tcl``  | No           | share/spack/modules          | share/spack/templates/modules/modulefile.tcl | Env. Modules/Lmod    |
+  +-----------+--------------+------------------------------+----------------------------------------------+----------------------+
+  |  ``lmod`` | Yes          | share/spack/lmod             | share/spack/templates/modules/modulefile.lua | Lmod                 |
+  +-----------+--------------+------------------------------+----------------------------------------------+----------------------+
 
 
 Spack ships with sensible defaults for the generation of module files, but
@@ -102,7 +110,7 @@ In general you can override or extend the default behavior by:
  2. writing specific rules in the ``modules.yaml`` configuration file
  3. writing your own templates to override or extend the defaults
 
-The former method let you express changes in the run-time environment
+The former method lets you express changes in the run-time environment
 that are needed to use the installed software properly, e.g. injecting variables
 from language interpreters into their extensions. The latter two instead permit to
 fine tune the filesystem layout, content and creation of module files to meet
@@ -110,79 +118,62 @@ site specific conventions.
 
 .. _overide-api-calls-in-package-py:
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Override API calls in ``package.py``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Setting environment variables dynamically in ``package.py``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-There are two methods that you can override in any ``package.py`` to affect the
-content of the module files generated by Spack. The first one:
+There are two methods that you can implement in any ``package.py`` to dynamically affect the
+content of the module files generated by Spack. The most important one is
+``setup_run_environment``, which can be used to set environment variables in the module file that
+depend on the spec:
 
 .. code-block:: python
 
    def setup_run_environment(self, env):
-       pass
+       if self.spec.satisfies("+foo"):
+           env.set("FOO", "bar")
 
-can alter the content of the module file associated with the same package where it is overridden.
-The second method:
+The second, less commonly used, is ``setup_dependent_run_environment(self, env, dependent_spec)``,
+which allows a dependency to set variables in the module file of its dependents. This is typically
+used in packages like ``python``, ``r``, or ``perl`` to prepend the dependent's prefix to the
+search path of the interpreter (``PYTHONPATH``, ``R_LIBS``, ``PERL5LIB`` resp.), so it can locate
+the packages at runtime.
+
+For example, a simplified version of the ``python`` package could look like this:
 
 .. code-block:: python
 
    def setup_dependent_run_environment(self, env, dependent_spec):
-       pass
+       if dependent_spec.package.extends(self.spec):
+           env.prepend_path("PYTHONPATH", dependent_spec.prefix.lib.python)
 
-can instead inject run-time environment modifications in the module files of packages
-that depend on it. In both cases you need to fill ``env`` with the desired
-list of environment modifications.
-
-.. admonition:: The ``r`` package and callback APIs
-
-  An example in which it is crucial to override both methods
-  is given by the ``r`` package. This package installs libraries and headers
-  in non-standard locations and it is possible to prepend the appropriate directory
-  to the corresponding environment variables:
-
-  ================== =================================
-   LD_LIBRARY_PATH    ``self.prefix/rlib/R/lib``
-   PKG_CONFIG_PATH    ``self.prefix/rlib/pkgconfig``
-  ================== =================================
-
-  with the following snippet:
-
-  .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
-     :pyobject: R.setup_run_environment
-
-  The ``r`` package also knows which environment variable should be modified
-  to make language extensions provided by other packages available, and modifies
-  it appropriately in the override of the second method:
-
-  .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
-     :pyobject: R.setup_dependent_run_environment
+and would make any package that ``extends("python")`` have its library directory added to the
+``PYTHONPATH`` environment variable in the module file. It's much more convenient to set this
+variable here, than to repeat it in every Python extension's ``setup_run_environment`` method.
 
 .. _modules-yaml:
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-Write a configuration file
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+The ``modules.yaml`` config file and module sets
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The configuration files that control module generation behavior
-are named ``modules.yaml``. The default configuration:
+The configuration files that control module generation behavior are named ``modules.yaml``. The
+default configuration looks like this:
 
 .. literalinclude:: _spack_root/etc/spack/defaults/modules.yaml
    :language: yaml
 
-activates the hooks to generate ``tcl`` module files and inspects
-the installation folder of each package for the presence of a set of subdirectories
-(``bin``, ``man``, ``share/man``, etc.). If any is found its full path is prepended
-to the environment variables listed below the folder name.
+You can define one or more **module sets**, each of which can be configured separately with regard
+to install location, naming scheme, inclusion and exclusion, autoloading, et cetera.
 
-Spack modules can be configured for multiple module sets. The default
-module set is named ``default``. All Spack commands which operate on
-modules default to apply the ``default`` module set, but can be
-applied to any module set in the configuration.
+The default module set is aptly named ``default``. All
+:ref:`Spack commands that operate on modules <maintaining-module-files>` apply to the ``default``
+module set, unless another module set is specified explicitly (with the ``--name`` flag).
 
-"""""""""""""""""""""""""
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
 Changing the modules root
-"""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 As shown in the table above, the default module root for ``lmod`` is
 ``$spack/share/spack/lmod`` and the default root for ``tcl`` is
@@ -198,7 +189,7 @@ set by changing the ``roots`` key of the configuration.
      my_custom_lmod_modules:
        roots:
          lmod: /path/to/install/custom/lmod/modules
-         ...
+         # ...
 
 This configuration will create two module sets. The default module set
 will install its ``tcl`` modules to ``/path/to/install/tcl/modules``
@@ -224,25 +215,32 @@ location could be confusing to users of your modules. In the next
 section, we will discuss enabling and disabling module types (module
 file generators) for each module set.
 
-""""""""""""""""""""
-Activate other hooks
-""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Automatically generating module files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Any other module file generator shipped with Spack can be activated adding it to the
-list under the ``enable`` key in the module file. Currently the only generator that
-is not active by default is ``lmod``, which produces hierarchical lua module files.
-
-Each module system can then be configured separately. In fact, you should list configuration
-options that affect a particular type of module files under a top level key corresponding
-to the generator being customized:
+Spack can be configured to automatically generate module files as part of package installation.
+This is done by adding the desired module systems to the ``enable`` list.
 
 .. code-block:: yaml
 
    modules:
      default:
        enable:
-         - tcl
-         - lmod
+       - tcl
+       - lmod
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Configuring ``tcl`` and ``lmod`` modules
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can configure the behavior of either module system separately, under a key corresponding to
+the generator being customized:
+
+.. code-block:: yaml
+
+   modules:
+     default:
        tcl:
          # contains environment modules specific customizations
        lmod:
@@ -253,16 +251,70 @@ either change the layout of the module files on the filesystem, or they will aff
 their content. For the latter point it is possible to use anonymous specs
 to fine tune the set of packages on which the modifications should be applied.
 
+.. _autoloading-dependencies:
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Autoloading and hiding dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A module file should set the variables that are needed for an application to work. But since an
+application often has many dependencies, where should all the environment variables for those be
+set? In Spack the rule is that each package sets the runtime variables that are needed by the
+package itself, and no more. This way, dependencies can be loaded standalone too, and duplication
+of environment variables is avoided.
+
+That means however that if you want to use an application, you need to load the modules for all its
+dependencies. Of course this is not something you would want users to do manually.
+
+Since Spack knows the dependency graph of every package, it can easily generate module files that
+automatically load the modules for its dependencies recursively. It is enabled by default for both
+Lmod and Environment Modules under the ``autoload: direct`` config option. The former system has
+builtin support through the ``depends_on`` function, the latter simply uses a ``module load``
+statement. Both module systems (at least in newer versions) do reference counting, so that if a
+module is loaded by two different modules, it will only be unloaded after the others are.
+
+The ``autoload`` key accepts the values ``none``, ``direct``, and ``all``. To disable it, use
+``none``, and to enable, it's best to stick to ``direct``, which only autoloads the direct link and
+run type dependencies, relying on recursive autoloading to load the rest.
+
+A common complaint about autoloading is the large number of modules that are visible to the user.
+Spack has a solution for this as well: ``hide_implicits: true``. This ensures that only those
+packages you've explicitly installed are exposed by ``module avail``, but still allows for
+autoloading of hidden dependencies. Lmod should support hiding implicits in general, while
+Environment Modules requires version 4.7 or higher.
+
+.. note::
+   If supported by your module system, we highly encourage the following configuration that enables
+   autoloading and hiding of implicits. It ensures all runtime variables are set correctly,
+   including those for dependencies, without overwhelming the user with a large number of available
+   modules. Further, it makes it easier to get readable module names without collisions, see the
+   section below on :ref:`modules-projections`.
+
+    .. code-block:: yaml
+  
+        modules:
+          default:
+            tcl:
+              hide_implicits: true
+              all:
+                autoload: direct
+            lmod:
+              hide_implicits: true
+              all:
+                autoload: direct
+
 .. _anonymous_specs:
 
-""""""""""""""""""""""""""""
-Selection by anonymous specs
-""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Setting environment variables for selected packages in config
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In the configuration file you can use *anonymous specs* (i.e. specs
-that **are not required to have a root package** and are thus used just
-to express constraints) to apply certain modifications on a selected set
-of the installed software. For instance, in the snippet below:
+In the configuration file you can filter particular specs, and make further changes to the
+environment variables that go into their module files. This is very powerful when you want to avoid
+:ref:`modifying the package itself <overide-api-calls-in-package-py>`, or when you want to set
+certain variables on multiple selected packages at once.
+
+For instance, in the snippet below:
 
 .. code-block:: yaml
 
@@ -305,12 +357,28 @@ the variable ``FOOBAR`` will be unset.
 .. note::
    Order does matter
      The modifications associated with the ``all`` keyword are always evaluated
-     first, no matter where they appear in the configuration file. All the other
-     spec constraints are instead evaluated top to bottom.
+     first, no matter where they appear in the configuration file. All the other changes to
+     environment variables for matching specs are evaluated from top to bottom.
 
-""""""""""""""""""""""""""""""""""""""""""""
+.. warning::
+
+     As general advice, it's often better to set as few unnecessary variables as possible. For
+     example, the following seemingly innocent and potentially useful configuration
+
+     .. code-block:: yaml
+
+        all:
+          environment:
+            set:
+              "{name}_ROOT": "{prefix}"
+
+     sets ``BINUTILS_ROOT`` to its prefix in modules for ``binutils``, which happens to break
+     the ``gcc`` compiler: it uses this variable as its default search path for certain object
+     files and libraries, and by merely setting it, everything fails to link.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Exclude or include specific module files
-""""""""""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You can use anonymous specs also to prevent module files from being written or
 to force them to be written. Consider the case where you want to hide from users
@@ -330,14 +398,19 @@ you will prevent the generation of module files for any package that
 is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
 or any ``llvm`` installation.
 
+It is safe to combine ``exclude`` and ``autoload``
+:ref:`mentioned above <autoloading-dependencies>`. When ``exclude`` prevents a module file to be
+generated for a dependency, the ``autoload`` feature will simply not generate a statement to load
+it.
+
 
 .. _modules-projections:
 
-"""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Customize the naming of modules
-"""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The names of environment modules generated by spack are not always easy to
+The names of environment modules generated by Spack are not always easy to
 fully comprehend due to the long hash in the name. There are three module
 configuration options to help with that. The first is a global setting to
 adjust the hash length. It can be set anywhere from 0 to 32 and has a default
@@ -353,6 +426,13 @@ shows how to set hash length in the module file names:
        tcl:
          hash_length: 7
 
+.. tip::
+
+   Using ``hide_implicits: true`` (see :ref:`autoloading-dependencies`) vastly reduces the number
+   modules exposed to the user. The hidden modules always contain the hash in their name, and are
+   not influenced by the ``hash_length`` setting. Hidden implicits thus make it easier to use a
+   short hash length or no hash at all, without risking name conflicts.
+
 To help make module names more readable, and to help alleviate name conflicts
 with a short hash, one can use the ``suffixes`` option in the modules
 configuration file. This option will add strings to modules that match a spec.
@@ -365,12 +445,12 @@ For instance, the following config options,
        tcl:
          all:
            suffixes:
-             ^python@2.7.12: 'python-2.7.12'
+             ^python@3.12: 'python-3.12'
              ^openblas: 'openblas'
 
-will add a ``python-2.7.12`` version string to any packages compiled with
-python matching the spec, ``python@2.7.12``. This is useful to know which
-version of python a set of python extensions is associated with. Likewise, the
+will add a ``python-3.12`` version string to any packages compiled with
+Python matching the spec, ``python@3.12``. This is useful to know which
+version of Python a set of Python extensions is associated with. Likewise, the
 ``openblas`` string is attached to any program that has openblas in the spec,
 most likely via the ``+blas`` variant specification.
 
@@ -468,41 +548,11 @@ that are already in the Lmod hierarchy.
    For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
    See `this discussion on the Lmod project <https://github.com/TACC/Lmod/issues/114>`_.
 
-""""""""""""""""""""""
-Select default modules
-""""""""""""""""""""""
-
-By default, when multiple modules of the same name share a directory,
-the highest version number will be the default module. This behavior
-of the ``module`` command can be overridden with a symlink named
-``default`` to the desired default module. If you wish to configure
-default modules with Spack, add a ``defaults`` key to your modules
-configuration:
-
-.. code-block:: yaml
-
-  modules:
-    my-module-set:
-      tcl:
-        defaults:
-        - gcc@10.2.1
-        - hdf5@1.2.10+mpi+hl%gcc
-
-These defaults may be arbitrarily specific. For any package that
-satisfies a default, Spack will generate the module file in the
-appropriate path, and will generate a default symlink to the module
-file as well.
-
-.. warning::
-  If Spack is configured to generate multiple default packages in the
-  same directory, the last modulefile to be generated will be the
-  default module.
-
 .. _customize-env-modifications:
 
-"""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Customize environment modifications
-"""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You can control which prefixes in a Spack package are added to
 environment variables with the ``prefix_inspections`` section; this
@@ -600,9 +650,9 @@ stack to users who are likely to inspect the modules to find full
 paths to software, when it is desirable to present the users with a
 simpler set of paths than those generated by the Spack install tree.
 
-""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Filter out environment modifications
-""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Modifications to certain environment variables in module files are there by
 default, for instance because they are generated by prefix inspections.
@@ -622,49 +672,37 @@ do so by using the ``exclude_env_vars``:
 The configuration above will generate module files that will not contain
 modifications to either ``CPATH`` or ``LIBRARY_PATH``.
 
+^^^^^^^^^^^^^^^^^^^^^^
+Select default modules
+^^^^^^^^^^^^^^^^^^^^^^
 
-.. _autoloading-dependencies:
-
-"""""""""""""""""""""
-Autoload dependencies
-"""""""""""""""""""""
-
-Often it is required for a module to have its (transient) dependencies loaded as well.
-One example where this is useful is when one package needs to use executables provided
-by its dependency; when the dependency is autoloaded, the executable will be in the
-PATH. Similarly for scripting languages such as Python, packages and their dependencies
-have to be loaded together.
-
-Autoloading is enabled by default for Lmod and Environment Modules. The former
-has builtin support for through the ``depends_on`` function. The latter uses
-``module load`` statement to load and track dependencies.
-
-Autoloading can also be enabled conditionally:
+By default, when multiple modules of the same name share a directory,
+the highest version number will be the default module. This behavior
+of the ``module`` command can be overridden with a symlink named
+``default`` to the desired default module. If you wish to configure
+default modules with Spack, add a ``defaults`` key to your modules
+configuration:
 
 .. code-block:: yaml
 
-    modules:
-      default:
-        tcl:
-          all:
-            autoload: none
-          ^python:
-            autoload: direct
+  modules:
+    my-module-set:
+      tcl:
+        defaults:
+        - gcc@10.2.1
+        - hdf5@1.2.10+mpi+hl%gcc
 
-The configuration file above will produce module files that will
-load their direct dependencies if the package installed depends on ``python``.
-The allowed values for the ``autoload`` statement are either ``none``,
-``direct`` or ``all``.
+These defaults may be arbitrarily specific. For any package that
+satisfies a default, Spack will generate the module file in the
+appropriate path, and will generate a default symlink to the module
+file as well.
 
-.. note::
-  Tcl prerequisites
-     In the ``tcl`` section of the configuration file it is possible to use
-     the ``prerequisites`` directive that accepts the same values as
-     ``autoload``. It will produce module files that have a ``prereq``
-     statement, which autoloads dependencies on Environment Modules when its
-     ``auto_handling`` configuration option is enabled. If Environment Modules
-     is installed with Spack, ``auto_handling`` is enabled by default starting
-     version 4.2. Otherwise it is enabled by default since version 5.0.
+.. warning::
+  If Spack is configured to generate multiple default packages in the
+  same directory, the last modulefile to be generated will be the
+  default module.
+
+.. _maintaining-module-files:
 
 ------------------------
 Maintaining Module Files

lib/spack/docs/packages_yaml.rst

@@ -647,6 +647,8 @@ manually placed files within the install prefix are owned by the
 assigned group. If no group is assigned, Spack will allow the OS
 default behavior to go as expected.
 
+.. _assigning-package-attributes:
+
 ----------------------------
 Assigning Package Attributes
 ----------------------------
@@ -657,10 +659,11 @@ You can assign class-level attributes in the configuration:
 
   packages:
     mpileaks:
-      # Override existing attributes
-      url: http://www.somewhereelse.com/mpileaks-1.0.tar.gz
-      # ... or add new ones
-      x: 1
+      package_attributes:
+        # Override existing attributes
+        url: http://www.somewhereelse.com/mpileaks-1.0.tar.gz
+        # ... or add new ones
+        x: 1
 
 Attributes set this way will be accessible to any method executed
 in the package.py file (e.g. the ``install()`` method). Values for these

lib/spack/docs/pipelines.rst

@@ -810,7 +810,7 @@ generated by ``spack ci generate``.  You also want your generated rebuild jobs
 .. code-block:: yaml
 
    spack:
-     ...
+     # ...
      ci:
        pipeline-gen:
        - build-job:

lib/spack/docs/repositories.rst

@@ -17,7 +17,7 @@ experimental software separately from the built-in repository. Spack
 allows you to configure local repositories using either the
 ``repos.yaml`` or the ``spack repo`` command.
 
-A package repository a directory structured like this::
+A package repository is a directory structured like this::
 
   repo/
       repo.yaml

lib/spack/docs/requirements.txt

@@ -2,12 +2,12 @@ sphinx==7.2.6
 sphinxcontrib-programoutput==0.17
 sphinx_design==0.5.0
 sphinx-rtd-theme==2.0.0
-python-levenshtein==0.23.0
+python-levenshtein==0.25.0
 docutils==0.20.1
 pygments==2.17.2
-urllib3==2.1.0
-pytest==7.4.4
+urllib3==2.2.0
+pytest==8.0.1
 isort==5.13.2
-black==23.12.1
+black==24.2.0
 flake8==7.0.0
 mypy==1.8.0

lib/spack/llnl/util/filesystem.py

@@ -171,7 +171,7 @@ def polite_path(components: Iterable[str]):
 @memoized
 def _polite_antipattern():
     # A regex of all the characters we don't want in a filename
-    return re.compile(r"[^A-Za-z0-9_.-]")
+    return re.compile(r"[^A-Za-z0-9_+.-]")
 
 
 def polite_filename(filename: str) -> str:
@@ -920,29 +920,35 @@ def get_filetype(path_name):
     return output.strip()
 
 
-@system_path_filter
-def is_nonsymlink_exe_with_shebang(path):
-    """
-    Returns whether the path is an executable script with a shebang.
-    Return False when the path is a *symlink* to an executable script.
-    """
+def has_shebang(path):
+    """Returns whether a path has a shebang line. Returns False if the file cannot be opened."""
     try:
-        st = os.lstat(path)
-        # Should not be a symlink
-        if stat.S_ISLNK(st.st_mode):
-            return False
-
-        # Should be executable
-        if not st.st_mode & (stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH):
-            return False
-
-        # Should start with a shebang
         with open(path, "rb") as f:
             return f.read(2) == b"#!"
-    except (IOError, OSError):
+    except OSError:
         return False
 
 
+@system_path_filter
+def is_nonsymlink_exe_with_shebang(path):
+    """Returns whether the path is an executable regular file with a shebang. Returns False too
+    when the path is a symlink to a script, and also when the file cannot be opened."""
+    try:
+        st = os.lstat(path)
+    except OSError:
+        return False
+
+    # Should not be a symlink
+    if stat.S_ISLNK(st.st_mode):
+        return False
+
+    # Should be executable
+    if not st.st_mode & (stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH):
+        return False
+
+    return has_shebang(path)
+
+
 @system_path_filter(arg_slice=slice(1))
 def chgrp_if_not_world_writable(path, group):
     """chgrp path to group if path is not world writable"""
@@ -1377,120 +1383,89 @@ def traverse_tree(
         yield (source_path, dest_path)
 
 
-def lexists_islink_isdir(path):
-    """Computes the tuple (lexists(path), islink(path), isdir(path)) in a minimal
-    number of stat calls on unix. Use os.path and symlink.islink methods for windows."""
-    if sys.platform == "win32":
-        if not os.path.lexists(path):
-            return False, False, False
-        return os.path.lexists(path), islink(path), os.path.isdir(path)
-    # First try to lstat, so we know if it's a link or not.
-    try:
-        lst = os.lstat(path)
-    except (IOError, OSError):
-        return False, False, False
-
-    is_link = stat.S_ISLNK(lst.st_mode)
-
-    # Check whether file is a dir.
-    if not is_link:
-        is_dir = stat.S_ISDIR(lst.st_mode)
-        return True, is_link, is_dir
-
-    # Check whether symlink points to a dir.
-    try:
-        st = os.stat(path)
-        is_dir = stat.S_ISDIR(st.st_mode)
-    except (IOError, OSError):
-        # Dangling symlink (i.e. it lexists but not exists)
-        is_dir = False
-
-    return True, is_link, is_dir
-
-
 class BaseDirectoryVisitor:
     """Base class and interface for :py:func:`visit_directory_tree`."""
 
-    def visit_file(self, root, rel_path, depth):
+    def visit_file(self, root: str, rel_path: str, depth: int) -> None:
         """Handle the non-symlink file at ``os.path.join(root, rel_path)``
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current file from ``root``
+            root: root directory
+            rel_path: relative path to current file from ``root``
             depth (int): depth of current file from the ``root`` directory"""
         pass
 
-    def visit_symlinked_file(self, root, rel_path, depth):
-        """Handle the symlink to a file at ``os.path.join(root, rel_path)``.
-        Note: ``rel_path`` is the location of the symlink, not to what it is
-        pointing to. The symlink may be dangling.
+    def visit_symlinked_file(self, root: str, rel_path: str, depth) -> None:
+        """Handle the symlink to a file at ``os.path.join(root, rel_path)``. Note: ``rel_path`` is
+        the location of the symlink, not to what it is pointing to. The symlink may be dangling.
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current symlink from ``root``
-            depth (int): depth of current symlink from the ``root`` directory"""
+            root: root directory
+            rel_path: relative path to current symlink from ``root``
+            depth: depth of current symlink from the ``root`` directory"""
         pass
 
-    def before_visit_dir(self, root, rel_path, depth):
+    def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         """Return True from this function to recurse into the directory at
         os.path.join(root, rel_path). Return False in order not to recurse further.
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current directory from ``root``
-            depth (int): depth of current directory from the ``root`` directory
+            root: root directory
+            rel_path: relative path to current directory from ``root``
+            depth: depth of current directory from the ``root`` directory
 
         Returns:
             bool: ``True`` when the directory should be recursed into. ``False`` when
             not"""
         return False
 
-    def before_visit_symlinked_dir(self, root, rel_path, depth):
-        """Return ``True`` to recurse into the symlinked directory and ``False`` in
-        order not to. Note: ``rel_path`` is the path to the symlink itself.
-        Following symlinked directories blindly can cause infinite recursion due to
-        cycles.
+    def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
+        """Return ``True`` to recurse into the symlinked directory and ``False`` in order not to.
+        Note: ``rel_path`` is the path to the symlink itself. Following symlinked directories
+        blindly can cause infinite recursion due to cycles.
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current symlink from ``root``
-            depth (int): depth of current symlink from the ``root`` directory
+            root: root directory
+            rel_path: relative path to current symlink from ``root``
+            depth: depth of current symlink from the ``root`` directory
 
         Returns:
             bool: ``True`` when the directory should be recursed into. ``False`` when
             not"""
         return False
 
-    def after_visit_dir(self, root, rel_path, depth):
-        """Called after recursion into ``rel_path`` finished. This function is not
-        called when ``rel_path`` was not recursed into.
+    def after_visit_dir(self, root: str, rel_path: str, depth: int) -> None:
+        """Called after recursion into ``rel_path`` finished. This function is not called when
+        ``rel_path`` was not recursed into.
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current directory from ``root``
-            depth (int): depth of current directory from the ``root`` directory"""
+            root: root directory
+            rel_path: relative path to current directory from ``root``
+            depth: depth of current directory from the ``root`` directory"""
         pass
 
-    def after_visit_symlinked_dir(self, root, rel_path, depth):
-        """Called after recursion into ``rel_path`` finished. This function is not
-        called when ``rel_path`` was not recursed into.
+    def after_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> None:
+        """Called after recursion into ``rel_path`` finished. This function is not called when
+        ``rel_path`` was not recursed into.
 
         Parameters:
-            root (str): root directory
-            rel_path (str): relative path to current symlink from ``root``
-            depth (int): depth of current symlink from the ``root`` directory"""
+            root: root directory
+            rel_path: relative path to current symlink from ``root``
+            depth: depth of current symlink from the ``root`` directory"""
         pass
 
 
-def visit_directory_tree(root, visitor, rel_path="", depth=0):
-    """Recurses the directory root depth-first through a visitor pattern using the
-    interface from :py:class:`BaseDirectoryVisitor`
+def visit_directory_tree(
+    root: str, visitor: BaseDirectoryVisitor, rel_path: str = "", depth: int = 0
+):
+    """Recurses the directory root depth-first through a visitor pattern using the interface from
+    :py:class:`BaseDirectoryVisitor`
 
     Parameters:
-        root (str): path of directory to recurse into
-        visitor (BaseDirectoryVisitor): what visitor to use
-        rel_path (str): current relative path from the root
-        depth (str): current depth from the root
+        root: path of directory to recurse into
+        visitor: what visitor to use
+        rel_path: current relative path from the root
+        depth: current depth from the root
     """
     dir = os.path.join(root, rel_path)
     dir_entries = sorted(os.scandir(dir), key=lambda d: d.name)
@@ -1498,26 +1473,19 @@ def visit_directory_tree(root, visitor, rel_path="", depth=0):
     for f in dir_entries:
         rel_child = os.path.join(rel_path, f.name)
         islink = f.is_symlink()
-        # On Windows, symlinks to directories are distinct from
-        # symlinks to files, and it is possible to create a
-        # broken symlink to a directory (e.g. using os.symlink
-        # without `target_is_directory=True`), invoking `isdir`
-        # on a symlink on Windows that is broken in this manner
-        # will result in an error. In this case we can work around
-        # the issue by reading the target and resolving the
-        # directory ourselves
+        # On Windows, symlinks to directories are distinct from symlinks to files, and it is
+        # possible to create a broken symlink to a directory (e.g. using os.symlink without
+        # `target_is_directory=True`), invoking `isdir` on a symlink on Windows that is broken in
+        # this manner will result in an error. In this case we can work around the issue by reading
+        # the target and resolving the directory ourselves
         try:
             isdir = f.is_dir()
         except OSError as e:
             if sys.platform == "win32" and hasattr(e, "winerror") and e.winerror == 5 and islink:
-                # if path is a symlink, determine destination and
-                # evaluate file vs directory
+                # if path is a symlink, determine destination and evaluate file vs directory
                 link_target = resolve_link_target_relative_to_the_link(f)
-                # link_target might be relative but
-                # resolve_link_target_relative_to_the_link
-                # will ensure that if so, that it is relative
-                # to the CWD and therefore
-                # makes sense
+                # link_target might be relative but resolve_link_target_relative_to_the_link
+                # will ensure that if so, that it is relative to the CWD and therefore makes sense
                 isdir = os.path.isdir(link_target)
             else:
                 raise e

lib/spack/llnl/util/link_tree.py

@@ -8,7 +8,7 @@
 import filecmp
 import os
 import shutil
-from collections import OrderedDict
+from typing import Callable, Dict, List, Optional, Tuple
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import BaseDirectoryVisitor, mkdirp, touch, traverse_tree
@@ -51,32 +51,32 @@ class SourceMergeVisitor(BaseDirectoryVisitor):
     - A list of merge conflicts in dst/
     """
 
-    def __init__(self, ignore=None):
+    def __init__(self, ignore: Optional[Callable[[str], bool]] = None):
         self.ignore = ignore if ignore is not None else lambda f: False
 
-        # When mapping <src root> to <dst root>/<projection>, we need
-        # to prepend the <projection> bit to the relative path in the
-        # destination dir.
-        self.projection = ""
+        # When mapping <src root> to <dst root>/<projection>, we need to prepend the <projection>
+        # bit to the relative path in the destination dir.
+        self.projection: str = ""
 
-        # When a file blocks another file, the conflict can sometimes
-        # be resolved / ignored (e.g. <prefix>/LICENSE or
-        # or <site-packages>/<namespace>/__init__.py conflicts can be
-        # ignored).
-        self.file_conflicts = []
+        # Two files f and g conflict if they are not os.path.samefile(f, g) and they are both
+        # projected to the same destination file. These conflicts are not necessarily fatal, and
+        # can be resolved or ignored. For example <prefix>/LICENSE or
+        # <site-packages>/<namespace>/__init__.py conflicts can be ignored).
+        self.file_conflicts: List[MergeConflict] = []
 
-        # When we have to create a dir where a file is, or a file
-        # where a dir is, we have fatal errors, listed here.
-        self.fatal_conflicts = []
+        # When we have to create a dir where a file is, or a file where a dir is, we have fatal
+        # errors, listed here.
+        self.fatal_conflicts: List[MergeConflict] = []
 
-        # What directories we have to make; this is an ordered set,
-        # so that we have a fast lookup and can run mkdir in order.
-        self.directories = OrderedDict()
+        # What directories we have to make; this is an ordered dict, so that we have a fast lookup
+        # and can run mkdir in order.
+        self.directories: Dict[str, Tuple[str, str]] = {}
 
-        # Files to link. Maps dst_rel to (src_root, src_rel)
-        self.files = OrderedDict()
+        # Files to link. Maps dst_rel to (src_root, src_rel). This is an ordered dict, where files
+        # are guaranteed to be grouped by src_root in the order they were visited.
+        self.files: Dict[str, Tuple[str, str]] = {}
 
-    def before_visit_dir(self, root, rel_path, depth):
+    def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         """
         Register a directory if dst / rel_path is not blocked by a file or ignored.
         """
@@ -104,7 +104,7 @@ def before_visit_dir(self, root, rel_path, depth):
             self.directories[proj_rel_path] = (root, rel_path)
             return True
 
-    def before_visit_symlinked_dir(self, root, rel_path, depth):
+    def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
         """
         Replace symlinked dirs with actual directories when possible in low depths,
         otherwise handle it as a file (i.e. we link to the symlink).
@@ -136,40 +136,56 @@ def before_visit_symlinked_dir(self, root, rel_path, depth):
         self.visit_file(root, rel_path, depth)
         return False
 
-    def visit_file(self, root, rel_path, depth):
+    def visit_file(self, root: str, rel_path: str, depth: int, *, symlink: bool = False) -> None:
         proj_rel_path = os.path.join(self.projection, rel_path)
 
         if self.ignore(rel_path):
             pass
         elif proj_rel_path in self.directories:
             # Can't create a file where a dir is; fatal error
-            src_a_root, src_a_relpath = self.directories[proj_rel_path]
             self.fatal_conflicts.append(
                 MergeConflict(
                     dst=proj_rel_path,
-                    src_a=os.path.join(src_a_root, src_a_relpath),
+                    src_a=os.path.join(*self.directories[proj_rel_path]),
                     src_b=os.path.join(root, rel_path),
                 )
             )
         elif proj_rel_path in self.files:
-            # In some cases we can resolve file-file conflicts
-            src_a_root, src_a_relpath = self.files[proj_rel_path]
-            self.file_conflicts.append(
-                MergeConflict(
-                    dst=proj_rel_path,
-                    src_a=os.path.join(src_a_root, src_a_relpath),
-                    src_b=os.path.join(root, rel_path),
+            # When two files project to the same path, they conflict iff they are distinct.
+            # If they are the same (i.e. one links to the other), register regular files rather
+            # than symlinks. The reason is that in copy-type views, we need a copy of the actual
+            # file, not the symlink.
+
+            src_a = os.path.join(*self.files[proj_rel_path])
+            src_b = os.path.join(root, rel_path)
+
+            try:
+                samefile = os.path.samefile(src_a, src_b)
+            except OSError:
+                samefile = False
+
+            if not samefile:
+                # Distinct files produce a conflict.
+                self.file_conflicts.append(
+                    MergeConflict(dst=proj_rel_path, src_a=src_a, src_b=src_b)
                 )
-            )
+                return
+
+            if not symlink:
+                # Remove the link in favor of the actual file. The del is necessary to maintain the
+                # order of the files dict, which is grouped by root.
+                del self.files[proj_rel_path]
+                self.files[proj_rel_path] = (root, rel_path)
+
         else:
             # Otherwise register this file to be linked.
             self.files[proj_rel_path] = (root, rel_path)
 
-    def visit_symlinked_file(self, root, rel_path, depth):
+    def visit_symlinked_file(self, root: str, rel_path: str, depth: int) -> None:
         # Treat symlinked files as ordinary files (without "dereferencing")
-        self.visit_file(root, rel_path, depth)
+        self.visit_file(root, rel_path, depth, symlink=True)
 
-    def set_projection(self, projection):
+    def set_projection(self, projection: str) -> None:
         self.projection = os.path.normpath(projection)
 
         # Todo, is this how to check in general for empty projection?
@@ -197,24 +213,19 @@ def set_projection(self, projection):
 
 
 class DestinationMergeVisitor(BaseDirectoryVisitor):
-    """DestinatinoMergeVisitor takes a SourceMergeVisitor
-    and:
+    """DestinatinoMergeVisitor takes a SourceMergeVisitor and:
 
-    a. registers additional conflicts when merging
-       to the destination prefix
-    b. removes redundant mkdir operations when
-       directories already exist in the destination
-       prefix.
+    a. registers additional conflicts when merging to the destination prefix
+    b. removes redundant mkdir operations when directories already exist in the destination prefix.
 
-    This also makes sure that symlinked directories
-    in the target prefix will never be merged with
+    This also makes sure that symlinked directories in the target prefix will never be merged with
     directories in the sources directories.
     """
 
-    def __init__(self, source_merge_visitor):
+    def __init__(self, source_merge_visitor: SourceMergeVisitor):
         self.src = source_merge_visitor
 
-    def before_visit_dir(self, root, rel_path, depth):
+    def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         # If destination dir is a file in a src dir, add a conflict,
         # and don't traverse deeper
         if rel_path in self.src.files:
@@ -236,7 +247,7 @@ def before_visit_dir(self, root, rel_path, depth):
         # don't descend into it.
         return False
 
-    def before_visit_symlinked_dir(self, root, rel_path, depth):
+    def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
         """
         Symlinked directories in the destination prefix should
         be seen as files; we should not accidentally merge
@@ -262,7 +273,7 @@ def before_visit_symlinked_dir(self, root, rel_path, depth):
         # Never descend into symlinked target dirs.
         return False
 
-    def visit_file(self, root, rel_path, depth):
+    def visit_file(self, root: str, rel_path: str, depth: int) -> None:
         # Can't merge a file if target already exists
         if rel_path in self.src.directories:
             src_a_root, src_a_relpath = self.src.directories[rel_path]
@@ -280,7 +291,7 @@ def visit_file(self, root, rel_path, depth):
                 )
             )
 
-    def visit_symlinked_file(self, root, rel_path, depth):
+    def visit_symlinked_file(self, root: str, rel_path: str, depth: int) -> None:
         # Treat symlinked files as ordinary files (without "dereferencing")
         self.visit_file(root, rel_path, depth)
 

lib/spack/spack/audit.py

@@ -244,7 +244,7 @@ def _search_duplicate_specs_in_externals(error_cls):
                 + lines
                 + ["as they might result in non-deterministic hashes"]
             )
-        except TypeError:
+        except (TypeError, AttributeError):
             details = []
 
         errors.append(error_cls(summary=error_msg, details=details))
@@ -292,12 +292,6 @@ def _avoid_mismatched_variants(error_cls):
     errors = []
     packages_yaml = spack.config.CONFIG.get_config("packages")
 
-    def make_error(config_data, summary):
-        s = io.StringIO()
-        s.write("Occurring in the following file:\n")
-        syaml.dump_config(config_data, stream=s, blame=True)
-        return error_cls(summary=summary, details=[s.getvalue()])
-
     for pkg_name in packages_yaml:
         # 'all:' must be more forgiving, since it is setting defaults for everything
         if pkg_name == "all" or "variants" not in packages_yaml[pkg_name]:
@@ -317,7 +311,7 @@ def make_error(config_data, summary):
                         f"Setting a preference for the '{pkg_name}' package to the "
                         f"non-existing variant '{variant.name}'"
                     )
-                    errors.append(make_error(preferences, summary))
+                    errors.append(_make_config_error(preferences, summary, error_cls=error_cls))
                     continue
 
                 # Variant cannot accept this value
@@ -329,11 +323,41 @@ def make_error(config_data, summary):
                         f"Setting the variant '{variant.name}' of the '{pkg_name}' package "
                         f"to the invalid value '{str(variant)}'"
                     )
-                    errors.append(make_error(preferences, summary))
+                    errors.append(_make_config_error(preferences, summary, error_cls=error_cls))
 
     return errors
 
 
+@config_packages
+def _wrongly_named_spec(error_cls):
+    """Warns if the wrong name is used for an external spec"""
+    errors = []
+    packages_yaml = spack.config.CONFIG.get_config("packages")
+    for pkg_name in packages_yaml:
+        if pkg_name == "all":
+            continue
+
+        externals = packages_yaml[pkg_name].get("externals", [])
+        is_virtual = spack.repo.PATH.is_virtual(pkg_name)
+        for entry in externals:
+            spec = spack.spec.Spec(entry["spec"])
+            regular_pkg_is_wrong = not is_virtual and pkg_name != spec.name
+            virtual_pkg_is_wrong = is_virtual and not any(
+                p.name == spec.name for p in spack.repo.PATH.providers_for(pkg_name)
+            )
+            if regular_pkg_is_wrong or virtual_pkg_is_wrong:
+                summary = f"Wrong external spec detected for '{pkg_name}': {spec}"
+                errors.append(_make_config_error(entry, summary, error_cls=error_cls))
+    return errors
+
+
+def _make_config_error(config_data, summary, error_cls):
+    s = io.StringIO()
+    s.write("Occurring in the following file:\n")
+    syaml.dump_config(config_data, stream=s, blame=True)
+    return error_cls(summary=summary, details=[s.getvalue()])
+
+
 #: Sanity checks on package directives
 package_directives = AuditClass(
     group="packages",
@@ -772,13 +796,33 @@ def check_virtual_with_variants(spec, msg):
                 except spack.repo.UnknownPackageError:
                     # This dependency is completely missing, so report
                     # and continue the analysis
-                    summary = (
-                        f"{pkg_name}: unknown package '{dep_name}' in " "'depends_on' directive"
-                    )
+                    summary = f"{pkg_name}: unknown package '{dep_name}' in 'depends_on' directive"
                     details = [f" in {filename}"]
                     errors.append(error_cls(summary=summary, details=details))
                     continue
 
+                # Check for self-referential specs similar to:
+                #
+                # depends_on("foo@X.Y", when="^foo+bar")
+                #
+                # That would allow clingo to choose whether to have foo@X.Y+bar in the graph.
+                problematic_edges = [
+                    x for x in when.edges_to_dependencies(dep_name) if not x.virtuals
+                ]
+                if problematic_edges and not dep.patches:
+                    summary = (
+                        f"{pkg_name}: dependency on '{dep.spec}' when '{when}' is self-referential"
+                    )
+                    details = [
+                        (
+                            f" please specify better using '^[virtuals=...] {dep_name}', or "
+                            f"substitute with an equivalent condition on '{pkg_name}'"
+                        ),
+                        f" in {filename}",
+                    ]
+                    errors.append(error_cls(summary=summary, details=details))
+                    continue
+
                 # check variants
                 dependency_variants = dep.spec.variants
                 for name, value in dependency_variants.items():

lib/spack/spack/bootstrap/core.py

@@ -542,7 +542,7 @@ def verify_patchelf(patchelf: "spack.util.executable.Executable") -> bool:
     return version >= spack.version.Version("0.13.1")
 
 
-def ensure_patchelf_in_path_or_raise() -> None:
+def ensure_patchelf_in_path_or_raise() -> spack.util.executable.Executable:
     """Ensure patchelf is in the PATH or raise."""
     # The old concretizer is not smart and we're doing its job: if the latest patchelf
     # does not concretize because the compiler doesn't support C++17, we try to

lib/spack/spack/bootstrap/environment.py

@@ -146,7 +146,7 @@ def mypy_root_spec() -> str:
 
 def black_root_spec() -> str:
     """Return the root spec used to bootstrap black"""
-    return _root_spec("py-black@:23.1.0")
+    return _root_spec("py-black@:24.1.0")
 
 
 def flake8_root_spec() -> str:

lib/spack/spack/build_systems/cached_cmake.py

@@ -199,6 +199,8 @@ def initconfig_mpi_entries(self):
                 mpiexec = "/usr/bin/srun"
             else:
                 mpiexec = os.path.join(spec["slurm"].prefix.bin, "srun")
+        elif hasattr(spec["mpi"].package, "mpiexec"):
+            mpiexec = spec["mpi"].package.mpiexec
         else:
             mpiexec = os.path.join(spec["mpi"].prefix.bin, "mpirun")
             if not os.path.exists(mpiexec):

lib/spack/spack/build_systems/cmake.py

@@ -58,6 +58,62 @@ def _maybe_set_python_hints(pkg: spack.package_base.PackageBase, args: List[str]
     )
 
 
+def _supports_compilation_databases(pkg: spack.package_base.PackageBase) -> bool:
+    """Check if this package (and CMake) can support compilation databases."""
+
+    # CMAKE_EXPORT_COMPILE_COMMANDS only exists for CMake >= 3.5
+    if not pkg.spec.satisfies("^cmake@3.5:"):
+        return False
+
+    # CMAKE_EXPORT_COMPILE_COMMANDS is only implemented for Makefile and Ninja generators
+    if not (pkg.spec.satisfies("generator=make") or pkg.spec.satisfies("generator=ninja")):
+        return False
+
+    return True
+
+
+def _conditional_cmake_defaults(pkg: spack.package_base.PackageBase, args: List[str]) -> None:
+    """Set a few default defines for CMake, depending on its version."""
+    cmakes = pkg.spec.dependencies("cmake", dt.BUILD)
+
+    if len(cmakes) != 1:
+        return
+
+    cmake = cmakes[0]
+
+    # CMAKE_INTERPROCEDURAL_OPTIMIZATION only exists for CMake >= 3.9
+    try:
+        ipo = pkg.spec.variants["ipo"].value
+    except KeyError:
+        ipo = False
+
+    if cmake.satisfies("@3.9:"):
+        args.append(CMakeBuilder.define("CMAKE_INTERPROCEDURAL_OPTIMIZATION", ipo))
+
+    # Disable Package Registry: export(PACKAGE) may put files in the user's home directory, and
+    # find_package may search there. This is not what we want.
+
+    # Do not populate CMake User Package Registry
+    if cmake.satisfies("@3.15:"):
+        # see https://cmake.org/cmake/help/latest/policy/CMP0090.html
+        args.append(CMakeBuilder.define("CMAKE_POLICY_DEFAULT_CMP0090", "NEW"))
+    elif cmake.satisfies("@3.1:"):
+        # see https://cmake.org/cmake/help/latest/variable/CMAKE_EXPORT_NO_PACKAGE_REGISTRY.html
+        args.append(CMakeBuilder.define("CMAKE_EXPORT_NO_PACKAGE_REGISTRY", True))
+
+    # Do not use CMake User/System Package Registry
+    # https://cmake.org/cmake/help/latest/manual/cmake-packages.7.html#disabling-the-package-registry
+    if cmake.satisfies("@3.16:"):
+        args.append(CMakeBuilder.define("CMAKE_FIND_USE_PACKAGE_REGISTRY", False))
+    elif cmake.satisfies("@3.1:3.15"):
+        args.append(CMakeBuilder.define("CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY", False))
+        args.append(CMakeBuilder.define("CMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY", False))
+
+    # Export a compilation database if supported.
+    if _supports_compilation_databases(pkg):
+        args.append(CMakeBuilder.define("CMAKE_EXPORT_COMPILE_COMMANDS", True))
+
+
 def generator(*names: str, default: Optional[str] = None):
     """The build system generator to use.
 
@@ -246,7 +302,10 @@ class CMakeBuilder(BaseBuilder):
     @property
     def archive_files(self):
         """Files to archive for packages based on CMake"""
-        return [os.path.join(self.build_directory, "CMakeCache.txt")]
+        files = [os.path.join(self.build_directory, "CMakeCache.txt")]
+        if _supports_compilation_databases(self):
+            files.append(os.path.join(self.build_directory, "compile_commands.json"))
+        return files
 
     @property
     def root_cmakelists_dir(self):
@@ -293,11 +352,6 @@ def std_args(pkg, generator=None):
         except KeyError:
             build_type = "RelWithDebInfo"
 
-        try:
-            ipo = pkg.spec.variants["ipo"].value
-        except KeyError:
-            ipo = False
-
         define = CMakeBuilder.define
         args = [
             "-G",
@@ -306,10 +360,6 @@ def std_args(pkg, generator=None):
             define("CMAKE_BUILD_TYPE", build_type),
         ]
 
-        # CMAKE_INTERPROCEDURAL_OPTIMIZATION only exists for CMake >= 3.9
-        if pkg.spec.satisfies("^cmake@3.9:"):
-            args.append(define("CMAKE_INTERPROCEDURAL_OPTIMIZATION", ipo))
-
         if primary_generator == "Unix Makefiles":
             args.append(define("CMAKE_VERBOSE_MAKEFILE", True))
 
@@ -318,6 +368,7 @@ def std_args(pkg, generator=None):
                 [define("CMAKE_FIND_FRAMEWORK", "LAST"), define("CMAKE_FIND_APPBUNDLE", "LAST")]
             )
 
+        _conditional_cmake_defaults(pkg, args)
         _maybe_set_python_hints(pkg, args)
 
         # Set up CMake rpath

lib/spack/spack/build_systems/intel.py

@@ -218,7 +218,7 @@ def pset_components(self):
             "+inspector": " intel-inspector",
             "+itac": " intel-itac intel-ta intel-tc" " intel-trace-analyzer intel-trace-collector",
             # Trace Analyzer and Collector
-            "+vtune": " intel-vtune"
+            "+vtune": " intel-vtune",
             # VTune, ..-profiler since 2020, ..-amplifier before
         }.items():
             if variant in self.spec:

lib/spack/spack/build_systems/lua.py

@@ -29,15 +29,12 @@ class LuaPackage(spack.package_base.PackageBase):
 
     with when("build_system=lua"):
         depends_on("lua-lang")
-        extends("lua", when="^lua")
-        with when("^lua-luajit"):
-            extends("lua-luajit")
-            depends_on("luajit")
-            depends_on("lua-luajit+lualinks")
-        with when("^lua-luajit-openresty"):
-            extends("lua-luajit-openresty")
-            depends_on("luajit")
-            depends_on("lua-luajit-openresty+lualinks")
+        with when("^[virtuals=lua-lang] lua"):
+            extends("lua")
+        with when("^[virtuals=lua-lang] lua-luajit"):
+            extends("lua-luajit+lualinks")
+        with when("^[virtuals=lua-lang] lua-luajit-openresty"):
+            extends("lua-luajit-openresty+lualinks")
 
     @property
     def lua(self):

lib/spack/spack/build_systems/oneapi.py

@@ -9,10 +9,13 @@
 import shutil
 from os.path import basename, isdir
 
-from llnl.util.filesystem import HeaderList, find_libraries, join_path, mkdirp
+from llnl.util import tty
+from llnl.util.filesystem import HeaderList, LibraryList, find_libraries, join_path, mkdirp
 from llnl.util.link_tree import LinkTree
 
+from spack.build_environment import dso_suffix
 from spack.directives import conflicts, variant
+from spack.package_base import InstallError
 from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
 
@@ -179,16 +182,72 @@ class IntelOneApiLibraryPackage(IntelOneApiPackage):
 
     """
 
+    def openmp_libs(self):
+        """Supply LibraryList for linking OpenMP"""
+
+        # NB: Hunting down explicit library files may be the Spack way of
+        # doing things, but it is better to add the compiler defined option
+        # e.g. -fopenmp
+
+        # If other packages use openmp, then all the packages need to
+        # support the same ABI. Spack usually uses the same compiler
+        # for all the packages, but you can force it if necessary:
+        #
+        # e.g. spack install blaspp%oneapi@2024 ^intel-oneapi-mkl%oneapi@2024
+        #
+        if self.spec.satisfies("%intel") or self.spec.satisfies("%oneapi"):
+            libname = "libiomp5"
+        elif self.spec.satisfies("%gcc"):
+            libname = "libgomp"
+        elif self.spec.satisfies("%clang"):
+            libname = "libomp"
+        else:
+            raise InstallError(
+                "OneAPI package with OpenMP threading requires one of %clang, %gcc, %oneapi, "
+                "or %intel"
+            )
+
+        # query the compiler for the library path
+        with self.compiler.compiler_environment():
+            omp_lib_path = Executable(self.compiler.cc)(
+                "--print-file-name", f"{libname}.{dso_suffix}", output=str
+            ).strip()
+
+        # Newer versions of clang do not give the full path to libomp. If that's
+        # the case, look in a path relative to the compiler where libomp is
+        # typically found. If it's not found there, error out.
+        if not os.path.exists(omp_lib_path) and self.spec.satisfies("%clang"):
+            compiler_root = os.path.dirname(os.path.dirname(os.path.realpath(self.compiler.cc)))
+            omp_lib_path_compiler = os.path.join(compiler_root, "lib", f"{libname}.{dso_suffix}")
+            if os.path.exists(omp_lib_path_compiler):
+                omp_lib_path = omp_lib_path_compiler
+
+        # if the compiler cannot find the file, it returns the input path
+        if not os.path.exists(omp_lib_path):
+            raise InstallError(f"OneAPI package cannot locate OpenMP library: {omp_lib_path}")
+
+        omp_libs = LibraryList(omp_lib_path)
+        tty.info(f"OneAPI package requires OpenMP library: {omp_libs}")
+        return omp_libs
+
+    # find_headers uses heuristics to determine the include directory
+    # that does not work for oneapi packages. Use explicit directories
+    # instead.
     def header_directories(self, dirs):
         h = HeaderList([])
         h.directories = dirs
+        # trilinos passes the directories to cmake, and cmake requires
+        # that the directory exists
+        for dir in dirs:
+            if not isdir(dir):
+                raise RuntimeError(f"{dir} does not exist")
         return h
 
     @property
     def headers(self):
-        return self.header_directories(
-            [self.component_prefix.include, self.component_prefix.include.join(self.component_dir)]
-        )
+        # This should match the directories added to CPATH by
+        # env/vars.sh for the component
+        return self.header_directories([self.component_prefix.include])
 
     @property
     def libs(self):

lib/spack/spack/build_systems/python.py

@@ -6,7 +6,8 @@
 import os
 import re
 import shutil
-from typing import Iterable, List, Mapping, Optional
+import stat
+from typing import Dict, Iterable, List, Mapping, Optional, Tuple
 
 import archspec
 
@@ -136,31 +137,52 @@ def view_file_conflicts(self, view, merge_map):
         return conflicts
 
     def add_files_to_view(self, view, merge_map, skip_if_exists=True):
-        if not self.extendee_spec:
+        # Patch up shebangs to the python linked in the view only if python is built by Spack.
+        if not self.extendee_spec or self.extendee_spec.external:
             return super().add_files_to_view(view, merge_map, skip_if_exists)
 
+        # We only patch shebangs in the bin directory.
+        copied_files: Dict[Tuple[int, int], str] = {}  # File identifier -> source
+        delayed_links: List[Tuple[str, str]] = []  # List of symlinks from merge map
+
         bin_dir = self.spec.prefix.bin
         python_prefix = self.extendee_spec.prefix
-        python_is_external = self.extendee_spec.external
-        global_view = fs.same_path(python_prefix, view.get_projection_for_spec(self.spec))
         for src, dst in merge_map.items():
-            if os.path.exists(dst):
+            if skip_if_exists and os.path.lexists(dst):
                 continue
-            elif global_view or not fs.path_contains_subdirectory(src, bin_dir):
+
+            if not fs.path_contains_subdirectory(src, bin_dir):
                 view.link(src, dst)
-            elif not os.path.islink(src):
+                continue
+
+            s = os.lstat(src)
+
+            # Symlink is delayed because we may need to re-target if its target is copied in view
+            if stat.S_ISLNK(s.st_mode):
+                delayed_links.append((src, dst))
+                continue
+
+            # If it's executable and has a shebang, copy and patch it.
+            if (s.st_mode & 0b111) and fs.has_shebang(src):
+                copied_files[(s.st_dev, s.st_ino)] = dst
                 shutil.copy2(src, dst)
-                is_script = fs.is_nonsymlink_exe_with_shebang(src)
-                if is_script and not python_is_external:
-                    fs.filter_file(
-                        python_prefix,
-                        os.path.abspath(view.get_projection_for_spec(self.spec)),
-                        dst,
-                    )
+                fs.filter_file(
+                    python_prefix, os.path.abspath(view.get_projection_for_spec(self.spec)), dst
+                )
             else:
-                orig_link_target = os.path.realpath(src)
-                new_link_target = os.path.abspath(merge_map[orig_link_target])
-                view.link(new_link_target, dst)
+                view.link(src, dst)
+
+        # Finally re-target the symlinks that point to copied files.
+        for src, dst in delayed_links:
+            try:
+                s = os.stat(src)
+                target = copied_files[(s.st_dev, s.st_ino)]
+            except (OSError, KeyError):
+                target = None
+            if target:
+                os.symlink(target, dst)
+            else:
+                view.link(src, dst, spec=self.spec)
 
     def remove_files_from_view(self, view, merge_map):
         ignore_namespace = False

lib/spack/spack/caches.py

@@ -35,9 +35,9 @@ def _misc_cache():
 
 
 #: Spack's cache for small data
-MISC_CACHE: Union[
-    spack.util.file_cache.FileCache, llnl.util.lang.Singleton
-] = llnl.util.lang.Singleton(_misc_cache)
+MISC_CACHE: Union[spack.util.file_cache.FileCache, llnl.util.lang.Singleton] = (
+    llnl.util.lang.Singleton(_misc_cache)
+)
 
 
 def fetch_cache_location():
@@ -91,6 +91,6 @@ def symlink(self, mirror_ref):
 
 
 #: Spack's local cache for downloaded source archives
-FETCH_CACHE: Union[
-    spack.fetch_strategy.FsCache, llnl.util.lang.Singleton
-] = llnl.util.lang.Singleton(_fetch_cache)
+FETCH_CACHE: Union[spack.fetch_strategy.FsCache, llnl.util.lang.Singleton] = (
+    llnl.util.lang.Singleton(_fetch_cache)
+)

lib/spack/spack/ci_needs_workaround.py

@@ -7,9 +7,7 @@
 get_job_name = lambda needs_entry: (
     needs_entry.get("job")
     if (isinstance(needs_entry, collections.abc.Mapping) and needs_entry.get("artifacts", True))
-    else needs_entry
-    if isinstance(needs_entry, str)
-    else None
+    else needs_entry if isinstance(needs_entry, str) else None
 )
 
 

lib/spack/spack/cmd/ci.py

@@ -6,6 +6,7 @@
 import json
 import os
 import shutil
+from urllib.parse import urlparse, urlunparse
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
@@ -157,7 +158,9 @@ def setup_parser(subparser):
         description=deindent(ci_reproduce.__doc__),
         help=spack.cmd.first_line(ci_reproduce.__doc__),
     )
-    reproduce.add_argument("job_url", help="URL of job artifacts bundle")
+    reproduce.add_argument(
+        "job_url", help="URL of GitLab job web page or artifact", type=_gitlab_artifacts_url
+    )
     reproduce.add_argument(
         "--runtime",
         help="Container runtime to use.",
@@ -792,11 +795,6 @@ def ci_reproduce(args):
     artifacts of the provided gitlab pipeline rebuild job's URL will be used to derive
     instructions for reproducing the build locally
     """
-    job_url = args.job_url
-    work_dir = args.working_dir
-    autostart = args.autostart
-    runtime = args.runtime
-
     # Allow passing GPG key for reprocuding protected CI jobs
     if args.gpg_file:
         gpg_key_url = url_util.path_to_file_url(args.gpg_file)
@@ -805,7 +803,47 @@ def ci_reproduce(args):
     else:
         gpg_key_url = None
 
-    return spack_ci.reproduce_ci_job(job_url, work_dir, autostart, gpg_key_url, runtime)
+    return spack_ci.reproduce_ci_job(
+        args.job_url, args.working_dir, args.autostart, gpg_key_url, args.runtime
+    )
+
+
+def _gitlab_artifacts_url(url: str) -> str:
+    """Take a URL either to the URL of the job in the GitLab UI, or to the artifacts zip file,
+    and output the URL to the artifacts zip file."""
+    parsed = urlparse(url)
+
+    if not parsed.scheme or not parsed.netloc:
+        raise ValueError(url)
+
+    parts = parsed.path.split("/")
+
+    if len(parts) < 2:
+        raise ValueError(url)
+
+    # Just use API endpoints verbatim, they're probably generated by Spack.
+    if parts[1] == "api":
+        return url
+
+    # If it's a URL to the job in the Gitlab UI, we may need to append the artifacts path.
+    minus_idx = parts.index("-")
+
+    # Remove repeated slashes in the remainder
+    rest = [p for p in parts[minus_idx + 1 :] if p]
+
+    # Now the format is jobs/X or jobs/X/artifacts/download
+    if len(rest) < 2 or rest[0] != "jobs":
+        raise ValueError(url)
+
+    if len(rest) == 2:
+        # replace jobs/X with jobs/X/artifacts/download
+        rest.extend(("artifacts", "download"))
+
+    # Replace the parts and unparse.
+    parts[minus_idx + 1 :] = rest
+
+    # Don't allow fragments / queries
+    return urlunparse(parsed._replace(path="/".join(parts), fragment="", query=""))
 
 
 def ci(parser, args):

lib/spack/spack/cmd/common/env_utility.py

@@ -115,7 +115,7 @@ def emulate_env_utility(cmd_name, context: Context, args):
             f"Not all dependencies of {spec.name} are installed. "
             f"Cannot setup {context} environment:",
             spec.tree(
-                status_fn=spack.spec.Spec.install_status,
+                install_status=True,
                 hashlen=7,
                 hashes=True,
                 # This shows more than necessary, but we cannot dynamically change deptypes

lib/spack/spack/cmd/develop.py

@@ -8,6 +8,7 @@
 import llnl.util.tty as tty
 
 import spack.cmd
+import spack.config
 import spack.spec
 import spack.util.path
 import spack.version
@@ -21,6 +22,7 @@
 
 def setup_parser(subparser):
     subparser.add_argument("-p", "--path", help="source location of package")
+    subparser.add_argument("-b", "--build-directory", help="build directory for the package")
 
     clone_group = subparser.add_mutually_exclusive_group()
     clone_group.add_argument(
@@ -151,4 +153,11 @@ def develop(parser, args):
     env = spack.cmd.require_active_env(cmd_name="develop")
     tty.debug("Updating develop config for {0} transactionally".format(env.name))
     with env.write_transaction():
+        if args.build_directory is not None:
+            spack.config.add(
+                "packages:{}:package_attributes:build_directory:{}".format(
+                    spec.name, args.build_directory
+                ),
+                env.scope_name,
+            )
         _update_config(spec, path)

lib/spack/spack/cmd/help.py

@@ -30,6 +30,7 @@
       @c{@min:max}                      version range (inclusive)
       @c{@min:}                         version <min> or higher
       @c{@:max}                         up to version <max> (inclusive)
+      @c{@=version}                     exact version
 
     compilers:
       @g{%compiler}                     build with <compiler>

lib/spack/spack/cmd/list.py

@@ -292,9 +292,11 @@ def head(n, span_id, title, anchor=None):
                 out.write("<dd>\n")
                 out.write(
                     ", ".join(
-                        d
-                        if d not in pkg_names
-                        else '<a class="reference internal" href="#%s">%s</a>' % (d, d)
+                        (
+                            d
+                            if d not in pkg_names
+                            else '<a class="reference internal" href="#%s">%s</a>' % (d, d)
+                        )
                         for d in deps
                     )
                 )

lib/spack/spack/cmd/logs.py

@@ -0,0 +1,71 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import errno
+import gzip
+import io
+import os
+import shutil
+import sys
+
+import spack.cmd
+import spack.spec
+import spack.util.compression as compression
+from spack.cmd.common import arguments
+from spack.main import SpackCommandError
+
+description = "print out logs for packages"
+section = "basic"
+level = "long"
+
+
+def setup_parser(subparser):
+    arguments.add_common_arguments(subparser, ["spec"])
+
+
+def _dump_byte_stream_to_stdout(instream: io.BufferedIOBase) -> None:
+    # Reopen stdout in binary mode so we don't have to worry about encoding
+    outstream = os.fdopen(sys.stdout.fileno(), "wb", closefd=False)
+    shutil.copyfileobj(instream, outstream)
+
+
+def _logs(cmdline_spec: spack.spec.Spec, concrete_spec: spack.spec.Spec):
+    if concrete_spec.installed:
+        log_path = concrete_spec.package.install_log_path
+    elif os.path.exists(concrete_spec.package.stage.path):
+        # TODO: `spack logs` can currently not show the logs while a package is being built, as the
+        # combined log file is only written after the build is finished.
+        log_path = concrete_spec.package.log_path
+    else:
+        raise SpackCommandError(f"{cmdline_spec} is not installed or staged")
+
+    try:
+        stream = open(log_path, "rb")
+    except OSError as e:
+        if e.errno == errno.ENOENT:
+            raise SpackCommandError(f"No logs are available for {cmdline_spec}") from e
+        raise SpackCommandError(f"Error reading logs for {cmdline_spec}: {e}") from e
+
+    with stream as f:
+        ext = compression.extension_from_magic_numbers_by_stream(f, decompress=False)
+        if ext and ext != "gz":
+            raise SpackCommandError(f"Unsupported storage format for {log_path}: {ext}")
+
+        # If the log file is gzip compressed, wrap it with a decompressor
+        _dump_byte_stream_to_stdout(gzip.GzipFile(fileobj=f) if ext == "gz" else f)
+
+
+def logs(parser, args):
+    specs = spack.cmd.parse_specs(args.spec)
+
+    if not specs:
+        raise SpackCommandError("You must supply a spec.")
+
+    if len(specs) != 1:
+        raise SpackCommandError("Too many specs. Supply only one.")
+
+    concrete_spec = spack.cmd.matching_spec_from_env(specs[0])
+
+    _logs(specs[0], concrete_spec)

lib/spack/spack/cmd/solve.py

@@ -135,8 +135,6 @@ def _process_result(result, show, required_format, kwargs):
 
 def solve(parser, args):
     # these are the same options as `spack spec`
-    install_status_fn = spack.spec.Spec.install_status
-
     fmt = spack.spec.DISPLAY_FORMAT
     if args.namespaces:
         fmt = "{namespace}." + fmt
@@ -146,7 +144,7 @@ def solve(parser, args):
         "format": fmt,
         "hashlen": None if args.very_long else 7,
         "show_types": args.types,
-        "status_fn": install_status_fn if args.install_status else None,
+        "install_status": args.install_status,
         "hashes": args.long or args.very_long,
     }
 

lib/spack/spack/cmd/spec.py

@@ -75,8 +75,6 @@ def setup_parser(subparser):
 
 
 def spec(parser, args):
-    install_status_fn = spack.spec.Spec.install_status
-
     fmt = spack.spec.DISPLAY_FORMAT
     if args.namespaces:
         fmt = "{namespace}." + fmt
@@ -86,7 +84,7 @@ def spec(parser, args):
         "format": fmt,
         "hashlen": None if args.very_long else 7,
         "show_types": args.types,
-        "status_fn": install_status_fn if args.install_status else None,
+        "install_status": args.install_status,
     }
 
     # use a read transaction if we are getting install status for every

lib/spack/spack/compilers/__init__.py

@@ -514,9 +514,10 @@ def get_compilers(config, cspec=None, arch_spec=None):
     for items in config:
         items = items["compiler"]
 
-        # NOTE: in principle this should be equality not satisfies, but config can still
-        # be written in old format gcc@10.1.0 instead of gcc@=10.1.0.
-        if cspec and not cspec.satisfies(items["spec"]):
+        # We might use equality here.
+        if cspec and not spack.spec.parse_with_version_concrete(
+            items["spec"], compiler=True
+        ).satisfies(cspec):
             continue
 
         # If an arch spec is given, confirm that this compiler

lib/spack/spack/compilers/msvc.py

@@ -7,6 +7,7 @@
 import re
 import subprocess
 import sys
+import tempfile
 from typing import Dict, List, Set
 
 import spack.compiler
@@ -15,7 +16,7 @@
 import spack.util.executable
 from spack.compiler import Compiler
 from spack.error import SpackError
-from spack.version import Version
+from spack.version import Version, VersionRange
 
 avail_fc_version: Set[str] = set()
 fc_path: Dict[str, str] = dict()
@@ -292,6 +293,15 @@ def setup_custom_environment(self, pkg, env):
             else:
                 env.set_path(env_var, int_env[env_var].split(os.pathsep))
 
+        # certain versions of ifx (2021.3.0:2023.1.0) do not play well with env:TMP
+        # that has a "." character in the path
+        # Work around by pointing tmp to the stage for the duration of the build
+        if self.fc and Version(self.fc_version(self.fc)).satisfies(
+            VersionRange("2021.3.0", "2023.1.0")
+        ):
+            new_tmp = tempfile.mkdtemp(dir=pkg.stage.path)
+            env.set("TMP", new_tmp)
+
         env.set("CC", self.cc)
         env.set("CXX", self.cxx)
         env.set("FC", self.fc)

lib/spack/spack/concretize.py

@@ -826,7 +826,6 @@ def __init__(self, spec):
 
 
 class InsufficientArchitectureInfoError(spack.error.SpackError):
-
     """Raised when details on architecture cannot be collected from the
     system"""
 

lib/spack/spack/config.py

@@ -63,10 +63,11 @@
 from spack.util.cpus import cpus_available
 
 #: Dict from section names -> schema for that section
-SECTION_SCHEMAS = {
+SECTION_SCHEMAS: Dict[str, Any] = {
     "compilers": spack.schema.compilers.schema,
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
+    "view": spack.schema.view.schema,
     "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
     "repos": spack.schema.repos.schema,
@@ -81,7 +82,7 @@
 
 # Same as above, but including keys for environments
 # this allows us to unify config reading between configs and environments
-_ALL_SCHEMAS = copy.deepcopy(SECTION_SCHEMAS)
+_ALL_SCHEMAS: Dict[str, Any] = copy.deepcopy(SECTION_SCHEMAS)
 _ALL_SCHEMAS.update({spack.schema.env.TOP_LEVEL_KEY: spack.schema.env.schema})
 
 #: Path to the default configuration
@@ -1096,7 +1097,7 @@ def read_config_file(
             data = syaml.load_config(f)
 
         if data:
-            if not schema:
+            if schema is None:
                 key = next(iter(data))
                 schema = _ALL_SCHEMAS[key]
             validate(data, schema)

lib/spack/spack/container/images.json

@@ -71,7 +71,7 @@
     "almalinux:9": {
       "bootstrap": {
         "template": "container/almalinux_9.dockerfile",
-        "image": "quay.io/almalinux/almalinux:9"
+        "image": "quay.io/almalinuxorg/almalinux:9"
       },
       "os_package_manager": "dnf_epel",
       "build": "spack/almalinux9",
@@ -79,13 +79,13 @@
         "develop": "latest"
       },
       "final": {
-        "image": "quay.io/almalinux/almalinux:9"
+        "image": "quay.io/almalinuxorg/almalinux:9"
       }
     },
     "almalinux:8": {
       "bootstrap": {
         "template": "container/almalinux_8.dockerfile",
-        "image": "quay.io/almalinux/almalinux:8"
+        "image": "quay.io/almalinuxorg/almalinux:8"
       },
       "os_package_manager": "dnf_epel",
       "build": "spack/almalinux8",
@@ -93,7 +93,7 @@
         "develop": "latest"
       },
       "final": {
-        "image": "quay.io/almalinux/almalinux:8"
+        "image": "quay.io/almalinuxorg/almalinux:8"
       }
     },
     "centos:stream": {

lib/spack/spack/deptypes.py

@@ -36,6 +36,9 @@
 #: Default dependency type if none is specified
 DEFAULT: DepFlag = BUILD | LINK
 
+#: A flag with no dependency types set
+NONE: DepFlag = 0
+
 #: An iterator of all flag components
 ALL_FLAGS: Tuple[DepFlag, DepFlag, DepFlag, DepFlag] = (BUILD, LINK, RUN, TEST)
 

lib/spack/spack/directives.py

@@ -34,7 +34,7 @@ class OpenMpi(Package):
 import functools
 import os.path
 import re
-from typing import Any, Callable, List, Optional, Set, Tuple, Union
+from typing import TYPE_CHECKING, Any, Callable, List, Optional, Set, Tuple, Union
 
 import llnl.util.lang
 import llnl.util.tty.color
@@ -57,6 +57,9 @@ class OpenMpi(Package):
     VersionLookupError,
 )
 
+if TYPE_CHECKING:
+    import spack.package_base
+
 __all__ = [
     "DirectiveError",
     "DirectiveMeta",
@@ -349,6 +352,7 @@ def remove_directives(arg):
         return _decorator
 
 
+SubmoduleCallback = Callable[["spack.package_base.PackageBase"], Union[str, List[str], bool]]
 directive = DirectiveMeta.directive
 
 
@@ -380,7 +384,7 @@ def version(
     tag: Optional[str] = None,
     branch: Optional[str] = None,
     get_full_repo: Optional[bool] = None,
-    submodules: Optional[bool] = None,
+    submodules: Union[SubmoduleCallback, Optional[bool]] = None,
     submodules_delete: Optional[bool] = None,
     # other version control
     svn: Optional[str] = None,

lib/spack/spack/environment/environment.py

@@ -21,7 +21,6 @@
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 import llnl.util.tty.color as clr
-from llnl.util.lang import dedupe
 from llnl.util.link_tree import ConflictingSpecsError
 from llnl.util.symlink import symlink
 
@@ -379,8 +378,8 @@ def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
         if not dev_specs:
             return
         for name, entry in dev_specs.items():
-            dev_path = entry["path"]
-            expanded_path = os.path.normpath(os.path.join(init_file_dir, entry["path"]))
+            dev_path = substitute_path_variables(entry["path"])
+            expanded_path = spack.util.path.canonicalize_path(dev_path, default_wd=init_file_dir)
 
             # Skip if the expanded path is the same (e.g. when absolute)
             if dev_path == expanded_path:
@@ -663,30 +662,26 @@ def __contains__(self, spec):
 
         return True
 
-    def specs_for_view(self, concretized_root_specs):
-        """
-        From the list of concretized user specs in the environment, flatten
-        the dags, and filter selected, installed specs, remove duplicates on dag hash.
-        """
-        # With deps, requires traversal
-        if self.link == "all" or self.link == "run":
-            deptype = ("run") if self.link == "run" else ("link", "run")
-            specs = list(
-                traverse.traverse_nodes(
-                    concretized_root_specs, deptype=deptype, key=traverse.by_dag_hash
-                )
-            )
+    def specs_for_view(self, concrete_roots: List[Spec]) -> List[Spec]:
+        """Flatten the DAGs of the concrete roots, keep only unique, selected, and installed specs
+        in topological order from root to leaf."""
+        if self.link == "all":
+            deptype = dt.LINK | dt.RUN
+        elif self.link == "run":
+            deptype = dt.RUN
         else:
-            specs = list(dedupe(concretized_root_specs, key=traverse.by_dag_hash))
+            deptype = dt.NONE
+
+        specs = traverse.traverse_nodes(
+            concrete_roots, order="topo", deptype=deptype, key=traverse.by_dag_hash
+        )
 
         # Filter selected, installed specs
         with spack.store.STORE.db.read_transaction():
-            specs = [s for s in specs if s in self and s.installed]
+            return [s for s in specs if s in self and s.installed]
 
-        return specs
-
-    def regenerate(self, concretized_root_specs):
-        specs = self.specs_for_view(concretized_root_specs)
+    def regenerate(self, concrete_roots: List[Spec]) -> None:
+        specs = self.specs_for_view(concrete_roots)
 
         # To ensure there are no conflicts with packages being installed
         # that cannot be resolved or have repos that have been removed
@@ -703,14 +698,14 @@ def regenerate(self, concretized_root_specs):
         old_root = self._current_root
 
         if new_root == old_root:
-            tty.debug("View at %s does not need regeneration." % self.root)
+            tty.debug(f"View at {self.root} does not need regeneration.")
             return
 
         _error_on_nonempty_view_dir(new_root)
 
         # construct view at new_root
         if specs:
-            tty.msg("Updating view at {0}".format(self.root))
+            tty.msg(f"Updating view at {self.root}")
 
         view = self.view(new=new_root)
 
@@ -720,7 +715,7 @@ def regenerate(self, concretized_root_specs):
         # Create a new view
         try:
             fs.mkdirp(new_root)
-            view.add_specs(*specs, with_dependencies=False)
+            view.add_specs(*specs)
 
             # create symlink from tmp_symlink_name to new_root
             if os.path.exists(tmp_symlink_name):
@@ -734,7 +729,7 @@ def regenerate(self, concretized_root_specs):
             try:
                 shutil.rmtree(new_root, ignore_errors=True)
                 os.unlink(tmp_symlink_name)
-            except (IOError, OSError):
+            except OSError:
                 pass
 
             # Give an informative error message for the typical error case: two specs, same package
@@ -876,9 +871,55 @@ def _process_definition(self, item):
             else:
                 self.spec_lists[name] = user_specs
 
+    def _process_view(self, env_view: Optional[Union[bool, str, Dict]]):
+        """Process view option(s), which can be boolean, string, or None.
+
+        A boolean environment view option takes precedence over any that may
+        be included. So ``view: True`` results in the default view only. And
+        ``view: False`` means the environment will have no view.
+
+        Args:
+            env_view: view option provided in the manifest or configuration
+        """
+
+        def add_view(name, values):
+            """Add the view with the name and the string or dict values."""
+            if isinstance(values, str):
+                self.views[name] = ViewDescriptor(self.path, values)
+            elif isinstance(values, dict):
+                self.views[name] = ViewDescriptor.from_dict(self.path, values)
+            else:
+                tty.error(f"Cannot add view named {name} for {type(values)} values {values}")
+
+        # If the configuration specifies 'view: False' then we are done
+        # processing views. If this is called with the environment's view
+        # view (versus an included view), then there are to be NO views.
+        if env_view is False:
+            return
+
+        # If the configuration specifies 'view: True' then only the default
+        # view will be created for the environment and we are done processing
+        # views.
+        if env_view is True:
+            add_view(default_view_name, self.view_path_default)
+            return
+
+        # Otherwise, the configuration has a subdirectory or dictionary.
+        if isinstance(env_view, str):
+            add_view(default_view_name, env_view)
+        elif env_view:
+            for name, values in env_view.items():
+                add_view(name, values)
+
+        # If we reach this point without an explicit view option then we
+        # provide the default view.
+        if self.views == dict():
+            self.views[default_view_name] = ViewDescriptor(self.path, self.view_path_default)
+
     def _construct_state_from_manifest(self):
         """Set up user specs and views from the manifest file."""
         self.spec_lists = collections.OrderedDict()
+        self.views = {}
 
         for item in spack.config.get("definitions", []):
             self._process_definition(item)
@@ -890,20 +931,7 @@ def _construct_state_from_manifest(self):
         )
         self.spec_lists[user_speclist_name] = user_specs
 
-        enable_view = env_configuration.get("view")
-        # enable_view can be boolean, string, or None
-        if enable_view is True or enable_view is None:
-            self.views = {default_view_name: ViewDescriptor(self.path, self.view_path_default)}
-        elif isinstance(enable_view, str):
-            self.views = {default_view_name: ViewDescriptor(self.path, enable_view)}
-        elif enable_view:
-            path = self.path
-            self.views = dict(
-                (name, ViewDescriptor.from_dict(path, values))
-                for name, values in enable_view.items()
-            )
-        else:
-            self.views = {}
+        self._process_view(spack.config.get("view", True))
 
     @property
     def user_specs(self):
@@ -2062,7 +2090,6 @@ def write(self, regenerate: bool = True) -> None:
 
         if regenerate:
             self.regenerate_views()
-            spack.hooks.post_env_write(self)
 
         self.new_specs.clear()
 
@@ -2185,7 +2212,7 @@ def _tree_to_display(spec):
         return spec.tree(
             recurse_dependencies=True,
             format=spack.spec.DISPLAY_FORMAT,
-            status_fn=spack.spec.Spec.install_status,
+            install_status=True,
             hashlen=7,
             hashes=True,
         )

lib/spack/spack/fetch_strategy.py

@@ -697,7 +697,6 @@ def __str__(self):
 
 @fetcher
 class GitFetchStrategy(VCSFetchStrategy):
-
     """
     Fetch strategy that gets source code from a git repository.
     Use like this in a package:
@@ -930,9 +929,12 @@ def clone(self, dest=None, commit=None, branch=None, tag=None, bare=False):
         git_commands = []
         submodules = self.submodules
         if callable(submodules):
-            submodules = list(submodules(self.package))
-            git_commands.append(["submodule", "init", "--"] + submodules)
-            git_commands.append(["submodule", "update", "--recursive"])
+            submodules = submodules(self.package)
+            if submodules:
+                if isinstance(submodules, str):
+                    submodules = [submodules]
+                git_commands.append(["submodule", "init", "--"] + submodules)
+                git_commands.append(["submodule", "update", "--recursive"])
         elif submodules:
             git_commands.append(["submodule", "update", "--init", "--recursive"])
 
@@ -1089,7 +1091,6 @@ def __str__(self):
 
 @fetcher
 class SvnFetchStrategy(VCSFetchStrategy):
-
     """Fetch strategy that gets source code from a subversion repository.
        Use like this in a package:
 
@@ -1184,7 +1185,6 @@ def __str__(self):
 
 @fetcher
 class HgFetchStrategy(VCSFetchStrategy):
-
     """
     Fetch strategy that gets source code from a Mercurial repository.
     Use like this in a package:

lib/spack/spack/filesystem_view.py

@@ -32,6 +32,7 @@
 from llnl.util.tty.color import colorize
 
 import spack.config
+import spack.paths
 import spack.projections
 import spack.relocate
 import spack.schema.projections
@@ -91,16 +92,16 @@ def view_copy(src: str, dst: str, view, spec: Optional[spack.spec.Spec] = None):
         prefix_to_projection[spack.store.STORE.layout.root] = view._root
 
         # This is vestigial code for the *old* location of sbang.
-        prefix_to_projection[
-            "#!/bin/bash {0}/bin/sbang".format(spack.paths.spack_root)
-        ] = sbang.sbang_shebang_line()
+        prefix_to_projection[f"#!/bin/bash {spack.paths.spack_root}/bin/sbang"] = (
+            sbang.sbang_shebang_line()
+        )
 
         spack.relocate.relocate_text(files=[dst], prefixes=prefix_to_projection)
 
     try:
         os.chown(dst, src_stat.st_uid, src_stat.st_gid)
     except OSError:
-        tty.debug("Can't change the permissions for %s" % dst)
+        tty.debug(f"Can't change the permissions for {dst}")
 
 
 def view_func_parser(parsed_name):
@@ -112,7 +113,7 @@ def view_func_parser(parsed_name):
     elif parsed_name in ("add", "symlink", "soft"):
         return view_symlink
     else:
-        raise ValueError("invalid link type for view: '%s'" % parsed_name)
+        raise ValueError(f"invalid link type for view: '{parsed_name}'")
 
 
 def inverse_view_func_parser(view_type):
@@ -270,9 +271,10 @@ def __init__(self, root, layout, **kwargs):
             # Ensure projections are the same from each source
             # Read projections file from view
             if self.projections != self.read_projections():
-                msg = "View at %s has projections file" % self._root
-                msg += " which does not match projections passed manually."
-                raise ConflictingProjectionsError(msg)
+                raise ConflictingProjectionsError(
+                    f"View at {self._root} has projections file"
+                    " which does not match projections passed manually."
+                )
 
         self._croot = colorize_root(self._root) + " "
 
@@ -313,11 +315,11 @@ def add_specs(self, *specs, **kwargs):
 
     def add_standalone(self, spec):
         if spec.external:
-            tty.warn(self._croot + "Skipping external package: %s" % colorize_spec(spec))
+            tty.warn(f"{self._croot}Skipping external package: {colorize_spec(spec)}")
             return True
 
         if self.check_added(spec):
-            tty.warn(self._croot + "Skipping already linked package: %s" % colorize_spec(spec))
+            tty.warn(f"{self._croot}Skipping already linked package: {colorize_spec(spec)}")
             return True
 
         self.merge(spec)
@@ -325,7 +327,7 @@ def add_standalone(self, spec):
         self.link_meta_folder(spec)
 
         if self.verbose:
-            tty.info(self._croot + "Linked package: %s" % colorize_spec(spec))
+            tty.info(f"{self._croot}Linked package: {colorize_spec(spec)}")
         return True
 
     def merge(self, spec, ignore=None):
@@ -393,7 +395,7 @@ def needs_file(spec, file):
 
         for file in files:
             if not os.path.lexists(file):
-                tty.warn("Tried to remove %s which does not exist" % file)
+                tty.warn(f"Tried to remove {file} which does not exist")
                 continue
 
             # remove if file is not owned by any other package in the view
@@ -404,7 +406,7 @@ def needs_file(spec, file):
             # we are currently removing, as we remove files before unlinking the
             # metadata directory.
             if len([s for s in specs if needs_file(s, file)]) <= 1:
-                tty.debug("Removing file " + file)
+                tty.debug(f"Removing file {file}")
                 os.remove(file)
 
     def check_added(self, spec):
@@ -477,14 +479,14 @@ def remove_standalone(self, spec):
         Remove (unlink) a standalone package from this view.
         """
         if not self.check_added(spec):
-            tty.warn(self._croot + "Skipping package not linked in view: %s" % spec.name)
+            tty.warn(f"{self._croot}Skipping package not linked in view: {spec.name}")
             return
 
         self.unmerge(spec)
         self.unlink_meta_folder(spec)
 
         if self.verbose:
-            tty.info(self._croot + "Removed package: %s" % colorize_spec(spec))
+            tty.info(f"{self._croot}Removed package: {colorize_spec(spec)}")
 
     def get_projection_for_spec(self, spec):
         """
@@ -558,9 +560,9 @@ def print_conflict(self, spec_active, spec_specified, level="error"):
         linked = tty.color.colorize("   (@gLinked@.)", color=color)
         specified = tty.color.colorize("(@rSpecified@.)", color=color)
         cprint(
-            self._croot + "Package conflict detected:\n"
-            "%s %s\n" % (linked, colorize_spec(spec_active))
-            + "%s %s" % (specified, colorize_spec(spec_specified))
+            f"{self._croot}Package conflict detected:\n"
+            f"{linked} {colorize_spec(spec_active)}\n"
+            f"{specified} {colorize_spec(spec_specified)}"
         )
 
     def print_status(self, *specs, **kwargs):
@@ -572,14 +574,14 @@ def print_status(self, *specs, **kwargs):
 
         for s, v in zip(specs, in_view):
             if not v:
-                tty.error(self._croot + "Package not linked: %s" % s.name)
+                tty.error(f"{self._croot}Package not linked: {s.name}")
             elif s != v:
                 self.print_conflict(v, s, level="warn")
 
         in_view = list(filter(None, in_view))
 
         if len(specs) > 0:
-            tty.msg("Packages linked in %s:" % self._croot[:-1])
+            tty.msg(f"Packages linked in {self._croot[:-1]}:")
 
             # Make a dict with specs keyed by architecture and compiler.
             index = index_by(specs, ("architecture", "compiler"))
@@ -589,20 +591,19 @@ def print_status(self, *specs, **kwargs):
                 if i > 0:
                     print()
 
-                header = "%s{%s} / %s{%s}" % (
-                    spack.spec.ARCHITECTURE_COLOR,
-                    architecture,
-                    spack.spec.COMPILER_COLOR,
-                    compiler,
+                header = (
+                    f"{spack.spec.ARCHITECTURE_COLOR}{{{architecture}}} "
+                    f"/ {spack.spec.COMPILER_COLOR}{{{compiler}}}"
                 )
                 tty.hline(colorize(header), char="-")
 
                 specs = index[(architecture, compiler)]
                 specs.sort()
 
-                format_string = "{name}{@version}"
-                format_string += "{%compiler}{compiler_flags}{variants}"
-                abbreviated = [s.cformat(format_string) for s in specs]
+                abbreviated = [
+                    s.cformat("{name}{@version}{%compiler}{compiler_flags}{variants}")
+                    for s in specs
+                ]
 
                 # Print one spec per line along with prefix path
                 width = max(len(s) for s in abbreviated)
@@ -634,22 +635,19 @@ def unlink_meta_folder(self, spec):
 
 
 class SimpleFilesystemView(FilesystemView):
-    """A simple and partial implementation of FilesystemView focused on
-    performance and immutable views, where specs cannot be removed after they
-    were added."""
+    """A simple and partial implementation of FilesystemView focused on performance and immutable
+    views, where specs cannot be removed after they were added."""
 
     def __init__(self, root, layout, **kwargs):
         super().__init__(root, layout, **kwargs)
 
     def _sanity_check_view_projection(self, specs):
-        """A very common issue is that we end up with two specs of the same
-        package, that project to the same prefix. We want to catch that as
-        early as possible and give a sensible error to the user. Here we use
-        the metadata dir (.spack) projection as a quick test to see whether
-        two specs in the view are going to clash. The metadata dir is used
-        because it's always added by Spack with identical files, so a
-        guaranteed clash that's easily verified."""
-        seen = dict()
+        """A very common issue is that we end up with two specs of the same package, that project
+        to the same prefix. We want to catch that as early as possible and give a sensible error to
+        the user. Here we use the metadata dir (.spack) projection as a quick test to see whether
+        two specs in the view are going to clash. The metadata dir is used because it's always
+        added by Spack with identical files, so a guaranteed clash that's easily verified."""
+        seen = {}
         for current_spec in specs:
             metadata_dir = self.relative_metadata_dir_for_spec(current_spec)
             conflicting_spec = seen.get(metadata_dir)
@@ -657,7 +655,8 @@ def _sanity_check_view_projection(self, specs):
                 raise ConflictingSpecsError(current_spec, conflicting_spec)
             seen[metadata_dir] = current_spec
 
-    def add_specs(self, *specs, **kwargs):
+    def add_specs(self, *specs: spack.spec.Spec) -> None:
+        """Link a root-to-leaf topologically ordered list of specs into the view."""
         assert all((s.concrete for s in specs))
         if len(specs) == 0:
             return
@@ -668,9 +667,6 @@ def add_specs(self, *specs, **kwargs):
                 tty.warn("Skipping external package: " + s.short_spec)
         specs = [s for s in specs if not s.external]
 
-        if kwargs.get("exclude", None):
-            specs = set(filter_exclude(specs, kwargs["exclude"]))
-
         self._sanity_check_view_projection(specs)
 
         # Ignore spack meta data folder.
@@ -695,13 +691,11 @@ def skip_list(file):
         # Inform about file-file conflicts.
         if visitor.file_conflicts:
             if self.ignore_conflicts:
-                tty.debug("{0} file conflicts".format(len(visitor.file_conflicts)))
+                tty.debug(f"{len(visitor.file_conflicts)} file conflicts")
             else:
                 raise MergeConflictSummary(visitor.file_conflicts)
 
-        tty.debug(
-            "Creating {0} dirs and {1} links".format(len(visitor.directories), len(visitor.files))
-        )
+        tty.debug(f"Creating {len(visitor.directories)} dirs and {len(visitor.files)} links")
 
         # Make the directory structure
         for dst in visitor.directories:

lib/spack/spack/hooks/__init__.py

@@ -15,13 +15,6 @@
     * post_install(spec, explicit)
     * pre_uninstall(spec)
     * post_uninstall(spec)
-    * on_install_start(spec)
-    * on_install_success(spec)
-    * on_install_failure(spec)
-    * on_phase_success(pkg, phase_name, log_file)
-    * on_phase_error(pkg, phase_name, log_file)
-    * on_phase_error(pkg, phase_name, log_file)
-    * post_env_write(env)
 
 This can be used to implement support for things like module
 systems (e.g. modules, lmod, etc.) or to add other custom
@@ -78,17 +71,5 @@ def __call__(self, *args, **kwargs):
 pre_install = _HookRunner("pre_install")
 post_install = _HookRunner("post_install")
 
-# These hooks are run within an install subprocess
 pre_uninstall = _HookRunner("pre_uninstall")
 post_uninstall = _HookRunner("post_uninstall")
-on_phase_success = _HookRunner("on_phase_success")
-on_phase_error = _HookRunner("on_phase_error")
-
-# These are hooks in installer.py, before starting install subprocess
-on_install_start = _HookRunner("on_install_start")
-on_install_success = _HookRunner("on_install_success")
-on_install_failure = _HookRunner("on_install_failure")
-on_install_cancel = _HookRunner("on_install_cancel")
-
-# Environment hooks
-post_env_write = _HookRunner("post_env_write")

lib/spack/spack/hooks/drop_redundant_rpaths.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
-from typing import IO, Optional, Tuple
+from typing import BinaryIO, Optional, Tuple
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import BaseDirectoryVisitor, visit_directory_tree
@@ -18,7 +18,7 @@ def should_keep(path: bytes) -> bool:
     return path.startswith(b"$") or (os.path.isabs(path) and os.path.lexists(path))
 
 
-def _drop_redundant_rpaths(f: IO) -> Optional[Tuple[bytes, bytes]]:
+def _drop_redundant_rpaths(f: BinaryIO) -> Optional[Tuple[bytes, bytes]]:
     """Drop redundant entries from rpath.
 
     Args:

lib/spack/spack/installer.py

@@ -1705,7 +1705,6 @@ def _install_task(self, task: BuildTask, install_status: InstallStatus) -> None:
         except spack.build_environment.StopPhase as e:
             # A StopPhase exception means that do_install was asked to
             # stop early from clients, and is not an error at this point
-            spack.hooks.on_install_failure(task.request.pkg.spec)
             pid = f"{self.pid}: " if tty.show_pid() else ""
             tty.debug(f"{pid}{str(e)}")
             tty.debug(f"Package stage directory: {pkg.stage.source_path}")
@@ -2011,7 +2010,6 @@ def install(self) -> None:
             if task is None:
                 continue
 
-            spack.hooks.on_install_start(task.request.pkg.spec)
             install_args = task.request.install_args
             keep_prefix = install_args.get("keep_prefix")
 
@@ -2037,9 +2035,6 @@ def install(self) -> None:
                     tty.warn(f"{pkg_id} does NOT actually have any uninstalled deps left")
                 dep_str = "dependencies" if task.priority > 1 else "dependency"
 
-                # Hook to indicate task failure, but without an exception
-                spack.hooks.on_install_failure(task.request.pkg.spec)
-
                 raise InstallError(
                     f"Cannot proceed with {pkg_id}: {task.priority} uninstalled "
                     f"{dep_str}: {','.join(task.uninstalled_deps)}",
@@ -2062,11 +2057,6 @@ def install(self) -> None:
                 tty.warn(f"{pkg_id} failed to install")
                 self._update_failed(task)
 
-                # Mark that the package failed
-                # TODO: this should also be for the task.pkg, but we don't
-                # model transitive yet.
-                spack.hooks.on_install_failure(task.request.pkg.spec)
-
                 if self.fail_fast:
                     raise InstallError(fail_fast_err, pkg=pkg)
 
@@ -2169,7 +2159,6 @@ def install(self) -> None:
                 tty.error(
                     f"Failed to install {pkg.name} due to " f"{exc.__class__.__name__}: {str(exc)}"
                 )
-                spack.hooks.on_install_cancel(task.request.pkg.spec)
                 raise
 
             except binary_distribution.NoChecksumException as exc:
@@ -2188,7 +2177,6 @@ def install(self) -> None:
 
             except (Exception, SystemExit) as exc:
                 self._update_failed(task, True, exc)
-                spack.hooks.on_install_failure(task.request.pkg.spec)
 
                 # Best effort installs suppress the exception and mark the
                 # package as a failure.
@@ -2372,9 +2360,6 @@ def run(self) -> bool:
         _print_timer(pre=self.pre, pkg_id=self.pkg_id, timer=self.timer)
         _print_installed_pkg(self.pkg.prefix)
 
-        # Send final status that install is successful
-        spack.hooks.on_install_success(self.pkg.spec)
-
         # preserve verbosity across runs
         return self.echo
 
@@ -2453,15 +2438,10 @@ def _real_install(self) -> None:
                         # Catch any errors to report to logging
                         self.timer.start(phase_fn.name)
                         phase_fn.execute()
-                        spack.hooks.on_phase_success(pkg, phase_fn.name, log_file)
                         self.timer.stop(phase_fn.name)
 
                 except BaseException:
                     combine_phase_logs(pkg.phase_log_files, pkg.log_path)
-                    spack.hooks.on_phase_error(pkg, phase_fn.name, log_file)
-
-                    # phase error indicates install error
-                    spack.hooks.on_install_failure(pkg.spec)
                     raise
 
                 # We assume loggers share echo True/False

lib/spack/spack/main.py

@@ -1038,9 +1038,9 @@ def finish_parse_and_run(parser, cmd_name, main_args, env_format_error):
     set_working_dir()
 
     # now we can actually execute the command.
-    if args.spack_profile or args.sorted_profile:
+    if main_args.spack_profile or main_args.sorted_profile:
         _profile_wrapper(command, parser, args, unknown)
-    elif args.pdb:
+    elif main_args.pdb:
         import pdb
 
         pdb.runctx("_invoke_command(command, parser, args, unknown)", globals(), locals())

lib/spack/spack/operating_systems/windows_os.py

@@ -9,6 +9,8 @@
 import platform
 import subprocess
 
+from llnl.util import tty
+
 from spack.error import SpackError
 from spack.util import windows_registry as winreg
 from spack.version import Version
@@ -83,11 +85,50 @@ def compiler_search_paths(self):
                     os.path.join(str(os.getenv("ONEAPI_ROOT")), "compiler", "*", "windows", "bin")
                 )
             )
+
         # Second strategy: Find MSVC via the registry
-        msft = winreg.WindowsRegistryView(
-            "SOFTWARE\\WOW6432Node\\Microsoft", winreg.HKEY.HKEY_LOCAL_MACHINE
-        )
-        vs_entries = msft.find_subkeys(r"VisualStudio_.*")
+        def try_query_registry(retry=False):
+            winreg_report_error = lambda e: tty.debug(
+                'Windows registry query on "SOFTWARE\\WOW6432Node\\Microsoft"'
+                f"under HKEY_LOCAL_MACHINE: {str(e)}"
+            )
+            try:
+                # Registry interactions are subject to race conditions, etc and can generally
+                # be flakey, do this in a catch block to prevent reg issues from interfering
+                # with compiler detection
+                msft = winreg.WindowsRegistryView(
+                    "SOFTWARE\\WOW6432Node\\Microsoft", winreg.HKEY.HKEY_LOCAL_MACHINE
+                )
+                return msft.find_subkeys(r"VisualStudio_.*", recursive=False)
+            except OSError as e:
+                # OSErrors propagated into caller by Spack's registry module are expected
+                # and indicate a known issue with the registry query
+                # i.e. user does not have permissions or the key/value
+                # doesn't exist
+                winreg_report_error(e)
+                return []
+            except winreg.InvalidRegistryOperation as e:
+                # Other errors raised by the Spack's reg module indicate
+                # an unexpected error type, and are handled specifically
+                # as the underlying cause is difficult/impossible to determine
+                # without manually exploring the registry
+                # These errors can also be spurious (race conditions)
+                # and may resolve on re-execution of the query
+                # or are permanent (specific types of permission issues)
+                # but the registry raises the same exception for all types of
+                # atypical errors
+                if retry:
+                    winreg_report_error(e)
+                return []
+
+        vs_entries = try_query_registry()
+        if not vs_entries:
+            # Occasional spurious race conditions can arise when reading the MS reg
+            # typically these race conditions resolve immediately and we can safely
+            # retry the reg query without waiting
+            # Note: Winreg does not support locking
+            vs_entries = try_query_registry(retry=True)
+
         vs_paths = []
 
         def clean_vs_path(path):
@@ -99,11 +140,8 @@ def clean_vs_path(path):
                 val = entry.get_subkey("Capabilities").get_value("ApplicationDescription").value
                 vs_paths.append(clean_vs_path(val))
             except FileNotFoundError as e:
-                if hasattr(e, "winerror"):
-                    if e.winerror == 2:
-                        pass
-                    else:
-                        raise
+                if hasattr(e, "winerror") and e.winerror == 2:
+                    pass
                 else:
                     raise
 

lib/spack/spack/relocate.py

@@ -7,6 +7,7 @@
 import os
 import re
 from collections import OrderedDict
+from typing import List, Optional
 
 import macholib.mach_o
 import macholib.MachO
@@ -47,7 +48,7 @@ def __init__(self, file_path, root_path):
 
 
 @memoized
-def _patchelf():
+def _patchelf() -> Optional[executable.Executable]:
     """Return the full path to the patchelf binary, if available, else None."""
     import spack.bootstrap
 
@@ -55,9 +56,7 @@ def _patchelf():
         return None
 
     with spack.bootstrap.ensure_bootstrap_configuration():
-        patchelf = spack.bootstrap.ensure_patchelf_in_path_or_raise()
-
-    return patchelf.path
+        return spack.bootstrap.ensure_patchelf_in_path_or_raise()
 
 
 def _elf_rpaths_for(path):
@@ -340,31 +339,34 @@ def macholib_get_paths(cur_path):
     return (rpaths, deps, ident)
 
 
-def _set_elf_rpaths(target, rpaths):
-    """Replace the original RPATH of the target with the paths passed
-    as arguments.
+def _set_elf_rpaths_and_interpreter(
+    target: str, rpaths: List[str], interpreter: Optional[str] = None
+) -> Optional[str]:
+    """Replace the original RPATH of the target with the paths passed as arguments.
 
     Args:
         target: target executable. Must be an ELF object.
         rpaths: paths to be set in the RPATH
+        interpreter: optionally set the interpreter
 
     Returns:
-        A string concatenating the stdout and stderr of the call
-        to ``patchelf`` if it was invoked
+        A string concatenating the stdout and stderr of the call to ``patchelf`` if it was invoked
     """
     # Join the paths using ':' as a separator
     rpaths_str = ":".join(rpaths)
 
-    patchelf, output = executable.Executable(_patchelf()), None
     try:
+        # TODO: error handling is not great here?
         # TODO: revisit the use of --force-rpath as it might be conditional
         # TODO: if we want to support setting RUNPATH from binary packages
-        patchelf_args = ["--force-rpath", "--set-rpath", rpaths_str, target]
-        output = patchelf(*patchelf_args, output=str, error=str)
+        args = ["--force-rpath", "--set-rpath", rpaths_str]
+        if interpreter:
+            args.extend(["--set-interpreter", interpreter])
+        args.append(target)
+        return _patchelf()(*args, output=str, error=str)
     except executable.ProcessError as e:
-        msg = "patchelf --force-rpath --set-rpath {0} failed with error {1}"
-        tty.warn(msg.format(target, e))
-    return output
+        tty.warn(str(e))
+        return None
 
 
 def needs_binary_relocation(m_type, m_subtype):
@@ -501,10 +503,12 @@ def new_relocate_elf_binaries(binaries, prefix_to_prefix):
 
     for path in binaries:
         try:
-            elf.replace_rpath_in_place_or_raise(path, prefix_to_prefix)
-        except elf.ElfDynamicSectionUpdateFailed as e:
-            # Fall back to the old `patchelf --set-rpath` method.
-            _set_elf_rpaths(path, e.new.decode("utf-8").split(":"))
+            elf.substitute_rpath_and_pt_interp_in_place_or_raise(path, prefix_to_prefix)
+        except elf.ElfCStringUpdatesFailed as e:
+            # Fall back to `patchelf --set-rpath ... --set-interpreter ...`
+            rpaths = e.rpath.new_value.decode("utf-8").split(":") if e.rpath else []
+            interpreter = e.pt_interp.new_value.decode("utf-8") if e.pt_interp else None
+            _set_elf_rpaths_and_interpreter(path, rpaths=rpaths, interpreter=interpreter)
 
 
 def relocate_elf_binaries(
@@ -546,10 +550,10 @@ def relocate_elf_binaries(
             new_rpaths = _make_relative(new_binary, new_root, new_norm_rpaths)
             # check to see if relative rpaths are changed before rewriting
             if sorted(new_rpaths) != sorted(orig_rpaths):
-                _set_elf_rpaths(new_binary, new_rpaths)
+                _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
         else:
             new_rpaths = _transform_rpaths(orig_rpaths, orig_root, new_prefixes)
-            _set_elf_rpaths(new_binary, new_rpaths)
+            _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
 
 
 def make_link_relative(new_links, orig_links):
@@ -596,7 +600,7 @@ def make_elf_binaries_relative(new_binaries, orig_binaries, orig_layout_root):
         orig_rpaths = _elf_rpaths_for(new_binary)
         if orig_rpaths:
             new_rpaths = _make_relative(orig_binary, orig_layout_root, orig_rpaths)
-            _set_elf_rpaths(new_binary, new_rpaths)
+            _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
 
 
 def warn_if_link_cant_be_relocated(link, target):

lib/spack/spack/schema/bootstrap.py

@@ -3,16 +3,17 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Schema for bootstrap.yaml configuration file."""
+from typing import Any, Dict
 
 #: Schema of a single source
-_source_schema = {
+_source_schema: Dict[str, Any] = {
     "type": "object",
     "properties": {"name": {"type": "string"}, "metadata": {"type": "string"}},
     "additionalProperties": False,
     "required": ["name", "metadata"],
 }
 
-properties = {
+properties: Dict[str, Any] = {
     "bootstrap": {
         "type": "object",
         "properties": {

lib/spack/spack/schema/buildcache_spec.py

@@ -6,27 +6,31 @@
 """Schema for a buildcache spec.yaml file
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/buildcache_spec.py
-   :lines: 13-
+   :lines: 15-
 """
+from typing import Any, Dict
+
 import spack.schema.spec
 
+properties: Dict[str, Any] = {
+    # `buildinfo` is no longer needed as of Spack 0.21
+    "buildinfo": {"type": "object"},
+    "spec": {
+        "type": "object",
+        "additionalProperties": True,
+        "items": spack.schema.spec.properties,
+    },
+    "binary_cache_checksum": {
+        "type": "object",
+        "properties": {"hash_algorithm": {"type": "string"}, "hash": {"type": "string"}},
+    },
+    "buildcache_layout_version": {"type": "number"},
+}
+
 schema = {
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "Spack buildcache specfile schema",
     "type": "object",
     "additionalProperties": False,
-    "properties": {
-        # `buildinfo` is no longer needed as of Spack 0.21
-        "buildinfo": {"type": "object"},
-        "spec": {
-            "type": "object",
-            "additionalProperties": True,
-            "items": spack.schema.spec.properties,
-        },
-        "binary_cache_checksum": {
-            "type": "object",
-            "properties": {"hash_algorithm": {"type": "string"}, "hash": {"type": "string"}},
-        },
-        "buildcache_layout_version": {"type": "number"},
-    },
+    "properties": properties,
 }

lib/spack/spack/schema/cdash.py

@@ -2,16 +2,15 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 """Schema for cdash.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/cdash.py
    :lines: 13-
 """
-
+from typing import Any, Dict
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "cdash": {
         "type": "object",
         "additionalProperties": False,

lib/spack/spack/schema/ci.py

@@ -2,12 +2,12 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 """Schema for gitlab-ci.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/ci.py
-   :lines: 13-
+   :lines: 16-
 """
+from typing import Any, Dict
 
 from llnl.util.lang import union_dicts
 
@@ -164,7 +164,7 @@
 }
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "ci": {
         "oneOf": [
             # TODO: Replace with core-shared-properties in Spack 0.23

lib/spack/spack/schema/compilers.py

@@ -2,16 +2,17 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 """Schema for compilers.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/compilers.py
-   :lines: 13-
+   :lines: 15-
 """
+from typing import Any, Dict
+
 import spack.schema.environment
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "compilers": {
         "type": "array",
         "items": {

lib/spack/spack/schema/concretizer.py

@@ -2,14 +2,14 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 """Schema for concretizer.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/concretizer.py
-   :lines: 13-
+   :lines: 12-
 """
+from typing import Any, Dict
 
-properties = {
+properties: Dict[str, Any] = {
     "concretizer": {
         "type": "object",
         "additionalProperties": False,

lib/spack/spack/schema/config.py

@@ -5,15 +5,16 @@
 """Schema for config.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/config.py
-   :lines: 13-
+   :lines: 17-
 """
+from typing import Any, Dict
 
 from llnl.util.lang import union_dicts
 
 import spack.schema.projections
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "config": {
         "type": "object",
         "default": {},

lib/spack/spack/schema/container.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Schema for the 'container' subsection of Spack environments."""
+from typing import Any, Dict
 
 _stages_from_dockerhub = {
     "type": "object",
@@ -85,4 +86,4 @@
     },
 }
 
-properties = {"container": container_schema}
+properties: Dict[str, Any] = {"container": container_schema}

lib/spack/spack/schema/cray_manifest.py

@@ -11,112 +11,115 @@
    This does not specify a configuration - it is an input format
    that is consumed and transformed into Spack DB records.
 """
+from typing import Any, Dict
+
+properties: Dict[str, Any] = {
+    "_meta": {
+        "type": "object",
+        "additionalProperties": False,
+        "properties": {
+            "file-type": {"type": "string", "minLength": 1},
+            "cpe-version": {"type": "string", "minLength": 1},
+            "system-type": {"type": "string", "minLength": 1},
+            "schema-version": {"type": "string", "minLength": 1},
+            # Older schemas use did not have "cpe-version", just the
+            # schema version; in that case it was just called "version"
+            "version": {"type": "string", "minLength": 1},
+        },
+    },
+    "compilers": {
+        "type": "array",
+        "items": {
+            "type": "object",
+            "additionalProperties": False,
+            "properties": {
+                "name": {"type": "string", "minLength": 1},
+                "version": {"type": "string", "minLength": 1},
+                "prefix": {"type": "string", "minLength": 1},
+                "executables": {
+                    "type": "object",
+                    "additionalProperties": False,
+                    "properties": {
+                        "cc": {"type": "string", "minLength": 1},
+                        "cxx": {"type": "string", "minLength": 1},
+                        "fc": {"type": "string", "minLength": 1},
+                    },
+                },
+                "arch": {
+                    "type": "object",
+                    "required": ["os", "target"],
+                    "additionalProperties": False,
+                    "properties": {
+                        "os": {"type": "string", "minLength": 1},
+                        "target": {"type": "string", "minLength": 1},
+                    },
+                },
+            },
+        },
+    },
+    "specs": {
+        "type": "array",
+        "items": {
+            "type": "object",
+            "required": ["name", "version", "arch", "compiler", "prefix", "hash"],
+            "additionalProperties": False,
+            "properties": {
+                "name": {"type": "string", "minLength": 1},
+                "version": {"type": "string", "minLength": 1},
+                "arch": {
+                    "type": "object",
+                    "required": ["platform", "platform_os", "target"],
+                    "additionalProperties": False,
+                    "properties": {
+                        "platform": {"type": "string", "minLength": 1},
+                        "platform_os": {"type": "string", "minLength": 1},
+                        "target": {
+                            "type": "object",
+                            "additionalProperties": False,
+                            "required": ["name"],
+                            "properties": {"name": {"type": "string", "minLength": 1}},
+                        },
+                    },
+                },
+                "compiler": {
+                    "type": "object",
+                    "required": ["name", "version"],
+                    "additionalProperties": False,
+                    "properties": {
+                        "name": {"type": "string", "minLength": 1},
+                        "version": {"type": "string", "minLength": 1},
+                    },
+                },
+                "dependencies": {
+                    "type": "object",
+                    "patternProperties": {
+                        "\\w[\\w-]*": {
+                            "type": "object",
+                            "required": ["hash"],
+                            "additionalProperties": False,
+                            "properties": {
+                                "hash": {"type": "string", "minLength": 1},
+                                "type": {
+                                    "type": "array",
+                                    "items": {"type": "string", "minLength": 1},
+                                },
+                            },
+                        }
+                    },
+                },
+                "prefix": {"type": "string", "minLength": 1},
+                "rpm": {"type": "string", "minLength": 1},
+                "hash": {"type": "string", "minLength": 1},
+                "parameters": {"type": "object"},
+            },
+        },
+    },
+}
 
 schema = {
     "$schema": "http://json-schema.org/schema#",
     "title": "CPE manifest schema",
     "type": "object",
     "additionalProperties": False,
-    "properties": {
-        "_meta": {
-            "type": "object",
-            "additionalProperties": False,
-            "properties": {
-                "file-type": {"type": "string", "minLength": 1},
-                "cpe-version": {"type": "string", "minLength": 1},
-                "system-type": {"type": "string", "minLength": 1},
-                "schema-version": {"type": "string", "minLength": 1},
-                # Older schemas use did not have "cpe-version", just the
-                # schema version; in that case it was just called "version"
-                "version": {"type": "string", "minLength": 1},
-            },
-        },
-        "compilers": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "additionalProperties": False,
-                "properties": {
-                    "name": {"type": "string", "minLength": 1},
-                    "version": {"type": "string", "minLength": 1},
-                    "prefix": {"type": "string", "minLength": 1},
-                    "executables": {
-                        "type": "object",
-                        "additionalProperties": False,
-                        "properties": {
-                            "cc": {"type": "string", "minLength": 1},
-                            "cxx": {"type": "string", "minLength": 1},
-                            "fc": {"type": "string", "minLength": 1},
-                        },
-                    },
-                    "arch": {
-                        "type": "object",
-                        "required": ["os", "target"],
-                        "additionalProperties": False,
-                        "properties": {
-                            "os": {"type": "string", "minLength": 1},
-                            "target": {"type": "string", "minLength": 1},
-                        },
-                    },
-                },
-            },
-        },
-        "specs": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "required": ["name", "version", "arch", "compiler", "prefix", "hash"],
-                "additionalProperties": False,
-                "properties": {
-                    "name": {"type": "string", "minLength": 1},
-                    "version": {"type": "string", "minLength": 1},
-                    "arch": {
-                        "type": "object",
-                        "required": ["platform", "platform_os", "target"],
-                        "additioanlProperties": False,
-                        "properties": {
-                            "platform": {"type": "string", "minLength": 1},
-                            "platform_os": {"type": "string", "minLength": 1},
-                            "target": {
-                                "type": "object",
-                                "additionalProperties": False,
-                                "required": ["name"],
-                                "properties": {"name": {"type": "string", "minLength": 1}},
-                            },
-                        },
-                    },
-                    "compiler": {
-                        "type": "object",
-                        "required": ["name", "version"],
-                        "additionalProperties": False,
-                        "properties": {
-                            "name": {"type": "string", "minLength": 1},
-                            "version": {"type": "string", "minLength": 1},
-                        },
-                    },
-                    "dependencies": {
-                        "type": "object",
-                        "patternProperties": {
-                            "\\w[\\w-]*": {
-                                "type": "object",
-                                "required": ["hash"],
-                                "additionalProperties": False,
-                                "properties": {
-                                    "hash": {"type": "string", "minLength": 1},
-                                    "type": {
-                                        "type": "array",
-                                        "items": {"type": "string", "minLength": 1},
-                                    },
-                                },
-                            }
-                        },
-                    },
-                    "prefix": {"type": "string", "minLength": 1},
-                    "rpm": {"type": "string", "minLength": 1},
-                    "hash": {"type": "string", "minLength": 1},
-                    "parameters": {"type": "object"},
-                },
-            },
-        },
-    },
+    "properties": properties,
 }

lib/spack/spack/schema/database_index.py

@@ -6,12 +6,41 @@
 """Schema for database index.json file
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/database_index.py
-   :lines: 36-
+   :lines: 17-
 """
+from typing import Any, Dict
+
 import spack.schema.spec
 
 # spack.schema.spec.properties
 
+properties: Dict[str, Any] = {
+    "database": {
+        "type": "object",
+        "required": ["installs", "version"],
+        "additionalProperties": False,
+        "properties": {
+            "installs": {
+                "type": "object",
+                "patternProperties": {
+                    r"^[\w\d]{32}$": {
+                        "type": "object",
+                        "properties": {
+                            "spec": spack.schema.spec.properties,
+                            "path": {"oneOf": [{"type": "string"}, {"type": "null"}]},
+                            "installed": {"type": "boolean"},
+                            "ref_count": {"type": "integer", "minimum": 0},
+                            "explicit": {"type": "boolean"},
+                            "installation_time": {"type": "number"},
+                        },
+                    }
+                },
+            },
+            "version": {"type": "string"},
+        },
+    }
+}
+
 #: Full schema with metadata
 schema = {
     "$schema": "http://json-schema.org/draft-07/schema#",
@@ -19,30 +48,5 @@
     "type": "object",
     "required": ["database"],
     "additionalProperties": False,
-    "properties": {
-        "database": {
-            "type": "object",
-            "required": ["installs", "version"],
-            "additionalProperties": False,
-            "properties": {
-                "installs": {
-                    "type": "object",
-                    "patternProperties": {
-                        r"^[\w\d]{32}$": {
-                            "type": "object",
-                            "properties": {
-                                "spec": spack.schema.spec.properties,
-                                "path": {"oneOf": [{"type": "string"}, {"type": "null"}]},
-                                "installed": {"type": "boolean"},
-                                "ref_count": {"type": "integer", "minimum": 0},
-                                "explicit": {"type": "boolean"},
-                                "installation_time": {"type": "number"},
-                            },
-                        }
-                    },
-                },
-                "version": {"type": "string"},
-            },
-        }
-    },
+    "properties": properties,
 }

lib/spack/spack/schema/definitions.py

@@ -6,13 +6,14 @@
 """Schema for definitions
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/definitions.py
-   :lines: 13-
+   :lines: 16-
 """
+from typing import Any, Dict
 
 import spack.schema
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "definitions": {
         "type": "array",
         "default": [],

lib/spack/spack/schema/develop.py

@@ -2,9 +2,9 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from typing import Any, Dict
 
-
-properties = {
+properties: Dict[str, Any] = {
     "develop": {
         "type": "object",
         "default": {},

lib/spack/spack/schema/env.py

@@ -6,8 +6,10 @@
 """Schema for env.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/env.py
-   :lines: 36-
+   :lines: 19-
 """
+from typing import Any, Dict
+
 from llnl.util.lang import union_dicts
 
 import spack.schema.gitlab_ci  # DEPRECATED
@@ -19,61 +21,31 @@
 
 projections_scheme = spack.schema.projections.properties["projections"]
 
+properties: Dict[str, Any] = {
+    "spack": {
+        "type": "object",
+        "default": {},
+        "additionalProperties": False,
+        "properties": union_dicts(
+            # Include deprecated "gitlab-ci" section
+            spack.schema.gitlab_ci.properties,
+            # merged configuration scope schemas
+            spack.schema.merged.properties,
+            # extra environment schema properties
+            {
+                "include": {"type": "array", "default": [], "items": {"type": "string"}},
+                "specs": spack.schema.spec_list_schema,
+            },
+        ),
+    }
+}
+
 schema = {
     "$schema": "http://json-schema.org/draft-07/schema#",
     "title": "Spack environment file schema",
     "type": "object",
     "additionalProperties": False,
-    "properties": {
-        "spack": {
-            "type": "object",
-            "default": {},
-            "additionalProperties": False,
-            "properties": union_dicts(
-                # Include deprecated "gitlab-ci" section
-                spack.schema.gitlab_ci.properties,
-                # merged configuration scope schemas
-                spack.schema.merged.properties,
-                # extra environment schema properties
-                {
-                    "include": {"type": "array", "default": [], "items": {"type": "string"}},
-                    "specs": spack.schema.spec_list_schema,
-                    "view": {
-                        "anyOf": [
-                            {"type": "boolean"},
-                            {"type": "string"},
-                            {
-                                "type": "object",
-                                "patternProperties": {
-                                    r"\w+": {
-                                        "required": ["root"],
-                                        "additionalProperties": False,
-                                        "properties": {
-                                            "root": {"type": "string"},
-                                            "link": {
-                                                "type": "string",
-                                                "pattern": "(roots|all|run)",
-                                            },
-                                            "link_type": {"type": "string"},
-                                            "select": {
-                                                "type": "array",
-                                                "items": {"type": "string"},
-                                            },
-                                            "exclude": {
-                                                "type": "array",
-                                                "items": {"type": "string"},
-                                            },
-                                            "projections": projections_scheme,
-                                        },
-                                    }
-                                },
-                            },
-                        ]
-                    },
-                },
-            ),
-        }
-    },
+    "properties": properties,
 }
 
 

lib/spack/spack/schema/environment.py

@@ -6,6 +6,7 @@
 schemas.
 """
 import collections.abc
+from typing import Any, Dict
 
 array_of_strings_or_num = {
     "type": "array",
@@ -18,7 +19,7 @@
     "patternProperties": {r"\w[\w-]*": {"anyOf": [{"type": "string"}, {"type": "number"}]}},
 }
 
-definition = {
+definition: Dict[str, Any] = {
     "type": "object",
     "default": {},
     "additionalProperties": False,

lib/spack/spack/schema/gitlab_ci.py

@@ -6,8 +6,9 @@
 """Schema for gitlab-ci.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/gitlab_ci.py
-   :lines: 13-
+   :lines: 15-
 """
+from typing import Any, Dict
 
 from llnl.util.lang import union_dicts
 
@@ -35,7 +36,7 @@
 
 runner_selector_schema = {
     "type": "object",
-    "additionalProperties": False,
+    "additionalProperties": True,
     "required": ["tags"],
     "properties": runner_attributes_schema_items,
 }
@@ -112,7 +113,7 @@
 }
 
 #: Properties for inclusion in other schemas
-properties = {"gitlab-ci": gitlab_ci_properties}
+properties: Dict[str, Any] = {"gitlab-ci": gitlab_ci_properties}
 
 #: Full schema with metadata
 schema = {

lib/spack/spack/schema/merged.py

@@ -6,8 +6,10 @@
 """Schema for configuration merged into one file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/merged.py
-   :lines: 39-
+   :lines: 32-
 """
+from typing import Any, Dict
+
 from llnl.util.lang import union_dicts
 
 import spack.schema.bootstrap
@@ -24,9 +26,10 @@
 import spack.schema.packages
 import spack.schema.repos
 import spack.schema.upstreams
+import spack.schema.view
 
 #: Properties for inclusion in other schemas
-properties = union_dicts(
+properties: Dict[str, Any] = union_dicts(
     spack.schema.bootstrap.properties,
     spack.schema.cdash.properties,
     spack.schema.compilers.properties,
@@ -41,6 +44,7 @@
     spack.schema.packages.properties,
     spack.schema.repos.properties,
     spack.schema.upstreams.properties,
+    spack.schema.view.properties,
 )
 
 

lib/spack/spack/schema/mirrors.py

@@ -6,8 +6,9 @@
 """Schema for mirrors.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/mirrors.py
-   :lines: 12-69
+   :lines: 13-
 """
+from typing import Any, Dict
 
 #: Common properties for connection specification
 connection = {
@@ -50,7 +51,7 @@
 }
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "mirrors": {
         "type": "object",
         "default": {},

lib/spack/spack/schema/modules.py

@@ -6,8 +6,10 @@
 """Schema for modules.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/modules.py
-   :lines: 13-
+   :lines: 16-
 """
+from typing import Any, Dict
+
 import spack.schema.environment
 import spack.schema.projections
 
@@ -141,7 +143,7 @@
 
 
 # Properties for inclusion into other schemas (requires definitions)
-properties = {
+properties: Dict[str, Any] = {
     "modules": {
         "type": "object",
         "additionalProperties": False,

lib/spack/spack/schema/packages.py

@@ -5,8 +5,10 @@
 """Schema for packages.yaml configuration files.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/packages.py
-   :lines: 13-
+   :lines: 14-
 """
+from typing import Any, Dict
+
 import spack.schema.environment
 
 permissions = {
@@ -91,7 +93,7 @@
 REQUIREMENT_URL = "https://spack.readthedocs.io/en/latest/packages_yaml.html#package-requirements"
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "packages": {
         "type": "object",
         "default": {},

lib/spack/spack/schema/projections.py

@@ -6,12 +6,12 @@
 """Schema for projections.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/projections.py
-   :lines: 13-
+   :lines: 14-
 """
-
+from typing import Any, Dict
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "projections": {"type": "object", "patternProperties": {r"all|\w[\w-]*": {"type": "string"}}}
 }
 

lib/spack/spack/schema/repos.py

@@ -6,12 +6,14 @@
 """Schema for repos.yaml configuration file.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/repos.py
-   :lines: 13-
+   :lines: 14-
 """
-
+from typing import Any, Dict
 
 #: Properties for inclusion in other schemas
-properties = {"repos": {"type": "array", "default": [], "items": {"type": "string"}}}
+properties: Dict[str, Any] = {
+    "repos": {"type": "array", "default": [], "items": {"type": "string"}}
+}
 
 
 #: Full schema with metadata

lib/spack/spack/schema/spack.py

@@ -0,0 +1,46 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Schema for spack environment
+
+.. literalinclude:: _spack_root/lib/spack/spack/schema/spack.py
+   :lines: 20-
+"""
+from typing import Any, Dict
+
+from llnl.util.lang import union_dicts
+
+import spack.schema
+import spack.schema.gitlab_ci as ci_schema  # DEPRECATED
+import spack.schema.merged as merged_schema
+
+#: Properties for inclusion in other schemas
+properties: Dict[str, Any] = {
+    "spack": {
+        "type": "object",
+        "default": {},
+        "additionalProperties": False,
+        "properties": union_dicts(
+            # Include deprecated "gitlab-ci" section
+            ci_schema.properties,
+            # merged configuration scope schemas
+            merged_schema.properties,
+            # extra environment schema properties
+            {
+                "include": {"type": "array", "default": [], "items": {"type": "string"}},
+                "specs": spack.schema.spec_list_schema,
+            },
+        ),
+    }
+}
+
+#: Full schema with metadata
+schema = {
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Spack environment file schema",
+    "type": "object",
+    "additionalProperties": False,
+    "properties": properties,
+}

lib/spack/spack/schema/spec.py

@@ -8,9 +8,9 @@
 TODO: This needs to be updated? Especially the hashes under properties.
 
 .. literalinclude:: _spack_root/lib/spack/spack/schema/spec.py
-   :lines: 13-
+   :lines: 15-
 """
-
+from typing import Any, Dict
 
 target = {
     "oneOf": [
@@ -57,7 +57,7 @@
 }
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "spec": {
         "type": "object",
         "additionalProperties": False,

lib/spack/spack/schema/upstreams.py

@@ -2,10 +2,10 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
+from typing import Any, Dict
 
 #: Properties for inclusion in other schemas
-properties = {
+properties: Dict[str, Any] = {
     "upstreams": {
         "type": "object",
         "default": {},

lib/spack/spack/schema/view.py

@@ -0,0 +1,49 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Schema for view
+
+.. literalinclude:: _spack_root/lib/spack/spack/schema/view.py
+   :lines: 15-
+"""
+from typing import Any, Dict
+
+import spack.schema
+
+projections_scheme = spack.schema.projections.properties["projections"]
+
+#: Properties for inclusion in other schemas
+properties: Dict[str, Any] = {
+    "view": {
+        "anyOf": [
+            {"type": "boolean"},
+            {"type": "string"},
+            {
+                "type": "object",
+                "patternProperties": {
+                    r"\w+": {
+                        "required": ["root"],
+                        "additionalProperties": False,
+                        "properties": {
+                            "root": {"type": "string"},
+                            "link": {"type": "string", "pattern": "(roots|all|run)"},
+                            "link_type": {"type": "string"},
+                            "select": {"type": "array", "items": {"type": "string"}},
+                            "exclude": {"type": "array", "items": {"type": "string"}},
+                            "projections": projections_scheme,
+                        },
+                    }
+                },
+            },
+        ]
+    }
+}
+
+#: Full schema with metadata
+schema = {
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Spack view configuration file schema",
+    "properties": properties,
+}

lib/spack/spack/solver/asp.py

@@ -19,51 +19,6 @@
 
 import archspec.cpu
 
-import spack.config as sc
-import spack.deptypes as dt
-import spack.parser
-import spack.paths as sp
-import spack.util.path as sup
-
-try:
-    import clingo  # type: ignore[import]
-
-    # There may be a better way to detect this
-    clingo_cffi = hasattr(clingo.Symbol, "_rep")
-except ImportError:
-    clingo = None  # type: ignore
-    clingo_cffi = False
-except AttributeError:
-    # Reaching this point indicates a broken clingo installation
-    # If Spack derived clingo, suggest user re-run bootstrap
-    # if non-spack, suggest user investigate installation
-
-    # assume Spack is not responsibe for broken clingo
-    msg = (
-        f"Clingo installation at {clingo.__file__} is incomplete or invalid."
-        "Please repair installation or re-install. "
-        "Alternatively, consider installing clingo via Spack."
-    )
-    # check whether Spack is responsible
-    if (
-        pathlib.Path(
-            sup.canonicalize_path(sc.get("bootstrap:root", sp.default_user_bootstrap_path))
-        )
-        in pathlib.Path(clingo.__file__).parents
-    ):
-        # Spack is responsible for the broken clingo
-        msg = (
-            "Spack bootstrapped copy of Clingo is broken, "
-            "please re-run the bootstrapping process via command `spack bootstrap now`."
-            " If this issue persists, please file a bug at: github.com/spack/spack"
-        )
-    raise RuntimeError(
-        "Clingo installation may be broken or incomplete, "
-        "please verify clingo has been installed correctly"
-        "\n\nClingo does not provide symbol clingo.Symbol"
-        f"{msg}"
-    )
-
 import llnl.util.lang
 import llnl.util.tty as tty
 
@@ -72,11 +27,14 @@
 import spack.cmd
 import spack.compilers
 import spack.config
+import spack.config as sc
+import spack.deptypes as dt
 import spack.directives
 import spack.environment as ev
 import spack.error
 import spack.package_base
 import spack.package_prefs
+import spack.parser
 import spack.platforms
 import spack.repo
 import spack.spec
@@ -89,13 +47,23 @@
 import spack.version.git_ref_lookup
 from spack import traverse
 
+from .core import (
+    AspFunction,
+    NodeArgument,
+    ast_sym,
+    ast_type,
+    clingo,
+    clingo_cffi,
+    extract_args,
+    fn,
+    parse_files,
+    parse_term,
+)
 from .counter import FullDuplicatesCounter, MinimalDuplicatesCounter, NoDuplicatesCounter
 
 GitOrStandardVersion = Union[spack.version.GitVersion, spack.version.StandardVersion]
 
-# these are from clingo.ast and bootstrapped later
-ASTType = None
-parse_files = None
+TransformFunction = Callable[["spack.spec.Spec", List[AspFunction]], List[AspFunction]]
 
 #: Enable the addition of a runtime node
 WITH_RUNTIME = sys.platform != "win32"
@@ -120,29 +88,13 @@
 
 def default_clingo_control():
     """Return a control object with the default settings used in Spack"""
-    control = clingo.Control()
+    control = clingo().Control()
     control.configuration.configuration = "tweety"
     control.configuration.solver.heuristic = "Domain"
     control.configuration.solver.opt_strategy = "usc,one"
     return control
 
 
-# backward compatibility functions for clingo ASTs
-def ast_getter(*names):
-    def getter(node):
-        for name in names:
-            result = getattr(node, name, None)
-            if result:
-                return result
-        raise KeyError("node has no such keys: %s" % names)
-
-    return getter
-
-
-ast_type = ast_getter("ast_type", "type")
-ast_sym = ast_getter("symbol", "term")
-
-
 class Provenance(enum.IntEnum):
     """Enumeration of the possible provenances of a version."""
 
@@ -301,86 +253,6 @@ def specify(spec):
     return spack.spec.Spec(spec)
 
 
-class AspObject:
-    """Object representing a piece of ASP code."""
-
-
-def _id(thing):
-    """Quote string if needed for it to be a valid identifier."""
-    if isinstance(thing, AspObject):
-        return thing
-    elif isinstance(thing, bool):
-        return '"%s"' % str(thing)
-    elif isinstance(thing, int):
-        return str(thing)
-    else:
-        return '"%s"' % str(thing)
-
-
-@llnl.util.lang.key_ordering
-class AspFunction(AspObject):
-    __slots__ = ["name", "args"]
-
-    def __init__(self, name, args=None):
-        self.name = name
-        self.args = () if args is None else tuple(args)
-
-    def _cmp_key(self):
-        return self.name, self.args
-
-    def __call__(self, *args):
-        """Return a new instance of this function with added arguments.
-
-        Note that calls are additive, so you can do things like::
-
-            >>> attr = AspFunction("attr")
-            attr()
-
-            >>> attr("version")
-            attr("version")
-
-            >>> attr("version")("foo")
-            attr("version", "foo")
-
-            >>> v = AspFunction("attr", "version")
-            attr("version")
-
-            >>> v("foo", "bar")
-            attr("version", "foo", "bar")
-
-        """
-        return AspFunction(self.name, self.args + args)
-
-    def symbol(self, positive=True):
-        def argify(arg):
-            if isinstance(arg, bool):
-                return clingo.String(str(arg))
-            elif isinstance(arg, int):
-                return clingo.Number(arg)
-            elif isinstance(arg, AspFunction):
-                return clingo.Function(arg.name, [argify(x) for x in arg.args], positive=positive)
-            else:
-                return clingo.String(str(arg))
-
-        return clingo.Function(self.name, [argify(arg) for arg in self.args], positive=positive)
-
-    def __str__(self):
-        return "%s(%s)" % (self.name, ", ".join(str(_id(arg)) for arg in self.args))
-
-    def __repr__(self):
-        return str(self)
-
-
-class AspFunctionBuilder:
-    def __getattr__(self, name):
-        return AspFunction(name)
-
-
-fn = AspFunctionBuilder()
-
-TransformFunction = Callable[[spack.spec.Spec, List[AspFunction]], List[AspFunction]]
-
-
 def remove_node(spec: spack.spec.Spec, facts: List[AspFunction]) -> List[AspFunction]:
     """Transformation that removes all "node" and "virtual_node" from the input list of facts."""
     return list(filter(lambda x: x.args[0] not in ("node", "virtual_node"), facts))
@@ -663,72 +535,6 @@ def _spec_with_default_name(spec_str, name):
     return spec
 
 
-def bootstrap_clingo():
-    global clingo, ASTType, parse_files
-
-    if not clingo:
-        import spack.bootstrap
-
-        with spack.bootstrap.ensure_bootstrap_configuration():
-            spack.bootstrap.ensure_core_dependencies()
-            import clingo
-
-    from clingo.ast import ASTType
-
-    try:
-        from clingo.ast import parse_files
-    except ImportError:
-        # older versions of clingo have this one namespace up
-        from clingo import parse_files
-
-
-class NodeArgument(NamedTuple):
-    id: str
-    pkg: str
-
-
-def intermediate_repr(sym):
-    """Returns an intermediate representation of clingo models for Spack's spec builder.
-
-    Currently, transforms symbols from clingo models either to strings or to NodeArgument objects.
-
-    Returns:
-        This will turn a ``clingo.Symbol`` into a string or NodeArgument, or a sequence of
-        ``clingo.Symbol`` objects into a tuple of those objects.
-    """
-    # TODO: simplify this when we no longer have to support older clingo versions.
-    if isinstance(sym, (list, tuple)):
-        return tuple(intermediate_repr(a) for a in sym)
-
-    try:
-        if sym.name == "node":
-            return NodeArgument(
-                id=intermediate_repr(sym.arguments[0]), pkg=intermediate_repr(sym.arguments[1])
-            )
-    except RuntimeError:
-        # This happens when using clingo w/ CFFI and trying to access ".name" for symbols
-        # that are not functions
-        pass
-
-    if clingo_cffi:
-        # Clingo w/ CFFI will throw an exception on failure
-        try:
-            return sym.string
-        except RuntimeError:
-            return str(sym)
-    else:
-        return sym.string or str(sym)
-
-
-def extract_args(model, predicate_name):
-    """Extract the arguments to predicates with the provided name from a model.
-
-    Pull out all the predicates with name ``predicate_name`` from the model, and
-    return their intermediate representation.
-    """
-    return [intermediate_repr(sym.arguments) for sym in model if sym.name == predicate_name]
-
-
 class ErrorHandler:
     def __init__(self, model):
         self.model = model
@@ -830,7 +636,7 @@ def raise_if_errors(self):
         if not initial_error_args:
             return
 
-        error_causation = clingo.Control()
+        error_causation = clingo().Control()
 
         parent_dir = pathlib.Path(__file__).parent
         errors_lp = parent_dir / "error_messages.lp"
@@ -881,54 +687,9 @@ def __init__(self, cores=True):
             cores (bool): whether to generate unsatisfiable cores for better
                 error reporting.
         """
-        bootstrap_clingo()
-
-        self.out = llnl.util.lang.Devnull()
         self.cores = cores
-
-        # These attributes are part of the object, but will be reset
-        # at each call to solve
+        # This attribute will be reset at each call to solve
         self.control = None
-        self.backend = None
-        self.assumptions = None
-
-    def title(self, name, char):
-        self.out.write("\n")
-        self.out.write("%" + (char * 76))
-        self.out.write("\n")
-        self.out.write("%% %s\n" % name)
-        self.out.write("%" + (char * 76))
-        self.out.write("\n")
-
-    def h1(self, name):
-        self.title(name, "=")
-
-    def h2(self, name):
-        self.title(name, "-")
-
-    def newline(self):
-        self.out.write("\n")
-
-    def fact(self, head):
-        """ASP fact (a rule without a body).
-
-        Arguments:
-            head (AspFunction): ASP function to generate as fact
-        """
-        symbol = head.symbol() if hasattr(head, "symbol") else head
-
-        # This is commented out to avoid evaluating str(symbol) when we have no stream
-        if not isinstance(self.out, llnl.util.lang.Devnull):
-            self.out.write(f"{str(symbol)}.\n")
-
-        atom = self.backend.add_atom(symbol)
-
-        # Only functions relevant for constructing bug reports for bad error messages
-        # are assumptions, and only when using cores.
-        choice = self.cores and symbol.name == "internal_error"
-        self.backend.add_rule([atom], [], choice=choice)
-        if choice:
-            self.assumptions.append(atom)
 
     def solve(self, setup, specs, reuse=None, output=None, control=None, allow_deprecated=False):
         """Set up the input and solve for dependencies of ``specs``.
@@ -948,49 +709,24 @@ def solve(self, setup, specs, reuse=None, output=None, control=None, allow_depre
             solve, and the internal statistics from clingo.
         """
         output = output or DEFAULT_OUTPUT_CONFIGURATION
-        # allow solve method to override the output stream
-        if output.out is not None:
-            self.out = output.out
-
         timer = spack.util.timer.Timer()
 
         # Initialize the control object for the solver
         self.control = control or default_clingo_control()
-        # set up the problem -- this generates facts and rules
-        self.assumptions = []
+
         timer.start("setup")
-        with self.control.backend() as backend:
-            self.backend = backend
-            setup.setup(self, specs, reuse=reuse, allow_deprecated=allow_deprecated)
+        asp_problem = setup.setup(specs, reuse=reuse, allow_deprecated=allow_deprecated)
+        if output.out is not None:
+            output.out.write(asp_problem)
+        if output.setup_only:
+            return Result(specs), None, None
         timer.stop("setup")
 
         timer.start("load")
-        # read in the main ASP program and display logic -- these are
-        # handwritten, not generated, so we load them as resources
-        parent_dir = os.path.dirname(__file__)
-
-        # extract error messages from concretize.lp by inspecting its AST
-        with self.backend:
-
-            def visit(node):
-                if ast_type(node) == ASTType.Rule:
-                    for term in node.body:
-                        if ast_type(term) == ASTType.Literal:
-                            if ast_type(term.atom) == ASTType.SymbolicAtom:
-                                name = ast_sym(term.atom).name
-                                if name == "internal_error":
-                                    arg = ast_sym(ast_sym(term.atom).arguments[0])
-                                    self.fact(AspFunction(name)(arg.string))
-
-            self.h1("Error messages")
-            path = os.path.join(parent_dir, "concretize.lp")
-            parse_files([path], visit)
-
-        # If we're only doing setup, just return an empty solve result
-        if output.setup_only:
-            return Result(specs), None, None
-
+        # Add the problem instance
+        self.control.add("base", [], asp_problem)
         # Load the file itself
+        parent_dir = os.path.dirname(__file__)
         self.control.load(os.path.join(parent_dir, "concretize.lp"))
         self.control.load(os.path.join(parent_dir, "heuristic.lp"))
         if spack.config.CONFIG.get("concretizer:duplicates:strategy", "none") != "none":
@@ -1016,12 +752,12 @@ def on_model(model):
             models.append((model.cost, model.symbols(shown=True, terms=True)))
 
         solve_kwargs = {
-            "assumptions": self.assumptions,
+            "assumptions": setup.assumptions,
             "on_model": on_model,
             "on_core": cores.append,
         }
 
-        if clingo_cffi:
+        if clingo_cffi():
             solve_kwargs["on_unsat"] = cores.append
 
         timer.start("solve")
@@ -1142,6 +878,7 @@ class SpackSolverSetup:
     def __init__(self, tests=False):
         self.gen = None  # set by setup()
 
+        self.assumptions = []
         self.declared_versions = collections.defaultdict(list)
         self.possible_versions = collections.defaultdict(set)
         self.deprecated_versions = collections.defaultdict(set)
@@ -1768,15 +1505,12 @@ def external_packages(self):
             for local_idx, spec in enumerate(external_specs):
                 msg = "%s available as external when satisfying %s" % (spec.name, spec)
 
-                def external_imposition(input_spec, _):
-                    return [fn.attr("external_conditions_hold", input_spec.name, local_idx)]
+                def external_imposition(input_spec, requirements):
+                    return requirements + [
+                        fn.attr("external_conditions_hold", input_spec.name, local_idx)
+                    ]
 
-                self.condition(
-                    spec,
-                    spack.spec.Spec(spec.name),
-                    msg=msg,
-                    transform_imposed=external_imposition,
-                )
+                self.condition(spec, spec, msg=msg, transform_imposed=external_imposition)
                 self.possible_versions[spec.name].add(spec.version)
                 self.gen.newline()
 
@@ -1881,36 +1615,7 @@ def _spec_clauses(
         """
         clauses = []
 
-        # TODO: do this with consistent suffixes.
-        class Head:
-            node = fn.attr("node")
-            virtual_node = fn.attr("virtual_node")
-            node_platform = fn.attr("node_platform_set")
-            node_os = fn.attr("node_os_set")
-            node_target = fn.attr("node_target_set")
-            variant_value = fn.attr("variant_set")
-            node_compiler = fn.attr("node_compiler_set")
-            node_compiler_version = fn.attr("node_compiler_version_set")
-            node_flag = fn.attr("node_flag_set")
-            node_flag_source = fn.attr("node_flag_source")
-            node_flag_propagate = fn.attr("node_flag_propagate")
-            variant_propagation_candidate = fn.attr("variant_propagation_candidate")
-
-        class Body:
-            node = fn.attr("node")
-            virtual_node = fn.attr("virtual_node")
-            node_platform = fn.attr("node_platform")
-            node_os = fn.attr("node_os")
-            node_target = fn.attr("node_target")
-            variant_value = fn.attr("variant_value")
-            node_compiler = fn.attr("node_compiler")
-            node_compiler_version = fn.attr("node_compiler_version")
-            node_flag = fn.attr("node_flag")
-            node_flag_source = fn.attr("node_flag_source")
-            node_flag_propagate = fn.attr("node_flag_propagate")
-            variant_propagation_candidate = fn.attr("variant_propagation_candidate")
-
-        f = Body if body else Head
+        f = _Body if body else _Head
 
         if spec.name:
             clauses.append(f.node(spec.name) if not spec.virtual else f.virtual_node(spec.name))
@@ -2506,12 +2211,11 @@ def define_concrete_input_specs(self, specs, possible):
 
     def setup(
         self,
-        driver: PyclingoDriver,
         specs: Sequence[spack.spec.Spec],
         *,
         reuse: Optional[List[spack.spec.Spec]] = None,
         allow_deprecated: bool = False,
-    ):
+    ) -> str:
         """Generate an ASP program with relevant constraints for specs.
 
         This calls methods on the solve driver to set up the problem with
@@ -2519,7 +2223,6 @@ def setup(
         specs, as well as constraints from the specs themselves.
 
         Arguments:
-            driver: driver instance of this solve
             specs: list of Specs to solve
             reuse: list of concrete specs that can be reused
             allow_deprecated: if True adds deprecated versions into the solve
@@ -2545,9 +2248,7 @@ def setup(
             if node.namespace is not None:
                 self.explicitly_required_namespaces[node.name] = node.namespace
 
-        # driver is used by all the functions below to add facts and
-        # rules to generate an ASP program.
-        self.gen = driver
+        self.gen = ProblemInstanceBuilder()
 
         if not allow_deprecated:
             self.gen.fact(fn.deprecated_versions_not_allowed())
@@ -2651,6 +2352,29 @@ def setup(
         self.gen.h1("Target Constraints")
         self.define_target_constraints()
 
+        self.gen.h1("Internal errors")
+        self.internal_errors()
+
+        return self.gen.value()
+
+    def internal_errors(self):
+        parent_dir = os.path.dirname(__file__)
+
+        def visit(node):
+            if ast_type(node) == clingo().ast.ASTType.Rule:
+                for term in node.body:
+                    if ast_type(term) == clingo().ast.ASTType.Literal:
+                        if ast_type(term.atom) == clingo().ast.ASTType.SymbolicAtom:
+                            name = ast_sym(term.atom).name
+                            if name == "internal_error":
+                                arg = ast_sym(ast_sym(term.atom).arguments[0])
+                                symbol = AspFunction(name)(arg.string)
+                                self.assumptions.append((parse_term(str(symbol)), True))
+                                self.gen.asp_problem.append(f"{{ {symbol} }}.\n")
+
+        path = os.path.join(parent_dir, "concretize.lp")
+        parse_files([path], visit)
+
     def define_runtime_constraints(self):
         """Define the constraints to be imposed on the runtimes"""
         recorder = RuntimePropertyRecorder(self)
@@ -2781,6 +2505,83 @@ def pkg_class(self, pkg_name: str) -> typing.Type["spack.package_base.PackageBas
         return spack.repo.PATH.get_pkg_class(request)
 
 
+class _Head:
+    """ASP functions used to express spec clauses in the HEAD of a rule"""
+
+    node = fn.attr("node")
+    virtual_node = fn.attr("virtual_node")
+    node_platform = fn.attr("node_platform_set")
+    node_os = fn.attr("node_os_set")
+    node_target = fn.attr("node_target_set")
+    variant_value = fn.attr("variant_set")
+    node_compiler = fn.attr("node_compiler_set")
+    node_compiler_version = fn.attr("node_compiler_version_set")
+    node_flag = fn.attr("node_flag_set")
+    node_flag_source = fn.attr("node_flag_source")
+    node_flag_propagate = fn.attr("node_flag_propagate")
+    variant_propagation_candidate = fn.attr("variant_propagation_candidate")
+
+
+class _Body:
+    """ASP functions used to express spec clauses in the BODY of a rule"""
+
+    node = fn.attr("node")
+    virtual_node = fn.attr("virtual_node")
+    node_platform = fn.attr("node_platform")
+    node_os = fn.attr("node_os")
+    node_target = fn.attr("node_target")
+    variant_value = fn.attr("variant_value")
+    node_compiler = fn.attr("node_compiler")
+    node_compiler_version = fn.attr("node_compiler_version")
+    node_flag = fn.attr("node_flag")
+    node_flag_source = fn.attr("node_flag_source")
+    node_flag_propagate = fn.attr("node_flag_propagate")
+    variant_propagation_candidate = fn.attr("variant_propagation_candidate")
+
+
+class ProblemInstanceBuilder:
+    """Provides an interface to construct a problem instance.
+
+    Once all the facts and rules have been added, the problem instance can be retrieved with:
+
+    >>> builder = ProblemInstanceBuilder()
+    >>> ...
+    >>> problem_instance = builder.value()
+
+    The problem instance can be added directly to the "control" structure of clingo.
+    """
+
+    def __init__(self):
+        self.asp_problem = []
+
+    def fact(self, atom: AspFunction) -> None:
+        symbol = atom.symbol() if hasattr(atom, "symbol") else atom
+        self.asp_problem.append(f"{str(symbol)}.\n")
+
+    def append(self, rule: str) -> None:
+        self.asp_problem.append(rule)
+
+    def title(self, header: str, char: str) -> None:
+        self.asp_problem.append("\n")
+        self.asp_problem.append("%" + (char * 76))
+        self.asp_problem.append("\n")
+        self.asp_problem.append(f"% {header}\n")
+        self.asp_problem.append("%" + (char * 76))
+        self.asp_problem.append("\n")
+
+    def h1(self, header: str) -> None:
+        self.title(header, "=")
+
+    def h2(self, header: str) -> None:
+        self.title(header, "-")
+
+    def newline(self):
+        self.asp_problem.append("\n")
+
+    def value(self) -> str:
+        return "".join(self.asp_problem)
+
+
 class RequirementParser:
     """Parses requirements from package.py files and configuration, and returns rules."""
 
@@ -3088,9 +2889,7 @@ def consume_facts(self):
         self._setup.gen.h2("Runtimes: rules")
         self._setup.gen.newline()
         for rule in self.rules:
-            if not isinstance(self._setup.gen.out, llnl.util.lang.Devnull):
-                self._setup.gen.out.write(rule)
-            self._setup.gen.control.add("base", [], rule)
+            self._setup.gen.append(rule)
 
         self._setup.gen.h2("Runtimes: conditions")
         for runtime_pkg in spack.repo.PATH.packages_with_tags("runtime"):

lib/spack/spack/solver/concretize.lp

@@ -698,6 +698,14 @@ requirement_group_satisfied(node(ID, Package), X) :-
   activate_requirement(node(ID, Package), X),
   requirement_group(Package, X).
 
+% Do not impose requirements, if the conditional requirement is not active
+do_not_impose(EffectID, node(ID, Package)) :-
+  trigger_condition_holds(TriggerID, node(ID, Package)),
+  pkg_fact(Package, condition_trigger(ConditionID, TriggerID)),
+  pkg_fact(Package, condition_effect(ConditionID, EffectID)),
+  requirement_group_member(ConditionID , Package, RequirementID),
+  not activate_requirement(node(ID, Package), RequirementID).
+
 % When we have a required provider, we need to ensure that the provider/2 facts respect
 % the requirement. This is particularly important for packages that could provide multiple
 % virtuals independently

lib/spack/spack/solver/core.py

@@ -0,0 +1,272 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+"""Low-level wrappers around clingo API."""
+import importlib
+import pathlib
+from types import ModuleType
+from typing import Any, Callable, NamedTuple, Optional, Tuple, Union
+
+from llnl.util import lang
+
+
+def _ast_getter(*names: str) -> Callable[[Any], Any]:
+    """Helper to retrieve AST attributes from different versions of the clingo API"""
+
+    def getter(node):
+        for name in names:
+            result = getattr(node, name, None)
+            if result:
+                return result
+        raise KeyError(f"node has no such keys: {names}")
+
+    return getter
+
+
+ast_type = _ast_getter("ast_type", "type")
+ast_sym = _ast_getter("symbol", "term")
+
+
+class AspObject:
+    """Object representing a piece of ASP code."""
+
+
+def _id(thing: Any) -> Union[str, AspObject]:
+    """Quote string if needed for it to be a valid identifier."""
+    if isinstance(thing, AspObject):
+        return thing
+    elif isinstance(thing, bool):
+        return f'"{str(thing)}"'
+    elif isinstance(thing, int):
+        return str(thing)
+    else:
+        return f'"{str(thing)}"'
+
+
+@lang.key_ordering
+class AspFunction(AspObject):
+    """A term in the ASP logic program"""
+
+    __slots__ = ["name", "args"]
+
+    def __init__(self, name: str, args: Optional[Tuple[Any, ...]] = None) -> None:
+        self.name = name
+        self.args = () if args is None else tuple(args)
+
+    def _cmp_key(self) -> Tuple[str, Optional[Tuple[Any, ...]]]:
+        return self.name, self.args
+
+    def __call__(self, *args: Any) -> "AspFunction":
+        """Return a new instance of this function with added arguments.
+
+        Note that calls are additive, so you can do things like::
+
+            >>> attr = AspFunction("attr")
+            attr()
+
+            >>> attr("version")
+            attr("version")
+
+            >>> attr("version")("foo")
+            attr("version", "foo")
+
+            >>> v = AspFunction("attr", "version")
+            attr("version")
+
+            >>> v("foo", "bar")
+            attr("version", "foo", "bar")
+
+        """
+        return AspFunction(self.name, self.args + args)
+
+    def _argify(self, arg: Any) -> Any:
+        """Turn the argument into an appropriate clingo symbol"""
+        if isinstance(arg, bool):
+            return clingo().String(str(arg))
+        elif isinstance(arg, int):
+            return clingo().Number(arg)
+        elif isinstance(arg, AspFunction):
+            return clingo().Function(arg.name, [self._argify(x) for x in arg.args], positive=True)
+        return clingo().String(str(arg))
+
+    def symbol(self):
+        """Return a clingo symbol for this function"""
+        return clingo().Function(
+            self.name, [self._argify(arg) for arg in self.args], positive=True
+        )
+
+    def __str__(self) -> str:
+        return f"{self.name}({', '.join(str(_id(arg)) for arg in self.args)})"
+
+    def __repr__(self) -> str:
+        return str(self)
+
+
+class _AspFunctionBuilder:
+    def __getattr__(self, name):
+        return AspFunction(name)
+
+
+#: Global AspFunction builder
+fn = _AspFunctionBuilder()
+
+_CLINGO_MODULE: Optional[ModuleType] = None
+
+
+def clingo() -> ModuleType:
+    """Lazy imports the Python module for clingo, and returns it."""
+    if _CLINGO_MODULE is not None:
+        return _CLINGO_MODULE
+
+    try:
+        clingo_mod = importlib.import_module("clingo")
+        # Make sure we didn't import an empty module
+        _ensure_clingo_or_raise(clingo_mod)
+    except ImportError:
+        clingo_mod = None
+
+    if clingo_mod is not None:
+        return _set_clingo_module_cache(clingo_mod)
+
+    clingo_mod = _bootstrap_clingo()
+    return _set_clingo_module_cache(clingo_mod)
+
+
+def _set_clingo_module_cache(clingo_mod: ModuleType) -> ModuleType:
+    """Sets the global cache to the lazy imported clingo module"""
+    global _CLINGO_MODULE
+    importlib.import_module("clingo.ast")
+    _CLINGO_MODULE = clingo_mod
+    return clingo_mod
+
+
+def _ensure_clingo_or_raise(clingo_mod: ModuleType) -> None:
+    """Ensures the clingo module can access expected attributes, otherwise raises an error."""
+    # These are imports that may be problematic at top level (circular imports). They are used
+    # only to provide exhaustive details when erroring due to a broken clingo module.
+    import spack.config
+    import spack.paths as sp
+    import spack.util.path as sup
+
+    try:
+        clingo_mod.Symbol
+    except AttributeError:
+        assert clingo_mod.__file__ is not None, "clingo installation is incomplete or invalid"
+        # Reaching this point indicates a broken clingo installation
+        # If Spack derived clingo, suggest user re-run bootstrap
+        # if non-spack, suggest user investigate installation
+        # assume Spack is not responsible for broken clingo
+        msg = (
+            f"Clingo installation at {clingo_mod.__file__} is incomplete or invalid."
+            "Please repair installation or re-install. "
+            "Alternatively, consider installing clingo via Spack."
+        )
+        # check whether Spack is responsible
+        if (
+            pathlib.Path(
+                sup.canonicalize_path(
+                    spack.config.CONFIG.get("bootstrap:root", sp.default_user_bootstrap_path)
+                )
+            )
+            in pathlib.Path(clingo_mod.__file__).parents
+        ):
+            # Spack is responsible for the broken clingo
+            msg = (
+                "Spack bootstrapped copy of Clingo is broken, "
+                "please re-run the bootstrapping process via command `spack bootstrap now`."
+                " If this issue persists, please file a bug at: github.com/spack/spack"
+            )
+        raise RuntimeError(
+            "Clingo installation may be broken or incomplete, "
+            "please verify clingo has been installed correctly"
+            "\n\nClingo does not provide symbol clingo.Symbol"
+            f"{msg}"
+        )
+
+
+def clingo_cffi() -> bool:
+    """Returns True if clingo uses the CFFI interface"""
+    return hasattr(clingo().Symbol, "_rep")
+
+
+def _bootstrap_clingo() -> ModuleType:
+    """Bootstraps the clingo module and returns it"""
+    import spack.bootstrap
+
+    with spack.bootstrap.ensure_bootstrap_configuration():
+        spack.bootstrap.ensure_core_dependencies()
+        clingo_mod = importlib.import_module("clingo")
+
+    return clingo_mod
+
+
+def parse_files(*args, **kwargs):
+    """Wrapper around clingo parse_files, that dispatches the function according
+    to clingo API version.
+    """
+    clingo()
+    try:
+        return importlib.import_module("clingo.ast").parse_files(*args, **kwargs)
+    except (ImportError, AttributeError):
+        return clingo().parse_files(*args, **kwargs)
+
+
+def parse_term(*args, **kwargs):
+    """Wrapper around clingo parse_term, that dispatches the function according
+    to clingo API version.
+    """
+    clingo()
+    try:
+        return importlib.import_module("clingo.symbol").parse_term(*args, **kwargs)
+    except (ImportError, AttributeError):
+        return clingo().parse_term(*args, **kwargs)
+
+
+class NodeArgument(NamedTuple):
+    """Represents a node in the DAG"""
+
+    id: str
+    pkg: str
+
+
+def intermediate_repr(sym):
+    """Returns an intermediate representation of clingo models for Spack's spec builder.
+
+    Currently, transforms symbols from clingo models either to strings or to NodeArgument objects.
+
+    Returns:
+        This will turn a ``clingo.Symbol`` into a string or NodeArgument, or a sequence of
+        ``clingo.Symbol`` objects into a tuple of those objects.
+    """
+    # TODO: simplify this when we no longer have to support older clingo versions.
+    if isinstance(sym, (list, tuple)):
+        return tuple(intermediate_repr(a) for a in sym)
+
+    try:
+        if sym.name == "node":
+            return NodeArgument(
+                id=intermediate_repr(sym.arguments[0]), pkg=intermediate_repr(sym.arguments[1])
+            )
+    except RuntimeError:
+        # This happens when using clingo w/ CFFI and trying to access ".name" for symbols
+        # that are not functions
+        pass
+
+    if clingo_cffi():
+        # Clingo w/ CFFI will throw an exception on failure
+        try:
+            return sym.string
+        except RuntimeError:
+            return str(sym)
+    else:
+        return sym.string or str(sym)
+
+
+def extract_args(model, predicate_name):
+    """Extract the arguments to predicates with the provided name from a model.
+
+    Pull out all the predicates with name ``predicate_name`` from the model, and
+    return their intermediate representation.
+    """
+    return [intermediate_repr(sym.arguments) for sym in model if sym.name == predicate_name]

lib/spack/spack/spec.py

@@ -186,11 +186,11 @@ class InstallStatus(enum.Enum):
     Options are artificially disjoint for display purposes
     """
 
-    installed = "@g{[+]}  "
-    upstream = "@g{[^]}  "
-    external = "@g{[e]}  "
-    absent = "@K{ - }  "
-    missing = "@r{[-]}  "
+    INSTALLED = "@g{[+]}"
+    UPSTREAM = "@g{[^]}"
+    EXTERNAL = "@g{[e]}"
+    ABSENT = "@K{ - }"
+    MISSING = "@r{[-]}"
 
 
 def colorize_spec(spec):
@@ -1499,9 +1499,11 @@ def edge_attributes(self) -> str:
         if not deptypes_str and not virtuals_str:
             return ""
         result = f"{deptypes_str} {virtuals_str}".strip()
-        return f"[{result}]"
+        return f"[{result}] "
 
-    def dependencies(self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.ALL):
+    def dependencies(
+        self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.ALL
+    ) -> List["Spec"]:
         """Return a list of direct dependencies (nodes in the DAG).
 
         Args:
@@ -1512,7 +1514,9 @@ def dependencies(self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.A
             deptype = dt.canonicalize(deptype)
         return [d.spec for d in self.edges_to_dependencies(name, depflag=deptype)]
 
-    def dependents(self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.ALL):
+    def dependents(
+        self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.ALL
+    ) -> List["Spec"]:
         """Return a list of direct dependents (nodes in the DAG).
 
         Args:
@@ -1636,23 +1640,23 @@ def _add_dependency(self, spec: "Spec", *, depflag: dt.DepFlag, virtuals: Tuple[
             self.add_dependency_edge(spec, depflag=depflag, virtuals=virtuals)
             return
 
-        # Keep the intersection of constraints when a dependency is added
-        # multiple times. Currently, we only allow identical edge types.
+        # Keep the intersection of constraints when a dependency is added multiple times.
+        # The only restriction, currently, is keeping the same dependency type
         orig = self._dependencies[spec.name]
         try:
             dspec = next(dspec for dspec in orig if depflag == dspec.depflag)
         except StopIteration:
-            current_deps = ", ".join(
-                dt.flag_to_chars(x.depflag) + " " + x.spec.short_spec for x in orig
-            )
+            edge_attrs = f"deptypes={dt.flag_to_chars(depflag).strip()}"
+            required_dep_str = f"^[{edge_attrs}] {str(spec)}"
+
             raise DuplicateDependencyError(
-                f"{self.short_spec} cannot depend on '{spec.short_spec}' multiple times.\n"
-                f"\tRequired: {dt.flag_to_chars(depflag)}\n"
-                f"\tDependency: {current_deps}"
+                f"{spec.name} is a duplicate dependency, with conflicting dependency types\n"
+                f"\t'{str(self)}' cannot depend on '{required_dep_str}'"
             )
 
         try:
             dspec.spec.constrain(spec)
+            dspec.update_virtuals(virtuals=virtuals)
         except spack.error.UnsatisfiableSpecError:
             raise DuplicateDependencyError(
                 f"Cannot depend on incompatible specs '{dspec.spec}' and '{spec}'"
@@ -4315,8 +4319,7 @@ def colorized(self):
         return colorize_spec(self)
 
     def format(self, format_string=DEFAULT_FORMAT, **kwargs):
-        r"""Prints out particular pieces of a spec, depending on what is
-        in the format string.
+        r"""Prints out particular pieces of a spec, depending on what is in the format string.
 
         Using the ``{attribute}`` syntax, any field of the spec can be
         selected.  Those attributes can be recursive. For example,
@@ -4442,6 +4445,9 @@ def write_attribute(spec, attribute, color):
             elif attribute == "spack_install":
                 write(morph(spec, spack.store.STORE.layout.root))
                 return
+            elif re.match(r"install_status", attribute):
+                write(self.install_status_symbol())
+                return
             elif re.match(r"hash(:\d)?", attribute):
                 col = "#"
                 if ":" in attribute:
@@ -4536,8 +4542,18 @@ def write_attribute(spec, attribute, color):
                 "Format string terminated while reading attribute." "Missing terminating }."
             )
 
+        # remove leading whitespace from directives that add it for internal formatting.
+        # Arch, compiler flags, and variants add spaces for spec format correctness, but
+        # we don't really want them in formatted string output. We do want to preserve
+        # whitespace from the format string.
         formatted_spec = out.getvalue()
-        return formatted_spec.strip()
+        whitespace_attrs = [r"{arch=[^}]*}", r"{architecture}", r"{compiler_flags}", r"{variants}"]
+        if any(re.match(rx, format_string) for rx in whitespace_attrs):
+            formatted_spec = formatted_spec.lstrip()
+        if any(re.search(f"{rx}$", format_string) for rx in whitespace_attrs):
+            formatted_spec = formatted_spec.rstrip()
+
+        return formatted_spec
 
     def cformat(self, *args, **kwargs):
         """Same as format, but color defaults to auto instead of False."""
@@ -4587,7 +4603,7 @@ def __str__(self):
             self.traverse(root=False), key=lambda x: (x.name, x.abstract_hash)
         )
         sorted_dependencies = [
-            d.format("{edge_attributes} " + DEFAULT_FORMAT) for d in sorted_dependencies
+            d.format("{edge_attributes}" + DEFAULT_FORMAT) for d in sorted_dependencies
         ]
         spec_str = " ^".join(root_str + sorted_dependencies)
         return spec_str.strip()
@@ -4607,20 +4623,25 @@ def colored_str(self):
     def install_status(self):
         """Helper for tree to print DB install status."""
         if not self.concrete:
-            return InstallStatus.absent
+            return InstallStatus.ABSENT
 
         if self.external:
-            return InstallStatus.external
+            return InstallStatus.EXTERNAL
 
         upstream, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
         if not record:
-            return InstallStatus.absent
+            return InstallStatus.ABSENT
         elif upstream and record.installed:
-            return InstallStatus.upstream
+            return InstallStatus.UPSTREAM
         elif record.installed:
-            return InstallStatus.installed
+            return InstallStatus.INSTALLED
         else:
-            return InstallStatus.missing
+            return InstallStatus.MISSING
+
+    def install_status_symbol(self):
+        """Get an install status symbol."""
+        status = self.install_status()
+        return clr.colorize(status.value)
 
     def _installed_explicitly(self):
         """Helper for tree to print DB install status."""
@@ -4646,7 +4667,7 @@ def tree(
         show_types: bool = False,
         depth_first: bool = False,
         recurse_dependencies: bool = True,
-        status_fn: Optional[Callable[["Spec"], InstallStatus]] = None,
+        install_status: bool = False,
         prefix: Optional[Callable[["Spec"], str]] = None,
     ) -> str:
         """Prints out this spec and its dependencies, tree-formatted
@@ -4667,8 +4688,7 @@ def tree(
             show_types: if True, show the (merged) dependency type of a node
             depth_first: if True, traverse the DAG depth first when representing it as a tree
             recurse_dependencies: if True, recurse on dependencies
-            status_fn: optional callable that takes a node as an argument and return its
-                installation status
+            install_status: if True, show installation status next to each spec
             prefix: optional callable that takes a node as an argument and return its
                 installation prefix
         """
@@ -4682,6 +4702,9 @@ def tree(
         ):
             node = dep_spec.spec
 
+            if install_status:
+                out += node.format("{install_status}  ")
+
             if prefix is not None:
                 out += prefix(node)
             out += " " * indent
@@ -4689,15 +4712,6 @@ def tree(
             if depth:
                 out += "%-4d" % d
 
-            if status_fn:
-                status = status_fn(node)
-                if status in list(InstallStatus):
-                    out += clr.colorize(status.value, color=color)
-                elif status:
-                    out += clr.colorize("@g{[+]}  ", color=color)
-                else:
-                    out += clr.colorize("@r{[-]}  ", color=color)
-
             if hashes:
                 out += clr.colorize("@K{%s}  ", color=color) % node.dag_hash(hashlen)
 

lib/spack/spack/stage.py

@@ -199,9 +199,11 @@ def get_stage_root():
 def _mirror_roots():
     mirrors = spack.config.get("mirrors")
     return [
-        sup.substitute_path_variables(root)
-        if root.endswith(os.sep)
-        else sup.substitute_path_variables(root) + os.sep
+        (
+            sup.substitute_path_variables(root)
+            if root.endswith(os.sep)
+            else sup.substitute_path_variables(root) + os.sep
+        )
         for root in mirrors.values()
     ]
 

lib/spack/spack/test/cmd/ci.py

@@ -16,6 +16,7 @@
 import spack
 import spack.binary_distribution
 import spack.ci as ci
+import spack.cmd.ci
 import spack.config
 import spack.environment as ev
 import spack.hash_types as ht
@@ -2028,6 +2029,43 @@ def fake_download_and_extract_artifacts(url, work_dir):
     assert expect_out in rep_out
 
 
+@pytest.mark.parametrize(
+    "url_in,url_out",
+    [
+        (
+            "https://example.com/api/v4/projects/1/jobs/2/artifacts",
+            "https://example.com/api/v4/projects/1/jobs/2/artifacts",
+        ),
+        (
+            "https://example.com/spack/spack/-/jobs/123456/artifacts/download",
+            "https://example.com/spack/spack/-/jobs/123456/artifacts/download",
+        ),
+        (
+            "https://example.com/spack/spack/-/jobs/123456",
+            "https://example.com/spack/spack/-/jobs/123456/artifacts/download",
+        ),
+        (
+            "https://example.com/spack/spack/-/jobs/////123456////?x=y#z",
+            "https://example.com/spack/spack/-/jobs/123456/artifacts/download",
+        ),
+    ],
+)
+def test_reproduce_build_url_validation(url_in, url_out):
+    assert spack.cmd.ci._gitlab_artifacts_url(url_in) == url_out
+
+
+def test_reproduce_build_url_validation_fails():
+    """Wrong URLs should cause an exception"""
+    with pytest.raises(SystemExit):
+        ci_cmd("reproduce-build", "example.com/spack/spack/-/jobs/123456/artifacts/download")
+
+    with pytest.raises(SystemExit):
+        ci_cmd("reproduce-build", "https://example.com/spack/spack/-/issues")
+
+    with pytest.raises(SystemExit):
+        ci_cmd("reproduce-build", "https://example.com/spack/spack/-")
+
+
 @pytest.mark.parametrize(
     "subcmd", [(""), ("generate"), ("rebuild-index"), ("rebuild"), ("reproduce-build")]
 )

lib/spack/spack/test/cmd/dev_build.py

@@ -215,6 +215,44 @@ def test_dev_build_env(tmpdir, install_mockery, mutable_mock_env_path):
         assert f.read() == spec.package.replacement_string
 
 
+def test_dev_build_env_with_vars(tmpdir, install_mockery, mutable_mock_env_path, monkeypatch):
+    """Test Spack does dev builds for packages in develop section of env (path with variables)."""
+    # setup dev-build-test-install package for dev build
+    build_dir = tmpdir.mkdir("build")
+    spec = spack.spec.Spec(f"dev-build-test-install@0.0.0 dev_path={build_dir}")
+    spec.concretize()
+
+    # store the build path in an environment variable that will be used in the environment
+    monkeypatch.setenv("CUSTOM_BUILD_PATH", build_dir)
+
+    with build_dir.as_cwd(), open(spec.package.filename, "w") as f:
+        f.write(spec.package.original_string)
+
+    # setup environment
+    envdir = tmpdir.mkdir("env")
+    with envdir.as_cwd():
+        with open("spack.yaml", "w") as f:
+            f.write(
+                """\
+spack:
+  specs:
+  - dev-build-test-install@0.0.0
+
+  develop:
+    dev-build-test-install:
+      spec: dev-build-test-install@0.0.0
+      path: $CUSTOM_BUILD_PATH
+"""
+            )
+        env("create", "test", "./spack.yaml")
+        with ev.read("test"):
+            install()
+
+    assert spec.package.filename in os.listdir(spec.prefix)
+    with open(os.path.join(spec.prefix, spec.package.filename), "r") as f:
+        assert f.read() == spec.package.replacement_string
+
+
 def test_dev_build_env_version_mismatch(tmpdir, install_mockery, mutable_mock_env_path):
     """Test Spack constraints concretization by develop specs."""
     # setup dev-build-test-install package for dev build

lib/spack/spack/test/cmd/develop.py

@@ -9,6 +9,7 @@
 
 import llnl.util.filesystem as fs
 
+import spack.config
 import spack.environment as ev
 import spack.spec
 from spack.main import SpackCommand
@@ -21,7 +22,7 @@
 
 @pytest.mark.usefixtures("mutable_mock_env_path", "mock_packages", "mock_fetch", "mutable_config")
 class TestDevelop:
-    def check_develop(self, env, spec, path=None):
+    def check_develop(self, env, spec, path=None, build_dir=None):
         path = path or spec.name
 
         # check in memory representation
@@ -41,6 +42,12 @@ def check_develop(self, env, spec, path=None):
         else:
             assert yaml_entry["path"] == path
 
+        if build_dir is not None:
+            scope = env.scope_name
+            assert build_dir == spack.config.get(
+                "packages:{}:package_attributes:build_directory".format(spec.name), scope
+            )
+
     def test_develop_no_path_no_clone(self):
         env("create", "test")
         with ev.read("test") as e:
@@ -72,6 +79,12 @@ def test_develop_no_args(self):
             develop()
             self.check_develop(e, spack.spec.Spec("mpich@=1.0"))
 
+    def test_develop_build_directory(self):
+        env("create", "test")
+        with ev.read("test") as e:
+            develop("-b", "test_build_dir", "mpich@1.0")
+            self.check_develop(e, spack.spec.Spec("mpich@=1.0"), None, "test_build_dir")
+
     def test_develop_twice(self):
         env("create", "test")
         with ev.read("test") as e:

lib/spack/spack/test/cmd/env.py

@@ -1471,8 +1471,8 @@ def test_env_view_fails_dir_file(tmpdir, mock_packages, mock_stage, mock_fetch,
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
-        add("view-dir-file")
-        add("view-dir-dir")
+        add("view-file")
+        add("view-dir")
         with pytest.raises(
             llnl.util.link_tree.MergeConflictSummary, match=os.path.join("bin", "x")
         ):
@@ -1486,8 +1486,8 @@ def test_env_view_succeeds_symlinked_dir_file(
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
-        add("view-dir-symlinked-dir")
-        add("view-dir-dir")
+        add("view-symlinked-dir")
+        add("view-dir")
         install()
         x_dir = os.path.join(str(view_dir), "bin", "x")
         assert os.path.exists(os.path.join(x_dir, "file_in_dir"))
@@ -2537,58 +2537,88 @@ def test_stack_view_no_activate_without_default(
         assert viewdir not in shell
 
 
+@pytest.mark.parametrize("include_views", [True, False, "split"])
 def test_stack_view_multiple_views(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery
+    tmp_path,
+    mock_fetch,
+    mock_packages,
+    mock_archive,
+    install_mockery,
+    mutable_config,
+    include_views,
 ):
-    filename = str(tmpdir.join("spack.yaml"))
-    default_viewdir = str(tmpdir.join("default-view"))
-    combin_viewdir = str(tmpdir.join("combinatorial-view"))
-    with open(filename, "w") as f:
-        f.write(
-            """\
-spack:
+    """Test multiple views as both included views (True), as both environment
+    views (False), or as one included and the other in the environment."""
+    # Write the view configuration and or manifest file
+    view_filename = tmp_path / "view.yaml"
+    base_content = """\
   definitions:
     - packages: [mpileaks, cmake]
-    - compilers: ['%%gcc', '%%clang']
+    - compilers: ['%gcc', '%clang']
   specs:
     - matrix:
         - [$packages]
         - [$compilers]
+"""
 
-  view:
-    default:
-      root: %s
-      select: ['%%gcc']
-    combinatorial:
-      root: %s
-      exclude: [callpath %%gcc]
-      projections:
-        'all': '{name}/{version}-{compiler.name}'"""
-            % (default_viewdir, combin_viewdir)
-        )
-    with tmpdir.as_cwd():
-        env("create", "test", "./spack.yaml")
-        with ev.read("test"):
-            install()
+    include_content = f"  include:\n    - {view_filename}\n"
+    view_line = "  view:\n"
 
-        shell = env("activate", "--sh", "test")
-        assert "PATH" in shell
-        assert os.path.join(default_viewdir, "bin") in shell
+    comb_dir = tmp_path / "combinatorial-view"
+    comb_view = """\
+{0}combinatorial:
+{0}  root: {1}
+{0}  exclude: [callpath%gcc]
+{0}  projections:
+"""
 
-        test = ev.read("test")
-        for spec in test._get_environment_specs():
+    projection = "    'all': '{name}/{version}-{compiler.name}'"
+
+    default_dir = tmp_path / "default-view"
+    default_view = """\
+{0}default:
+{0}  root: {1}
+{0}  select: ['%gcc']
+"""
+
+    content = "spack:\n"
+    indent = "  "
+    if include_views is True:
+        # Include both the gcc and combinatorial views
+        view = "view:\n" + default_view.format(indent, str(default_dir))
+        view += comb_view.format(indent, str(comb_dir)) + indent + projection
+        view_filename.write_text(view)
+        content += include_content + base_content
+    elif include_views == "split":
+        # Include the gcc view and inline the combinatorial view
+        view = "view:\n" + default_view.format(indent, str(default_dir))
+        view_filename.write_text(view)
+        content += include_content + base_content + view_line
+        indent += "  "
+        content += comb_view.format(indent, str(comb_dir)) + indent + projection
+    else:
+        # Inline both the gcc and combinatorial views in the environment.
+        indent += "  "
+        content += base_content + view_line
+        content += default_view.format(indent, str(default_dir))
+        content += comb_view.format(indent, str(comb_dir)) + indent + projection
+
+    filename = tmp_path / ev.manifest_name
+    filename.write_text(content)
+
+    env("create", "test", str(filename))
+    with ev.read("test"):
+        install()
+
+    with ev.read("test") as e:
+        assert os.path.exists(str(default_dir / "bin"))
+        for spec in e._get_environment_specs():
+            spec_subdir = f"{spec.version}-{spec.compiler.name}"
+            comb_spec_dir = str(comb_dir / spec.name / spec_subdir)
             if not spec.satisfies("callpath%gcc"):
-                assert os.path.exists(
-                    os.path.join(
-                        combin_viewdir, spec.name, "%s-%s" % (spec.version, spec.compiler.name)
-                    )
-                )
+                assert os.path.exists(comb_spec_dir)
             else:
-                assert not os.path.exists(
-                    os.path.join(
-                        combin_viewdir, spec.name, "%s-%s" % (spec.version, spec.compiler.name)
-                    )
-                )
+                assert not os.path.exists(comb_spec_dir)
 
 
 def test_env_activate_sh_prints_shell_output(tmpdir, mock_stage, mock_fetch, install_mockery):
@@ -3714,3 +3744,191 @@ def test_environment_created_from_lockfile_has_view(mock_packages, temporary_sto
     # Make sure the view was created
     with ev.Environment(env_b) as e:
         assert os.path.isdir(e.view_path_default)
+
+
+def test_env_view_disabled(tmp_path, mutable_mock_env_path):
+    """Ensure an inlined view being disabled means not even the default view
+    is created (since the case doesn't appear to be covered in this module)."""
+    spack_yaml = tmp_path / ev.manifest_name
+    spack_yaml.write_text(
+        """\
+spack:
+  specs:
+  - mpileaks
+  view: false
+"""
+    )
+    env("create", "disabled", str(spack_yaml))
+    with ev.read("disabled") as e:
+        e.concretize()
+
+    assert len(e.views) == 0
+    assert not os.path.exists(e.view_path_default)
+
+
+@pytest.mark.parametrize("first", ["false", "true", "custom"])
+def test_env_include_mixed_views(tmp_path, mutable_mock_env_path, mutable_config, first):
+    """Ensure including path and boolean views in different combinations result
+    in the creation of only the first view if it is not disabled."""
+    false_yaml = tmp_path / "false-view.yaml"
+    false_yaml.write_text("view: false\n")
+
+    true_yaml = tmp_path / "true-view.yaml"
+    true_yaml.write_text("view: true\n")
+
+    custom_name = "my-test-view"
+    custom_view = tmp_path / custom_name
+    custom_yaml = tmp_path / "custom-view.yaml"
+    custom_yaml.write_text(
+        f"""
+view:
+  {custom_name}:
+    root: {custom_view}
+"""
+    )
+
+    if first == "false":
+        order = [false_yaml, true_yaml, custom_yaml]
+    elif first == "true":
+        order = [true_yaml, custom_yaml, false_yaml]
+    else:
+        order = [custom_yaml, false_yaml, true_yaml]
+    includes = [f"  - {yaml}\n" for yaml in order]
+
+    spack_yaml = tmp_path / ev.manifest_name
+    spack_yaml.write_text(
+        f"""\
+spack:
+  include:
+{''.join(includes)}
+  specs:
+  - mpileaks
+  packages:
+    mpileaks:
+      compiler: [gcc]
+"""
+    )
+
+    env("create", "test", str(spack_yaml))
+    with ev.read("test") as e:
+        concretize()
+
+    # Only the first included view should be created if view not disabled by it
+    assert len(e.views) == 0 if first == "false" else 1
+    if first == "true":
+        assert os.path.exists(e.view_path_default)
+    else:
+        assert not os.path.exists(e.view_path_default)
+
+    if first == "custom":
+        assert os.path.exists(custom_view)
+    else:
+        assert not os.path.exists(custom_view)
+
+
+def test_stack_view_multiple_views_same_name(
+    tmp_path, mock_fetch, mock_packages, mock_archive, install_mockery, mutable_config
+):
+    """Test multiple views with the same name combine settings with precedence
+    given to the options in spack.yaml."""
+    # Write the view configuration and or manifest file
+
+    view_filename = tmp_path / "view.yaml"
+    default_dir = tmp_path / "default-view"
+    default_view = f"""\
+view:
+  default:
+    root: {default_dir}
+    select: ['%gcc']
+    projections:
+      all: '{{name}}/{{version}}-{{compiler.name}}'
+"""
+    view_filename.write_text(default_view)
+
+    view_dir = tmp_path / "view"
+    content = f"""\
+spack:
+  include:
+  - {view_filename}
+  definitions:
+    - packages: [mpileaks, cmake]
+    - compilers: ['%gcc', '%clang']
+  specs:
+    - matrix:
+        - [$packages]
+        - [$compilers]
+
+  view:
+    default:
+      root: {view_dir}
+      exclude: ['cmake']
+      projections:
+        all: '{{name}}/{{compiler.name}}-{{version}}'
+"""
+
+    filename = tmp_path / ev.manifest_name
+    filename.write_text(content)
+
+    env("create", "test", str(filename))
+    with ev.read("test"):
+        install()
+
+    with ev.read("test") as e:
+        # the view root in the included view should NOT exist
+        assert not os.path.exists(str(default_dir))
+
+        for spec in e._get_environment_specs():
+            # no specs will exist in the included view projection
+            included_spec_subdir = f"{spec.version}-{spec.compiler.name}"
+            included_spec_dir = str(view_dir / spec.name / included_spec_subdir)
+            assert not os.path.exists(included_spec_dir)
+
+            # only specs compiled with %gcc (selected in the included view) that
+            # are also not cmake (excluded in the environment view) should exist
+            env_spec_subdir = f"{spec.compiler.name}-{spec.version}"
+            env_spec_dir = str(view_dir / spec.name / env_spec_subdir)
+            if spec.satisfies("cmake") or spec.satisfies("%clang"):
+                assert not os.path.exists(env_spec_dir)
+            else:
+                assert os.path.exists(env_spec_dir)
+
+
+def test_env_view_resolves_identical_file_conflicts(tmp_path, install_mockery, mock_fetch):
+    """When files clash in a view, but refer to the same file on disk (for example, the dependent
+    symlinks to a file in the dependency at the same relative path), Spack links the first regular
+    file instead of symlinks. This is important for copy type views where we need the underlying
+    file to be copied instead of the symlink (when a symlink would be copied, it would become a
+    self-referencing symlink after relocation). The test uses a symlink type view though, since
+    that keeps track of the original file path."""
+    with ev.create("env", with_view=tmp_path / "view") as e:
+        add("view-resolve-conflict-top")
+        install()
+        top = e.matching_spec("view-resolve-conflict-top").prefix
+        bottom = e.matching_spec("view-file").prefix
+
+    # In this example we have `./bin/x` in 3 prefixes, two links, one regular file. We expect the
+    # regular file to be linked into the view. There are also 2 links at `./bin/y`, but no regular
+    # file, so we expect standard behavior: first entry is linked into the view.
+
+    #   view-resolve-conflict-top/bin/
+    #     x -> view-file/bin/x
+    #     y -> view-resolve-conflict-middle/bin/y    # expect this y to be linked
+    #   view-resolve-conflict-middle/bin/
+    #     x -> view-file/bin/x
+    #     y -> view-file/bin/x
+    #   view-file/bin/
+    #     x                                          # expect this x to be linked
+
+    assert os.readlink(tmp_path / "view" / "bin" / "x") == bottom.bin.x
+    assert os.readlink(tmp_path / "view" / "bin" / "y") == top.bin.y
+
+
+def test_env_view_ignores_different_file_conflicts(tmp_path, install_mockery, mock_fetch):
+    """Test that file-file conflicts for two unique files in environment views are ignored, and
+    that the dependent's file is linked into the view, not the dependency's file."""
+    with ev.create("env", with_view=tmp_path / "view") as e:
+        add("view-ignore-conflict")
+        install()
+        prefix_dependent = e.matching_spec("view-ignore-conflict").prefix
+    # The dependent's file is linked into the view
+    assert os.readlink(tmp_path / "view" / "bin" / "x") == prefix_dependent.bin.x

lib/spack/spack/test/cmd/logs.py

@@ -0,0 +1,119 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import gzip
+import os
+import sys
+import tempfile
+from contextlib import contextmanager
+from io import BytesIO, TextIOWrapper
+
+import pytest
+
+import spack
+from spack.main import SpackCommand
+
+logs = SpackCommand("logs")
+install = SpackCommand("install")
+
+
+@contextmanager
+def stdout_as_buffered_text_stream():
+    """Attempt to simulate "typical" interface for stdout when user is
+    running Spack/Python from terminal. "spack log" should not be run
+    for all possible cases of what stdout might look like, in
+    particular some programmatic redirections of stdout like StringIO
+    are not meant to be supported by this command; more-generally,
+    mechanisms that depend on decoding binary output prior to write
+    are not supported for "spack log".
+    """
+    original_stdout = sys.stdout
+
+    with tempfile.TemporaryFile(mode="w+b") as tf:
+        sys.stdout = TextIOWrapper(tf)
+        try:
+            yield tf
+        finally:
+            sys.stdout = original_stdout
+
+
+def _rewind_collect_and_decode(rw_stream):
+    rw_stream.seek(0)
+    return rw_stream.read().decode("utf-8")
+
+
+@pytest.fixture
+def disable_capture(capfd):
+    with capfd.disabled():
+        yield
+
+
+def test_logs_cmd_errors(install_mockery, mock_fetch, mock_archive, mock_packages):
+    spec = spack.spec.Spec("libelf").concretized()
+    assert not spec.installed
+
+    with pytest.raises(spack.main.SpackCommandError, match="is not installed or staged"):
+        logs("libelf")
+
+    with pytest.raises(spack.main.SpackCommandError, match="Too many specs"):
+        logs("libelf mpi")
+
+    install("libelf")
+    os.remove(spec.package.install_log_path)
+    with pytest.raises(spack.main.SpackCommandError, match="No logs are available"):
+        logs("libelf")
+
+
+def _write_string_to_path(string, path):
+    """Write a string to a file, preserving newline format in the string."""
+    with open(path, "wb") as f:
+        f.write(string.encode("utf-8"))
+
+
+def test_dump_logs(install_mockery, mock_fetch, mock_archive, mock_packages, disable_capture):
+    """Test that ``spack log`` can find (and print) the logs for partial
+    builds and completed installs.
+
+    Also make sure that for compressed logs, that we automatically
+    decompress them.
+    """
+    cmdline_spec = spack.spec.Spec("libelf")
+    concrete_spec = cmdline_spec.concretized()
+
+    # Sanity check, make sure this test is checking what we want: to
+    # start with
+    assert not concrete_spec.installed
+
+    stage_log_content = "test_log stage output\nanother line"
+    installed_log_content = "test_log install output\nhere to test multiple lines"
+
+    with concrete_spec.package.stage:
+        _write_string_to_path(stage_log_content, concrete_spec.package.log_path)
+        with stdout_as_buffered_text_stream() as redirected_stdout:
+            spack.cmd.logs._logs(cmdline_spec, concrete_spec)
+            assert _rewind_collect_and_decode(redirected_stdout) == stage_log_content
+
+    install("libelf")
+
+    # Sanity check: make sure a path is recorded, regardless of whether
+    # it exists (if it does exist, we will overwrite it with content
+    # in this test)
+    assert concrete_spec.package.install_log_path
+
+    with gzip.open(concrete_spec.package.install_log_path, "wb") as compressed_file:
+        bstream = BytesIO(installed_log_content.encode("utf-8"))
+        compressed_file.writelines(bstream)
+
+    with stdout_as_buffered_text_stream() as redirected_stdout:
+        spack.cmd.logs._logs(cmdline_spec, concrete_spec)
+        assert _rewind_collect_and_decode(redirected_stdout) == installed_log_content
+
+    with concrete_spec.package.stage:
+        _write_string_to_path(stage_log_content, concrete_spec.package.log_path)
+        # We re-create the stage, but "spack log" should ignore that
+        # if the package is installed
+        with stdout_as_buffered_text_stream() as redirected_stdout:
+            spack.cmd.logs._logs(cmdline_spec, concrete_spec)
+            assert _rewind_collect_and_decode(redirected_stdout) == installed_log_content

lib/spack/spack/test/cmd/url.py

@@ -98,13 +98,9 @@ def test_url_list(mock_packages):
 def test_url_summary(mock_packages):
     """Test the URL summary command."""
     # test url_summary, the internal function that does the work
-    (
-        total_urls,
-        correct_names,
-        correct_versions,
-        name_count_dict,
-        version_count_dict,
-    ) = url_summary(None)
+    (total_urls, correct_names, correct_versions, name_count_dict, version_count_dict) = (
+        url_summary(None)
+    )
 
     assert 0 < correct_names <= sum(name_count_dict.values()) <= total_urls
     assert 0 < correct_versions <= sum(version_count_dict.values()) <= total_urls

lib/spack/spack/test/cmd/view.py

@@ -191,7 +191,7 @@ def test_view_files_not_ignored(
     pkg.do_install()
     pkg.assert_installed(spec.prefix)
 
-    install("view-dir-file")  # Arbitrary package to add noise
+    install("view-file")  # Arbitrary package to add noise
 
     viewpath = str(tmpdir.mkdir("view_{0}".format(cmd)))
 
@@ -205,7 +205,7 @@ def test_view_files_not_ignored(
         prefix_in_view = viewpath
         args = []
 
-    view(cmd, *(args + [viewpath, "view-not-ignored", "view-dir-file"]))
+    view(cmd, *(args + [viewpath, "view-not-ignored", "view-file"]))
     pkg.assert_installed(prefix_in_view)
 
     view("remove", viewpath, "view-not-ignored")

lib/spack/spack/test/cmd_extensions.py

@@ -103,9 +103,9 @@ def hello_world_with_module_in_root(extension_creator):
 
     @contextlib.contextmanager
     def _hwwmir(extension_name=None):
-        with extension_creator(
-            extension_name
-        ) if extension_name else extension_creator() as extension:
+        with (
+            extension_creator(extension_name) if extension_name else extension_creator()
+        ) as extension:
             # Note that the namespace of the extension is derived from the
             # fixture.
             extension.add_command(

lib/spack/spack/test/compilers/basics.py

@@ -11,7 +11,7 @@
 import llnl.util.filesystem as fs
 
 import spack.compiler
-import spack.compilers as compilers
+import spack.compilers
 import spack.spec
 import spack.util.environment
 from spack.compiler import Compiler
@@ -25,12 +25,14 @@ class MockOs:
             pass
 
         compiler_name = "gcc"
-        compiler_cls = compilers.class_for_compiler_name(compiler_name)
+        compiler_cls = spack.compilers.class_for_compiler_name(compiler_name)
         monkeypatch.setattr(compiler_cls, "cc_version", lambda x: version)
 
-        compiler_id = compilers.CompilerID(os=MockOs, compiler_name=compiler_name, version=None)
-        variation = compilers.NameVariation(prefix="", suffix="")
-        return compilers.DetectVersionArgs(
+        compiler_id = spack.compilers.CompilerID(
+            os=MockOs, compiler_name=compiler_name, version=None
+        )
+        variation = spack.compilers.NameVariation(prefix="", suffix="")
+        return spack.compilers.DetectVersionArgs(
             id=compiler_id, variation=variation, language="cc", path=path
         )
 
@@ -56,7 +58,7 @@ def test_multiple_conflicting_compiler_definitions(mutable_config):
     mutable_config.update_config("compilers", compiler_config)
 
     arch_spec = spack.spec.ArchSpec(("test", "test", "test"))
-    cmp = compilers.compiler_for_spec("clang@=0.0.0", arch_spec)
+    cmp = spack.compilers.compiler_for_spec("clang@=0.0.0", arch_spec)
     assert cmp.f77 == "f77"
 
 
@@ -64,7 +66,7 @@ def test_get_compiler_duplicates(config):
     # In this case there is only one instance of the specified compiler in
     # the test configuration (so it is not actually a duplicate), but the
     # method behaves the same.
-    cfg_file_to_duplicates = compilers.get_compiler_duplicates(
+    cfg_file_to_duplicates = spack.compilers.get_compiler_duplicates(
         "gcc@4.5.0", spack.spec.ArchSpec("cray-CNL-xeon")
     )
 
@@ -74,7 +76,7 @@ def test_get_compiler_duplicates(config):
 
 
 def test_all_compilers(config):
-    all_compilers = compilers.all_compilers()
+    all_compilers = spack.compilers.all_compilers()
     filtered = [x for x in all_compilers if str(x.spec) == "clang@=3.3"]
     filtered = [x for x in filtered if x.operating_system == "SuSE11"]
     assert len(filtered) == 1
@@ -88,7 +90,7 @@ def test_version_detection_is_empty(
     make_args_for_version, input_version, expected_version, expected_error
 ):
     args = make_args_for_version(version=input_version)
-    result, error = compilers.detect_version(args)
+    result, error = spack.compilers.detect_version(args)
     if not error:
         assert result.id.version == expected_version
 
@@ -104,7 +106,7 @@ def test_compiler_flags_from_config_are_grouped():
         "modules": None,
     }
 
-    compiler = compilers.compiler_from_dict(compiler_entry)
+    compiler = spack.compilers.compiler_from_dict(compiler_entry)
     assert any(x == "-foo-flag foo-val" for x in compiler.flags["cflags"])
 
 
@@ -288,7 +290,7 @@ def flag_value(flag, spec):
     else:
         compiler_entry = copy(default_compiler_entry)
         compiler_entry["spec"] = spec
-        compiler = compilers.compiler_from_dict(compiler_entry)
+        compiler = spack.compilers.compiler_from_dict(compiler_entry)
 
     return getattr(compiler, flag)
 
@@ -657,8 +659,8 @@ def test_xl_r_flags():
     [("gcc@4.7.2", False), ("clang@3.3", False), ("clang@8.0.0", True)],
 )
 def test_detecting_mixed_toolchains(compiler_spec, expected_result, config):
-    compiler = compilers.compilers_for_spec(compiler_spec).pop()
-    assert compilers.is_mixed_toolchain(compiler) is expected_result
+    compiler = spack.compilers.compilers_for_spec(compiler_spec).pop()
+    assert spack.compilers.is_mixed_toolchain(compiler) is expected_result
 
 
 @pytest.mark.regression("14798,13733")
@@ -737,6 +739,49 @@ def module(*args):
     assert version == test_version
 
 
+@pytest.mark.regression("42679")
+def test_get_compilers(config):
+    """Tests that we can select compilers whose versions differ only for a suffix."""
+    common = {
+        "flags": {},
+        "operating_system": "ubuntu23.10",
+        "target": "x86_64",
+        "modules": [],
+        "environment": {},
+        "extra_rpaths": [],
+    }
+    with_suffix = {
+        "spec": "gcc@13.2.0-suffix",
+        "paths": {
+            "cc": "/usr/bin/gcc-13.2.0-suffix",
+            "cxx": "/usr/bin/g++-13.2.0-suffix",
+            "f77": "/usr/bin/gfortran-13.2.0-suffix",
+            "fc": "/usr/bin/gfortran-13.2.0-suffix",
+        },
+        **common,
+    }
+    without_suffix = {
+        "spec": "gcc@13.2.0",
+        "paths": {
+            "cc": "/usr/bin/gcc-13.2.0",
+            "cxx": "/usr/bin/g++-13.2.0",
+            "f77": "/usr/bin/gfortran-13.2.0",
+            "fc": "/usr/bin/gfortran-13.2.0",
+        },
+        **common,
+    }
+
+    compilers = [{"compiler": without_suffix}, {"compiler": with_suffix}]
+
+    assert spack.compilers.get_compilers(
+        compilers, cspec=spack.spec.CompilerSpec("gcc@=13.2.0-suffix")
+    ) == [spack.compilers._compiler_from_config_entry(with_suffix)]
+
+    assert spack.compilers.get_compilers(
+        compilers, cspec=spack.spec.CompilerSpec("gcc@=13.2.0")
+    ) == [spack.compilers._compiler_from_config_entry(without_suffix)]
+
+
 def test_compiler_get_real_version_fails(working_env, monkeypatch, tmpdir):
     # Test variables
     test_version = "2.2.2"

lib/spack/spack/test/compilers/detection.py

@@ -422,7 +422,7 @@ def test_xl_version_detection(version_str, expected_version):
         ("pgi", "19.1"),
         ("pgi", "19.1a"),
         ("intel", "9.0.0"),
-        ("intel", "0.0.0-foobar")
+        ("intel", "0.0.0-foobar"),
         # ('oneapi', '2021.1'),
         # ('oneapi', '2021.1-foobar')
     ],

lib/spack/spack/test/concretize.py

@@ -1522,6 +1522,30 @@ def test_sticky_variant_in_package(self):
         s = Spec("sticky-variant %clang").concretized()
         assert s.satisfies("%clang") and s.satisfies("~allow-gcc")
 
+    @pytest.mark.regression("42172")
+    @pytest.mark.only_clingo("Original concretizer cannot use sticky variants")
+    @pytest.mark.parametrize(
+        "spec,allow_gcc",
+        [
+            ("sticky-variant@1.0+allow-gcc", True),
+            ("sticky-variant@1.0~allow-gcc", False),
+            ("sticky-variant@1.0", False),
+        ],
+    )
+    def test_sticky_variant_in_external(self, spec, allow_gcc):
+        # setup external for sticky-variant+allow-gcc
+        config = {"externals": [{"spec": spec, "prefix": "/fake/path"}], "buildable": False}
+        spack.config.set("packages:sticky-variant", config)
+
+        maybe = llnl.util.lang.nullcontext if allow_gcc else pytest.raises
+        with maybe(spack.error.SpackError):
+            s = Spec("sticky-variant-dependent%gcc").concretized()
+
+        if allow_gcc:
+            assert s.satisfies("%gcc")
+            assert s["sticky-variant"].satisfies("+allow-gcc")
+            assert s["sticky-variant"].external
+
     @pytest.mark.only_clingo("Use case not supported by the original concretizer")
     def test_do_not_invent_new_concrete_versions_unless_necessary(self):
         # ensure we select a known satisfying version rather than creating

lib/spack/spack/test/concretize_requirements.py

@@ -1133,3 +1133,46 @@ def test_conflict_packages_yaml(packages_yaml, spec_str, concretize_scope, mock_
     update_packages_config(packages_yaml)
     with pytest.raises(UnsatisfiableSpecError):
         Spec(spec_str).concretized()
+
+
+@pytest.mark.parametrize(
+    "spec_str,expected,not_expected",
+    [
+        (
+            "forward-multi-value +cuda cuda_arch=10 ^dependency-mv~cuda",
+            ["cuda_arch=10", "^dependency-mv~cuda"],
+            ["cuda_arch=11", "^dependency-mv cuda_arch=10", "^dependency-mv cuda_arch=11"],
+        ),
+        (
+            "forward-multi-value +cuda cuda_arch=10 ^dependency-mv+cuda",
+            ["cuda_arch=10", "^dependency-mv cuda_arch=10"],
+            ["cuda_arch=11", "^dependency-mv cuda_arch=11"],
+        ),
+        (
+            "forward-multi-value +cuda cuda_arch=11 ^dependency-mv+cuda",
+            ["cuda_arch=11", "^dependency-mv cuda_arch=11"],
+            ["cuda_arch=10", "^dependency-mv cuda_arch=10"],
+        ),
+        (
+            "forward-multi-value +cuda cuda_arch=10,11 ^dependency-mv+cuda",
+            ["cuda_arch=10,11", "^dependency-mv cuda_arch=10,11"],
+            [],
+        ),
+    ],
+)
+def test_forward_multi_valued_variant_using_requires(
+    spec_str, expected, not_expected, config, mock_packages
+):
+    """Tests that a package can forward multivalue variants to dependencies, using
+    `requires` directives of the form:
+
+        for _val in ("shared", "static"):
+            requires(f"^some-virtual-mv libs={_val}", when=f"libs={_val} ^some-virtual-mv")
+    """
+    s = Spec(spec_str).concretized()
+
+    for constraint in expected:
+        assert s.satisfies(constraint)
+
+    for constraint in not_expected:
+        assert not s.satisfies(constraint)

lib/spack/spack/test/conftest.py

@@ -1851,7 +1851,7 @@ def binary_with_rpaths(prefix_tmpdir):
     paths are encoded with `$ORIGIN` prepended.
     """
 
-    def _factory(rpaths, message="Hello world!"):
+    def _factory(rpaths, message="Hello world!", dynamic_linker="/lib64/ld-linux.so.2"):
         source = prefix_tmpdir.join("main.c")
         source.write(
             """
@@ -1867,10 +1867,10 @@ def _factory(rpaths, message="Hello world!"):
         executable = source.dirpath("main.x")
         # Encode relative RPATHs using `$ORIGIN` as the root prefix
         rpaths = [x if os.path.isabs(x) else os.path.join("$ORIGIN", x) for x in rpaths]
-        rpath_str = ":".join(rpaths)
         opts = [
             "-Wl,--disable-new-dtags",
-            "-Wl,-rpath={0}".format(rpath_str),
+            f"-Wl,-rpath={':'.join(rpaths)}",
+            f"-Wl,--dynamic-linker,{dynamic_linker}",
             str(source),
             "-o",
             str(executable),

lib/spack/spack/test/database.py

@@ -60,13 +60,9 @@ def test_spec_installed_upstream(
     upstream_and_downstream_db, mock_custom_repository, config, monkeypatch
 ):
     """Test whether Spec.installed_upstream() works."""
-    (
-        upstream_write_db,
-        upstream_db,
-        upstream_layout,
-        downstream_db,
-        downstream_layout,
-    ) = upstream_and_downstream_db
+    (upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout) = (
+        upstream_and_downstream_db
+    )
 
     # a known installed spec should say that it's installed
     with spack.repo.use_repositories(mock_custom_repository):
@@ -90,13 +86,9 @@ def test_spec_installed_upstream(
 
 @pytest.mark.usefixtures("config")
 def test_installed_upstream(upstream_and_downstream_db, tmpdir):
-    (
-        upstream_write_db,
-        upstream_db,
-        upstream_layout,
-        downstream_db,
-        downstream_layout,
-    ) = upstream_and_downstream_db
+    (upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout) = (
+        upstream_and_downstream_db
+    )
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("x")
@@ -132,13 +124,9 @@ def test_installed_upstream(upstream_and_downstream_db, tmpdir):
 
 @pytest.mark.usefixtures("config")
 def test_removed_upstream_dep(upstream_and_downstream_db, tmpdir):
-    (
-        upstream_write_db,
-        upstream_db,
-        upstream_layout,
-        downstream_db,
-        downstream_layout,
-    ) = upstream_and_downstream_db
+    (upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout) = (
+        upstream_and_downstream_db
+    )
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("z")
@@ -168,13 +156,9 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db, tmpdir):
     DB. When a package is recorded as installed in both, the results should
     refer to the downstream DB.
     """
-    (
-        upstream_write_db,
-        upstream_db,
-        upstream_layout,
-        downstream_db,
-        downstream_layout,
-    ) = upstream_and_downstream_db
+    (upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout) = (
+        upstream_and_downstream_db
+    )
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("x")

lib/spack/spack/test/git_fetch.py

@@ -363,3 +363,30 @@ def test_gitsubmodules_delete(
         assert not os.path.isdir(file_path)
         file_path = os.path.join(s.package.stage.source_path, "third_party/submodule1")
         assert not os.path.isdir(file_path)
+
+
+@pytest.mark.disable_clean_stage_check
+def test_gitsubmodules_falsey(
+    mock_git_repository, default_mock_concretization, mutable_mock_repo, monkeypatch
+):
+    """
+    Test GitFetchStrategy behavior when callable submodules returns Falsey
+    """
+
+    def submodules_callback(package):
+        return False
+
+    type_of_test = "tag-branch"
+    t = mock_git_repository.checks[type_of_test]
+
+    # Construct the package under test
+    s = default_mock_concretization("git-test")
+    args = copy.copy(t.args)
+    args["submodules"] = submodules_callback
+    monkeypatch.setitem(s.package.versions, Version("git"), args)
+    s.package.do_stage()
+    with working_dir(s.package.stage.source_path):
+        file_path = os.path.join(s.package.stage.source_path, "third_party/submodule0/r0_file_0")
+        assert not os.path.isfile(file_path)
+        file_path = os.path.join(s.package.stage.source_path, "third_party/submodule1/r0_file_1")
+        assert not os.path.isfile(file_path)

lib/spack/spack/test/llnl/util/filesystem.py

@@ -13,8 +13,7 @@
 import pytest
 
 import llnl.util.filesystem as fs
-import llnl.util.symlink
-from llnl.util.symlink import SymlinkError, _windows_can_symlink, islink, symlink
+from llnl.util.symlink import islink, symlink
 
 import spack.paths
 
@@ -754,93 +753,6 @@ def test_is_nonsymlink_exe_with_shebang(tmpdir):
         assert not fs.is_nonsymlink_exe_with_shebang("symlink_to_executable_script")
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Unix-only test.")
-def test_lexists_islink_isdir(tmpdir):
-    root = str(tmpdir)
-
-    # Create a directory and a file, an a bunch of symlinks.
-    dir = os.path.join(root, "dir")
-    file = os.path.join(root, "file")
-    nonexistent = os.path.join(root, "does_not_exist")
-    symlink_to_dir = os.path.join(root, "symlink_to_dir")
-    symlink_to_file = os.path.join(root, "symlink_to_file")
-    dangling_symlink = os.path.join(root, "dangling_symlink")
-    symlink_to_dangling_symlink = os.path.join(root, "symlink_to_dangling_symlink")
-    symlink_to_symlink_to_dir = os.path.join(root, "symlink_to_symlink_to_dir")
-    symlink_to_symlink_to_file = os.path.join(root, "symlink_to_symlink_to_file")
-
-    os.mkdir(dir)
-    with open(file, "wb") as f:
-        f.write(b"file")
-
-    symlink("dir", symlink_to_dir)
-    symlink("file", symlink_to_file)
-    symlink("does_not_exist", dangling_symlink)
-    symlink("dangling_symlink", symlink_to_dangling_symlink)
-    symlink("symlink_to_dir", symlink_to_symlink_to_dir)
-    symlink("symlink_to_file", symlink_to_symlink_to_file)
-
-    assert fs.lexists_islink_isdir(dir) == (True, False, True)
-    assert fs.lexists_islink_isdir(file) == (True, False, False)
-    assert fs.lexists_islink_isdir(nonexistent) == (False, False, False)
-    assert fs.lexists_islink_isdir(symlink_to_dir) == (True, True, True)
-    assert fs.lexists_islink_isdir(symlink_to_file) == (True, True, False)
-    assert fs.lexists_islink_isdir(symlink_to_dangling_symlink) == (True, True, False)
-    assert fs.lexists_islink_isdir(symlink_to_symlink_to_dir) == (True, True, True)
-    assert fs.lexists_islink_isdir(symlink_to_symlink_to_file) == (True, True, False)
-
-
-@pytest.mark.skipif(sys.platform != "win32", reason="For Windows Only")
-@pytest.mark.parametrize("win_can_symlink", [True, False])
-def test_lexists_islink_isdir_windows(tmpdir, monkeypatch, win_can_symlink):
-    """Run on windows without elevated privileges to test junctions and hard links which have
-    different results from the lexists_islink_isdir method.
-    """
-    if win_can_symlink and not _windows_can_symlink():
-        pytest.skip("Cannot test dev mode behavior without dev mode enabled.")
-    with tmpdir.as_cwd():
-        monkeypatch.setattr(llnl.util.symlink, "_windows_can_symlink", lambda: win_can_symlink)
-        dir = str(tmpdir.join("dir"))
-        file = str(tmpdir.join("file"))
-        nonexistent = str(tmpdir.join("does_not_exist"))
-        symlink_to_dir = str(tmpdir.join("symlink_to_dir"))
-        symlink_to_file = str(tmpdir.join("symlink_to_file"))
-        dangling_symlink = str(tmpdir.join("dangling_symlink"))
-        symlink_to_dangling_symlink = str(tmpdir.join("symlink_to_dangling_symlink"))
-        symlink_to_symlink_to_dir = str(tmpdir.join("symlink_to_symlink_to_dir"))
-        symlink_to_symlink_to_file = str(tmpdir.join("symlink_to_symlink_to_file"))
-
-        os.mkdir(dir)
-        assert fs.lexists_islink_isdir(dir) == (True, False, True)
-
-        symlink("dir", symlink_to_dir)
-        assert fs.lexists_islink_isdir(dir) == (True, False, True)
-        assert fs.lexists_islink_isdir(symlink_to_dir) == (True, True, True)
-
-        with open(file, "wb") as f:
-            f.write(b"file")
-        assert fs.lexists_islink_isdir(file) == (True, False, False)
-
-        symlink("file", symlink_to_file)
-        if win_can_symlink:
-            assert fs.lexists_islink_isdir(file) == (True, False, False)
-        else:
-            assert fs.lexists_islink_isdir(file) == (True, True, False)
-        assert fs.lexists_islink_isdir(symlink_to_file) == (True, True, False)
-
-        with pytest.raises(SymlinkError):
-            symlink("does_not_exist", dangling_symlink)
-            symlink("dangling_symlink", symlink_to_dangling_symlink)
-
-        symlink("symlink_to_dir", symlink_to_symlink_to_dir)
-        symlink("symlink_to_file", symlink_to_symlink_to_file)
-
-        assert fs.lexists_islink_isdir(nonexistent) == (False, False, False)
-        assert fs.lexists_islink_isdir(symlink_to_dangling_symlink) == (False, False, False)
-        assert fs.lexists_islink_isdir(symlink_to_symlink_to_dir) == (True, True, True)
-        assert fs.lexists_islink_isdir(symlink_to_symlink_to_file) == (True, True, False)
-
-
 class RegisterVisitor(fs.BaseDirectoryVisitor):
     """A directory visitor that keeps track of all visited paths"""