Set version to v0.23.1

* Fix hash change due to None vs {}

* Enforce null for empty list of external_modules

.github/workflows/unit_tests.yaml

@@ -52,7 +52,13 @@ jobs:
           # Needed for unit tests
           sudo apt-get -y install \
               coreutils cvs gfortran graphviz gnupg2 mercurial ninja-build \
-              cmake bison libbison-dev kcov
+              cmake bison libbison-dev subversion
+    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
+    - name: Install kcov with brew
+      run: "brew install kcov"
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest pytest-xdist pytest-cov
@@ -99,7 +105,13 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for shell tests
-          sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
+          sudo apt-get install -y coreutils csh zsh tcsh fish dash bash subversion
+    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
+    - name: Install kcov with brew
+      run: "brew install kcov"
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest coverage[toml] pytest-xdist
@@ -134,7 +146,7 @@ jobs:
     - name: Setup repo and non-root user
       run: |
           git --version
-          git config --global --add safe.directory /__w/spack/spack
+          git config --global --add safe.directory '*'
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test

.github/workflows/valid-style.yml

@@ -74,7 +74,7 @@ jobs:
       - name: Setup repo and non-root user
         run: |
           git --version
-          git config --global --add safe.directory /__w/spack/spack
+          git config --global --add safe.directory '*'
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test

CHANGELOG.md

@@ -1,3 +1,395 @@
+# v0.23.1 (2025-02-19)
+
+## Bugfixes
+- Fix a correctness issue of `ArchSpec.intersects` (#48741)
+- Make `extra_attributes` order independent in Spec hashing (#48615, #48854)
+- Fix issue where system proxy settings were not respected in OCI build caches (#48783)
+- Fix an issue where the `--test` concretizer flag was not forwarded correctly (#48417)
+- Fix an issue where `codesign` and `install_name_tool` would not preserve hardlinks on
+  Darwin (#47808)
+- Fix an issue on Darwin where codesign would run on unmodified binaries (#48568)
+- Patch configure scripts generated with libtool < 2.5.4, to avoid redundant flags when
+  creating shared libraries on Darwin (#48671)
+- Fix issue related to mirror URL paths on Windows (#47898)
+- Esnure proper UTF-8 encoding/decoding in logging (#48005)
+- Fix issues related to `filter_file` (#48038, #48108)
+- Fix issue related to creating bootstrap source mirrors (#48235)
+- Fix issue where command line config arguments were not always top level (#48255)
+- Fix an incorrect typehint of `concretized()` (#48504)
+- Improve mention of next Spack version in warning (#47887)
+- Tests: fix forward compatibility with Python 3.13 (#48209)
+- Docs: encourage use of `--oci-username-variable` and `--oci-password-variable` (#48189)
+- Docs: ensure Getting Started has bootstrap list output in correct place (#48281)
+- CI: allow GitHub actions to run on forks of Spack with different project name (#48041)
+- CI: make unit tests work on Ubuntu 24.04 (#48151)
+- CI: re-enable cray pipelines (#47697)
+
+## Package updates
+- `qt-base`: fix rpath for dependents (#47424)
+- `gdk-pixbuf`: fix outdated URL (#47825)
+
+# v0.23.0 (2024-11-13)
+
+`v0.23.0` is a major feature release.
+
+We are planning to make this the last major release before Spack `v1.0`
+in June 2025. Alongside `v0.23`, we will be making pre-releases (alpha,
+beta, etc.)  of `v1.0`, and we encourage users to try them and send us
+feedback, either on GitHub or on Slack. You can track the road to
+`v1.0` here:
+
+  * https://github.com/spack/spack/releases
+  * https://github.com/spack/spack/discussions/30634
+
+## Features in this Release
+
+1. **Language virtuals**
+
+   Your packages can now explicitly depend on the languages they require.
+   Historically, Spack has considered C, C++, and Fortran compiler
+   dependencies to be implicit. In `v0.23`, you should ensure that
+   new packages add relevant C, C++, and Fortran dependencies like this:
+
+   ```python
+   depends_on("c", type="build")
+   depends_on("cxx", type="build")
+   depends_on("fortran", type="build")
+   ```
+
+   We encourage you to add these annotations to your packages now, to prepare
+   for Spack `v1.0.0`. In `v1.0.0`, these annotations will be necessary for
+   your package to use C, C++, and Fortran compilers. Note that you should
+   *not* add language dependencies to packages that don't need them, e.g.,
+   pure python packages.
+
+   We have already auto-generated these dependencies for packages in the
+   `builtin` repository (see #45217), based on the types of source files
+   present in each package's source code. We *may* have added too many or too
+   few language dependencies, so please submit pull requests to correct
+   packages if you find that the language dependencies are incorrect.
+
+   Note that we have also backported support for these dependencies to
+   `v0.21.3` and `v0.22.2`, to make all of them forward-compatible with
+   `v0.23`. This should allow you to move easily between older and newer Spack
+   releases without breaking your packages.
+
+2. **Spec splicing**
+
+   We are working to make binary installation more seamless in Spack. `v0.23`
+   introduces "splicing", which allows users to deploy binaries using local,
+   optimized versions of a binary interface, even if they were not built with
+   that interface. For example, this would allow you to build binaries in the
+   cloud using `mpich` and install them on a system using a local, optimized
+   version of `mvapich2` *without rebuilding*. Spack preserves full provenance
+   for the installed packages and knows that they were built one way but
+   deployed another.
+
+   Our intent is to leverage this across many key HPC binary packages,
+   e.g. MPI, CUDA, ROCm, and libfabric.
+
+   Fundamentally, splicing allows Spack to redeploy an existing spec with
+   different dependencies than how it was built. There are two interfaces to
+   splicing.
+
+   a. Explicit Splicing
+
+      #39136 introduced the explicit splicing interface. In the
+      concretizer config, you can specify a target spec and a replacement
+      by hash.
+
+      ```yaml
+      concretizer:
+        splice:
+          explicit:
+          - target: mpi
+            replacement: mpich/abcdef
+      ```
+
+      Here, every installation that would normally use the target spec will
+      instead use its replacement. Above, any spec using *any* `mpi` will be
+      spliced to depend on the specific `mpich` installation requested. This
+      *can* go wrong if you try to replace something built with, e.g.,
+      `openmpi` with `mpich`, and it is on the user to ensure ABI
+      compatibility between target and replacement specs. This currently
+      requires some expertise to use, but it will allow users to reuse the
+      binaries they create across more machines and environments.
+
+   b. Automatic Splicing (experimental)
+
+      #46729 introduced automatic splicing. In the concretizer config, enable
+      automatic splicing:
+
+      ```yaml
+      concretizer:
+        splice:
+          automatic: true
+      ```
+
+      or run:
+
+      ```console
+      spack config add concretizer:splice:automatic:true
+      ```
+
+      The concretizer will select splices for ABI compatibility to maximize
+      package reuse. Packages can denote ABI compatibility using the
+      `can_splice` directive. No packages in Spack yet use this directive, so
+      if you want to use this feature you will need to add `can_splice`
+      annotations to your packages. We are working on ways to add more ABI
+      compatibility information to the Spack package repository, and this
+      directive may change in the future.
+
+   See the documentation for more details:
+   * https://spack.readthedocs.io/en/latest/build_settings.html#splicing
+   * https://spack.readthedocs.io/en/latest/packaging_guide.html#specifying-abi-compatibility
+
+3. Broader variant propagation
+
+   Since #42931, you can specify propagated variants like `hdf5
+   build_type==RelWithDebInfo` or `trilinos ++openmp` to propagate a variant
+   to all dependencies for which it is relevant. This is valid *even* if the
+   variant does not exist on the package or its dependencies.
+
+   See https://spack.readthedocs.io/en/latest/basic_usage.html#variants.
+
+4. Query specs by namespace
+
+   #45416 allows a package's namespace (indicating the repository it came from)
+   to be treated like a variant. You can request packages from particular repos
+   like this:
+
+   ```console
+   spack find zlib namespace=builtin
+   spack find zlib namespace=myrepo
+   ```
+
+   Previously, the spec syntax only allowed namespaces to be prefixes of spec
+   names, e.g. `builtin.zlib`. The previous syntax still works.
+
+5. `spack spec` respects environment settings and `unify:true`
+
+   `spack spec` did not previously respect environment lockfiles or
+   unification settings, which made it difficult to see exactly how a spec
+   would concretize within an environment. Now it does, so the output you get
+   with `spack spec` will be *the same* as what your environment will
+   concretize to when you run `spack concretize`. Similarly, if you provide
+   multiple specs on the command line with `spack spec`, it will concretize
+   them together if `unify:true` is set.
+
+   See #47556 and #44843.
+
+6. Less noisy `spack spec` output
+
+   `spack spec` previously showed output like this:
+
+   ```console
+    > spack spec /v5fn6xo
+    Input spec
+    --------------------------------
+     -   /v5fn6xo
+
+    Concretized
+    --------------------------------
+    [+]  openssl@3.3.1%apple-clang@16.0.0~docs+shared arch=darwin-sequoia-m1
+    ...
+   ```
+
+   But the input spec is redundant, and we know we run `spack spec` to concretize
+   the input spec. `spack spec` now *only* shows the concretized spec. See #47574.
+
+7. Better output for `spack find -c`
+
+   In an environmnet, `spack find -c` lets you search the concretized, but not
+   yet installed, specs, just as you would the installed ones. As with `spack
+   spec`, this should make it easier for you to see what *will* be built
+   before building and installing it. See #44713.
+
+8. `spack -C <env>`: use an environment's configuration without activation
+
+   Spack environments allow you to associate:
+   1. a set of (possibly concretized) specs, and
+   2. configuration
+
+   When you activate an environment, you're using both of these. Previously, we
+   supported:
+   * `spack -e <env>` to run spack in the context of a specific environment, and
+   * `spack -C <directory>` to run spack using a directory with configuration files.
+
+   You can now also pass an environment to `spack -C` to use *only* the environment's
+   configuration, but not the specs or lockfile. See #45046.
+
+## New commands, options, and directives
+
+* The new `spack env track` command (#41897) takes a non-managed Spack
+  environment and adds a symlink to Spack's `$environments_root` directory, so
+  that it will be included for reference counting for commands like `spack
+  uninstall` and `spack gc`. If you use free-standing directory environments,
+  this is useful for preventing Spack from removing things required by your
+  environments. You can undo this tracking with the `spack env untrack`
+  command.
+
+* Add `-t` short option for `spack --backtrace` (#47227)
+
+  `spack -d / --debug` enables backtraces on error, but it can be very
+  verbose, and sometimes you just want the backtrace. `spack -t / --backtrace`
+  provides that option.
+
+* `gc`: restrict to specific specs (#46790)
+
+  If you only want to garbage-collect specific packages, you can now provide
+  them on the command line. This gives users finer-grained control over what
+  is uninstalled.
+
+* oci buildcaches now support `--only=package`. You can now push *just* a
+  package and not its dependencies to an OCI registry. This allows dependents
+  of non-redistributable specs to be stored in OCI registries without an
+  error. See #45775.
+
+## Notable refactors
+* Variants are now fully conditional
+
+  The `variants` dictionary on packages was previously keyed by variant name,
+  and allowed only one definition of any given variant. Spack is now smart
+  enough to understand that variants may have different values and defaults
+  for different versions. For example, `warpx` prior to `23.06` only supported
+  builds for one dimensionality, and newer `warpx` versions could be built
+  with support for many different dimensions:
+
+  ```python
+  variant(
+      "dims",
+      default="3",
+      values=("1", "2", "3", "rz"),
+      multi=False,
+      description="Number of spatial dimensions",
+      when="@:23.05",
+  )
+  variant(
+      "dims",
+      default="1,2,rz,3",
+      values=("1", "2", "3", "rz"),
+      multi=True,
+      description="Number of spatial dimensions",
+      when="@23.06:",
+  )
+  ```
+
+  Previously, the default for the old version of `warpx` was not respected and
+  had to be specified manually. Now, Spack will select the right variant
+  definition for each version at concretization time. This allows variants to
+  evolve more smoothly over time. See #44425 for details.
+
+## Highlighted bugfixes
+
+1. Externals no longer override the preferred provider (#45025).
+
+   External definitions could interfere with package preferences. Now, if
+   `openmpi` is the preferred `mpi`, and an external `mpich` is defined, a new
+   `openmpi` *will* be built if building it is possible. Previously we would
+   prefer `mpich` despite the preference.
+
+2. Composable `cflags` (#41049).
+
+   This release fixes a longstanding bug that concretization would fail if
+   there were different `cflags` specified in `packages.yaml`,
+   `compilers.yaml`, or on `the` CLI. Flags and their ordering are now tracked
+   in the concretizer and flags from multiple sources will be merged.
+
+3. Fix concretizer Unification for included environments (#45139).
+
+## Deprecations, removals, and syntax changes
+
+1. The old concretizer has been removed from Spack, along with the
+   `config:concretizer` config option. Spack will emit a warning if the option
+   is present in user configuration, since it now has no effect. Spack now
+   uses a simpler bootstrapping mechanism, where a JSON prototype is tweaked
+   slightly to get an initial concrete spec to download. See #45215.
+
+2. Best-effort expansion of spec matrices has been removed. This feature did
+   not work with the "new" ASP-based concretizer, and did not work with
+   `unify: True` or `unify: when_possible`. Use the
+   [exclude key](https://spack.readthedocs.io/en/latest/environments.html#spec-matrices)
+   for the environment to exclude invalid components, or use multiple spec
+   matrices to combine the list of specs for which the constraint is valid and
+   the list of specs for which it is not. See #40792.
+
+3. The old Cray `platform` (based on Cray PE modules) has been removed, and
+   `platform=cray` is no longer supported. Since `v0.19`, Spack has handled
+   Cray machines like Linux clusters with extra packages, and we have
+   encouraged using this option to support Cray. The new approach allows us to
+   correctly handle Cray machines with non-SLES operating systems, and it is
+   much more reliable than making assumptions about Cray modules. See the
+   `v0.19` release notes and #43796 for more details.
+
+4. The `config:install_missing_compilers` config option has been deprecated,
+   and it is a no-op when set in `v0.23`. Our new compiler dependency model
+   will replace it with a much more reliable and robust mechanism in `v1.0`.
+   See #46237.
+
+5. Config options that deprecated in `v0.21` have been removed in `v0.23`. You
+   can now only specify preferences for `compilers`, `targets`, and
+   `providers` globally via the `packages:all:` section. Similarly, you can
+   only specify `versions:` locally for a specific package. See #44061 and
+   #31261 for details.
+
+6. Spack's old test interface has been removed (#45752), having been
+   deprecated in `v0.22.0` (#34236). All `builtin` packages have been updated
+   to use the new interface. See the [stand-alone test documentation](
+   https://spack.readthedocs.io/en/latest/packaging_guide.html#stand-alone-tests)
+
+7. The `spack versions --safe-only` option, deprecated since `v0.21.0`, has
+   been removed. See #45765.
+
+* The `--dependencies` and `--optimize` arguments to `spack ci` have been
+  deprecated. See #45005.
+
+## Binary caches
+1. Public binary caches now include an ML stack for Linux/aarch64 (#39666)We
+   now build an ML stack for Linux/aarch64 for all pull requests and on
+   develop. The ML stack includes both CPU-only and CUDA builds for Horovod,
+   Hugging Face, JAX, Keras, PyTorch,scikit-learn, TensorBoard, and
+   TensorFlow, and related packages. The CPU-only stack also includes XGBoost.
+   See https://cache.spack.io/tag/develop/?stack=ml-linux-aarch64-cuda.
+
+2. There is also now an stack of developer tools for macOS (#46910), which is
+   analogous to the Linux devtools stack. You can use this to avoid building
+   many common build dependencies. See
+   https://cache.spack.io/tag/develop/?stack=developer-tools-darwin.
+
+## Architecture support
+* archspec has been updated to `v0.2.5`, with support for `zen5`
+* Spack's CUDA package now supports the Grace Hopper `9.0a` compute capability (#45540)
+
+## Windows
+* Windows bootstrapping: `file` and `gpg` (#41810)
+* `scripts` directory added to PATH on Windows for python extensions (#45427)
+* Fix `spack load --list` and `spack unload` on Windows (#35720)
+
+## Other notable changes
+* Bugfix: `spack find -x` in environments (#46798)
+* Spec splices are now robust to duplicate nodes with the same name in a spec (#46382)
+* Cache per-compiler libc calculations for performance (#47213)
+* Fixed a bug in external detection for openmpi (#47541)
+* Mirror configuration allows username/password as environment variables (#46549)
+* Default library search caps maximum depth (#41945)
+* Unify interface for `spack spec` and `spack solve` commands (#47182)
+* Spack no longer RPATHs directories in the default library search path (#44686)
+* Improved performance of Spack database (#46554)
+* Enable package reuse for packages with versions from git refs (#43859)
+* Improved handling for `uuid` virtual on macos (#43002)
+* Improved tracking of task queueing/requeueing in the installer (#46293)
+
+## Spack community stats
+
+* Over 2,000 pull requests updated package recipes
+* 8,307 total packages, 329 new since `v0.22.0`
+    * 140 new Python packages
+    * 14 new R packages
+* 373 people contributed to this release
+    * 357 committers to packages
+    * 60 committers to core
+
+
 # v0.22.2 (2024-09-21)
 
 ## Bugfixes

lib/spack/docs/binary_caches.rst

@@ -265,25 +265,30 @@ infrastructure, or to cache Spack built binaries in Github Actions and
 GitLab CI.
 
 To get started, configure an OCI mirror using ``oci://`` as the scheme,
-and optionally specify a username and password (or personal access token):
+and optionally specify variables that hold the username and password (or
+personal access token) for the registry:
 
 .. code-block:: console
 
-    $ spack mirror add --oci-username username --oci-password password my_registry oci://example.com/my_image
+    $ spack mirror add --oci-username-variable REGISTRY_USER \
+                       --oci-password-variable REGISTRY_TOKEN \
+                       my_registry oci://example.com/my_image
 
 Spack follows the naming conventions of Docker, with Dockerhub as the default
 registry. To use Dockerhub, you can omit the registry domain:
 
 .. code-block:: console
 
-    $ spack mirror add --oci-username username --oci-password password my_registry oci://username/my_image
+    $ spack mirror add ... my_registry oci://username/my_image
 
 From here, you can use the mirror as any other build cache:
 
 .. code-block:: console
 
+    $ export REGISTRY_USER=...
+    $ export REGISTRY_TOKEN=...
     $ spack buildcache push my_registry <specs...>  # push to the registry
-    $ spack install <specs...> # install from the registry
+    $ spack install <specs...>  # or install from the registry
 
 A unique feature of buildcaches on top of OCI registries is that it's incredibly
 easy to generate get a runnable container image with the binaries installed. This

lib/spack/docs/containers.rst

@@ -38,9 +38,11 @@ just have to configure and OCI registry and run ``spack buildcache push``.
    spack -e . install
 
    # Configure the registry
-   spack -e . mirror add --oci-username ... --oci-password ... container-registry oci://example.com/name/image
+   spack -e . mirror add --oci-username-variable REGISTRY_USER \
+                         --oci-password-variable REGISTRY_TOKEN \
+                        container-registry oci://example.com/name/image
 
-   # Push the image
+   # Push the image (do set REGISTRY_USER and REGISTRY_TOKEN)
    spack -e . buildcache push --update-index --base-image ubuntu:22.04 --tag my_env container-registry
 
 The resulting container image can then be run as follows:

lib/spack/docs/getting_started.rst

@@ -148,20 +148,22 @@ The first time you concretize a spec, Spack will bootstrap automatically:
    --------------------------------
    zlib@1.2.13%gcc@9.4.0+optimize+pic+shared build_system=makefile arch=linux-ubuntu20.04-icelake
 
+The default bootstrap behavior is to use pre-built binaries. You can verify the
+active bootstrap repositories with:
+
+.. command-output:: spack bootstrap list
+
 If for security concerns you cannot bootstrap ``clingo`` from pre-built
 binaries, you have to disable fetching the binaries we generated with Github Actions.
 
 .. code-block:: console
 
-   $ spack bootstrap disable github-actions-v0.4
-   ==> "github-actions-v0.4" is now disabled and will not be used for bootstrapping
-   $ spack bootstrap disable github-actions-v0.3
-   ==> "github-actions-v0.3" is now disabled and will not be used for bootstrapping
-
-You can verify that the new settings are effective with:
-
-.. command-output:: spack bootstrap list
+   $ spack bootstrap disable github-actions-v0.6
+   ==> "github-actions-v0.6" is now disabled and will not be used for bootstrapping
+   $ spack bootstrap disable github-actions-v0.5
+   ==> "github-actions-v0.5" is now disabled and will not be used for bootstrapping
 
+You can verify that the new settings are effective with ``spack bootstrap list``.
 
 .. note::
 

lib/spack/llnl/util/filesystem.py

@@ -24,6 +24,7 @@
     Callable,
     Deque,
     Dict,
+    Generator,
     Iterable,
     List,
     Match,
@@ -300,35 +301,32 @@ def filter_file(
     ignore_absent: bool = False,
     start_at: Optional[str] = None,
     stop_at: Optional[str] = None,
+    encoding: Optional[str] = "utf-8",
 ) -> None:
     r"""Like sed, but uses python regular expressions.
 
-    Filters every line of each file through regex and replaces the file
-    with a filtered version.  Preserves mode of filtered files.
+    Filters every line of each file through regex and replaces the file with a filtered version.
+    Preserves mode of filtered files.
 
-    As with re.sub, ``repl`` can be either a string or a callable.
-    If it is a callable, it is passed the match object and should
-    return a suitable replacement string.  If it is a string, it
-    can contain ``\1``, ``\2``, etc. to represent back-substitution
-    as sed would allow.
+    As with re.sub, ``repl`` can be either a string or a callable. If it is a callable, it is
+    passed the match object and should return a suitable replacement string.  If it is a string, it
+    can contain ``\1``, ``\2``, etc. to represent back-substitution as sed would allow.
 
     Args:
-        regex (str): The regular expression to search for
-        repl (str): The string to replace matches with
-        *filenames: One or more files to search and replace
-        string (bool): Treat regex as a plain string. Default it False
-        backup (bool): Make backup file(s) suffixed with ``~``. Default is False
-        ignore_absent (bool): Ignore any files that don't exist.
-            Default is False
-        start_at (str): Marker used to start applying the replacements. If a
-            text line matches this marker filtering is started at the next line.
-            All contents before the marker and the marker itself are copied
-            verbatim. Default is to start filtering from the first line of the
-            file.
-        stop_at (str): Marker used to stop scanning the file further. If a text
-            line matches this marker filtering is stopped and the rest of the
-            file is copied verbatim. Default is to filter until the end of the
-            file.
+        regex: The regular expression to search for
+        repl: The string to replace matches with
+        *filenames: One or more files to search and replace string: Treat regex as a plain string.
+            Default it False backup: Make backup file(s) suffixed with ``~``. Default is False
+        ignore_absent: Ignore any files that don't exist. Default is False
+        start_at: Marker used to start applying the replacements. If a text line matches this
+            marker filtering is started at the next line. All contents before the marker and the
+            marker itself are copied verbatim. Default is to start filtering from the first line of
+            the file.
+        stop_at: Marker used to stop scanning the file further. If a text line matches this marker
+            filtering is stopped and the rest of the file is copied verbatim. Default is to filter
+            until the end of the file.
+        encoding: The encoding to use when reading and writing the files. Default is None, which
+            uses the system's default encoding.
     """
     # Allow strings to use \1, \2, etc. for replacement, like sed
     if not callable(repl):
@@ -344,72 +342,56 @@ def groupid_to_group(x):
 
     if string:
         regex = re.escape(regex)
-    for filename in path_to_os_path(*filenames):
-        msg = 'FILTER FILE: {0} [replacing "{1}"]'
-        tty.debug(msg.format(filename, regex))
-
-        backup_filename = filename + "~"
-        tmp_filename = filename + ".spack~"
-
-        if ignore_absent and not os.path.exists(filename):
-            msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.'
-            tty.debug(msg.format(filename))
+    regex_compiled = re.compile(regex)
+    for path in path_to_os_path(*filenames):
+        if ignore_absent and not os.path.exists(path):
+            tty.debug(f'FILTER FILE: file "{path}" not found. Skipping to next file.')
             continue
+        else:
+            tty.debug(f'FILTER FILE: {path} [replacing "{regex}"]')
 
-        # Create backup file. Don't overwrite an existing backup
-        # file in case this file is being filtered multiple times.
-        if not os.path.exists(backup_filename):
-            shutil.copy(filename, backup_filename)
+        fd, temp_path = tempfile.mkstemp(
+            prefix=f"{os.path.basename(path)}.", dir=os.path.dirname(path)
+        )
+        os.close(fd)
 
-        # Create a temporary file to read from. We cannot use backup_filename
-        # in case filter_file is invoked multiple times on the same file.
-        shutil.copy(filename, tmp_filename)
+        shutil.copy(path, temp_path)
+        errored = False
 
         try:
-            # Open as a text file and filter until the end of the file is
-            # reached, or we found a marker in the line if it was specified
-            #
-            # To avoid translating line endings (\n to \r\n and vice-versa)
-            # we force os.open to ignore translations and use the line endings
-            # the file comes with
-            with open(tmp_filename, mode="r", errors="surrogateescape", newline="") as input_file:
-                with open(filename, mode="w", errors="surrogateescape", newline="") as output_file:
-                    do_filtering = start_at is None
-                    # Using iter and readline is a workaround needed not to
-                    # disable input_file.tell(), which will happen if we call
-                    # input_file.next() implicitly via the for loop
-                    for line in iter(input_file.readline, ""):
-                        if stop_at is not None:
-                            current_position = input_file.tell()
+            # Open as a text file and filter until the end of the file is reached, or we found a
+            # marker in the line if it was specified. To avoid translating line endings (\n to
+            # \r\n and vice-versa) use newline="".
+            with open(
+                temp_path, mode="r", errors="surrogateescape", newline="", encoding=encoding
+            ) as input_file, open(
+                path, mode="w", errors="surrogateescape", newline="", encoding=encoding
+            ) as output_file:
+                if start_at is None and stop_at is None:  # common case, avoids branching in loop
+                    for line in input_file:
+                        output_file.write(re.sub(regex_compiled, repl, line))
+                else:
+                    # state is -1 before start_at; 0 between; 1 after stop_at
+                    state = 0 if start_at is None else -1
+                    for line in input_file:
+                        if state == 0:
                             if stop_at == line.strip():
-                                output_file.write(line)
-                                break
-                        if do_filtering:
-                            filtered_line = re.sub(regex, repl, line)
-                            output_file.write(filtered_line)
-                        else:
-                            do_filtering = start_at == line.strip()
-                            output_file.write(line)
-                    else:
-                        current_position = None
-
-            # If we stopped filtering at some point, reopen the file in
-            # binary mode and copy verbatim the remaining part
-            if current_position and stop_at:
-                with open(tmp_filename, mode="rb") as input_binary_buffer:
-                    input_binary_buffer.seek(current_position)
-                    with open(filename, mode="ab") as output_binary_buffer:
-                        output_binary_buffer.writelines(input_binary_buffer.readlines())
+                                state = 1
+                            else:
+                                line = re.sub(regex_compiled, repl, line)
+                        elif state == -1 and start_at == line.strip():
+                            state = 0
+                        output_file.write(line)
 
         except BaseException:
-            # clean up the original file on failure.
-            shutil.move(backup_filename, filename)
+            # restore the original file
+            os.rename(temp_path, path)
+            errored = True
             raise
 
         finally:
-            os.remove(tmp_filename)
-            if not backup and os.path.exists(backup_filename):
-                os.remove(backup_filename)
+            if not errored and not backup:
+                os.unlink(temp_path)
 
 
 class FileFilter:
@@ -2838,6 +2820,25 @@ def temporary_dir(
         remove_directory_contents(tmp_dir)
 
 
+@contextmanager
+def edit_in_place_through_temporary_file(file_path: str) -> Generator[str, None, None]:
+    """Context manager for modifying ``file_path`` in place, preserving its inode and hardlinks,
+    for functions or external tools that do not support in-place editing. Notice that this function
+    is unsafe in that it works with paths instead of a file descriptors, but this is by design,
+    since we assume the call site will create a new inode at the same path."""
+    tmp_fd, tmp_path = tempfile.mkstemp(
+        dir=os.path.dirname(file_path), prefix=f"{os.path.basename(file_path)}."
+    )
+    # windows cannot replace a file with open fds, so close since the call site needs to replace.
+    os.close(tmp_fd)
+    try:
+        shutil.copyfile(file_path, tmp_path, follow_symlinks=True)
+        yield tmp_path
+        shutil.copyfile(tmp_path, file_path, follow_symlinks=True)
+    finally:
+        os.unlink(tmp_path)
+
+
 def filesummary(path, print_bytes=16) -> Tuple[int, bytes]:
     """Create a small summary of the given file. Does not error
     when file does not exist.

lib/spack/llnl/util/tty/log.py

@@ -879,10 +879,13 @@ def _writer_daemon(
     write_fd.close()
 
     # 1. Use line buffering (3rd param = 1) since Python 3 has a bug
-    # that prevents unbuffered text I/O.
-    # 2. Python 3.x before 3.7 does not open with UTF-8 encoding by default
+    #    that prevents unbuffered text I/O. [needs citation]
+    # 2. Enforce a UTF-8 interpretation of build process output with errors replaced by '?'.
+    #    The downside is that the log file will not contain the exact output of the build process.
     # 3. closefd=False because Connection has "ownership"
-    read_file = os.fdopen(read_fd.fileno(), "r", 1, encoding="utf-8", closefd=False)
+    read_file = os.fdopen(
+        read_fd.fileno(), "r", 1, encoding="utf-8", errors="replace", closefd=False
+    )
 
     if stdin_fd:
         stdin_file = os.fdopen(stdin_fd.fileno(), closefd=False)
@@ -928,11 +931,7 @@ def _writer_daemon(
                     try:
                         while line_count < 100:
                             # Handle output from the calling process.
-                            try:
-                                line = _retry(read_file.readline)()
-                            except UnicodeDecodeError:
-                                # installs like --test=root gpgme produce non-UTF8 logs
-                                line = "<line lost: output was not encoded as UTF-8>\n"
+                            line = _retry(read_file.readline)()
 
                             if not line:
                                 return
@@ -946,6 +945,13 @@ def _writer_daemon(
                                 output_line = clean_line
                                 if filter_fn:
                                     output_line = filter_fn(clean_line)
+                                enc = sys.stdout.encoding
+                                if enc != "utf-8":
+                                    # On Python 3.6 and 3.7-3.14 with non-{utf-8,C} locale stdout
+                                    # may not be able to handle utf-8 output. We do an inefficient
+                                    # dance of re-encoding with errors replaced, so stdout.write
+                                    # does not raise.
+                                    output_line = output_line.encode(enc, "replace").decode(enc)
                                 sys.stdout.write(output_line)
 
                             # Stripped output to log file.

lib/spack/spack/__init__.py

@@ -11,7 +11,7 @@
 import spack.util.git
 
 #: PEP440 canonical <major>.<minor>.<micro>.<devN> string
-__version__ = "0.23.0.dev0"
+__version__ = "0.23.1"
 spack_version = __version__
 
 

lib/spack/spack/audit.py

@@ -1366,14 +1366,8 @@ def _test_detection_by_executable(pkgs, debug_log, error_cls):
 
             def _compare_extra_attribute(_expected, _detected, *, _spec):
                 result = []
-                # Check items are of the same type
-                if not isinstance(_detected, type(_expected)):
-                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
-                    _details = [f"{_detected} was detected instead"]
-                    return [error_cls(summary=_summary, details=_details)]
-
                 # If they are string expected is a regex
-                if isinstance(_expected, str):
+                if isinstance(_expected, str) and isinstance(_detected, str):
                     try:
                         _regex = re.compile(_expected)
                     except re.error:
@@ -1389,7 +1383,7 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         _details = [f"{_detected} does not match the regex"]
                         return [error_cls(summary=_summary, details=_details)]
 
-                if isinstance(_expected, dict):
+                elif isinstance(_expected, dict) and isinstance(_detected, dict):
                     _not_detected = set(_expected.keys()) - set(_detected.keys())
                     if _not_detected:
                         _summary = f"{pkg_name}: cannot detect some attributes for spec {_spec}"
@@ -1404,6 +1398,10 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         result.extend(
                             _compare_extra_attribute(_expected[_key], _detected[_key], _spec=_spec)
                         )
+                else:
+                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
+                    _details = [f"{_detected} was detected instead"]
+                    return [error_cls(summary=_summary, details=_details)]
 
                 return result
 

lib/spack/spack/binary_distribution.py

@@ -2332,7 +2332,9 @@ def is_backup_file(file):
             if not codesign:
                 return
             for binary in changed_files:
-                codesign("-fs-", binary)
+                # preserve the original inode by running codesign on a copy
+                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
+                    codesign("-fs-", tmp_binary)
 
     # If we are installing back to the same location
     # relocate the sbang location if the spack directory changed

lib/spack/spack/build_systems/autotools.py

@@ -357,6 +357,13 @@ def _do_patch_libtool_configure(self):
             )
             # Support Libtool 2.4.2 and older:
             x.filter(regex=r'^(\s*test \$p = "-R")(; then\s*)$', repl=r'\1 || test x-l = x"$p"\2')
+            # Configure scripts generated with libtool < 2.5.4 have a faulty test for the
+            # -single_module linker flag. A deprecation warning makes it think the default is
+            # -multi_module, triggering it to use problematic linker flags (such as ld -r). The
+            # linker default is `-single_module` from (ancient) macOS 10.4, so override by setting
+            # `lt_cv_apple_cc_single_mod=yes`. See the fix in libtool commit
+            # 82f7f52123e4e7e50721049f7fa6f9b870e09c9d.
+            x.filter("lt_cv_apple_cc_single_mod=no", "lt_cv_apple_cc_single_mod=yes", string=True)
 
     @spack.builder.run_after("configure")
     def _do_patch_libtool(self):

lib/spack/spack/cmd/__init__.py

@@ -25,6 +25,7 @@
 import spack.extensions
 import spack.parser
 import spack.paths
+import spack.repo
 import spack.spec
 import spack.store
 import spack.traverse as traverse
@@ -166,7 +167,9 @@ def quote_kvp(string: str) -> str:
 
 
 def parse_specs(
-    args: Union[str, List[str]], concretize: bool = False, tests: bool = False
+    args: Union[str, List[str]],
+    concretize: bool = False,
+    tests: spack.concretize.TestsType = False,
 ) -> List[spack.spec.Spec]:
     """Convenience function for parsing arguments from specs.  Handles common
     exceptions and dies if there are errors.
@@ -178,11 +181,13 @@ def parse_specs(
     if not concretize:
         return specs
 
-    to_concretize = [(s, None) for s in specs]
+    to_concretize: List[spack.concretize.SpecPairInput] = [(s, None) for s in specs]
     return _concretize_spec_pairs(to_concretize, tests=tests)
 
 
-def _concretize_spec_pairs(to_concretize, tests=False):
+def _concretize_spec_pairs(
+    to_concretize: List[spack.concretize.SpecPairInput], tests: spack.concretize.TestsType = False
+) -> List[spack.spec.Spec]:
     """Helper method that concretizes abstract specs from a list of abstract,concrete pairs.
 
     Any spec with a concrete spec associated with it will concretize to that spec. Any spec
@@ -193,7 +198,7 @@ def _concretize_spec_pairs(to_concretize, tests=False):
     # Special case for concretizing a single spec
     if len(to_concretize) == 1:
         abstract, concrete = to_concretize[0]
-        return [concrete or abstract.concretized()]
+        return [concrete or abstract.concretized(tests=tests)]
 
     # Special case if every spec is either concrete or has an abstract hash
     if all(

lib/spack/spack/cmd/bootstrap.py

@@ -29,7 +29,7 @@
 
 
 # Tarball to be downloaded if binary packages are requested in a local mirror
-BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.4/bootstrap-buildcache.tar.gz"
+BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.6/bootstrap-buildcache.tar.gz"
 
 #: Subdirectory where to create the mirror
 LOCAL_MIRROR_DIR = "bootstrap_cache"
@@ -51,9 +51,9 @@
     },
 }
 
-CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/clingo.json"
-GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/gnupg.json"
-PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/patchelf.json"
+CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/clingo.json"
+GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/gnupg.json"
+PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/patchelf.json"
 
 # Metadata for a generated source mirror
 SOURCE_METADATA = {

lib/spack/spack/cmd/common/arguments.py

@@ -528,6 +528,7 @@ def __call__(self, parser, namespace, values, option_string):
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
         # specified on the command line.
+        spack.config.CONFIG.ensure_scope_ordering()
         spack.config.set(self.config_path, self.const, scope="command_line")
 
 

lib/spack/spack/cmd/license.py

@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import datetime
 import os
 import re
 from collections import defaultdict
@@ -97,7 +96,7 @@ def list_files(args):
 OLD_LICENSE, SPDX_MISMATCH, GENERAL_MISMATCH = range(1, 4)
 
 #: Latest year that copyright applies. UPDATE THIS when bumping copyright.
-latest_year = datetime.date.today().year
+latest_year = 2024  # year of 0.23 release
 strict_date = r"Copyright 2013-%s" % latest_year
 
 #: regexes for valid license lines at tops of files

lib/spack/spack/cmd/spec.py

@@ -82,14 +82,6 @@ def spec(parser, args):
     if args.namespaces:
         fmt = "{namespace}." + fmt
 
-    tree_kwargs = {
-        "cover": args.cover,
-        "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,
-    }
-
     # use a read transaction if we are getting install status for every
     # spec in the DAG.  This avoids repeatedly querying the DB.
     tree_context = lang.nullcontext
@@ -99,46 +91,35 @@ def spec(parser, args):
     env = ev.active_environment()
 
     if args.specs:
-        input_specs = spack.cmd.parse_specs(args.specs)
-        concretized_specs = spack.cmd.parse_specs(args.specs, concretize=True)
-        specs = list(zip(input_specs, concretized_specs))
+        concrete_specs = spack.cmd.parse_specs(args.specs, concretize=True)
     elif env:
         env.concretize()
-        specs = env.concretized_specs()
-
-        if not args.format:
-            # environments are printed together in a combined tree() invocation,
-            # except when using --yaml or --json, which we print spec by spec below.
-            tree_kwargs["key"] = spack.traverse.by_dag_hash
-            tree_kwargs["hashes"] = args.long or args.very_long
-            print(spack.spec.tree([concrete for _, concrete in specs], **tree_kwargs))
-            return
+        concrete_specs = env.concrete_roots()
     else:
         tty.die("spack spec requires at least one spec or an active environment")
 
-    for input, output in specs:
-        # With --yaml or --json, just print the raw specs to output
-        if args.format:
+    # With --yaml, --json, or --format, just print the raw specs to output
+    if args.format:
+        for spec in concrete_specs:
             if args.format == "yaml":
                 # use write because to_yaml already has a newline.
-                sys.stdout.write(output.to_yaml(hash=ht.dag_hash))
+                sys.stdout.write(spec.to_yaml(hash=ht.dag_hash))
             elif args.format == "json":
-                print(output.to_json(hash=ht.dag_hash))
+                print(spec.to_json(hash=ht.dag_hash))
             else:
-                print(output.format(args.format))
-            continue
+                print(spec.format(args.format))
+        return
 
-        with tree_context():
-            # Only show the headers for input specs that are not concrete to avoid
-            # repeated output. This happens because parse_specs outputs concrete
-            # specs for `/hash` inputs.
-            if not input.concrete:
-                tree_kwargs["hashes"] = False  # Always False for input spec
-                print("Input spec")
-                print("--------------------------------")
-                print(input.tree(**tree_kwargs))
-                print("Concretized")
-                print("--------------------------------")
-
-            tree_kwargs["hashes"] = args.long or args.very_long
-            print(output.tree(**tree_kwargs))
+    with tree_context():
+        print(
+            spack.spec.tree(
+                concrete_specs,
+                cover=args.cover,
+                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,
+                hashes=args.long or args.very_long,
+                key=spack.traverse.by_dag_hash,
+            )
+        )

lib/spack/spack/cmd/tutorial.py

@@ -24,7 +24,7 @@
 
 
 # tutorial configuration parameters
-tutorial_branch = "releases/v0.22"
+tutorial_branch = "releases/v0.23"
 tutorial_mirror = "file:///mirror"
 tutorial_key = os.path.join(spack.paths.share_path, "keys", "tutorial.pub")
 

lib/spack/spack/concretize.py

@@ -6,7 +6,7 @@
 import sys
 import time
 from contextlib import contextmanager
-from typing import Iterable, Optional, Sequence, Tuple, Union
+from typing import Iterable, List, Optional, Sequence, Tuple, Union
 
 import llnl.util.tty as tty
 
@@ -36,6 +36,7 @@ def enable_compiler_existence_check():
     CHECK_COMPILER_EXISTENCE = saved
 
 
+SpecPairInput = Tuple[Spec, Optional[Spec]]
 SpecPair = Tuple[Spec, Spec]
 SpecLike = Union[Spec, str]
 TestsType = Union[bool, Iterable[str]]
@@ -60,8 +61,8 @@ def concretize_specs_together(
 
 
 def concretize_together(
-    spec_list: Sequence[SpecPair], tests: TestsType = False
-) -> Sequence[SpecPair]:
+    spec_list: Sequence[SpecPairInput], tests: TestsType = False
+) -> List[SpecPair]:
     """Given a number of specs as input, tries to concretize them together.
 
     Args:
@@ -77,8 +78,8 @@ def concretize_together(
 
 
 def concretize_together_when_possible(
-    spec_list: Sequence[SpecPair], tests: TestsType = False
-) -> Sequence[SpecPair]:
+    spec_list: Sequence[SpecPairInput], tests: TestsType = False
+) -> List[SpecPair]:
     """Given a number of specs as input, tries to concretize them together to the extent possible.
 
     See documentation for ``unify: when_possible`` concretization for the precise definition of
@@ -114,8 +115,8 @@ def concretize_together_when_possible(
 
 
 def concretize_separately(
-    spec_list: Sequence[SpecPair], tests: TestsType = False
-) -> Sequence[SpecPair]:
+    spec_list: Sequence[SpecPairInput], tests: TestsType = False
+) -> List[SpecPair]:
     """Concretizes the input specs separately from each other.
 
     Args:

lib/spack/spack/config.py

@@ -431,6 +431,19 @@ def ensure_unwrapped(self) -> "Configuration":
         """Ensure we unwrap this object from any dynamic wrapper (like Singleton)"""
         return self
 
+    def highest(self) -> ConfigScope:
+        """Scope with highest precedence"""
+        return next(reversed(self.scopes.values()))  # type: ignore
+
+    @_config_mutator
+    def ensure_scope_ordering(self):
+        """Ensure that scope order matches documented precedent"""
+        # FIXME: We also need to consider that custom configurations and other orderings
+        # may not be preserved correctly
+        if "command_line" in self.scopes:
+            # TODO (when dropping python 3.6): self.scopes.move_to_end
+            self.scopes["command_line"] = self.remove_scope("command_line")
+
     @_config_mutator
     def push_scope(self, scope: ConfigScope) -> None:
         """Add a higher precedence scope to the Configuration."""

lib/spack/spack/environment/environment.py

@@ -3044,11 +3044,13 @@ def prepare_config_scope(self) -> None:
         """Add the manifest's scopes to the global configuration search path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.push_scope(scope)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):

lib/spack/spack/mirror.py

@@ -180,7 +180,7 @@ def ensure_mirror_usable(self, direction: str = "push"):
         if errors:
             msg = f"invalid {direction} configuration for mirror {self.name}: "
             msg += "\n    ".join(errors)
-            raise spack.mirror.MirrorError(msg)
+            raise MirrorError(msg)
 
     def _update_connection_dict(self, current_data: dict, new_data: dict, top_level: bool):
         # Only allow one to exist in the config

lib/spack/spack/oci/opener.py

@@ -397,6 +397,7 @@ def create_opener():
     """Create an opener that can handle OCI authentication."""
     opener = urllib.request.OpenerDirector()
     for handler in [
+        urllib.request.ProxyHandler(),
         urllib.request.UnknownHandler(),
         urllib.request.HTTPSHandler(context=spack.util.web.ssl_create_default_context()),
         spack.util.web.SpackHTTPDefaultErrorHandler(),

lib/spack/spack/relocate.py

@@ -13,6 +13,7 @@
 import macholib.mach_o
 import macholib.MachO
 
+import llnl.util.filesystem as fs
 import llnl.util.lang
 import llnl.util.tty as tty
 from llnl.util.lang import memoized
@@ -275,10 +276,10 @@ def modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths):
 
     # Deduplicate and flatten
     args = list(itertools.chain.from_iterable(llnl.util.lang.dedupe(args)))
+    install_name_tool = executable.Executable("install_name_tool")
     if args:
-        args.append(str(cur_path))
-        install_name_tool = executable.Executable("install_name_tool")
-        install_name_tool(*args)
+        with fs.edit_in_place_through_temporary_file(cur_path) as temp_path:
+            install_name_tool(*args, temp_path)
 
 
 def macholib_get_paths(cur_path):
@@ -717,8 +718,8 @@ def fixup_macos_rpath(root, filename):
         # No fixes needed
         return False
 
-    args.append(abspath)
-    executable.Executable("install_name_tool")(*args)
+    with fs.edit_in_place_through_temporary_file(abspath) as temp_path:
+        executable.Executable("install_name_tool")(*args, temp_path)
     return True
 
 

lib/spack/spack/relocate_text.py

@@ -209,7 +209,7 @@ def _apply_to_file(self, f):
         # but it's nasty to deal with matches across boundaries, so let's stick to
         # something simple.
 
-        modified = True
+        modified = False
 
         for match in self.regex.finditer(f.read()):
             # The matching prefix (old) and its replacement (new)

lib/spack/spack/schema/config.py

@@ -106,8 +106,8 @@
             {
                 "names": ["install_missing_compilers"],
                 "message": "The config:install_missing_compilers option has been deprecated in "
-                "Spack v0.23, and is currently ignored. It will be removed from config in "
-                "Spack v0.25.",
+                "Spack v0.23, and is currently ignored. It will be removed from config after "
+                "Spack v1.0.",
                 "error": False,
             },
         ],

lib/spack/spack/solver/asp.py

@@ -3839,12 +3839,21 @@ def splice_at_hash(
         self._splices.setdefault(parent_node, []).append(splice)
 
     def _resolve_automatic_splices(self):
-        """After all of the specs have been concretized, apply all immediate
-        splices in size order. This ensures that all dependencies are resolved
+        """After all of the specs have been concretized, apply all immediate splices.
+
+        Use reverse topological order to ensure that all dependencies are resolved
         before their parents, allowing for maximal sharing and minimal copying.
+
         """
         fixed_specs = {}
-        for node, spec in sorted(self._specs.items(), key=lambda x: len(x[1])):
+
+        # create a mapping from dag hash to an integer representing position in reverse topo order.
+        specs = self._specs.values()
+        topo_order = list(traverse.traverse_nodes(specs, order="topo", key=traverse.by_dag_hash))
+        topo_lookup = {spec.dag_hash(): index for index, spec in enumerate(reversed(topo_order))}
+
+        # iterate over specs, children before parents
+        for node, spec in sorted(self._specs.items(), key=lambda x: topo_lookup[x[1].dag_hash()]):
             immediate = self._splices.get(node, [])
             if not immediate and not any(
                 edge.spec in fixed_specs for edge in spec.edges_to_dependencies()

lib/spack/spack/spec.py

@@ -448,6 +448,9 @@ def _target_satisfies(self, other: "ArchSpec", strict: bool) -> bool:
         return bool(self._target_intersection(other))
 
     def _target_constrain(self, other: "ArchSpec") -> bool:
+        if self.target is None and other.target is None:
+            return False
+
         if not other._target_satisfies(self, strict=False):
             raise UnsatisfiableArchitectureSpecError(self, other)
 
@@ -496,21 +499,56 @@ def _target_intersection(self, other):
                     if (not s_min or o_comp >= s_min) and (not s_max or o_comp <= s_max):
                         results.append(o_min)
                 else:
-                    # Take intersection of two ranges
-                    # Lots of comparisons needed
-                    _s_min = _make_microarchitecture(s_min)
-                    _s_max = _make_microarchitecture(s_max)
-                    _o_min = _make_microarchitecture(o_min)
-                    _o_max = _make_microarchitecture(o_max)
+                    # Take the "min" of the two max, if there is a partial ordering.
+                    n_max = ""
+                    if s_max and o_max:
+                        _s_max = _make_microarchitecture(s_max)
+                        _o_max = _make_microarchitecture(o_max)
+                        if _s_max.family != _o_max.family:
+                            continue
+                        if _s_max <= _o_max:
+                            n_max = s_max
+                        elif _o_max < _s_max:
+                            n_max = o_max
+                        else:
+                            continue
+                    elif s_max:
+                        n_max = s_max
+                    elif o_max:
+                        n_max = o_max
+
+                    # Take the "max" of the two min.
+                    n_min = ""
+                    if s_min and o_min:
+                        _s_min = _make_microarchitecture(s_min)
+                        _o_min = _make_microarchitecture(o_min)
+                        if _s_min.family != _o_min.family:
+                            continue
+                        if _s_min >= _o_min:
+                            n_min = s_min
+                        elif _o_min > _s_min:
+                            n_min = o_min
+                        else:
+                            continue
+                    elif s_min:
+                        n_min = s_min
+                    elif o_min:
+                        n_min = o_min
+
+                    if n_min and n_max:
+                        _n_min = _make_microarchitecture(n_min)
+                        _n_max = _make_microarchitecture(n_max)
+                        if _n_min.family != _n_max.family or not _n_min <= _n_max:
+                            continue
+                        if n_min == n_max:
+                            results.append(n_min)
+                        else:
+                            results.append(f"{n_min}:{n_max}")
+                    elif n_min:
+                        results.append(f"{n_min}:")
+                    elif n_max:
+                        results.append(f":{n_max}")
 
-                    n_min = s_min if _s_min >= _o_min else o_min
-                    n_max = s_max if _s_max <= _o_max else o_max
-                    _n_min = _make_microarchitecture(n_min)
-                    _n_max = _make_microarchitecture(n_max)
-                    if _n_min == _n_max:
-                        results.append(n_min)
-                    elif not n_min or not n_max or _n_min < _n_max:
-                        results.append("%s:%s" % (n_min, n_max))
         return results
 
     def constrain(self, other: "ArchSpec") -> bool:
@@ -1431,8 +1469,6 @@ def tree(
 class Spec:
     #: Cache for spec's prefix, computed lazily in the corresponding property
     _prefix = None
-    #: Cache for spec's length, computed lazily in the corresponding property
-    _length = None
     abstract_hash = None
 
     @staticmethod
@@ -1502,9 +1538,8 @@ def __init__(
         self._external_path = external_path
         self.external_modules = Spec._format_module_list(external_modules)
 
-        # This attribute is used to store custom information for
-        # external specs. None signal that it was not set yet.
-        self.extra_attributes = None
+        # This attribute is used to store custom information for external specs.
+        self.extra_attributes: dict = {}
 
         # This attribute holds the original build copy of the spec if it is
         # deployed differently than it was built. None signals that the spec
@@ -2219,8 +2254,8 @@ def to_node_dict(self, hash=ht.dag_hash):
             d["external"] = syaml.syaml_dict(
                 [
                     ("path", self.external_path),
-                    ("module", self.external_modules),
-                    ("extra_attributes", self.extra_attributes),
+                    ("module", self.external_modules or None),
+                    ("extra_attributes", syaml.sorted_dict(self.extra_attributes)),
                 ]
             )
 
@@ -2958,7 +2993,7 @@ def _finalize_concretization(self):
         for spec in self.traverse():
             spec._cached_hash(ht.dag_hash)
 
-    def concretized(self, tests: Union[bool, Iterable[str]] = False) -> "spack.spec.Spec":
+    def concretized(self, tests: Union[bool, Iterable[str]] = False) -> "Spec":
         """This is a non-destructive version of concretize().
 
         First clones, then returns a concrete version of this package
@@ -3081,18 +3116,13 @@ def constrain(self, other, deps=True):
             if not self.variants[v].compatible(other.variants[v]):
                 raise vt.UnsatisfiableVariantSpecError(self.variants[v], other.variants[v])
 
-        # TODO: Check out the logic here
         sarch, oarch = self.architecture, other.architecture
-        if sarch is not None and oarch is not None:
-            if sarch.platform is not None and oarch.platform is not None:
-                if sarch.platform != oarch.platform:
-                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
-            if sarch.os is not None and oarch.os is not None:
-                if sarch.os != oarch.os:
-                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
-            if sarch.target is not None and oarch.target is not None:
-                if sarch.target != oarch.target:
-                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
+        if (
+            sarch is not None
+            and oarch is not None
+            and not self.architecture.intersects(other.architecture)
+        ):
+            raise UnsatisfiableArchitectureSpecError(sarch, oarch)
 
         changed = False
 
@@ -3115,18 +3145,12 @@ def constrain(self, other, deps=True):
 
         changed |= self.compiler_flags.constrain(other.compiler_flags)
 
-        old = str(self.architecture)
         sarch, oarch = self.architecture, other.architecture
-        if sarch is None or other.architecture is None:
-            self.architecture = sarch or oarch
-        else:
-            if sarch.platform is None or oarch.platform is None:
-                self.architecture.platform = sarch.platform or oarch.platform
-            if sarch.os is None or oarch.os is None:
-                sarch.os = sarch.os or oarch.os
-            if sarch.target is None or oarch.target is None:
-                sarch.target = sarch.target or oarch.target
-        changed |= str(self.architecture) != old
+        if sarch is not None and oarch is not None:
+            changed |= self.architecture.constrain(other.architecture)
+        elif oarch is not None:
+            self.architecture = oarch
+            changed = True
 
         if deps:
             changed |= self._constrain_dependencies(other)
@@ -3702,18 +3726,6 @@ def __getitem__(self, name: str):
 
         return child
 
-    def __len__(self):
-        if not self.concrete:
-            raise spack.error.SpecError(f"Cannot get length of abstract spec: {self}")
-
-        if not self._length:
-            self._length = 1 + sum(len(dep) for dep in self.dependencies())
-        return self._length
-
-    def __bool__(self):
-        # Need to define this so __len__ isn't used by default
-        return True
-
     def __contains__(self, spec):
         """True if this spec or some dependency satisfies the spec.
 
@@ -4472,7 +4484,7 @@ def clear_caches(self, ignore=()):
             if h.attr not in ignore:
                 if hasattr(self, h.attr):
                     setattr(self, h.attr, None)
-        for attr in ("_dunder_hash", "_prefix", "_length"):
+        for attr in ("_dunder_hash", "_prefix"):
             if attr not in ignore:
                 setattr(self, attr, None)
 
@@ -4849,8 +4861,8 @@ def from_node_dict(cls, node):
                 spec.external_modules = node["external"]["module"]
                 if spec.external_modules is False:
                     spec.external_modules = None
-                spec.extra_attributes = node["external"].get(
-                    "extra_attributes", syaml.syaml_dict()
+                spec.extra_attributes = (
+                    node["external"].get("extra_attributes") or syaml.syaml_dict()
                 )
 
         # specs read in are concrete unless marked abstract

lib/spack/spack/stage.py

@@ -487,7 +487,7 @@ def _generate_fetchers(self, mirror_only=False) -> Generator["fs.FetchStrategy",
             # Insert fetchers in the order that the URLs are provided.
             fetchers[:0] = (
                 fs.from_url_scheme(
-                    url_util.join(mirror.fetch_url, self.mirror_layout.path),
+                    url_util.join(mirror.fetch_url, *self.mirror_layout.path.split(os.sep)),
                     checksum=digest,
                     expand=expand,
                     extension=extension,

lib/spack/spack/test/abi_splicing.py

@@ -10,9 +10,6 @@
 
 import spack.config
 import spack.deptypes as dt
-import spack.package_base
-import spack.paths
-import spack.repo
 import spack.solver.asp
 from spack.installer import PackageInstaller
 from spack.spec import Spec
@@ -232,3 +229,19 @@ def test_spliced_build_deps_only_in_build_spec(splicing_setup):
         assert _has_build_dependency(build_spec, "splice-z")
         # Spliced build dependencies are removed
         assert len(concr_goal.dependencies(None, dt.BUILD)) == 0
+
+
+def test_spliced_transitive_dependency(splicing_setup):
+    cache = ["splice-depends-on-t@1.0 ^splice-h@1.0.1"]
+    goal_spec = Spec("splice-depends-on-t^splice-h@1.0.2")
+
+    with CacheManager(cache):
+        spack.config.set("packages", _make_specs_non_buildable(["splice-depends-on-t"]))
+        _enable_splicing()
+        concr_goal = goal_spec.concretized()
+        # Spec has been spliced
+        assert concr_goal._build_spec is not None
+        assert concr_goal["splice-t"]._build_spec is not None
+        assert concr_goal.satisfies(goal_spec)
+        # Spliced build dependencies are removed
+        assert len(concr_goal.dependencies(None, dt.BUILD)) == 0

lib/spack/spack/test/cmd/init_py_functions.py

@@ -4,9 +4,11 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import pytest
 
+import spack.config
 import spack.environment as ev
 import spack.error
 import spack.solver.asp as asp
+import spack.store
 from spack.cmd import (
     CommandNameError,
     PythonNameError,

lib/spack/spack/test/cmd/pkg.py

@@ -315,6 +315,7 @@ def test_pkg_grep(mock_packages, capfd):
             "depends-on-manyvariants",
             "manyvariants",
             "splice-a",
+            "splice-depends-on-t",
             "splice-h",
             "splice-t",
             "splice-vh",

lib/spack/spack/test/cmd/spec.py

@@ -7,6 +7,7 @@
 
 import pytest
 
+import spack.config
 import spack.environment as ev
 import spack.error
 import spack.spec

lib/spack/spack/test/config.py

@@ -1532,3 +1532,30 @@ def test_config_path_dsl(path, it_should_work, expected_parsed):
     else:
         with pytest.raises(ValueError):
             spack.config.ConfigPath._validate(path)
+
+
+@pytest.mark.regression("48254")
+def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
+    """Check that the "command_line" scope remains the highest priority scope, when we activate,
+    or deactivate, environments.
+    """
+    expected_cl_scope = spack.config.CONFIG.highest()
+    assert expected_cl_scope.name == "command_line"
+
+    # Creating an environment pushes a new scope
+    ev.create("test")
+    with ev.read("test"):
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # No active environment pops the scope
+        with ev.no_active_environment():
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # Switch the environment to another one
+        ev.create("test-2")
+        with ev.read("test-2"):
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+    assert spack.config.CONFIG.highest() == expected_cl_scope

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

@@ -1249,3 +1249,14 @@ def test_find_input_types(tmp_path: pathlib.Path):
 
     with pytest.raises(TypeError):
         fs.find(1, "file.txt")  # type: ignore
+
+
+def test_edit_in_place_through_temporary_file(tmp_path):
+    (tmp_path / "example.txt").write_text("Hello")
+    current_ino = os.stat(tmp_path / "example.txt").st_ino
+    with fs.edit_in_place_through_temporary_file(tmp_path / "example.txt") as temporary:
+        os.unlink(temporary)
+        with open(temporary, "w") as f:
+            f.write("World")
+    assert (tmp_path / "example.txt").read_text() == "World"
+    assert os.stat(tmp_path / "example.txt").st_ino == current_ino

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

@@ -298,30 +298,6 @@ def inner():
     top-level raised TypeError: ok"""
     )
 
-    full_message = h.grouped_message(with_tracebacks=True)
-    no_line_numbers = re.sub(r"line [0-9]+,", "line xxx,", full_message)
-
-    assert (
-        no_line_numbers
-        == dedent(
-            """\
-    due to the following failures:
-    inner method raised ValueError: wow!
-      File "{0}", \
-line xxx, in test_grouped_exception
-        inner()
-      File "{0}", \
-line xxx, in inner
-        raise ValueError("wow!")
-
-    top-level raised TypeError: ok
-      File "{0}", \
-line xxx, in test_grouped_exception
-        raise TypeError("ok")
-    """
-        ).format(__file__)
-    )
-
 
 def test_grouped_exception_base_type():
     h = llnl.util.lang.GroupedExceptionHandler()

lib/spack/spack/test/llnl/util/tty/log.py

@@ -57,18 +57,16 @@ def test_log_python_output_without_echo(capfd, tmpdir):
         assert capfd.readouterr()[0] == ""
 
 
-def test_log_python_output_with_invalid_utf8(capfd, tmpdir):
-    with tmpdir.as_cwd():
-        with log.log_output("foo.txt"):
-            sys.stdout.buffer.write(b"\xc3\x28\n")
+def test_log_python_output_with_invalid_utf8(capfd, tmp_path):
+    tmp_file = str(tmp_path / "foo.txt")
+    with log.log_output(tmp_file, echo=True):
+        sys.stdout.buffer.write(b"\xc3helloworld\n")
 
-        expected = b"<line lost: output was not encoded as UTF-8>\n"
-        with open("foo.txt", "rb") as f:
-            written = f.read()
-            assert written == expected
+    # we should be able to read this as valid utf-8
+    with open(tmp_file, "r", encoding="utf-8") as f:
+        assert f.read() == "<EFBFBD>helloworld\n"
 
-        # nothing on stdout or stderr
-        assert capfd.readouterr()[0] == ""
+    assert capfd.readouterr().out == "<EFBFBD>helloworld\n"
 
 
 def test_log_python_output_and_echo_output(capfd, tmpdir):

lib/spack/spack/test/spack_yaml.py

@@ -138,3 +138,19 @@ def test_round_trip_configuration(initial_content, expected_final_content, tmp_p
         expected_final_content = initial_content
 
     assert final_content.getvalue() == expected_final_content
+
+
+def test_sorted_dict():
+    assert syaml.sorted_dict(
+        {
+            "z": 0,
+            "y": [{"x": 0, "w": [2, 1, 0]}, 0],
+            "v": ({"u": 0, "t": 0, "s": 0}, 0, {"r": 0, "q": 0}),
+            "p": 0,
+        }
+    ) == {
+        "p": 0,
+        "v": ({"s": 0, "t": 0, "u": 0}, 0, {"q": 0, "r": 0}),
+        "y": [{"w": [2, 1, 0], "x": 0}, 0],
+        "z": 0,
+    }

lib/spack/spack/test/spec_semantics.py

@@ -1842,6 +1842,16 @@ def test_abstract_contains_semantic(lhs, rhs, expected, mock_packages):
         # Different virtuals intersect if there is at least package providing both
         (Spec, "mpi", "lapack", (True, False, False)),
         (Spec, "mpi", "pkgconfig", (False, False, False)),
+        # Intersection among target ranges for different architectures
+        (Spec, "target=x86_64:", "target=ppc64le:", (False, False, False)),
+        (Spec, "target=x86_64:", "target=:power9", (False, False, False)),
+        (Spec, "target=:haswell", "target=:power9", (False, False, False)),
+        (Spec, "target=:haswell", "target=ppc64le:", (False, False, False)),
+        # Intersection among target ranges for the same architecture
+        (Spec, "target=:haswell", "target=x86_64:", (True, True, True)),
+        (Spec, "target=:haswell", "target=x86_64_v4:", (False, False, False)),
+        # Edge case of uarch that split in a diamond structure, from a common ancestor
+        (Spec, "target=:cascadelake", "target=:cannonlake", (False, False, False)),
     ],
 )
 def test_intersects_and_satisfies(factory, lhs_str, rhs_str, results):
@@ -1891,6 +1901,16 @@ def test_intersects_and_satisfies(factory, lhs_str, rhs_str, results):
         # Flags
         (Spec, "cppflags=-foo", "cppflags=-foo", False, "cppflags=-foo"),
         (Spec, "cppflags=-foo", "cflags=-foo", True, "cppflags=-foo cflags=-foo"),
+        # Target ranges
+        (Spec, "target=x86_64:", "target=x86_64:", False, "target=x86_64:"),
+        (Spec, "target=x86_64:", "target=:haswell", True, "target=x86_64:haswell"),
+        (
+            Spec,
+            "target=x86_64:haswell",
+            "target=x86_64_v2:icelake",
+            True,
+            "target=x86_64_v2:haswell",
+        ),
     ],
 )
 def test_constrain(factory, lhs_str, rhs_str, result, constrained_str):

lib/spack/spack/test/spec_yaml.py

@@ -21,6 +21,7 @@
 import pytest
 import ruamel.yaml
 
+import spack.config
 import spack.hash_types as ht
 import spack.paths
 import spack.repo
@@ -144,86 +145,83 @@ def descend_and_check(iterable, level=0):
     assert level >= 5
 
 
-def test_ordered_read_not_required_for_consistent_dag_hash(config, mock_packages):
+@pytest.mark.parametrize("spec_str", ["mpileaks ^zmpi", "dttop", "dtuse"])
+def test_ordered_read_not_required_for_consistent_dag_hash(
+    spec_str, mutable_config: spack.config.Configuration, mock_packages
+):
     """Make sure ordered serialization isn't required to preserve hashes.
 
-    For consistent hashes, we require that YAML and json documents
-    have their keys serialized in a deterministic order. However, we
-    don't want to require them to be serialized in order. This
-    ensures that is not required.
-    """
-    specs = ["mpileaks ^zmpi", "dttop", "dtuse"]
-    for spec in specs:
-        spec = Spec(spec)
-        spec.concretize()
+    For consistent hashes, we require that YAML and JSON serializations have their keys in a
+    deterministic order. However, we don't want to require them to be serialized in order. This
+    ensures that is not required."""
 
-        #
-        # Dict & corresponding YAML & JSON from the original spec.
-        #
-        spec_dict = spec.to_dict()
-        spec_yaml = spec.to_yaml()
-        spec_json = spec.to_json()
+    # Make sure that `extra_attributes` of externals is order independent for hashing.
+    extra_attributes = {
+        "compilers": {"c": "/some/path/bin/cc", "cxx": "/some/path/bin/c++"},
+        "foo": "bar",
+        "baz": "qux",
+    }
+    mutable_config.set(
+        "packages:dtuse",
+        {
+            "buildable": False,
+            "externals": [
+                {"spec": "dtuse@=1.0", "prefix": "/usr", "extra_attributes": extra_attributes}
+            ],
+        },
+    )
 
-        #
-        # Make a spec with reversed OrderedDicts for every
-        # OrderedDict in the original.
-        #
-        reversed_spec_dict = reverse_all_dicts(spec.to_dict())
+    spec = spack.spec.Spec(spec_str).concretized()
 
-        #
-        # Dump to YAML and JSON
-        #
-        yaml_string = syaml.dump(spec_dict, default_flow_style=False)
-        reversed_yaml_string = syaml.dump(reversed_spec_dict, default_flow_style=False)
-        json_string = sjson.dump(spec_dict)
-        reversed_json_string = sjson.dump(reversed_spec_dict)
+    if spec_str == "dtuse":
+        assert spec.external and spec.extra_attributes == extra_attributes
 
-        #
-        # Do many consistency checks
-        #
+    spec_dict = spec.to_dict(hash=ht.dag_hash)
+    spec_yaml = spec.to_yaml()
+    spec_json = spec.to_json()
 
-        # spec yaml is ordered like the spec dict
-        assert yaml_string == spec_yaml
-        assert json_string == spec_json
+    # Make a spec with dict keys reversed recursively
+    spec_dict_rev = reverse_all_dicts(spec_dict)
 
-        # reversed string is different from the original, so it
-        # *would* generate a different hash
-        assert yaml_string != reversed_yaml_string
-        assert json_string != reversed_json_string
+    # Dump to YAML and JSON
+    yaml_string = syaml.dump(spec_dict, default_flow_style=False)
+    yaml_string_rev = syaml.dump(spec_dict_rev, default_flow_style=False)
+    json_string = sjson.dump(spec_dict)
+    json_string_rev = sjson.dump(spec_dict_rev)
 
-        # build specs from the "wrongly" ordered data
-        round_trip_yaml_spec = Spec.from_yaml(yaml_string)
-        round_trip_json_spec = Spec.from_json(json_string)
-        round_trip_reversed_yaml_spec = Spec.from_yaml(reversed_yaml_string)
-        round_trip_reversed_json_spec = Spec.from_yaml(reversed_json_string)
+    # spec yaml is ordered like the spec dict
+    assert yaml_string == spec_yaml
+    assert json_string == spec_json
 
-        # Strip spec if we stripped the yaml
-        spec = spec.copy(deps=ht.dag_hash.depflag)
+    # reversed string is different from the original, so it *would* generate a different hash
+    assert yaml_string != yaml_string_rev
+    assert json_string != json_string_rev
 
-        # specs are equal to the original
-        assert spec == round_trip_yaml_spec
-        assert spec == round_trip_json_spec
+    # build specs from the "wrongly" ordered data
+    from_yaml = Spec.from_yaml(yaml_string)
+    from_json = Spec.from_json(json_string)
+    from_yaml_rev = Spec.from_yaml(yaml_string_rev)
+    from_json_rev = Spec.from_json(json_string_rev)
 
-        assert spec == round_trip_reversed_yaml_spec
-        assert spec == round_trip_reversed_json_spec
-        assert round_trip_yaml_spec == round_trip_reversed_yaml_spec
-        assert round_trip_json_spec == round_trip_reversed_json_spec
-        # dag_hashes are equal
-        assert spec.dag_hash() == round_trip_yaml_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_json_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_reversed_yaml_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_reversed_json_spec.dag_hash()
+    # Strip spec if we stripped the yaml
+    spec = spec.copy(deps=ht.dag_hash.depflag)
 
-        # dag_hash is equal after round-trip by dag_hash
-        spec.concretize()
-        round_trip_yaml_spec.concretize()
-        round_trip_json_spec.concretize()
-        round_trip_reversed_yaml_spec.concretize()
-        round_trip_reversed_json_spec.concretize()
-        assert spec.dag_hash() == round_trip_yaml_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_json_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_reversed_yaml_spec.dag_hash()
-        assert spec.dag_hash() == round_trip_reversed_json_spec.dag_hash()
+    # specs and their hashes are equal to the original
+    assert (
+        spec.process_hash()
+        == from_yaml.process_hash()
+        == from_json.process_hash()
+        == from_yaml_rev.process_hash()
+        == from_json_rev.process_hash()
+    )
+    assert (
+        spec.dag_hash()
+        == from_yaml.dag_hash()
+        == from_json.dag_hash()
+        == from_yaml_rev.dag_hash()
+        == from_json_rev.dag_hash()
+    )
+    assert spec == from_yaml == from_json == from_yaml_rev == from_json_rev
 
 
 @pytest.mark.parametrize("module", [spack.spec, spack.version])
@@ -294,13 +292,10 @@ def visit_Call(self, node):
 def reverse_all_dicts(data):
     """Descend into data and reverse all the dictionaries"""
     if isinstance(data, dict):
-        return syaml_dict(
-            reversed([(reverse_all_dicts(k), reverse_all_dicts(v)) for k, v in data.items()])
-        )
+        return type(data)((k, reverse_all_dicts(v)) for k, v in reversed(list(data.items())))
     elif isinstance(data, (list, tuple)):
         return type(data)(reverse_all_dicts(elt) for elt in data)
-    else:
-        return data
+    return data
 
 
 def check_specs_equal(original_spec, spec_yaml_path):

lib/spack/spack/util/filesystem.py

@@ -13,7 +13,7 @@
 import sys
 
 from llnl.util import tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import edit_in_place_through_temporary_file
 from llnl.util.lang import memoized
 
 from spack.util.executable import Executable, which
@@ -81,12 +81,11 @@ def fix_darwin_install_name(path):
     Parameters:
         path (str): directory in which .dylib files are located
     """
-    libs = glob.glob(join_path(path, "*.dylib"))
+    libs = glob.glob(os.path.join(path, "*.dylib"))
+    install_name_tool = Executable("install_name_tool")
+    otool = Executable("otool")
     for lib in libs:
-        # fix install name first:
-        install_name_tool = Executable("install_name_tool")
-        install_name_tool("-id", lib, lib)
-        otool = Executable("otool")
+        args = ["-id", lib]
         long_deps = otool("-L", lib, output=str).split("\n")
         deps = [dep.partition(" ")[0][1::] for dep in long_deps[2:-1]]
         # fix all dependencies:
@@ -98,5 +97,8 @@ def fix_darwin_install_name(path):
                 # but we don't know builddir (nor how symbolic links look
                 # in builddir). We thus only compare the basenames.
                 if os.path.basename(dep) == os.path.basename(loc):
-                    install_name_tool("-change", dep, loc, lib)
+                    args.extend(("-change", dep, loc))
                     break
+
+        with edit_in_place_through_temporary_file(lib) as tmp:
+            install_name_tool(*args, tmp)

lib/spack/spack/util/spack_yaml.py

@@ -447,20 +447,13 @@ def _dump_annotated(handler, data, stream=None):
         return getvalue()
 
 
-def sorted_dict(dict_like):
-    """Return an ordered dict with all the fields sorted recursively.
-
-    Args:
-        dict_like (dict): dictionary to be sorted
-
-    Returns:
-        dictionary sorted recursively
-    """
-    result = syaml_dict(sorted(dict_like.items()))
-    for key, value in result.items():
-        if isinstance(value, collections.abc.Mapping):
-            result[key] = sorted_dict(value)
-    return result
+def sorted_dict(data):
+    """Descend into data and sort all dictionary keys."""
+    if isinstance(data, dict):
+        return type(data)((k, sorted_dict(v)) for k, v in sorted(data.items()))
+    elif isinstance(data, (list, tuple)):
+        return type(data)(sorted_dict(v) for v in data)
+    return data
 
 
 def extract_comments(data):

share/spack/gitlab/cloud_pipelines/.gitlab-ci.yml

@@ -14,10 +14,10 @@ default:
   image: { "name": "ghcr.io/spack/e4s-ubuntu-18.04:v2021-10-18", "entrypoint": [""] }
 
 # CI Platform-Arch
-.cray_rhel_zen4:
+.cray_rhel_x86_64_v3:
   variables:
     SPACK_TARGET_PLATFORM: "cray-rhel"
-    SPACK_TARGET_ARCH: "zen4"
+    SPACK_TARGET_ARCH: "x86_64_v3"
 
 .cray_sles_zen4:
   variables:
@@ -876,7 +876,7 @@ aws-pcluster-build-neoverse_v1:
     - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
 
 .generate-cray-rhel:
-  tags: [ "cray-rhel-zen4", "public" ]
+  tags: [ "cray-rhel-x86_64_v3", "public" ]
   extends: [ ".generate-cray" ]
 
 .generate-cray-sles:
@@ -888,7 +888,7 @@ aws-pcluster-build-neoverse_v1:
 # E4S - Cray RHEL
 #######################################
 .e4s-cray-rhel:
-  extends: [ ".cray_rhel_zen4" ]
+  extends: [ ".cray_rhel_x86_64_v3" ]
   variables:
     SPACK_CI_STACK_NAME: e4s-cray-rhel
 
@@ -896,7 +896,6 @@ e4s-cray-rhel-generate:
   extends: [ ".generate-cray-rhel", ".e4s-cray-rhel" ]
 
 e4s-cray-rhel-build:
-  allow_failure: true  # libsci_cray.so broken, misses DT_NEEDED for libdl.so
   extends: [ ".build", ".e4s-cray-rhel" ]
   trigger:
     include:
@@ -915,10 +914,10 @@ e4s-cray-rhel-build:
   variables:
     SPACK_CI_STACK_NAME: e4s-cray-sles
 
-e4s-cray-sles-generate:
+.e4s-cray-sles-generate:
   extends: [ ".generate-cray-sles", ".e4s-cray-sles" ]
 
-e4s-cray-sles-build:
+.e4s-cray-sles-build:
   allow_failure: true  # libsci_cray.so broken, misses DT_NEEDED for libdl.so
   extends: [ ".build", ".e4s-cray-sles" ]
   trigger:

share/spack/gitlab/cloud_pipelines/configs/cray-rhel/compilers.yaml

@@ -1,31 +1,27 @@
 compilers:
 - compiler:
-    spec: cce@15.0.1
+    spec: cce@=18.0.0
     paths:
-      cc: cc
-      cxx: CC
-      f77: ftn
-      fc: ftn
+      cc: /opt/cray/pe/cce/18.0.0/bin/craycc
+      cxx: /opt/cray/pe/cce/18.0.0/bin/crayCC
+      f77: /opt/cray/pe/cce/18.0.0/bin/crayftn
+      fc: /opt/cray/pe/cce/18.0.0/bin/crayftn
     flags: {}
     operating_system: rhel8
-    target: any
-    modules:
-    - PrgEnv-cray/8.3.3
-    - cce/15.0.1
-    environment:
-      set:
-        MACHTYPE: x86_64
-- compiler:
-    spec: gcc@11.2.0
-    paths:
-      cc: gcc
-      cxx: g++
-      f77: gfortran
-      fc: gfortran
-    flags: {}
-    operating_system: rhel8
-    target: any
-    modules:
-    - PrgEnv-gnu
-    - gcc/11.2.0
+    target: x86_64
+    modules: []
     environment: {}
+    extra_rpaths: []
+- compiler:
+    spec: gcc@=8.5.0
+    paths:
+      cc: /usr/bin/gcc
+      cxx: /usr/bin/g++
+      f77: /usr/bin/gfortran
+      fc: /usr/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules: []
+    environment: {}
+    extra_rpaths: []

share/spack/gitlab/cloud_pipelines/configs/cray-rhel/packages.yaml

@@ -1,16 +1,15 @@
 packages:
-  # EXTERNALS
   cray-mpich:
     buildable: false
     externals:
-    - spec: cray-mpich@8.1.25 %cce@15.0.1
-      prefix: /opt/cray/pe/mpich/8.1.25/ofi/cray/10.0
+    - spec: cray-mpich@8.1.30 %cce
+      prefix: /opt/cray/pe/mpich/8.1.30/ofi/cray/18.0
       modules:
-      - cray-mpich/8.1.25
+      - cray-mpich/8.1.30
   cray-libsci:
     buildable: false
     externals:
-    - spec: cray-libsci@23.02.1.1 %cce@15.0.1
-      prefix: /opt/cray/pe/libsci/23.02.1.1/CRAY/9.0/x86_64/
+    - spec: cray-libsci@24.07.0 %cce
+      prefix: /opt/cray/pe/libsci/24.07.0/CRAY/18.0/x86_64/
       modules:
-      - cray-libsci/23.02.1.1
+      - cray-libsci/24.07.0

share/spack/gitlab/cloud_pipelines/configs/cray-rhel/x86_64_v3/ci.yaml

@@ -0,0 +1,4 @@
+ci:
+  pipeline-gen:
+  - build-job:
+      tags: ["cray-rhel-x86_64_v3"]

share/spack/gitlab/cloud_pipelines/configs/cray-rhel/zen4/ci.yaml

@@ -1,4 +0,0 @@
-ci:
-  pipeline-gen:
-  - build-job:
-      tags: ["cray-rhel-zen4"]

share/spack/gitlab/cloud_pipelines/stacks/e4s-cray-rhel/spack.yaml

@@ -10,8 +10,7 @@ spack:
 
   packages:
     all:
-      prefer:
-      - "%cce"
+      require: "%cce@18.0.0 target=x86_64_v3"
       compiler: [cce]
       providers:
         blas: [cray-libsci]
@@ -19,17 +18,15 @@ spack:
         mpi: [cray-mpich]
         tbb: [intel-tbb]
         scalapack: [netlib-scalapack]
-      target: [zen4]
       variants: +mpi
-
+    ncurses:
+      require: +termlib ldflags=-Wl,--undefined-version
     tbb:
       require: "intel-tbb"
     binutils:
       variants: +ld +gold +headers +libiberty ~nls
     boost:
       variants: +python +filesystem +iostreams +system
-    cuda:
-      version: [11.7.0]
     elfutils:
       variants: ~nls
       require: "%gcc"
@@ -39,20 +36,14 @@ spack:
       variants: +fortran +hl +shared
     libfabric:
       variants: fabrics=sockets,tcp,udp,rxm
-    libunwind:
-      variants: +pic +xz
     mgard:
       require:
         - "@2023-01-10:"
     mpich:
       variants: ~wrapperrpath
-    ncurses:
-      variants: +termlib
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
-    python:
-      version: [3.8.13]
+      require: "~qt ^[virtuals=gl] osmesa"
     trilinos:
       require:
       - one_of: [+amesos +amesos2 +anasazi +aztec +boost +epetra +epetraext +ifpack
@@ -63,12 +54,6 @@ spack:
       - one_of: [~ml ~muelu ~zoltan2 ~teko, +ml +muelu +zoltan2 +teko]
       - one_of: [+superlu-dist, ~superlu-dist]
       - one_of: [+shylu, ~shylu]
-    xz:
-      variants: +pic
-    mesa:
-      version: [21.3.8]
-    unzip:
-      require: "%gcc"
 
   specs:
   # CPU
@@ -76,62 +61,43 @@ spack:
   - aml
   - arborx
   - argobots
-  - bolt
-  - butterflypack
   - boost +python +filesystem +iostreams +system
   - cabana
-  - caliper
   - chai
-  - charliecloud
   - conduit
-  # - cp2k +mpi         # libxsmm: ftn-78 ftn: ERROR in command linel; The -f option has an invalid argument, "tree-vectorize".
   - datatransferkit
   - flecsi
   - flit
-  - flux-core
-  - fortrilinos
   - ginkgo
   - globalarrays
   - gmp
   - gotcha
   - h5bench
   - hdf5-vol-async
-  - hdf5-vol-cache
+  - hdf5-vol-cache cflags=-Wno-error=incompatible-function-pointer-types
   - hdf5-vol-log
   - heffte +fftw
-  - hpx max_cpu_count=512 networking=mpi
   - hypre
   - kokkos +openmp
   - kokkos-kernels +openmp
-  - lammps
   - legion
   - libnrm
-  #- libpressio +bitgrooming +bzip2 ~cuda ~cusz +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp +json +remote +netcdf +mgard # mgard: 
   - libquo
   - libunwind
   - mercury
   - metall
   - mfem
-  # - mgard +serial +openmp +timing +unstructured ~cuda # mgard
   - mpark-variant
-  - mpifileutils ~xattr
+  - mpifileutils ~xattr cflags=-Wno-error=implicit-function-declaration
   - nccmp
   - nco
-  - netlib-scalapack
-  - omega-h
-  - openmpi
+  - netlib-scalapack cflags=-Wno-error=implicit-function-declaration
   - openpmd-api ^adios2~mgard
-  - papi
   - papyrus
   - pdt
   - petsc
-  - plumed
   - precice
   - pumi
-  - py-h5py +mpi
-  - py-h5py ~mpi
-  - py-libensemble +mpi +nlopt
-  - py-petsc4py
   - qthreads scheduler=distrib
   - raja
   - slate ~cuda
@@ -144,8 +110,7 @@ spack:
   - swig@4.0.2-fortran
   - sz3
   - tasmanian
-  - tau +mpi +python
-  - trilinos@13.0.1 +belos +ifpack2 +stokhos
+  - trilinos +belos +ifpack2 +stokhos
   - turbine
   - umap
   - umpire
@@ -155,27 +120,47 @@ spack:
   # - alquimia            # pflotran: petsc-3.19.4-c6pmpdtpzarytxo434zf76jqdkhdyn37/lib/petsc/conf/rules:169: material_aux.o] Error 1: fortran errors
   # - amrex               # disabled temporarily pending resolution of unreproducible CI failure
   # - axom                # axom: CMake Error at axom/sidre/cmake_install.cmake:154 (file): file INSTALL cannot find "/tmp/gitlab-runner-2/spack-stage/spack-stage-axom-0.8.1-jvol6riu34vuyqvrd5ft2gyhrxdqvf63/spack-build-jvol6ri/lib/fortran/axom_spio.mod": No such file or directory.
+  # - bolt                # ld.lld: error: CMakeFiles/bolt-omp.dir/kmp_gsupport.cpp.o: symbol GOMP_atomic_end@@GOMP_1.0 has undefined version GOMP_1.0
   # - bricks              # bricks: clang-15: error: clang frontend command failed with exit code 134 (use -v to see invocation)
+  # - butterflypack ^netlib-scalapack cflags=-Wno-error=implicit-function-declaration # ftn-2116 ftn: INTERNAL "driver" was terminated due to receipt of signal 01:  Hangup.
+  # - caliper             # papi: papi_internal.c:124:3: error: use of undeclared identifier '_papi_hwi_my_thread'; did you mean '_papi_hwi_read'?
+  # - charliecloud        # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - cp2k +mpi           # libxsmm: ftn-78 ftn: ERROR in command linel; The -f option has an invalid argument, "tree-vectorize".
   # - dealii              # llvm@14.0.6: ?; intel-tbb@2020.3: clang-15: error: unknown argument: '-flifetime-dse=1'; assimp@5.2.5: clang-15: error: clang frontend command failed with exit code 134 (use -v to see invocation)
   # - dyninst             # requires %gcc
   # - ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 +paraview +pnetcdf +sz +unifyfs +veloc ~visit +vtkm +zfp ^hdf5@1.14 # llvm@14.0.6: ?;
   # - exaworks            # rust: ld.lld: error: relocation R_X86_64_32 cannot be used against local symbol; recompile with -fPIC'; defined in /opt/cray/pe/cce/15.0.1/cce/x86_64/lib/no_mmap.o, referenced by /opt/cray/pe/cce/15.0.1/cce/x86_64/lib/no_mmap.o:(__no_mmap_for_malloc)
+  # - flux-core           # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - fortrilinos         # trilinos-14.0.0: packages/teuchos/core/src/Teuchos_BigUIntDecl.hpp:67:8: error: no type named 'uint32_t' in namespace 'std'
   # - gasnet              # configure error: User requested --enable-ofi but I don't know how to build ofi programs for your system
   # - gptune              # py-scipy: meson.build:82:0: ERROR: Unknown compiler(s): [['/home/gitlab-runner-3/builds/dWfnZWPh/0/spack/spack/lib/spack/env/cce/ftn']]
   # - hpctoolkit          # dyninst requires %gcc
+  # - hpx max_cpu_count=512 networking=mpi  # libxcrypt-4.4.35
+  # - lammps              # lammps-20240829.1: Reversed (or previously applied) patch detected!  Assume -R? [n] 
+  # - libpressio +bitgrooming +bzip2 ~cuda ~cusz +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp +json +remote +netcdf +mgard # mgard: 
+  # - mgard +serial +openmp +timing +unstructured ~cuda # mgard
   # - nrm                 # py-scipy: meson.build:82:0: ERROR: Unknown compiler(s): [['/home/gitlab-runner-3/builds/dWfnZWPh/0/spack/spack/lib/spack/env/cce/ftn']]
   # - nvhpc               # requires %gcc
+  # - omega-h             # trilinos-13.4.1: packages/kokkos/core/src/impl/Kokkos_MemoryPool.cpp:112:48: error: unknown type name 'uint32_t'
+  # - openmpi             # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - papi                # papi_internal.c:124:3: error: use of undeclared identifier '_papi_hwi_my_thread'; did you mean '_papi_hwi_read'?
   # - parsec ~cuda        # parsec: parsec/fortran/CMakeFiles/parsec_fortran.dir/parsecf.F90.o: ftn-2103 ftn: WARNING in command line. The -W extra option is not supported or invalid and will be ignored.
   # - phist               # fortran_bindings/CMakeFiles/phist_fort.dir/phist_testing.F90.o: ftn-78 ftn: ERROR in command line. The -f option has an invalid argument, "no-math-errno".
   # - plasma              # %cce conflict
+  # - plumed              # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - py-h5py +mpi        # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - py-h5py ~mpi        # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
   # - py-jupyterhub       # rust: ld.lld: error: relocation R_X86_64_32 cannot be used against local symbol; recompile with -fPIC'; defined in /opt/cray/pe/cce/15.0.1/cce/x86_64/lib/no_mmap.o, referenced by /opt/cray/pe/cce/15.0.1/cce/x86_64/lib/no_mmap.o:(__no_mmap_for_malloc)
+  # - py-libensemble +mpi +nlopt  # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
+  # - py-petsc4py         # libxcrypt-4.4.35: ld.lld: error: version script assignment of 'XCRYPT_2.0' to symbol 'xcrypt_r' failed: symbol not defined
   # - quantum-espresso    # quantum-espresso: CMake Error at cmake/FindSCALAPACK.cmake:503 (message): A required library with SCALAPACK API not found.  Please specify library
   # - scr                 # scr: make[2]: *** [examples/CMakeFiles/test_ckpt_F.dir/build.make:112: examples/test_ckpt_F] Error 1: /opt/cray/pe/cce/15.0.1/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: /opt/cray/pe/mpich/8.1.25/ofi/cray/10.0/lib/libmpi_cray.so: undefined reference to `PMI_Barrier'
   # - strumpack ~slate    # strumpack: [test/CMakeFiles/test_HSS_seq.dir/build.make:117: test/test_HSS_seq] Error 1: ld.lld: error: undefined reference due to --no-allow-shlib-undefined: mpi_abort_
+  # - tau +mpi +python    # libelf: configure: error: installation or configuration problem: C compiler cannot create executables.; papi: papi_internal.c:124:3: error: use of undeclared identifier '_papi_hwi_my_thread'; did you mean '_papi_hwi_read'?
   # - upcxx               # upcxx: configure error: User requested --enable-ofi but I don't know how to build ofi programs for your system
   # - variorum            # variorum: /opt/cray/pe/cce/15.0.1/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: /opt/cray/pe/lib64/libpals.so.0: undefined reference to `json_array_append_new@@libjansson.so.4'
-  # - xyce +mpi +shared +pymi +pymi_static_tpls ^trilinos~shylu # openblas: ftn-2307 ftn: ERROR in command line: The "-m" option must be followed by 0, 1, 2, 3 or 4.; make[2]: *** [<builtin>: spotrf2.o] Error 1; make[1]: *** [Makefile:27: lapacklib] Error 2; make: *** [Makefile:250: netlib] Error 2
   # - warpx +python       # py-scipy: meson.build:82:0: ERROR: Unknown compiler(s): [['/home/gitlab-runner-3/builds/dWfnZWPh/0/spack/spack/lib/spack/env/cce/ftn']]
+  # - xyce +mpi +shared +pymi +pymi_static_tpls ^trilinos~shylu # openblas: ftn-2307 ftn: ERROR in command line: The "-m" option must be followed by 0, 1, 2, 3 or 4.; make[2]: *** [<builtin>: spotrf2.o] Error 1; make[1]: *** [Makefile:27: lapacklib] Error 2; make: *** [Makefile:250: netlib] Error 2
 
   cdash:
     build-group: E4S Cray

share/spack/qa/run-shell-tests

@@ -36,7 +36,7 @@ export QA_DIR=$(realpath $QA_DIR)
 cd "$SPACK_ROOT"
 
 # Run bash tests with coverage enabled, but pipe output to /dev/null
-# because it seems that kcov seems to undo the script's redirection
+# because it seems that kcov undoes the script's redirection
 if [ "$COVERAGE" = true ]; then
     kcov "$SPACK_ROOT/coverage" "$QA_DIR/setup-env-test.sh" &> /dev/null
     kcov "$SPACK_ROOT/coverage" "$QA_DIR/completion-test.sh" &> /dev/null

var/spack/repos/builtin.mock/packages/splice-depends-on-t/package.py

@@ -0,0 +1,22 @@
+# 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)
+
+from spack.package import *
+
+
+class SpliceDependsOnT(Package):
+    """Package that depends on splice-t"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/splice-depends-on-t-1.0.tar.gz"
+
+    version("1.0", md5="0123456789abcdef0123456789abcdef")
+
+    depends_on("splice-t")
+
+    def install(self, spec, prefix):
+        with open(prefix.join("splice-depends-on-t"), "w") as f:
+            f.write("splice-depends-on-t: {0}".format(prefix))
+            f.write("splice-t: {0}".format(spec["splice-t"].prefix))

var/spack/repos/builtin/packages/gdk-pixbuf/package.py

@@ -12,33 +12,36 @@ class GdkPixbuf(MesonPackage):
     GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3."""
 
     homepage = "https://gitlab.gnome.org/GNOME/gdk-pixbuf"
-    url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/2.40/gdk-pixbuf-2.40.0.tar.xz"
     git = "https://gitlab.gnome.org/GNOME/gdk-pixbuf"
-    list_url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/"
+    url = "https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/archive/2.40.0/gdk-pixbuf-2.40.0.tar.gz"
+
+    # Falling back to the gitlab source since the mirror here seems to be broken
+    # url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/2.40/gdk-pixbuf-2.40.0.tar.xz"
+    # list_url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/"
     list_depth = 1
 
     license("LGPL-2.1-or-later", checked_by="wdconinc")
 
-    version("2.42.12", sha256="b9505b3445b9a7e48ced34760c3bcb73e966df3ac94c95a148cb669ab748e3c7")
+    version("2.42.12", sha256="d41966831b3d291fcdfe31f683bea4b3f03241d591ddbe550b5db873af3da364")
     # https://nvd.nist.gov/vuln/detail/CVE-2022-48622
     version(
         "2.42.10",
-        sha256="ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b",
+        sha256="87a086c51d9705698b22bd598a795efaccf61e4db3a96f439dcb3cd90506dab8",
         deprecated=True,
     )
     version(
         "2.42.9",
-        sha256="28f7958e7bf29a32d4e963556d241d0a41a6786582ff6a5ad11665e0347fc962",
+        sha256="226d950375907857b23c5946ae6d30128f08cd75f65f14b14334c7a9fb686e36",
         deprecated=True,
     )
     version(
         "2.42.6",
-        sha256="c4a6b75b7ed8f58ca48da830b9fa00ed96d668d3ab4b1f723dcf902f78bde77f",
+        sha256="c4f3a84a04bc7c5f4fbd97dce7976ab648c60628f72ad4c7b79edce2bbdb494d",
         deprecated=True,
     )
     version(
         "2.42.2",
-        sha256="83c66a1cfd591d7680c144d2922c5955d38b4db336d7cd3ee109f7bcf9afef15",
+        sha256="249b977279f761979104d7befbb5ee23f1661e29d19a36da5875f3a97952d13f",
         deprecated=True,
     )
 

var/spack/repos/builtin/packages/qt-base/package.py

@@ -65,9 +65,15 @@ def cmake_args(self):
             if re_qt.match(dep.name):
                 qt_prefix_path.append(self.spec[dep.name].prefix)
 
-        # Now append all qt-* dependency prefixex into a prefix path
+        # Now append all qt-* dependency prefixes into a prefix path
         args.append(self.define("QT_ADDITIONAL_PACKAGES_PREFIX_PATH", ":".join(qt_prefix_path)))
 
+        # Make our CMAKE_INSTALL_RPATH redundant:
+        # for prefix of current package ($ORIGIN/../lib type of rpaths),
+        args.append(self.define("QT_DISABLE_RPATH", True))
+        # for prefixes of dependencies
+        args.append(self.define("QT_NO_DISABLE_CMAKE_INSTALL_RPATH_USE_LINK_PATH", True))
+
         return args
 
     @run_after("install")