Update list of excluded variables in `from_sourcing_file` function to
cover all variables specific to Environment Modules or Lmod. Add
specifically variables relative to the definition of `module()`, `ml()`
and `_module_raw()` Bash functions.
Fixes#13504
Update `env.set` command and underlying `SetEnv` object to add the `raw`
boolean attribute. `raw` is optional and set to False by default. When
set to True, value format is skipped for object when generating
environment modifications.
With this change it is now possible to define environment variable
whose value contains variable reference syntax (like `{foo}` or `{}`)
that should be set as-is.
Fixes#29578
Update Tcl modulefile template to use the `depends-on` command to
autoload modules if Lmod is the current module tool.
Autoloading modules with `module load` command in Tcl modulefile does
not work well for Lmod at some extend. An attempt to unload then load
designated module is performed each time such command is encountered. It
may lead to a load storm that may not end correctly with large number of
module dependencies.
`depends-on` command should be used for Lmod instead of `module load`,
as it checks if module is already loaded, and does not attempt to reload
this module.
Lua modulefile template already uses `depends_on` command to autoload
dependencies. Thus it is already considered that to use Lmod with Spack,
it must support `depends_on` command (version 7.6+).
Environment Modules copes well with `module load` command to autoload
dependencies (version 3.2+). `depends-on` command is supported starting
version 5.1 (as an alias of `prereq-all` command) which was relased last
year.
This change introduces a test to determine if current module tool that
evaluates modulefile is Lmod. If so, autoload dependencies are defined
with `depends-on` command. Otherwise `module load` command is used.
Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set
by Lmod starting version 5.1.
Fixes#36764
Update modulefile templates to append a trailing delimiter to MANPATH
environment variable, if the modulefile sets it.
With a trailing delimiter at ends of MANPATH's value, man will search
the system man pages after searching the specific paths set.
Using append-path/append_path to add this element, the module tool
ensures it is appended only once. When modulefile is unloaded, the
number of append attempt is decreased, thus the trailing delimiter is
removed only if this number equals 0.
Disclaimer: no path element should be appended to MANPATH by generated
modulefiles. It should always be prepended to ensure this variable's
value ends with the trailing delimiter.
Fixes#11355.
* Improve lib/spack/spack/test/cmd/compiler.py
* Use "tmp_path" in the "mock_executable" fixture
* Return a pathlib.Path from mock_executable
* Fix mock_executable fixture on Windows
"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication
* Remove wrong compiler cache, fix compiler removal
fixes#37996
_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.
Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
In the past, Spack did not allow two different versions of the
same package within a DAG. That led to difficulties with packages
that still required Python 2 while other packages had already
switched to Python 3.
The libxcb and xcb-proto packages did not have Python 3 support
for a time. To get around this issue, Spack maintainers disabled
their dependency on an internal (i.e., Spack-provided) Python
(see #4145),forcing these packages to look for a system-provided
Python (see #7646).
This has worked for us all right, but with the arrival of our most
recent platform we seem to be missing the critical xcbgen Python
module on the system. Since most software has largely moved on to
Python 3 now, let's re-enable internal Spack dependencies for the
libxcb and xcb-proto packages.
fa7719a changed syntax for specifying exact versions, which are
required for some compiler specs (including those read as part
of parsing a Cray manifest). This fixes that and also makes a
couple other improvements to manifest parsing.
* Instantiate compiler specs with exact versions (fixes#37893)
* fix slingshot network detection (CPE 22.10+ has libcxi.so
in /usr/lib64)
* "spack external find": add arg to ignore default dir for cray
manifests
Make it clear that copy-only pipelines are not supported while still
using the deprecated ci config format. Also ensure that the deprecated
stack does not fail on spack pipelines for tags.
* Fix reporting of packageless specs as having no tests
* Add test_test_output_multiple_specs with update to simple-standalone-test (and tests)
* Refactored test status summary; added more tests or checks
MSVC compiler logic was using string parsing to extract version
from compiler spec, which was fragile. This broke in #37572, so has
been fixed and made more robust by using attribute access.
Ensure that requirements `packages:*:require:@x` and preferences `packages:*:version:[x]`
fail concretization when no version defined in the package satisfies `x`. This always holds
except for git versions -- they are defined on the fly.
Two bugs came in from #37438
1. `unify: when_possible` was broken, because of an incorrect assertion. abstract/concrete
spec pairs were compared against the results that were in the process of being computed,
rather than against the previous results.
2. `unify: true` had an ordering bug that could mix the association between abstract and
concrete specs
- [x] 1 is resolved by creating a lookup from old concrete specs to old abstract specs,
and we use that to associate the "new" concrete specs that happen to be the old
ones with their abstract specs (since those are stripped out for concretization
- [x] 2 is resolved by combining the new and old abstract as lists instead of combining
them as sets. This is important because `set() | set()` does not make any ordering
promises, even though set ordering is otherwise guaranteed in `python@3.7:`
Spack displays package code context when it shouldn't (e.g., on `FetchError`s)
and doesn't display it when it should (e.g., when errors occur in builder classes.
The line attribution can sometimes be off by one, as well.
- [x] Display package context when errors occur in a subclass of `PackageBase`
- [x] Display package context when errors occur in a subclass of `BaseBuilder`
- [x] Do not display package context when errors occur in `PackageBase`,
`BaseBuilder` or other core code that is not in a `package.py` file.
- [x] Fix off-by-one error for core code (don't subtract one from the line number *unless*
it's in an actual `package.py` file.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
We currently throw a nasty error if you try to reuse packages from some other namespace
(e.g., OLCF), but we should be able to reuse patched local versions of builtin packages.
Right now the only obstacle to that is that we try to look up virtual info for unknown
namespaces, and we can't get the package from the repo to do that. We *can* assume that
a package with a known namespace is similar, and that its virtual provider information
is reasonably accurate, so we now do that. This isn't 100% accurate, but neither is
relying on the package itself, as it may have gone out of date.
The real solution here is virtual edge information, but this is a stopgap until we have
that.
`spec_clauses()` attempts to look up package information for concrete specs in order to
determine which virtuals they may provide. This fails for renamed/deleted dependencies
of buildcaches and installed packages.
This will eventually be fixed by #35258, which adds virtual information on edges, but we
need a workaround to make older buildcaches usable.
- [x] make an exception for renamed packages and omit their virtual constraints
- [x] add a note that this will be solved by adding virtuals to edges
The concretizer can fail with `reuse:true` if a buildcache or installation contains a
package with a dependency that has been renamed or deleted in the main repo (e.g.,
`netcdf` was refactored to `netcdf-c`, `netcdf-fortran`, etc., but there are still
binary packages with dependencies called `netcdf`).
We should still be able to install things for which we are missing `package.py` files.
`Spec.inject_patches_variant()` was failing this requirement by attempting to look up
the package class for concrete specs. This isn't needed -- we can skip it.
- [x] swap two conditions in `Spec.inject_patches_variant()`
The @= in `spack find` output adds a bit of noise. Remove it as we
did for `spack spec` and `spack concretize`.
This modifies display_specs so it actually covers other places we use that routine, as
well, e.g., `spack buildcache list`.
before:
```
-- linux-ubuntu20.04-aarch64 / gcc@=11.1.0 -----------------------
ofdlcpi libpressio@0.88.0
```
after:
```
-- linux-ubuntu20.04-aarch64 / gcc@11.1.0 -----------------------
ofdlcpi libpressio@0.88.0
```
If a user does not explicitly `--force` the concretization of an entire environment,
Spack will try to reuse the concrete specs that are already in the lockfile.
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* gitlab ci: release fixes and improvements
- use rules to reduce boilerplate in .gitlab-ci.yml
- support copy-only pipeline jobs
- make pipelines for release branches rebuild everything
- make pipelines for protected tags copy-only
* gitlab ci: remove url changes used in testing
* gitlab ci: tag mirrors need public key
Make sure that mirrors associated with release branches and tags
contain the public key needed to verify the signed binaries. This
also ensures that when stack-specific mirror contents are copied
to the root, the root mirror has the public key as well.
* review: be more specific about tags, curl flags
* Make the check in ci.yaml consistent with the .gitlab-ci.yml
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
Currently, specs on buildcache mirrors must be referenced by their full description. This PR allows buildcache specs to be referenced by their hashes, rather than their full description.
### How it works
Hash resolution has been moved from `SpecParser` into `Spec`, and now includes the ability to execute a `BinaryCacheQuery` after checking the local store, but before concluding that the hash doesn't exist.
### Side-effects of Proposed Changes
Failures will take longer when nonexistent hashes are parsed, as mirrors will now be scanned.
### Other Changes
- `BinaryCacheIndex.update` has been modified to fail appropriately only when mirrors have been configured.
- Tests of hash failures have been updated to use `mutable_empty_config` so they don't needlessly search mirrors.
- Documentation has been clarified for `BinaryCacheQuery`, and more documentation has been added to the hash resolution functions added to `Spec`.
* py-rsatoolbox: add 0.0.5, 0.1.0 and 0.1.2 from wheels
* py-setuptools: add 63.4.3
* remove wheels and open up requirements
* Fix style
* Update var/spack/repos/builtin/packages/py-rsatoolbox/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-rsatoolbox/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Change version for python restriction
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-mne: add 1.4.0 and py-importlib-resources: add 5.12.0
* Fix style
* Update var/spack/repos/builtin/packages/py-mne/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR ensures that we'll get a comprehensible error message whenever an old
version of Spack tries to use a DB or a lockfile that is "too new".
* Fix error message when using a too new DB
* Add a unit-test to ensure we have a comprehensible error message
* py-pysam: adding version 0.21.0
* Update var/spack/repos/builtin/packages/py-pysam/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Add a section to the lock file to track the Spack version/commit that produced
an environment. This should (eventually) enhance reproducibility, though we
do not currently do anything with the information. It just adds to provenance
at the moment.
Changes include:
- [x] adding the version/commit to `spack.lock`
- [x] refactor `spack.main.get_version()
- [x] fix a couple of environment lock file-related typos
* add a virtual dependency name instead of complete package name
* add OneAPI components as providers of virtual packages
* Revert the default of tbb
---------
Co-authored-by: Nisarg Patel <nisarg.patel@lrz.de>
The flags --mirror-name / --mirror-url / --directory were deprecated in
favor of just passing a positional name, url or directory, and letting spack
figure it out.
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Prior to this PR, the HOMEDRIVE environment variable was used to
detect what drive we are operating in. This variable is not available
for service account logins (like what is used for CI), so switch to
extracting the drive from PROGRAMFILES (which is more-widely defined).
On Windows, several commonly available system tools for decompression
are unreliable (gz/bz2/xz). This commit refactors `decompressor_for`
to call out to a Windows or Unix-specific method:
* The decompressor_for_nix method behaves the same as before and
generally treats the Python/system support options for decompression
as interchangeable (although avoids using Python's built-in tar
support since that has had issues with permissions).
* The decompressor_for_win method can only use Python support for
gz/bz2/xz, although for a tar.gz it does use system support for
untar (after the decompression step). .zip uses the system tar
utility, and .Z depends on external support (i.e. that the user
has installed 7zip).
A naming scheme has been introduced for the various _decompression
methods:
* _system_gunzip means to use a system tool (and fail if it's not
available)
* _py_gunzip means to use Python's built-in support for decompressing
.gzip files (and fail if it's not available)
* _gunzip is a method that can do either
* fix(hdf5): h5pfc link failure
develop branch doesn't need linking any more.
See: acb186f6e5
* [@spackbot] updating style on behalf of hyoklee
---------
Co-authored-by: hyoklee <hyoklee@users.noreply.github.com>
This is a refactor of Spack's stand-alone test process to be more spack- and pytest-like.
It is more spack-like in that test parts are no longer "hidden" in a package's run_test()
method and pytest-like in that any package method whose name starts test_
(i.e., a "test" method) is a test part. We also support the ability to embed test parts in a
test method when that makes sense.
Test methods are now implicit test parts. The docstring is the purpose for the test part.
The name of the method is the name of the test part. The working directory is the active
spec's test stage directory. You can embed test parts using the test_part context manager.
Functionality added by this commit:
* Adds support for multiple test_* stand-alone package test methods, each of which is
an implicit test_part for execution and reporting purposes;
* Deprecates package use of run_test();
* Exposes some functionality from run_test() as optional helper methods;
* Adds a SkipTest exception that can be used to flag stand-alone tests as being skipped;
* Updates the packaging guide section on stand-alone tests to provide more examples;
* Restores the ability to run tests "inherited" from provided virtual packages;
* Prints the test log path (like we currently do for build log paths);
* Times and reports the post-install process (since it can include post-install tests);
* Corrects context-related error message to distinguish test recipes from build recipes.
* hip: get_paths for hipify-clang
* fix: need to actually use get_paths now to get hipify-clang path
* set hipify-clang path differentluy for external vs spack-installed case
* [@spackbot] updating style on behalf of eugeneswalker
fixes#22341
Using double quotes creates issues with shell variable substitutions,
in particular when the manifest has "definitions:" in it. Use single
quotes instead.
Add a "require" directive to packages, which functions exactly like
requirements specified in packages.yaml (uses the same fact-generation
logic); update both to allow making the requirement conditional.
* Packages may now use "require" to add constraints. This can be useful
for something like "require(%gcc)" (where before we had to add a
conflict for every compiler except gcc).
* Requirements (in packages.yaml or in a "require" directive) can be
conditional on a spec, e.g. "require(%gcc, when=@1.0.0)" (version
1.0.0 can only build with gcc).
* Requirements may include a message which clarifies why they are needed.
The concretizer assigns a high priority to errors which generate these
messages (in particular over errors for unsatisfied requirements that
do not produce messages, but also over a number of more-generic
errors).
## Version types, parsing and printing
- The version classes have changed: `VersionBase` is removed, there is now a
`ConcreteVersion` base class. `StandardVersion` and `GitVersion` both inherit
from this.
- The public api (`Version`, `VersionRange`, `ver`) has changed a bit:
1. `Version` produces either `StandardVersion` or `GitVersion` instances.
2. `VersionRange` produces a `ClosedOpenRange`, but this shouldn't affect the user.
3. `ver` produces any of `VersionList`, `ClosedOpenRange`, `StandardVersion`
or `GitVersion`.
- No unexpected type promotion, so that the following is no longer an identity:
`Version(x) != VersionRange(x, x)`.
- `VersionList.concrete` now returns a version if it contains only a single element
subtyping `ConcreteVersion` (i.e. `StandardVersion(...)` or `GitVersion(...)`)
- In version lists, the parser turns `@x` into `VersionRange(x, x)` instead
of `Version(x)`.
- The above also means that `ver("x")` produces a range, whereas
`ver("=x")` produces a `StandardVersion`. The `=` is part of _VersionList_
syntax.
- `VersionList.__str__` now outputs `=x.y.z` for specific version entries,
and `x.y.z` as a short-hand for ranges `x.y.z:x.y.z`.
- `Spec.format` no longer aliases `{version}` to `{versions}`, but pulls the
concrete version out of the list and prints that -- except when the list is
is not concrete, then is falls back to `{versions}` to avoid a pedantic error.
For projections of concrete specs, `{version}` should be used to render
`1.2.3` instead of `=1.2.3` (which you would get with `{versions}`).
The default `Spec` format string used in `Spec.__str__` now uses
`{versions}` so that `str(Spec(string)) == string` holds.
## Changes to `GitVersion`
- `GitVersion` is a small wrapper around `StandardVersion` which enriches it
with a git ref. It no longer inherits from it.
- `GitVersion` _always_ needs to be able to look up an associated Spack version
if it was not assigned (yet). It throws a `VersionLookupError` whenever `ref_version`
is accessed but it has no means to look up the ref; in the past Spack would
not error and use the commit sha as a literal version, which was incorrect.
- `GitVersion` is never equal to `StandardVersion`, nor is satisfied by it. This
is such that we don't lose transitivity. This fixes the following bug on `develop`
where `git_version_a == standard_version == git_version_b` does not imply
`git_version_a == git_version_b`. It also ensures equality always implies equal
hash, which is also currently broken on develop; inclusion tests of a set of
versions + git versions would behave differently from inclusion tests of a
list of the same objects.
- The above means `ver("ref=1.2.3) != ver("=1.2.3")` could break packages that branch
on specific versions, but that was brittle already, since the same happens with
externals: `pkg@1.2.3-external` suffixes wouldn't be exactly equal either. Instead,
those checks should be `x.satisfies("@1.2.3")` which works both for git versions and
custom version suffixes.
- `GitVersion` from commit will now print as `<hash>=<version>` once the
git ref is resolved to a spack version. This is for reliability -- version is frozen
when added to the database and queried later. It also improves performance
since there is no need to clone all repos of all git versions after `spack clean -m`
is run and something queries the database, triggering version comparison, such
as potentially reuse concretization.
- The "empty VerstionStrComponent trick" for `GitVerison` is dropped since it wasn't
representable as a version string (by design). Instead, it's replaced by `git`,
so you get `1.2.3.git.4` (which reads 4 commits after a tag 1.2.3). This means
that there's an edge case for version schemes `1.1.1`, `1.1.1a`, since the
generated git version `1.1.1.git.1` (1 commit after `1.1.1`) compares larger
than `1.1.1a`, since `a < git` are compared as strings. This is currently a
wont-fix edge case, but if really required, could be fixed by special casing
the `git` string.
- Saved, concrete specs (database, lock file, ...) that only had a git sha as their
version, but have no means to look the effective Spack version anymore, will
now see their version mapped to `hash=develop`. Previously these specs
would always have their sha literally interpreted as a version string (even when
it _could_ be looked up). This only applies to databases, lock files and spec.json
files created before Spack 0.20; after this PR, we always have a Spack version
associated to the relevant GitVersion).
- Fixes a bug where previously `to_dict` / `from_dict` (de)serialization would not
reattach the repo to the GitVersion, causing the git hash to be used as a literal
(bogus) version instead of the resolved version. This was in particularly breaking
version comparison in the build process on macOS/Windows.
## Installing or matching specific versions
- In the past, `spack install pkg@3.2` would install `pkg@=3.2` if it was a
known specific version defined in the package, even when newer patch releases
`3.2.1`, `3.2.2`, `...` were available. This behavior was only there because
there was no syntax to distinguish between `3.2` and `3.2.1`. Since there is
syntax for this now through `pkg@=3.2`, the old exact matching behavior is
removed. This means that `spack install pkg@3.2` constrains the `pkg` version
to the range `3.2`, and `spack install pkg@=3.2` constrains it to the specific
version `3.2`.
- Also in directives such as `depends_on("pkg@2.3")` and their when
conditions `conflicts("...", when="@2.3")` ranges are ranges, and specific
version matches require `@=2.3.`.
- No matching version: in the case `pkg@3.2` matches nothing, concretization
errors. However, if you run `spack install pkg@=3.2` and this version
doesn't exist, Spack will define it; this allows you to install non-registered
versions.
- For consistency, you can now do `%gcc@10` and let it match a configured
`10.x.y` compiler. It errors when there is no matching compiler.
In the past it was interpreted like a specific `gcc@=10` version, which
would get bootstrapped.
- When compiler _bootstrapping_ is enabled, `%gcc@=10.2.0` can be used to
bootstrap a specific compiler version.
## Other changes
- Externals, compilers, and develop spec definitions are backwards compatible.
They are typically defined as `pkg@3.2.1` even though they should be
saying `pkg@=3.2.1`. Spack now transforms `pkg@3` into `pkg@=3` in those cases.
- Finally, fix strictness of `version(...)` directive/declaration. It just does a simple
type check, and now requires strings/integers. Floats are not allowed because
they are ambiguous `str(3.10) == "3.1"`.
`spack buildcache create` is a misnomer cause it's the only way to push to
an existing buildcache (and it in fact calls binary_distribution.push).
Also we have `spack buildcache update-index` but for create the flag is
`--rebuild-index`, which is confusing (and also... why "rebuild"
something if the command is "create" in the first place, that implies it
wasn't there to begin with).
So, after this PR, you can use either
```
spack buildcache create --rebuild-index
```
or
```
spack buildcache push --update-index
```
Also, alias `spack buildcache rebuild-index` to `spack buildcache
update-index`.
Spack never parsed `nagfor` linker arguments put on the compiler line:
```
nagfor -Wl,-Wl,,-rpath,,/path
````
so, let's continue not attempting to parse that.
`buildcache create --rel`: deprecate this because there is no point in
making things relative before tarballing; on install you need to expand
`$ORIGIN` / `@loader_path` / relative symlinks anyways because some
dependencies may actually be in an upstream, or have different
projections.
`buildcache install --allow-root`: this flag was propagated through a
lot of functions but was ultimately unused.
* py-amici, py-python-libsbml: new packages
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Swig and cmake are build-only dependencies
* cmake as a run dependency after all
* py-amici: default boost and hdf5 variants to True
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When building perl with posix jobserver, it seems to eat jobs, which
reduces parallelism to 1 in many cases, and is rather annoying. This is
solved in GNU Make 4.4 (fifo is more stable than file descriptors), but
that version is typically not available.
So, fix this issue by simply unsetting MAKEFLAGS for the duration of
./Configure. That's enough, and the build phase runs perfectly in
parallel again.
This switches the default Make build type to `build_type=Release`.
This offers:
- higher optimization level, including loop vectorization on older GCC
- adds NDEBUG define, which disables assertions, which could cause speedups if assertions are in loops etc
- no `-g` means smaller install size
Downsides are:
- worse backtraces (though this does NOT strip symbols)
- perf reports may be useless
- no function arguments / local variables in debugger (could be of course)
- no file path / line numbers in debugger
The downsides can be mitigated by overriding to `build_type=RelWithDebInfo` in `packages.yaml`,
if needed. The upside is that builds will be MUCH smaller (and faster) with this change.
---------
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* Vendor ruamel.yaml v0.17.21
* Add unit test for whitespace regression
* Add an abstraction layer in Spack to wrap ruamel.yaml
All YAML operations are routed through spack.util.spack_yaml
The custom classes have been adapted to the new ruamel.yaml
class hierarchy.
Fixed line annotation issue in "spack config blame"
This ensures that:
a) no externals are added to the tarball metadata file
b) no externals are added to the prefix to prefix map on install, also
for old tarballs that did include externals
c) ensure that the prefix -> prefix map is always string to string, and
doesn't contain None in case for some reason a hash is missing
* libiconv can be provided by libc, so update packages which depend on
libiconv to require the iconv virtual instead
* Many packages need special consideration when locating iconv depending
on whether it is provided by libc (no prefix provided) or the libiconv
package (in that case we want to provide a prefix)
* It was also noticed that when an iconv external was provided, that
there was interference with linking (this should generally be handled
by Spack's compiler wrappers and bears further investigation)
* Like iconv, libintl can be provided by libc or another package, namely
gettext. It is not converted to a provider like libiconv because it
provides additional routines. The logic is similar to that of iconv
but instead of checking the provider, we check whether the gettext
installation includes libintl.
* Provide openmp from rocm-open-extras for roblas test
* Addressing the prechecks/audit/package-audits check
* Correcting style check errors.
* rocm-openmp-extras path veriable restricting for test
* Correcting the env variable to run_tests
* Guard use of OpenMP to make it optional in rocblas test
* Removing unused patch
* Patch to handle file reorg changes for the tests
* Correcting patch file name
* Limiting hipify-clang path to 5.4 and later
* Set hipify-clang path env in CMake
* Disable module generation by default (#35564)
a) It's used by site administrators, so it's niche
b) If it's used by site administrators, they likely need to modify the config anyhow, so the default config only serves as an example to get started
c) it's too arbitrary to enable tcl, but disable lmod
* Remove leftover from old module file schema
* Warn if module file config is detected and generation is disabled
---------
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Change the signature of the Environment.__init__ method to have
a single argument, i.e. the directory where the environment manifest
is located. Initializing that directory is now delegated to a function
taking care of all the error handling upfront. Environment objects
require a "spack.yaml" to be available to be constructed.
Add a class to manage the environment manifest file. The environment
now delegates to an attribute of that class the responsibility of keeping
track of changes modifying the manifest. This allows simplifying the
updates of the manifest file, and helps keeping in sync the spec lists in
memory with the spack.yaml on disk.
* generax: adding new package generax
* muscle5: adding new package muscle5
* py-custom-inherit: adding new package py-custom-inherit
* py-ete3: adding new package py-ete3
* py-itolapi: adding new package py-itolapi
* py-opentree: adding new package py-opentree
* py-pypng: adding new package py-pypng
* py-toyplot: adding new package py-toyplot
* py-toytree: adding new package py-toytree
* py-pastml: adding new package py-pastml
* raxml-ng: adding new version 1.1.0
* py-topiary: adding new package py-topiary
* generax: adding master branch version
generax: adding version 2.0.1
generax: add mpi variant
* py-topiary: add main
* generax: correcting commit for 2.0.1
* Update var/spack/repos/builtin/packages/py-itolapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-opentree/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-topiary-asr: rename package, requested changes.
* Update var/spack/repos/builtin/packages/py-topiary-asr/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Make sure to append additional flags needed for specific compilers
in the flag_handler instead of adding them as separate cmake define
lines that override the main spack cflags.
Spack comes to a crawl post-install of nvhpc, which is partly thanks to
this post install hook which has a lot of redundancy, and isn't correct.
1. There's no need to store "type" because that _is_ "mode".
2. There are more file types than "symlink", "dir", "file".
3. Don't checksum device type things
4. Don't run 3 stat calls (exists, stat, isdir/islink), but one lstat
call
5. Don't read entire files into memory
I also don't know why `spack.crypto` wasn't used for checksumming, but I
guess it's too late for that now. Finally md5 would've been the faster
algorithm, which would've been fine given that a non cryptographicall
checksum was used anyways.
The bricks package uses header from the opencl-clhpp package when built with
the cuda variant activated. In order to find the header files, the bricks
CMakeLists.txt uses the `find_package(OpenCL 2.0)` statement. The CMake
FindOpenCL module searches several paths to find the header files. Eventually
it will search for header files in the local /usr/include directories. If
OpenCL headers are found, but CUDA is not installed locally, then the build
will fail.
One of the CMake variables searched for a path to the OpenCL headers is
OCL_ROOT. This fix utilizes the OCL_ROOT variable to identify the correct path
to the install opencl-clhpp package within Spack. Also, if the cuda variant is
not used, then the OpenCL build is disabled to prevent a build failure due to
improperly-identified locally-installed OpenCL header files.
The default behavior of the build process has not changed. An external variable
definitions must be made to activate these features. Specifically, to disable
the OpenCL build, this flag must be provided to CMake:
-DBRICK_USE_OPENCL=OFF
The Spack build process explicitly uses this option unless the cuda variant is
specified. If the cuda variant is specified, then the BRICK_USE_OPENCL variable
is set to ON and the OCL_ROOT variable is set to the path of the opencl-clhpp
include directory.
* "new py-subword-nmt package"
* [@spackbot] updating style on behalf of Sangu-Mbekelu
* Update package.py
updating package based on review
* [@spackbot] updating style on behalf of Sangu-Mbekelu
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* [py-breathe] New version 4.35.0
* Update var/spack/repos/builtin/packages/py-breathe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [py-sphinx-design] New versions 0.4.0, 0.4.1
* conflicts() -> depends_on()
Per @adamjstewart
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding py-ipyrad for testing
* py-ipyrad: placating flake8
* py-ipyrad: adding version 0.9.90, fixing hard coded path.
* py-ipyrad: use join_path instead of hard coded linux path
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipyrad: Removing unneeded dependencies
* py-ipyrad: Readded future (see ipyrad setup.py)
* py-ipyrad: Switch to an anchored link in the docs
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipyrad: Removed patch decorator
---------
Co-authored-by: snehring <snehring@iastate.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* elfutils cannot build against libarchive@3.62+iconv
* elfutils needs libmicrohttpd version 0.9.50 or older
* elfutils: explicitly depend on pkg-config
* libmicrohttpd: Add several new versions
* Add patch for MacOS M1/M2 machines to fix segfault when using gmp
* Update var/spack/repos/builtin/packages/gmp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Restrict patch to v6.2.1
* Update var/spack/repos/builtin/packages/gmp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The patch for the zziplib package applied for version 0.13.69 and
earlier includes a reference to Creative Commons
Attribution-NonCommercial-ShareAlike 2.0 Generic license, which
causes Flexera's ~expensive perl script~ FlexNet Code Insights open
source license and compliance tool to flag Spack as a non-commercial
product. This patch narrows the diff context in the patch to exclude
this text. The semantics of the patch file are unchanged.
We have successfully been building silo@4.10.2 against hdf5@1.10.4 from
some time. Refinement of #34275 (which was concerned with 4.11 but
unnecessarily restricted 4.10).
* py-numpy: set openblas `symbol_suffix` in site.cfg
This writes the correct `symbol_suffix` variant value from the `openblas` in the spec into the `site.cfg`. Fixes#37133.
* py-numpy: fix style
* py-numpy: handle symbol_suffix == "none"
* py-codecov: deprecate since not on pypi anymore
* codecov: new package
* [@spackbot] updating style on behalf of wdconinc
* codecov: use github URL instead, multi-platform
* fix: install to prefix.bin.codecov
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* codecov: use versions lookup dict
* codecov: versions -> _versions, fix style
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Silence make
Set a fixed and large NUM_THREADS by default, to avoid that it gets initialized with the host # CPUs.
Set OMP_NUM_THREADS/OPENBLAS_NUM_THREADS in terms of make_jobs so that tests don't need excessive CPU.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
If we modify both Path and PATH, on Windows they will clobber one
another. This PR updates the shell modification logic to automatically
convert variable names to upper-case on Windows.
Paths with spaces are an issue on Windows and our current powershell
scripts are not sufficiently hardended against their use.
This PR removes promlematic commandlets that do not work well with paths
with spaces and adds escape quotes in other areas where this could be an
issue.
* glib: new version 2.76.1
This adds a new stable version of glib, 2.76.1 (skipping the 2.75 unstable series).
`mkenums.py` check now is specified as a dict, after r62dca6c1cf. The `filter_file` should disable both old and new. Better (maybe, but more complicated) would be to add the `can_fail` flag for this test.
The `iconv` argument was already deprecated and has now been removed. It is now resolved through meson itself, e71ecc8771.
Builds successfully on my system (and several dependents on top of it):
```console
==> glib: Successfully installed glib-2.76.1-7iy4mee2evabd357gviozbtyh5yxi27t
```
as does the previous 2.74.6 version
* glib: patch for 2.76.1, new version 2.74.7
Replace my initial libintl check with the much nicer check for
"intl" in self.spec["gettext"].libs.names. Thanks to Chris Green!
Co-authored-by: Bernhard Kaindl <bkaindl@gmail.com>
* initial commit for enabling test for rccl hsakmt-roct and rocm-opencl
* fix styling and cleaning code
* adding missing imports and minor fixes
* minor style fix
* moidfying hsakmt-roct test to run right after installation
* osg-ca-certs: igtf link should point to version, not 'current'
* osg-ca-certs: new version 1.110.igtf.1.119
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* ants: add version 2.4.3
- add version 2.4.3
- deprecate old git version
* [@spackbot] updating style on behalf of glennpj
---------
Co-authored-by: glennpj <glennpj@users.noreply.github.com>
* Add new package MozJPEG
MozJPEG is a patched version of libjpeg-turbo which improves JPEG compression efficiency achieving higher visual quality and smaller file sizes at the same time.
* MozJPEG: Add myself as a maintainer and fix style
* google-cloud-cli: add new package
* black fixes
* Less verbose
* [@spackbot] updating style on behalf of adamjstewart
* More robust if ver doesn't exist for platform
* Deprecate ancient GEE
* Fix ppc64le bug
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
- [x] Replace `version(ver, checksum=None, **kwargs)` signature with
`version(ver, checksum=None, *, sha256=..., ...)` explicitly listing all arguments.
- [x] Fix various issues in packages:
- `tags` instead of `tag`
- `default` instead of `preferred`
- `sha26` instead of `sha256`
- etc
Also, use `sha256=...` consistently.
Note: setting `sha256` currently doesn't validate the checksum length, so you could do
`sha256="a"*32` and it would get checked as `md5`... but that's something for another PR.
* py-torch: define property cmake_prefix_paths
`py-torch` installs `libtorch` and a cmake config in a non-standard location. This points downstream code to the relevant locations. From there it should pick up the correctly library and include paths for C++ projects.
* py-torch: python_platlib suggestion
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of wdconinc
* py-torch: back to self.spec["python"].package.platlib
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Add mfem v4.5.2 and related updates/tweaks in other packages
* [mfem] Add the release source link for MFEM v4.5.2
* [mfem] Remove 'goxberry' (his request) from MFEM's maintainers list
This means that `spack install` will now build the minimal set of packages
required to install the root(s).
To opt out of build edge pruning, use `spack install --include-build-deps`.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.
- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.
- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
fixes#36628
Fix using compilers that declare "target: any" in their
configuration. This should happen only on Cray with the
module based programming environment.
* Simplify test/cmd/ci.py::test_ci_generate_with_custom_scripts
* Rearrange the build-job logic in generate_gitlab_ci_yaml
* Preserve all unknown attributes in build jobs
* Slip tests for custom attributes in the tests for other job types
* Support custom artifacts
* [@spackbot] updating style on behalf of blue42u
* Don't bother sorting needs
---------
Co-authored-by: blue42u <blue42u@users.noreply.github.com>
* DaV SDK: Enable ParaView raytracing with in SDK
* CI: Drop swr testing from Data Vis SDK
* ISPC: extend LLVM requirement to main
* DaV SDK: Disallow concretizing develop unifyfs
No longer needed after mochi-margo patch
* New packages: py-ogb, py-outdated, py-littleutils
* Update var/spack/repos/builtin/packages/py-outdated/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.
- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.
- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
* lmod modules: allow users to remove items from hierarchy per-spec
This allows MPI wrappers that depend on MPI to be removed from the MPI portion of
the hierarchy and be made available when the appropriate compiler is loaded.
module load gcc
module load mpi-wrapper # implicitly loads mpi
module load hdf5
This allows users to treat an mpi wrapper like an mpi program
This adds the new LTS version of Qt5. No build system changes needed.
The bundled libjpeg and sqlite versions were updated, but it is unclear if these are actual build requirements, and we have not been tracking these specific versions in the version dependencies (likely due to exactly this lack of clarity).
Compare: https://github.com/qt/qtbase/compare/v5.15.8-lts-lgpl...v5.15.9-lts-lgpl
* Add NetCDF95 package.
NetCDF95 is an alternative Fortran interface to the NetCDF library which uses Fortran 2003 features.
* [@spackbot] updating style on behalf of RemiLacroix-IDRIS
---------
Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com>
* libmypaint: change extend to append
For same reason as #36939, `extend` takes a list as argument, while `append` takes list entry. Here `append` should be used.
* libmypaint: depends_on intltool
starting with the 5.0.x release stream the cuda related configury
items in Open MPI once again need --with-cuda-libdir so that
libcuda.so can be found at configure time, otherwise no cuda
support unless someone copies libcuda.so to
$CUDA_HOME/lib64
related to #36760
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Updating torchgeo to 0.4.1
* Added some commas
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Changed fiona bounds
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* upcxx: Enhance auto-detection for HPE Cray EX platforms
1. Some Cray EX systems use ALPS instead of SLURM, ensure we default
the pmi-runcmd appropriately.
2. Some Cray EX systems run a stock kernel and lack a Cray PrgEnv
(yes, really), so add a check for libfabric CXI provider as a
last resort for detecting Cray EX, and ensure we don't choke on
a lack of `$CRAYPE_DIR`.
* upcxx: Cray XC improvements
1. Future-proof Cray XC detection, in case Spack ever starts reporting
it as "linux".
2. Revert cray-libsci workaround for ALCF Theta. The workaround no longer
appears to be necessary, and is actually causing failures on Theta now.
* upcxx: Add level_zero variant detection
This commit changes the environment modifications class to escape
strings with double quotes instead of single quotes.
Single quotes prevent the expansion of enviornment variables that are
nested within environment variable definitions.
Fixes#36689
- The "base" builder class should be last in the MRO
- `filter_compiler_wrappers` needs to be moved to builders
- Decorating a function from a mixin class require using
the correct metaclass for the mixin
* py-dask-mpi: remove jupyter-server-proxy
This dependency isn't a 'hard' one; it optionally simplifies getting access to the web consoles.
See: https://github.com/dask/dask-mpi/pull/102
* Add patch to remove unnecessary dependency
* review comments
* pass formatting
* Update m4
For %oneapi & %intel, we explicitly set -O0 so dependents of m4 do not break
# The default optimization level for icx/icpx is "-O2",
# but building m4 with this level breaks the build of dependents.
# So we set it explicitely to "-O0".
* [@spackbot] updating style on behalf of hpcnpatel
This aims to resolve#34164 by resolving the <include-fragment> tags
that GitHub has started using for their release pages, see
https://github.github.io/include-fragment-element/.
This feels a bit hacky but intended as a starting point for discussion.
After reading a page during spidering, it first parses for
include-fragments, gets them all, and treats them all as separate pages.
Then it looks for href links in both the page itself and the fragments.
Co-authored-by: Alec Scott <alec@bcs.sh>
* py-torch: Update conflicts for +/~tensorpipe
* [@spackbot] updating style on behalf of blue42u
* Update var/spack/repos/builtin/packages/py-torch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of blue42u
---------
Co-authored-by: blue42u <blue42u@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
MSVC compilers rely on vcvars environment setup scripts to establish
build environement variables neccesary for all projects to build
successfully. Prior to this we were only piping LIB, INCLUDE, and PATH
change through.
Instead we need to propegate all changes to the env variables made by
VCVARs in order to establish robust support for the MSVC compiler.
This most significantly impacts projects that need to be build with
NMake and MSBuild
No changes to the build recipe required. Changelog at https://github.com/xrootd/xrootd/compare/v5.5.3...v5.5.4.
Built successfully on my test system:
```console
[+] /opt/software/linux-ubuntu23.04-skylake/gcc-12.2.0/xrootd-5.5.4-cgyz43ivwwqkc7bhdofnxhl2fusysg3m
```
* CI: Fixup docs for bootstrap.
* CI: Add compatibility shim
* Add an update method for CI
Update requires manually renaming section to `ci`. After
this patch, updating and using the deprecated `gitlab-ci` section
should be possible.
* Fix typos in generate warnings
* Fixup CI schema validation
* Add unit tests for legacy CI
* Add deprecated CI stack for continuous testing
* Allow updating gitlab-ci section directly with env update
* Make warning give good advice for updating gitlab-ci
* Fix typo in CI name
* Remove white space
* Remove unneeded component of deprected-ci
* cppzmq: new versions 4.8.1, 4.9.0 (updated cmake dependency)
No important changes in the build system, https://github.com/zeromq/cppzmq/compare/v4.7.1...v4.9.0, other than the more recent cmake required starting with 4.8.0.
There is also a patch version 4.8.0, but presumably 4.8.1 is preferred.
* cppzmq: add maintainer
* Extract a method to warn when the manifest is not up-to-date
* Extract methods to update the repository and ensure dir exists
* Simplify further the write method, add failing unit-test
* Fix the function computing YAML equivalence between two instances
* ECP-SDK: enable hdf5 VOL adapters
- When +hdf5, enable VOL adapters suitable for the SDK.
- Each VOL package must prepend to the HDF5_PLUGIN_PATH.
- hdf5: 1.13.3 will break existing VOL packages, constrain
VOLs related to SDK and add note to keep 1.13.2 available.
- hdf5-vol-async:
- Do not set HDF5_VOL_CONNECTOR, consumers must opt-in.
- Enforce DAG constraints on MPI to require threaded version.
- Depend on an explicit version of argbots to relax
concretization issues in other spack environments.
- paraview: fix compiler flag usage for the 110 ABI (followup to #33617).
* ECP Data and ViS: Add constraits for HDF5 VOLS
* CI: HDF5 1.14 builds without VisIt
* hdf5-vol-async: Update docs string
---------
Co-authored-by: Stephen McDowell <stephen.mcdowell@kitware.com>
* Fix py-torch build on Linux >=6.0.3
* Update var/spack/repos/builtin/packages/py-torch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
VeloC/SCR component releases needed for upcoming VeloC release.
* AXL v0.8.0
* ER v0.4.0
* KVTree v1.4.0
* Rankstr v0.3.0
* Redset v0.3.0
* Shuffile v0.3.0
* Spath v0.3.0
Added some dependency compatibility restraints as the new componenet
versions have a change to how their cmake config works.
* add cuDNN variant and make RDKit optional
* [@spackbot] updating style on behalf of RMeli
* add newer version of rdkit
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* archspec: add v0.2.0, deprecate old versions
* Simplify version ranges
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-setuptools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Rename PIKA_WITH_P2300_REFERENCE_IMPLEMENTATION CMake option in pika package
* Remove unnecessary use of self in pika package
* Use append instead of list += for single options in pika package
* Add pika 0.14.0
* add tandem package
* apply black
* fix import
* fix year of license
* add version 1.0 and associated compile fix
* change git to property
* add conflict to intel
* Kokkos: add release 4.0.0
* Kokkos: updating default c++ standard requirement
Now Kokkos requires c++17 as its new minimum c++ standard library.
* Kokkos: adding support for new GPU architectures
The new updates include NVIDIA Hopper and AMD Navi
* Kokkos: fixing style...
* paraview +rocm: constrain kokkos dep to @:3.7.01
---------
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* initial commit for enabling test for rocm-smi-lib, rocm-cmake and rocm-clang-ocl
* fix styling and cleaning code
* disabling some tests for rocm-smi-lib
* fix style errors
* msmpi has no wrappers so don't set MPI_CXX_COMPILER etc. for that
MPI implementation
* hdf5 on Windows does not have h5cc etc., so do not try to filter
them on Windows
* py-uproot: new versions 5.0.4, 5.0.5
No changed in dependency versions
* py-awkward-cpp: new versions
* py-awkward: new versions
* py-awkward: new version in 1.10.* series
Previously `spack -e bla config update <section>` would treat the
environment config scope as standard config file instead of a single
file config scope. This fixes that.
When app is uninstalled, if it matches a default, then remove the
default symlink targeting its modulefile.
Until now, when a default were uninstalled, the default symlink were
left pointing to a nonexistent modulefile.
- Update default image to Ubuntu 22.04 (previously was still Ubuntu 18.04)
- Optionally use depfiles to install the environment within the container
- Allow extending Dockerfile Jinja2 template
- Allow extending Singularity definition file Jinja2 template
- Deprecate previous options to add extra instructions
Unless the amdgpu_target is overriden, the libraries will default to
being built for cuda, since amdgpu_target=none is both default and in
conflict with +rocm. This requires a custom Disjoint set to include
both the 'auto' variant used by the rocm mathlibs and the 'none'
variant used by ROCmPackage.
* Fix search for hip+cuda in hipcub@5.1 and later
This patch is not strictly necessary, but it may fix the search for HIP
in certain environments.
* Backport fix for CUDA 11.5 to hipsparse
* Reduce effort on grounding by employing cardinality constraints
If we use a cardinality constraint instead of a rule
using pair of values, we'll end up grounding 1 rule
instead of all the possible pair combinations of the
allowed values.
* Display all errors from concretization, instead of just one
If clingo produces multiple "error" facts, we now print all
of them in the error message. Before we were printing just
the one with the least priority.
Consolidate a few common patterns in concretize.lp to ensure
that certain node attributes have one and only one value
assigned.
All errors are displayed, so use a single criterion
instead of three.
* Account for weights in concretize.lp
To recover the optimization order we had before, account
for weights of errors when minimizing.
The priority is mapped to powers of 10, so to effectively
get back the same results as with priorities.
openblas likes to concurrently writes to the same archive from different
targets, and solves that through .NOTPARALLEL: all
We run `make x y z` which is not affected by `NOTPARALLEL`, running into
races.
When generating modulefile, correctly detect software installation asked
by user as explicit installation.
Explicit installation status were previously fetched from database
record of spec, which was only set after modulefile generation.
Code is updated to pass down the explicit status of software
installation to the object that generates modulefiles.
Fixes#34730.
Fixes#12105.
A value for the explicit argument has to be set when creating a new
installation, but for operations on existing installation, this value is
retrieved from database. Such operations are: module rm, module refresh,
module setdefaults or when get_module function is used.
Update on the way tests that mimics an installation, thus explicit
argument has to be set under such situation.
Original Author of this change: Chris Green <greenc@fnal.gov>
Two changes:
- Remove adding the library path using -L: It is obsolete now
that we have the library paths in before the system paths.
- Link with -linto only if the gettext recipe provides it:
When we are on a glibc system, we can use external gettext,
which means we use the libintl inside libc.so: no -lintl then.
This change was already submitted in #35450 and reviewed but is
stuck in this big PR which is trying to do too in a single PR.
This fixes a bug in the Windows build of Perl.
An attribute defined in package class is inaccessible from the install
method due to builder: refactor it to be a method.
Add `config:stage_name` which is a Spec format string that can
customize the names of stages created by Spack. This was primarily
created to allow generating shorter stage names on Windows (along
with `config:build_stage`, this can be used to create stages with
short absolute paths).
By default, this is not set and the prior name stage format is used.
This also removes the username component that is always added to
Stage paths on Windows (if users want to include this, they can
add it to the `build_stage`).
* py-aioitertools: add v0.11.0
* Update var/spack/repos/builtin/packages/py-aioitertools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* compiler wrapper: fix -Xlinker parsing
* handle the case of -rpath without value; avoid that we drop the flag
* also handle the -Xlinker -rpath -Xlinker without further args case...
* fix test
* get rid of global $rp var, reduce branching
* Ascent: Drop VTK-h dependency for 0.9
* Ascent: Remove duplicate OpenMP constraints
* Ascent: 0.9.0 cannot build with vtk-m@2
* Ascent: Only needs vtkm when using vtkh
* Ascent: Require fides when building with ADIOS2
* QE v7.1 add post-processing tools installation
Quantum-Espersso@7.1 ships with an incoplete CMakeLists.txt that prevents the installation of post-processing tools.
Added patches, is fixed in two different commits in upstream.
* fixed style
* removed spaces
* added MR references
* Add new libfabric versions 1.17.1, 1.17.0, 1.16.0, 1.15.2.
* Add libfabric dependency on numactl and linux-headers when building
with OPX provider support.
* Set libfabric flag_handler to pass compiler flags as arguments to
configure.
Fix patching old boost versions to account for builders.
Add a proper version constraint on boost for recent dyninst.
The constraint can be found in dyninst source code under
"cmake/Boost.cmake" which contains:
set(_boost_min_version 1.70.0)
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Current develop spack.bat file cannot handle any reserved characters
being passed via the CLI, particularly '=' and '?'. To address this,
re-do the CLI parsing for loop to use custom logic to allow for more
granular handling of CLI args.
* We take a less-than-ideal approach to escaping local scope and
handling unset variables as well as the actual parsing of CL
arguments. To address this, don't quote the args and then try to
parse the quotes we just added (resulting in spack flags being
undefined). Instead, leverage batch script features. Since we are
not unnecessarily quoting things, we don't need to think about
removing them, and in the case of paths with spaces, we should _not_
be removing the quotes as we currently do.
Corrects libs detection with a more specific root, otherwise there
can be inconsistencies between version of WGL requested and the
version picked up by `find_libraries`.
Corrects headers detection - win-sdk, win-wdk, and WGL headers all
exist under the same directory, so we can compute the headers for WGL
without querying the spec for win-sdk (which causes errors).
This commit also removes the `plat` variant of `wgl`, which is
redundant with the Spec's target.
- [x] Specs that define 'new' versions in the require: section need to generate associated facts to indicate that those versions are valid.
- [x] add test to verify success with unknown versions.
- [x] remove unneeded check that was leading to extra complexity and test
failures (at this point, all `hash=version` does not require listing out that version
in `packages.yaml`)
- [x] unique index for origin (dont reuse 0)
Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
* Add v8.4.1, and a few other changes.
Minor adjustments for better alignment between Spack and ESMF native
build. For ESMF >= 8.3.1 now Spack defaults to using
external-parallelio. Before use internal version, which was PIO-1 all
the way up to v8.3.0b10 anyway! Xerces is disabled by default.
* Deal with two long lines flagged by prechecks/style.
* Try to satisfy prechecks/style.
* Try to satisfy flake8 rules wrt indentation of continuation lines.
* Now trying to satisfy "black reformatting".
* For "black" formatting really put that ugly comma at the end before
closing parentheses. Interesting.
* Support building against external-parallelio even w/o mpi, but select the
external-parallelio dependency accordingly.
* Correct C compiler setting.
* Handle `pnetcdf` variant consistent with how `ParallelIO` does it. And
also pass the `pnetcdf` variant down to the `external-parallelio`
dependency if set.
* Long line formatting again.
* Simplify handling of tarball URL construction and update sha256
checksums.
* Align version check with recommended self.spec.satisfies().
* Deprecate v8.4.0 which has a bug that can cause memory corruption, fixed
in v8.4.1.
* Use double quotes vs single quotes as per style-check... although
https://spack-tutorial.readthedocs.io/en/latest/tutorial_packaging.html#querying-spec-versions
clearly shows it with single quotes.
* ispc: attempts at getting more recent versions to work
* ispc: more attempts to get newer versions to build
* ispc: cleanup
* llvm: remove ispc_patches variant again
* ispc: unpin ncurses
* ispc: satisfy style checks
* ispc: 1.19 is only compatible with LLVM 13-15
otherwise it would not build against develop, as this now has LLVM 16
* ispc: relax LLVM version to what ispc requires itself
verified that it builds against LLVM 13, 14, 15, but not 12 and 16
* ispc: use spec.satisfies instead of version comparison
according to suggestions from review and docs, this is the canonical way to do it
* ispc: checksum 1.18.1
just in order to include all versions, also checked that it builds
---------
Co-authored-by: Martin Aumüller <aumuell@reserv.at>
Add a `find_first` method that locates one instance of a file
that matches a specified pattern by recursively searching a directory
tree. Unlike other `find` methods, this only locates one file at most,
so can use optimizations that avoid searching the entire tree:
Typically the relevant files are at low depth, so it makes sense to
locate files through iterative deepening and early exit.
Update tcl and lmod modulefile template to provide more information on
help message (name, version and target) like done on whatis for lmod
modulefiles.
This resolves a loose end from #36241 (missed due to package name). `libpthread-stubs` is another package from the xcb project that is now tracked through https://gitlab.freedesktop.org/xorg/ instead. No new versions; no changed hashes.
* py-iniconfig: new version 2.0.0 (-> hatchling)
py-iniconfig switched to hatchling with v2.0.0:
https://github.com/pytest-dev/iniconfig/blob/v2.0.0/pyproject.toml
```
==> py-iniconfig: Successfully installed py-iniconfig-2.0.0-ttoip2aalmxqqybv3vnozcabk47vg2yn
```
* Update var/spack/repos/builtin/packages/py-iniconfig/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Adapt tcl and lmod modulefile templates to generate append-path or
remove-path commands in modulefile when respectively append_flags or
remove_flags commands are defined in package for run environment.
Fixes#10299.
* Add option to optionally build with CMake
* Autotools is preferred where available
* Unlike the autotools-based build, the CMake-based build creates
either static or shared libs, not both (the default is shared
and is controlled with a new "shared" variant that only exists
when building with cmake)
* Note that `cmake~ownlibs` depends on expat, so would require
`expat build_system=autotools` (to avoid a cyclic dependency)
Simplify environment modification block in modulefile Tcl template by
always setting a path delimiter to the prepend-path, append-path and
remove-path commands.
Remove --delim option to the setenv command as this command does not
allow such option.
Update test_prepend_path_separator test to explicitly check the 6
path-like commands that should be present in generated modulefile.
* Add a pre-check job that just bootstrap the environment on Python 3.6
* py-typing-extension: restore information on Python 3.6 installation
* Fix job name, try to run quick test on installed python packages
fixes#36339
We were missing a rule that enforced a match between
the `node_compiler` and the compiler used to satisfy
a requirement.
Fix compiler with custom, made up version too
* gcc: fix for apple-clang conflict
* Update var/spack/repos/builtin/packages/gcc/package.py
Use variant by @adamjstewart
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Specs that define 'new' versions in the require: section need to generate
associated facts to indicate that those versions are valid.
* add test to verify success with unknown versions.
Since environment-modules has support for autoloading since 4.2,
and Spack-builds of it enable it by default, use the same autoload
default for tcl as lmod.
* add opppy-0_1_6 and opppy-0_1_7 releases to the spack recipes
* update urls
* remove sphinx from the dependency list
* cleanup OPPPY versions to capture OPPPY-0_1_1 tag descrepency
* one more attempt at fixing the url for opppy-0_1_1 (simpler fix)
---------
Co-authored-by: Cleveland <cleveland@lanl.gov>
Co-authored-by: clevelam <clevelam@users.noreply.github.com>
* update python package
* change package inheritance
* small update
* enable cpp tests
* small update
* Add flaky package
* Restructure PennyLane deps and order
* Change Lightning defaults and add libomp support for MacOS
* Replace explicit git url with PyPI
* Add Flaky support
* Update PennyLane and PennyLane Lightning support
* fix format
* update packages versioning
* Add patching and default updates for lightning package
* Format
* fix patch version
* update py-flaky package
* update py-pennylane-lightning package
* update py-pennylane package
* remove explicity python dependence
* Remove redundant lines from patch-file
* Update SHA for new patch
* Initial commit for PLLKokkos.
* Comment verbose variant.
* Update develop commit version and restore verbose option.
* Add backends.
* Add mesa package dep (libxml2). Fix rocm install for py-pennylane-lightning-kokkos.
* Restore sycl backend.
* Revert mesa package.
* Make py-pe-li-kokkos into CudaPackage, ROCmPackage.
* Do not force kokkos+wrapper when +cuda
* Few mods following comments on py-pll.
* Update versions of py-pennylane*.
* Remove py-pennylane-lightning patch.
* Remove redundant preferred=True.
* Fix lint in py-pennylane-lightning-kokkos.
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Ninja and pip not required at runtime. Set lower bound on PL/PLL versions.
* Remove v0.29.0 from pennylane.
* Add AmintorDusko as maintainer.
---------
Co-authored-by: AmintorDusko <amintor_dusko@hotmail.com>
Co-authored-by: Lee J. O'Riordan <lee@xanadu.ai>
Co-authored-by: Amintor Dusko <87949283+AmintorDusko@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The xcb-utils have been migrated to the gitlab.freedesktop.org, from the
previous separate location. That means that a URL change is needed to
pick up newer version
([ref](https://lists.freedesktop.org/archives/xcb/2022-October/011422.html)).
This replaces the `homepage` and `url` with the latest (to an `xz`
file), adds a `url_for_version` function to resolve past versions, and
add the latest versions. Because of the `url_for_version` I don't think
we can use the `xorg_mirror_path` approach here.
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
netcdf-cxx and netcdf-c now build with CMake rather than Autotools.
netcdf-c can still optionally build with Autotools (but defaults to
CMake). With some additional patches to the CMake files, netcdf-c
can use CMake to build on Windows.
* abinit: add version 9.8.3
* require hdf5 up to 1.8 and libxc up to version 5
* abinit: constrained versions of libxc and hdf5
* fixed bad syntax for format
* fixed error looking for fftw in spec.
* Changed to look for fftw-api in spec.
* Update var/spack/repos/builtin/packages/abinit/package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Xorg apps: updated versions to current latest
This updates all xorg apps to the latest versions, adding updated
requirements where needed.
No major version increases in any packages.
Minor version increases in some packages (build changes, if any, are
indicated below):
- rgb
- xauth
- xcalc
- xclock
- xeyes: xi >= 1.7, x11-xcb xcb-present >= 1.9 xcb-xfixes xcb-damage
- xfontsel
- xfs: xfont2 >= 2.0.1
- xinit
- xpr
- xrdb
Bugfix version increases in many packages, with no expected impact on
dependencies or interfaces.
Summary of dependency changes:
- xeyes:
- depends_on("libxi@1.7:", when="@1.2:")
- depends_on("libxcb@1.9:", when="@1.2:")
- xfs:
- depends_on("libxfont@1.4.5:", when="@:1.1")
- depends_on("libxfont2@2.0.1:", when="@1.2:")
* setxkbmap: depends_on libxrandr when @1.3.3:
* constype: new version
Add support for building with CMake and make it the default build
system on all platforms. By doing this, lz4 can now be built on
Windows. The makefile-based build remains as an option.
* wayland: new versions, new build system (meson)
* wayland-protocols: new version, new build system (meson)
* [@spackbot] updating style on behalf of wdconinc
* wayland-protocols: added maintainer
* wayland: added maintainer
* wayland-protocols: no need to import build systems, per flake8
* wayland: no need to import build system, per flake8
* Update var/spack/repos/builtin/packages/wayland/package.py
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
If you have a "require:" section in your packages config, and you
use it to specify a list of requirements, the list elements can
now include strings (before this, each element in the list had to
be a `one_of` or `any_of` specification, which is awkward if you
wanted to apply just one spec with no alternatives).
* py-pdf2image: new package
* py-pdf2image: 1.16.3 source now available on pypi
* Update var/spack/repos/builtin/packages/py-pdf2image/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Example one:
```
spack install --add x y z
```
is equivalent to
```
spack add x y z
spack concretize
spack install --only-concrete
```
where `--only-concrete` installs without modifying spack.yaml/spack.lock
Example two:
```
spack install
```
concretizes current spack.yaml if outdated and installs all specs.
Example three:
```
spack install x y z
```
concretizes current spack.yaml if outdated and installs *only* concrete
specs in the environment that match abstract specs `x`, `y`, or `z`.
* update versions and arch flags
* style update
* more style issues
* fix hashes and testing problem
* return the old versions, but they are really bad
* fix style
---------
Co-authored-by: Gerald Ragghianti <gerald@ragghianti.com>
The `ignore` parameter was only used for `spack activate/deactivate`, and it isn't used
by Spack Environments which have their own handling of file conflicts. We should remove it.
Everything that handles `ignore=` was removed in #29317 and included in 0.19, when we
removed `spack activate` and `spack deactivate` in favor of environments. So all of these
usages removed here were already being ignored by Spack.
Adapt tcl modulefile template to call "module load" on autoload
dependency without testing if this dependency is already loaded or not.
The is-loaded test is not necessary, as module commands know how to cope
with an already loaded module. With environment-modules 4.2+ (released
in 2018) it is also important to have this "module load" command even if
dependency is already loaded in order to record that the modulefile
declares such dependency. This is important if you want to keep a
consistent environment when a dependent module is unloaded.
The "Autoloading" verbose message is also removed as recent module
commands will report such information to the user (depending on the
verbosity configured for the module command).
Such change has been test successfully with Modules 3.2 (EL7), 4.5 (EL8)
and 5.2 (latest) and also with Lmod 7 and 8 (as it is mentionned in
Spack docs that Lmod can be used along with tcl modules). Dependencies
are correctly loaded or unloaded, whether they are loaded/unloaded or
not.
This change fixes Tcl quoting issue introduced in #32853.
Fixes#19155.
* py-setuptools-git-versioning: new package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-hepunits: new versions 2.2.0, 2.2.1, 2.3.0, 2.3.1
Python 2 support dropped in 2.2 series.
Ref: https://github.com/scikit-hep/hepunits/compare/v2.1.1...v2.3.1
* py-hepunits: py-hatchling as of version 2.3
* [@spackbot] updating style on behalf of wdconinc
* py-hepunits: only depends_on toml through 2.1.1
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
In the Windows filesystem logic for creating a symlink, we intend to
fall back to a copy when the symlink cannot be created (for some
configuration settings on Windows it is not possible for the user
to create a symlink). It turns out we were overly-broad in which
exceptions lead to this fallback, and the subsequent copy would
also fail: at least one case where this occurred is when we
attempted to create a symlink that already existed.
The updated logic expressly avoids falling back to a copy when the
file/symlink already exists.
* Bazel: limit parallelism
* Patch packages that don't directly invoke bazel
* Style fixes
* flag comes after build, not bazel
* flag comes after build, not bazel
* command is only attribute if specific package
* ASP-based solver: use satisfies instead of intersects
They are semantically equivalent for concrete versions,
but the GitVersion.intersects implementation is buggy
* Mitigation for git version bug
fixes#36134
This commit works around the issue in #36134, by using
GitVersion.satisfies instead of GitVersion.intersects
There are still underlying issues when trying to infer the
"reference version" when no explicit one is given, but:
1. They are not reproducible with our synthetic repo
2. They occur only when the `git.<xxx>` form of Git version
is used
Here we just work around the user facing issue and ensure
the tests are correct with our synthetic repository.
* py-pytorch-lightning: add v2.0.0
* py-lightning-utilities: add v0.8.0
* Update all PyTorch packages
* Open-CE does not yet have patches for PyTorch 2 on ppc64le
For `spack install --test=all gromacs`
* remove the `test` target from the `check()` call and just use
the `check` target, in accordance with usual GROMACS test protocol
* build the test binaries explicitly during the build phase
Additional minor updates are necessary. This change
updates the package structure to the newer format with a
separate Builder class so we can override `check()`.
However, note that additional modernization should be
undertaken with care.
This PR does 2 unrelated things:
1. It changes the encoding of the compilers
2. It tweaks the heuristic for the solves in a0d8817907
Both were initially motivated by trying to get a performance gain but, while 2 showed significant speed-ups[^1], 1 instead didn't. I kept it anyhow, since I think the code related to compilers is more consolidated with the new encoding and we might get some performance improvement out of it if we can base our errors on the `node_compiler(Package, CompilerID)` atoms instead of `attrs`.
[^1]: In general the changes in the heuristic brought a ~10% speed-up on the tests I did. I'll post detailed results below.
Add a warning about compilers.yaml that is triggered if there are multiple compilers with the same spec, os and
target (since they can't be selected by users with the spec syntax only).
* [openmpi] 5.0.0.rc10 onwards needs munge
This is the error you will see when munge is missing from `PKG_CONFIG_PATH`:
```
configure:63942: checking for pmix pkg-config cflags
configure:63956: check_package_pkgconfig_run_results=Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63959: $? = 1
configure:63966: pkg-config output: Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63972: result: error
configure:63974: error: An error occurred retrieving pmix cppflags from pkg-config
```
* Use same PKG_CONFIG_PATH defaults for ompi+pmix+prrte
The issue I tried to fix in https://github.com/spack/spack/pull/36105 comes from
different default search paths in different `pkg-config` executables used in
`openmpi` and `pmix` package. As these tools (`openmpi`, `pmix`, and `prrte`)
all use the same mechanisms to detect dependencies, the `pkg-config` environment
they use should also be equal.
Since GPG clear-sign cannot deal with lines longer than 19995 characters
and doesn't even error but simply truncates those linese (don't ask me
why...), we have to be careful not to hit that line limit when reducing
the filesize.
So, instead this PR sets the indent level to 0 and drops the whitespace
after `: `, which still reduces file size by 50% or so.
Per feedback from the UCX community, we rarely do update
releases to anything but the current and one previous main
release stream.
Update comments in the UCX spack file to reflect this.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* py-pyshacl: patch dependency typo
* py-pyshacl: satisfy flake8
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Adds builders appropriate for building these packages on Windows.
It is intended that builds on other platforms are unaffected (e.g.
they build with Autotools as before on Linux).
* py-pint: new versions
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-antspyx: new package
Also adds required dependencies.
Requires options to ITK to enable the right support libraries, and
patches to remove tune the setup and provide resources rather than
downloading libraries/"submodules" on the fly.
* Fix patch URL
* Style fixes.
* bump version and re-include `git clone ...` as resource
... and use colors in disambiguate message for clarity.
This commit avoids the loop:
```
for root in roots:
for dep in deps(root):
...
```
instead it ensures each node is visited once and only once.
Also adds a small optimization when searching for concrete specs, since
we can assume uniqueness of dag hash, so it's fine to early exit.
This adds a new mode for `concretizer:reuse` called `dependencies`,
which only reuses dependencies. Currently, `spack install foo` will
reuse older versions of `foo`, which might be surprising to users.
* update mda dependencies
* apply black
* mdanalysis draft
* update
* small fixes
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ci: version bump for ghcr.io/spack/e4s-amazonlinux-2
This new image comes with GnuPG v2.4.0
* py-cython: upperbounds for Python versions
* fix py-gevent nonsense
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* CI configuration boilerplate reduction and refactor
Configuration:
- New notation for list concatenation (prepend/append)
- New notation for string concatenation (prepend/append)
- Break out configuration files for: ci.yaml, cdash.yaml, view.yaml
- Spack CI section refactored to improve self-consistency and
composability
- Scripts are now lists of lists and/or lists of strings
- Job attributes are now listed under precedence ordered list that are
composed/merged using Spack config merge rules.
- "service-jobs" are identified explicitly rather than as a batch
CI:
- Consolidate common, platform, and architecture configurations for all CI stacks into composable configuration files
- Make padding consistent across all stacks (256)
- Merge all package -> runner mappings to be consistent across all
stacks
Unit Test:
- Refactor CI module unit-tests for refactor configuration
Docs:
- Add docs for new notations in configuration.rst
- Rewrite docs on CI pipelines to be consistent with refactored CI
workflow
* Script verbose environ, dev bootstrap
* Port #35409
By setting the traversal depth to 1, only specs matching the changed
package and direct dependents of those (and of course all dependencies
of that set) are removed from pruning candidacy.
* py-deap: newer version can use newer setuptools
* Update var/spack/repos/builtin/packages/py-deap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The overlapping dependency version ranges caused the concretizer to pick
version 7.1 even though version 8.0 is available:
```
==> Error: No version for 'cubelib' satisfies '@4.7.1' and '@4.8'
```
Moreover, Score-P 8.0 requires libbfd:
```
configure: error: bfd.h required
```
* Provide openmp from rocm-open-extras when tensile uses openmp
* Correcting audit check failure in rocm-openmp-extras dependency
* Fixing style check error
* rocm-openmp-extras required instead of llvm-amdgpu both varient
When untouched spec pruning is enabled, specs possibly affected
by a change cannot be pruned from a pipeline.
Previously spack looked at all specs matching changed package
names, and traversed dependents of each, all the way to the
environment root, to compute the set of environment specs
possibly affected by a change (and thus, not candidates for
pruning).
With this PR, when untouched spec pruning is enabled, a new
environment variable can control how far towards the root spack
traverses to compute the set of specs possibly affected by a
change. SPACK_UNTOUCHED_PRUNING_DEPENDENT_DEPTH can be set
to any numeric value before the "spack ci generate" command
is called to control this traversal depth parameter. Setting
it to "0" traverses only touched specs, setting it to "1"
traverses only touched specs and their direct dependents, and
so on. Omitting the variable results in the previous behavior
of traversing all the way to the root. Setting it to a negative
value means no traversal is done, and always yields an empty
set of possibly affected specs (which would result in the max
pruning possible).
Currently `spack buildcache create` creates compressed tarballs that
differ between each invocation, thanks to:
1. The gzip header containing mtime set to time.time()
2. The generated buildinfo file which has a different mtime every time.
To avoid this, you have to explicitly construct GZipFile yourself, since
the Python API doesn't expose the mtime arg, and we have to manually
create the tarinfo object for the buildinfo metadata file.
Normalize mode: regular files & hardlinks executable by user, dirs, symlinks: set 0o755 permissions in tarfile; other files use 0o644
* "new py-thop package"
* [@spackbot] updating style on behalf of Sangu-Mbekelu
* Update package.py
modified the url and dependencies
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* py-openmesh: new package
* Update var/spack/repos/builtin/packages/py-openmesh/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit formalizes `satisfies(lhs, rhs, strict=True/False)`
and splits it into two functions: `satisfies(lhs, rhs)` and
`intersects(lhs, rhs)`.
- `satisfies(lhs, rhs)` means: all concrete specs matching the
left hand side also match the right hand side
- `intersects(lhs, rhs)` means: there exist concrete specs
matching both lhs and rhs.
`intersects` now has the property that it's commutative,
which previously was not guaranteed.
For abstract specs, `intersects(lhs, rhs)` implies that
`constrain(lhs, rhs)` works.
What's *not* done in this PR is ensuring that
`intersects(concrete, abstract)` returns false when the
abstract spec has additional properties not present in the
concrete spec, but `constrain(concrete, abstract)` will
raise an error.
To accomplish this, some semantics have changed, as well
as bugfixes to ArchSpec:
- GitVersion is now interpreted as a more constrained
version
- Compiler flags are interpreted as strings since their
order is important
- Abstract specs respect variant type (bool / multivalued)
* New package: py-imbalanced-learn
* Fix typo
* [@spackbot] updating style on behalf of meyersbs
* Update var/spack/repos/builtin/packages/py-imbalanced-learn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update/fix py-meldmd; update openmm
* Restrict filter_file based on openmm version
* Updates based on Adam's feedback
* [@spackbot] updating style on behalf of meyersbs
* Break up long filter_file
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Cray fortran compiler names fortran modules in uppercase by
default. Compile with the "-ef" flag to produce the lowercase
name that singularity-eos is expecting.
Two fixes:
1. `-Wl,a,b,c,d` is a comma separated list of linker arguments, we
incorrectly assume key/value pairs, which runs into issues with for
example `-Wl,--enable-new-dtags,-rpath,/x`
2. `-Xlinker,xxx` is not a think, so it shouldn't be parsed.
* httpie: add v3.2.1
* Add additional 3.2.1 dependencies to httpie
* Add version condition to dependency
* Reorder dependencies for efficiency
* Update var/spack/repos/builtin/packages/httpie/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* awscli: add v1.27.84
* Add botocore dependency to awscli
* Update var/spack/repos/builtin/packages/awscli/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-botocore@1.29.84 dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update mda dependencies
* apply black
* Update var/spack/repos/builtin/packages/py-gsd/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove numpy upper bound
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gsd/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update proj
* re-add autotools support
* style
* Setup env in builders
* Drop direct windows conflict for older versions
* Default to CMake
Add new style class definiton
* Proj: setup_run_environment in package not builder
* Proj: move run env changes to pkg, rm cmake arg
* Set PROJ_LIB during build
* Style
* Rm redundant configure arg
Currently, if two compilers with the same spec differ on the flags, the concretizer will:
1. mix both sets of flags for the spec in the ASP program
2. error noting that the set of flags from the compiler (both of them) doesn't match the set from the lower priority compiler
This PR fixes both -- only flags from the highest priority compiler with a given spec are considered.
* py-elasticsearch: new versions
Also add py-elastic-transport as a new dependency
* py-elasticsearch: py-urllib3 is no longer a dependency
* Update var/spack/repos/builtin/packages/py-elasticsearch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`mypy` only understands `sys.platform == "win32"`, not indirect assignments of that
value to things like `is_windows`. If we don't use the accepted platform checks, `mypy`
registers many Windows-only symbols as not present on Linux, when it should skip the
checks for platform-specific code.
* add 2.14.2 py-astroid version
* add py-pylint 2.26.2
* fix black
* fix py-dill depends_on
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix py-astroid minor versionning
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* modify typing_extensions depends_on
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Start using paths found in extra_rpaths in compilers.yaml when building
* running black and changing maintainer list
* changing import order to pass isort
---------
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
Update `spack.util.environment` to remove legacy idioms.
* Remove kwargs from method signature and use a class for traces
* Uppercase a few global variables
* spack.util.environment: add type-hints
* Improve docstrings
* Fixed most style issues reported by pylint
* py-ipdb: updating versions
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* py-ipdb: fixing versions problem and deleting 10.1 which is too old for Python > 3.6
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: removed useless dependencies
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: missing @
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e3sm-scorpio: add e3sm-scorpio package
This is the Scorpio package from the e3sm.org site.
* fixed style errors
* removed unneeded dependency on cmake
Use correct `shlib_symbol_version` for Julia 1.8, work around issue where libuv-julia's git checkout has arbitrary mtime, causing make to regenerate configure scripts, sometimes.
* Add a `py-gmxapi` package.
This package provides the Python package for the GROMACS
public API. The Python package is not strongly coupled to
a specific GROMACS _version_, but its compiled extension module
is strongly coupled to a specific GROMACS _installation_.
* Update conflict info.
In order to allow `^gromacs@2022.1` while rejecting `^gromacs@2022`,
we need to compare to `gromacs@2022.0`.
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review.
* Simplify build system structure.
* Update dependencies for completeness.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Per code review, pretend gmxapi <0.4 doesn't exist, for simplicity.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
a shared library /lib64/libcxi.so, which seems to also appear on other
non-slingshot systems. This patch also checks to make sure that there
is a Cray programming enviornment in /opt/cray/pe in addition to the
shared library.
* py-pygments 2.12; fix py-docutils, again
`2.12` is the latest for which our style hack works, beyond that we need
our own package to make a plugin.
Old docutils needs old setuptools
* py-setuptools is always a dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update the range
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Intel OneAPI's extreme pickiness continues to bring out
buggy/noncompliant code.
This patch fixes an error in the configure.in embedded 'c' test code
and also in a file with an initialized, but unused, variable.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Updates to release 0.6.
* Dep updates
* Dep version fix
* Another version fix
* Fix typo
* UFL version fix
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fenics-ffcx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Some updates following review
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* More updates
* More updates
* build/run updates
* Small fix
* Fix version number.
* specify lower bounds for python dependencies
* address style issues
* address style issues
* address PR comments
* amend setuptools dependency to be of type build only
* amend setuptools dependency to be of type run and build for ffcx and ufl
* add build dependency to ensure import tests pass
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
* py-dask-mpi: new package with dependencies
* py-hatch-jupyter-builder is not needed after all
* skip_modules seems cleaner
* Update var/spack/repos/builtin/packages/py-jupyter-server-proxy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-simpervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Flags `-fallow-argument-mismatch -fallow-invalid-boz` set in `FFLAGS`/`FCFLAGS`
environment variables don't really have effect in older versions of WRF, we need
to force them in the compiler wrappers.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
With the last merge request for OOMMF [1], the intention was to have version
20b0_20220930 as the preferred version, and provide 20b0_20220930-vanilla as an
additional version for the unlikely case anybody needed that.
I made the (wrong) assumption that the `version` listed first in the `package.py` file
would be the preferred version. This merge request is to correct that by
explicitly tagging the preferred version with `preferred=True`.
[1] https://github.com/spack/spack/pull/33072/files
If the docbook packages
- docbook-xml
- docbook-xsl
are installed in a spack environment view the catalog files will be in
conflict in the view directory. This PR resolves that by adding an
appropriate prefix to each catalog name so that they are unique in the
view. The resulting XML_CATALOG_FILES environment variable will then be
able to point to both of them.
1. add version 2023.03.01
2. add variant 'python' that supports unwinding python source
3. clean up some things with the cray variant
4. require the latest libmonitor
5. fix sha256 checksum for url patch
6. delete rocm 5.3 from older versions
* cleaned up style, linked to external htslib
* removed htslib/bcfrools/samtools deps, use bundled libs instead
the pysam package includes the necessary libs to link to, so it wasn't even using linked libs when building
* fixed style
* revert to using external htslib
currently uses bundled samtools and bcftools, and there is no way to use external versions for those dependencies
* added libs property to htslibs package
added support for lib64
* added htslib name
* onednn: add variant to use Arm Compute Library on aarch64
* Update cmake version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Shorten macro definition
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update cpu/gpu_runtime variants
* Update acl variant when 1.7+
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of annop-w
* Add dependencies for new runtimes
* Fix dependency package name to oneapi-level-zero
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: new version 1.10.*, 2.0.*
Lots of changes in 2.0.*, see https://github.com/scikit-hep/awkward/releases. This will need some extra testing.
* py-awkward: hatchling
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* py-scikit-build-core: new and improved py-scikit-build
* py-awkward-cpp: new package
* py-awkward: add depends_on py-awkward-cpp
* py-awkward: depends_on py-packaging
* py-awkward-cpp: new versions pinned by py-awkward
* py-scikit-build-core: additional depends_on
* py-awkward: branch master deprecated
* py-pytest-subprocess: new package
* py-pytest: new version 7.2.1
* py-scikit-build-core: add tests dependencies
* [@spackbot] updating style on behalf of wdconinc
* py-scikit-build-core: two more test dependencies
* py-pytest: depends_on py-exceptiongroup
* py-awkward: add pytest support
* py-pytest: suggestions from review
* py-scikit-build-core: suggestions from review
* Update var/spack/repos/builtin/packages/py-awkward-cpp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: depends_on pyyaml when @:1, order old deps last
* [@spackbot] updating style on behalf of wdconinc
* py-awkward: move some opt deps to test, order test deps
* py-awkward: remove test dependencies
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
if dump file existed it was not truncating the file, resulting in
a file with unaltered filesize, with the new content at the beginning,
"padded" with the tail of the old content, since the new content was
not enough to overwrite it.
`colify` is an old module in Spack that still uses `**kwargs` liberally.
We should be more explicit. Doing this eliminates the need for many
checks (can't pass the wrong arg if it isn't allowed) and makes the
function documentation more clear.
Fixes a bug introduced in 44ed0de8c0
where the push method of binary_distribution now takes named args
include_root and include_depedencies, to avoid the **kwarg hole.
But the call site wasn't update and we passed a dict of keys/values instead
of arguments, which resulted in a call like this:
```
push(include_root={"include_root": True, "include_dependencies": False})
```
This commit fixes that, and adds a test to see if we push the correct packages.
This error shows up a lot, typically it's harmless because an error
happened before the source build even started, in which case we don't
have build logs to copy. So, warn instead of error, cause it distracts
from the actual CI error.
Currently we attempt to setup the build environment even when
dependencies are not installed, which typically results in error while
searching for libraries or executables in a dependency's prefix.
With this change, we get a more user friendly error:
```
$ spack build-env perl
==> Error: Not all dependencies of perl are installed, cannot setup build environment:
- qpj6dw5 perl@5.36.0%apple-clang@14.0.0+cpanm+open+shared+threads build_system=generic arch=darwin-ventura-m1
- jq2plbe ^berkeley-db@18.1.40%apple-clang@14.0.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=darwin-ventura-m1
...
$ echo $?
1
```
* Allow users to specify root env dir
Environments managed by spack have some advantages over anonymous Environments
but they are tucked away inside spack's directory tree. This PR gives
users the ability to specify where the environments should live.
See #32823
This is also taken as an opportunity to ensure that all references are to "managed environments",
rather than "named environments". Prior to this PR some references to the latter persisted.
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* Update exago w/ 1.5.1 and small updates to hiop.
* Fix styling.
* Add RAJA back to ExaGO package.
* Update RAJA requirement for ExaGO and HiOp.
* Update last RAJA requirement in HiOp.
* Add new sphinx rtd theme release 1.2.0
The new release helps with supporting more recent version of docutils
* set docutils officially supported version
* add jquery dependency for sphinx-rtd-theme
* add conflict with jquery version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* correct dependency
* fix version dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* set sphinx version
* fix sha256
* add version for flit-core
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The call:
```
x.satisfies(y[, strict=False])
```
is commutative, and tests non-empty intersection, whereas:
```
x.satsifies(y, strict=True)
```
is not commutative, and tests set-inclusion.
There are 2 fast paths. When strict=False both self and other need to
be concrete, when strict=True we can optimize when other is concrete.
a) It's used by site administrators, so it's niche
b) If it's used by site administrators, they likely need to modify the config anyhow, so the default config only serves as an example to get started
c) it's too arbitrary to enable tcl, but disable lmod
Spack generally ignores file-file projection clashes in environment
views, but would eventually error when linking the `.spack` directory
for two specs of the same package.
This leads to obscure errors where users have no clue what the issue is
and how to fix it. On top of that, the error comes very late, since it
happens when the .spack dir contents are linked (which happens after
everything else)
This PR improves that by doing a quick check ahead of time if clashes
are going to be anticipated (by simply checking for clashes in the
projection of each spec's .spack metadir). If there are clashes, a
human-readable error is thrown which shows two of the conflicting specs,
and tells users to user unify:true, view:false, or set up custom
projections.
* add pytng
* black
* add setuptools
* fix
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pytng/package.py
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Kokkos when compiled by spack without +wrapper could potentially capture the spack compiler wrappers, resulting in cmake configs and kokkos_launch_compiler trying to run the spack compiler wrapper after installation.
The checksum exception was not detailed enough and not reraised when using cache only, resulting in useless error messages.
Now it dumps the file path, expected
hash, computed hash, and the downloaded file summary.
Batch scripts in general will not function without carriage return line
endings on Windows. We rely on these scripts to support cmd, so we
should not allow these scripts to be converted to lf.
Note: Windows 11 supports lf line endings due to the use of Windows
Terminal. Once support for Windows 10 is dropped, this change can be
reverted.
When running many concurrent spack install processes that need to write
to the db, Spack regularly times out. This is because writing to the DB
after another process has written to it requires deserialization of the
db, mutating it in memory, and serializing it again, which takes some
time. On top of that, I believe there's a 1 second retry when a write
lock cannot be obtained, so I think this means only 3 processes can
really write to the DB at the same time before timing out.
* Style: black 23, skip magic trailing commas
* isort should use same line length as black
* Fix unused import
* Update version of black used in CI
* Update new packages
* Update new packages
* Update package.py
Initial new stuff
* Update package.py
* Update package.py
* Update package.py
* fix targets
* non-llvm backends
* ooops
* fix style
* Somehow that was not caught?
Somehow that was not caught?
* style
* Last fix
make capitalization consistent with Halide not LLVM...
* py-cmake-format: new version, new variants
* Update var/spack/repos/builtin/packages/py-cmake-format/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cufflinks: new package version with 0.17.3
* Update var/spack/repos/builtin/packages/py-cufflinks/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Specs that did not contribute any files to an env view caused a problem
where zip(specs, files grouped by prefix) got "out of sync", causing the
wrong merge map to be passed to a package's `add_files_to_view`, which
specifically caused an issue where *sometimes* bin/python ended up as a
symlink instead of a copy.
One such example is kokkos + kokkos-nvcc-wrapper, as the latter package
only provides the file bin/nvcc_wrapper, which is also added to view by
kokkos, causing kokkos-nvcc-wrapper to contribute 0 files.
The test feels a bit contrived, but it captures the problem... pkg a is
added first and has 0 files to contribute, pkg b adds a single file, and
we check if pkg b receives a merge map (and a does not).
* pfunit: add v4.6.3
* pfunit: use CMakePackage methods to define arguments
* pfunit: deprecate v3.X, make a variant conditional
* pfunit: simplify setting up environment variables
Reading the docs it seems only v3
needs F90_VENDOR to be set
* pfunit: fix option names
The names set before were unused
* pfunit: shared libraries seem not to be supported
See https://github.com/Goddard-Fortran-Ecosystem/pFUnit/issues/308#issuecomment-874725759
* Add py-mlflow and its dependencies
* mlflow: fix syntax error in package.py
* py-mlflow: cleanup
Process review remarks, add missing dependencies, add skinny variant
* Apply suggestions from code review
* Fix flake8 issues
* More formatting fixes
* Fix py-waitress dependency version
* py-mlflow: platform-specific dependency
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Process review remarks
* Fix typo in dependency version
* py-shap: fix dependencies
* py-arrow: fix dependencies
* py-slicer: remove py-setuptools explicit version
* py-pyarrow: dataset variant and pass options through environment
It appears there are some issues when using `pip install` instead of
`python setup.py` - this setup_build_environment should fix that.
* py-pyarrow: review remark
* Decouple setup_build_environment from install_options
* py-pyarrow: style
* Bump licenses to 2023
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
`spack gc` removes build deps of explicitly installed specs, but somehow
if you take one of the specs that `spack gc` would remove, and feed it
to `spack uninstall /<hash>` by hash, it complains about all the
dependents that still rely on it.
This resolves the inconsistency by only following run/link type deps in
spack uninstall.
That way you can finally do `spack uninstall cmake` without having to
remove all packages built with cmake.
Default package requirements might contain
variants that are not defined in each package,
so we shouldn't verify them when emitting facts
for the ASP solver.
Account for group when enforcing requirements
packages:all : don't emit facts for requirement conditions
that can't apply to current spec
* Update package.py
Several libraries are need to be present at run time so that the code can be run in parallel.
I have added them as dependencies and to LD_LIBRARY_PATH. Orca comes as a binary so the libraries cannot be added as RPATH at compilation time.
Also, orca 5.0.3 was compiled against 4.1.1, not 4.1.2.
* fortls
* Update var/spack/repos/builtin/packages/py-fortls/package.py
* review
* Update var/spack/repos/builtin/packages/py-fortls/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fixes
* review
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new py-amplpy package
* [@spackbot] updating style on behalf of sm2939
* Update package.py
* Rename var/spack/repos/builtin/py-amplpy/package.py to var/spack/repos/builtin/packages/py-amplpy/package.py
* Edited file to change copyright year/dependencies and changed the directory of the file
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
#35098 added the correct extraction of toolset version for the MSVC
compiler. This updates the associated method in MSBuilder to retrieve
the (now correct) property.
Meme 4.5.0 has the first occurrence of the string
```
use XML::Simple
```
I found this by doing a binary search manually extracting tarballs until `grep` came up empty.
* new ampltools package
* [@spackbot] updating style on behalf of sm2939
* Update and rename var/spack/repos/builtin/py-ampltools/package.py to var/spack/repos/builtin/packages/py-ampltools/package.py
Edited file to change copyright year/dependencies and edited directory
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* Add Score-P 8.0 and Cube 4.7/4.8 packages.
* Score-P 8.0 requires 4.8, not 4.7, Cube packages
* Add maintainer
* Add CUDA and HIP variants. Add version checks for CUDA (Score-P 8 requires CUDA 7), ROCm (variant only valid as of Score-P 8), and MPI (Score-P 7 requires at least version 2.2 of the MPI standard).
* Deprecate everything pre-7.0.
* Fix HIP dependencies and enable CUDA and HIP variants for configure.
* Deprecate OTF2 pre-2.3 and Cube pre-4.6
* Add "fake" mpi compiler wrappers to msmpi: msmpi doesn't actually
provide wrappers, so this just assigns the wrappers to be whatever
compiler that a dependent is using. Packages referencing the
wrappers would otherwise break. This is assumed to be workable
because build scripts will need to assemble appropriate information
to pass to the compiler anyway
* Fix msmpi detection stanza ('executable' is not the correct name of
the property)
* Fix compiler pkg dereference
* add initial package.
* Update package.py
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* Hopefully this will be fine.
* Update package.py
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cvise: new package
* cvise: colordiff as optional dependency
* cvise: remove old versions and correctly name master version
* cvise: update license date
* cvise: use maintainers directive
* Remove @olupton as maintainer
After live discussion: it's been too long since he did anything with this package.
* add halide package.
* some style changes.
* small fix
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
add comment to requirements.txt
* Update package.py
Fix version order.
* Update package.py
style
* Update package.py
Removed unneeded vars.
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Fix some deps
* Update package.py
* Fix finding llvm cmake info
* Update package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR enables the successful execution of the spack binary cache
tutorial on Windows. It assumes gnupg and file are available (they
can be installed with choco).
* Fix handling of args with quotes in spack.bat
* `file` utility can be installed on Windows (e.g. with choco): update
error message accordingly
I don't know if this is new in version 7.0, but to build `info`, which is a required executable at the end of the recipe, it is necessary to have a terminal library, otherwise you get
```
[...]
checking for tgetent in -ltinfo... no
checking for tgetent in -lncurses... no
checking for tgetent in -lcurses... no
checking for tgetent in -ltermlib... no
checking for tgetent in -ltermcap... no
checking for tgetent in -lterminfo... no
configure: WARNING: info needs a terminal library, one of: tinfo ncurses curses termlib termcap terminfo
[...]
configure: WARNING: Could not find a terminal library among tinfo ncurses curses termlib termcap terminfo
configure: WARNING: The programs from `info' directory will not be built.
```
then compilation runs, `info` is not built and installation fails according to Spack because the required executable is missing.
* Support packages for using scitokens on OSG
The Open Science Grid (OSG) encourages scitokens to provide
certain services (e.g. writing to xrootd). Spack already
supports this through scitokens-cpp and xrootd +scitokens-cpp.
This adds py-htgettoken, a python utility to get a scitoken
from a vault through web authentication. To support htgettoken,
this also adds py-gssapi.
This also adds the OSG CA cert collection which is typically
at /etc/grid-security but pointed to in user installations by
the X509_CERTS_DIR variable.
This allows userspace through spack for functionality that
otherwise depends on installing the RPMs provided by OSG.
* fine, I'll fix style myself then
* fix maintainers
* py-gssapi: version before depends_on
* remove list_url
* add documentation on reason for git describe version numbers
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* better BEARER_TOKEN definition
* import os
* remove older version that don't build with setuptools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
At least with ZSH, prefix inspections containing `./bin` result in a
`$PREFIX/./bin` and result in strange `$PATH` handling.
I.e., `module load git` will prepend `/path/to/git/./bin`, `which git`
will find the right executable, but `git --version` will print the
system one. Normalize the relative path to avoid this behavior.
See also spack/spack#31867.
* changes to enable LLVM_ENABLE_RUNTIMES for libcxx and libcxxabi
* remove version update for 5.3.0 as it is done thru PR #33320 to enable
ci and reviews
* initial commit for rocm-5.4.0 release
* update the versions for more packages for 5.4.0 release
* update the gallium patch for mesa for libllvm-15 for ROCm-5.4.0 release
* update rocm-openmp-extras and rocwmma recipes for 5.4.0 release
* fix build error for rocfft for 5.4.0
* address review comments for rocfft for 5.4.0 change
* undo the removal of the older patch file
* bump up the version for hipfft for 5.4.0
* fix the failure after the merge with develop
* add recipes updates for 5.4.0 for migraphx.miopen-hip,miopen-opencl
* address the review comments on the mesa patch.update the rdc package for
5.4.0 release
* fix style errors
* acts: new versions 21.1.1, 22.0.1, 23.0.0
New versions:
- [major 23.0.0](https://github.com/acts-project/acts/compare/v22.0.0...v23.0.0):
- new option `ACTS_BUILD_PLUGIN_GEANT4` -> enabled with existing variant `geant4`
- new option `ACTS_BUILD_EXAMPLES_BINARIES`:
- it is my understanding that the binaries for examples are deprecated (in favor of python examples); warnings to this effect have been printed for a few versions, and now the building of binaries is disabled by default,
- rather than introducing a variant to enable deprecated behavior for only one or two versions, I propose that we just follow the default and keep this disabled.
- [bugfix 22.0.1](https://github.com/acts-project/acts/compare/v22.0.0...v22.0.1) (no build system changes)
- [bugfix 21.1.1](https://github.com/acts-project/acts/compare/v21.1.0...v21.1.1) (no build system changes)
* acts: correct 23.0.0 sha
Co-authored-by: Hadrien G. <knights_of_ni@gmx.com>
As of 2.4.113, the flag for man-pages is now a feature,
so true/false is now enabled/disabled. Other similarly
changed options are not used in the spack recipe (i.e.
experimental kms drivers).
* qt: new versions 6.4.0, 6.4.1
- New libpsl vendored dependency in qt-base.
- New embree and tinyexr dependency in qt-quick3d.
We need to figure out a better way to deal with these vendored
dependencies in src/3rdparty. Removing them was a way to make sure
they are not used unintentionally. Many of these dependencies cannot
be overridden with a QT_FEATURE_system_* flag and are included directly
in cpp files. Many change versions from release to release, so even if
they use system (ie spack managed) versions we need to support this in
the depends_on lines.
What we can rely on?
- src/3rdparty is where vendored stuff is stored
- not much else...
Possible ways to deal with this:
- Change vendor_deps_to_keep to dict with versions, eg
```
vendor_deps_to_keep = {
"xatlas": "@6:",
"embree": "@6.4:",
"tinyexr": "@6.4:",
}
```
- Similarly introduce system_deps_to_use:
```
system_deps_to_use = {
"assimp@5.2:": "@6:",
}
```
and derive depends_on and QT_FEATURE_system_* from this dict.
* qt-*: new version 6.4.2, invert vendored pkgs logic
* qt-base: fix vendor_deps_to_avoid typo
* qt-*: move lots into QtPackage base layer
* py-minkowskiengine: new package (sparse tensor autodiff by Nvidia)
This python package (with cuda support) provides torch support for sparse
tensors. The `pybind11` headers are not found without the patch to `setup.py`.
* [@spackbot] updating style on behalf of wdconinc
* py-minkowskiengine: depends_on numpy, pybind11 type=link; no patch
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
The fastqc script was using the system perl. This PR sets the script to
use the spack built/provided perl. This PR also removes the code that
adds the java path. That should be handled by module loading as far as I
know.
* Add HDF5 version 1.13.3.
* Remove maintainers no longer with The HDFGroup.
* Add version hdf5-vol-async@1.4
* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.
* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.
* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.
* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.
* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.
* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.
* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.
* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.
* Don't guard ParaView patch on HDF5 variant
ParaView always needsd HDF5 and ignores the variant.
* py-h5py: Newer versions of HDF5 introduce breaking API changes
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* Add trilinos-solvers variant to nalu-wind package.
This allows nalu-wind to be built against a trilinos installation
which doesn't have amesos2, belos, ifpack2, or muelu enabled, if
the nalu-wind user provides the spec 'nalu-wind@master~trilinos-solvers'
Support for these solver-packages remains on by default.
* Fixed a style issue reported by CI.
* Incorporate change in wording suggested from review comments.
... to clarify that at least one, or both, of hypre and/or
trilinos-solvers must be enabled. The error condition is if
both are disabled.
* That style checker is picky...
* It really did want a trailing comma...
* py-jinja2-cli: new package
* Update var/spack/repos/builtin/packages/py-jinja2-cli/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-docker@5:
* [@spackbot] updating style on behalf of spoutn1k
* Ignore `tls` variant
* Update var/spack/repos/builtin/packages/py-docker/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* `py-docker`: `py-paramiko` version fix
---------
Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The gfx906:xnack- and gfx908:xnack- targets were introduced in ROCm 4.1
and replaced gfx906 and gfx908 as default build targets, but the library
can still be built for gfx906 and gfx908 if requested.
* e4s: restore builds builds
* gitlab ci: allow UO to build protected binaries for signing
* use newer image; comment out failing builds
* gitlab-ci: Some tweaks for e4s power builds
- fix tags (no longer require generate jobs to run on aws)
- fix resource requests for generation jobs resource requests
- remove SPACK_SIGNING_KEY from protected power build jobs
- update UO signing key path
- change the CDash build group to reflect stack name
- retry pipeline generation jobs *always*
* correct double packages: section
* gitlab-ci:script: modernize
* remove new gnu make, not for ppc64le
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
* Added e4s-cl package
* Version order change
* Added e4s-cl dependencies
* Added python-sotools dependency
* [@spackbot] updating style on behalf of spoutn1k
* Add missing versions to py- packages
* Fix style
* [@spackbot] updating style on behalf of spoutn1k
* Update var/spack/repos/builtin/packages/e4s-cl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/e4s-cl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-python-sotools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add docker removing patch for e4s-cl
Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nexusforge: add with dependencies
* py-pyshacl, py-sseclient: more style
* py-hjson, py-nexus-sdk, py-nexusforge, py-puremagic: more style
* py-pyshacl: license update
* py-nexusforge, py-prettytable, py-pyshacl: review remarks
* py-nexusforge: make the variant mean something
Too hasty to commit...
* py-ipyparallel: add 8.4.1, which builds with py-hatchling
* py-ipyparallel: copyright and redundant py-setuptools dependency
* py-ipyparallel: py-packaging was dropped after 8.0.0
fixes#34879
This commit adds a new maintainer directive,
which by default extend the list of maintainers
for a given package.
The directive is backward compatible with the current
practice of having a "maintainers" list declared at
the class level.
Move the relocation of binary text in its own class
Drop threaded text replacement, since the current bottleneck
is decompression. It would be better to parallellize over packages,
instead of over files per package.
A small improvement with separate classes for text replacement is that we
now compile the regex in the constructor; previously it was compiled per
binary to be relocated.
The regex doesn't actually work because dollar signs and parentheses have to be
escaped. Also, compiling with OpenMPI requires defining the macro
`MPI2SUPPORT`.
This commit makes explicit the format version of the spec file
we are reading from.
Before there were different functions capable of reading some
part of the spec file at multiple format versions. The decision
was implicit, since checks were based on the structure of the
JSON without ever checking a format version number.
The refactor makes also explicit which spec file format is used
by which database and lockfile format, since the information is
stored in global mappings.
To ensure we don't change the hash of old specs, JSON representations
of specs have been added as data. A unit tests checks that we read
the correct hash in, and that the hash stays the same when we
re-serialize the spec using the most recent format version.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
```
File ".../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/site-packages/h5py/_hl/base.py", line 19, in <module>
from collections import (Mapping, MutableMapping, KeysView,
ImportError: cannot import name 'Mapping' from 'collections' (.../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/collections/__init__.py)
```
Fixed in https://github.com/h5py/h5py/pull/1069 which was first merged
in v2.9.
* py-flatten-dict: require poetry to build.
The sources seem to contain a bundled, auto-generated `setup.py`.
Building with `pip` insist on using Poetry as mentioned in
`pyproject.toml`, so require it as a build dependency.
* Update var/spack/repos/builtin/packages/py-flatten-dict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-flatten-dict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Currently we print "sha256 checksum failed for [file]. Expected X but
got Y".
This PR extends that message with file size and contents info:
"... but got Y. File size = 123456 bytes. Contents = b'abc...def'"
That way we can immediately see if the file was downloaded only
partially, or if we downloaded a text page instead of a binary, etc.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
py-scipy 1.6 and older come with pre cython-ized files that
use the _PyGen_Send symbol that was removed from python 3.10.0.161,
so do not build these old versions with python 3.10.1 and later
Parts of libgcrypt should not be optimized with -O1/2/3, so it's best to
let the build system do that; the build system cannot know the compiler
wrapper would inject optimization flags
When running unit-test the test/ci.py module is leaving
garbage (help.sh, test.sh files) in the current working
directory.
This commit changes the current working directory to a
temporary path before those files are created.
* freeimage: fails to compile with c++17, use c++14
Only `opencascade` when a (non-default) variant depends on `freeimage`, which seems to have gone unmaintained. There are c++17 standard violations [[1]]( https://en.cppreference.com/w/cpp/language/except_spec) in the code, so we can at most expect c++14. Since some compilers default to c++17 (gcc-12) we need to be explicit.
* freeimage: install directly in prefix
* freeimage: fix inverted patch
* environments: don't rewrite relative view path, expand path on cli ahead of time
Currently if you have a spack.yaml that specifies a view by relative
path, Spack expands it to an absolute path on `spack -e . install` and
persists that to disk.
This is rather annoying when you have a `spack.yaml` file inside a git
repo, cause you want to use relative paths to make it relocatable, but
you constantly have to undo the changes made to spack.yaml by Spack.
So, as an alternative:
1. Always stick to paths as they are provided in spack.yaml, never
replace them with a canonicalized version
2. Turn relative paths on the command line into absolute paths before
storing to spack.yaml. This way you can do `spack env create --dir
./env --with-view ./view` and both `./env` and `./view` are resolved
to the current working dir, as expected (not `./env/view`). This
corresponds to the old behavior of `spack env create`.
* create --with-view always takes a value
All packages with explicit Windows support can be found with
`spack list --tags=windows`.
This also removes the documentation which explicitly lists
supported packages on Windows (which is currently out of date and
is now unnecessary with the added tags).
Note that if a package does not appear in this list, it *may*
still build on Windows, but it likely means that no explicit
attempt has been made to support it.
* nextflow recipe: added latest stable version
* tower-cli recipe: added latest release
* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli
* recipes nf-tower-agent and nf-tower-cli: small fix
* nf-core-tools recipe: added most py- dependencies
* nf-core-tools: recipe without galaxy-tool-util (for testing)
* fixed typos in py-yacman recipe
* fixed typos in py-pytest-workflow recipe
* fixed typo in nf-core-tools recipe
* fixed typos in py-yacman recipe
* fixes in recipes for py-questionary and py-url-normalize
* fixes to py-yacman recipe
* style fixes to py- packages that are dependencies to nf-core-tools
* fix in py-requests-cache recipe
* added missing dep in py-requests-cache recipe
* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper
* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util
* nf-core-tools: new version with extra dependency
* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps
* nextflow and nf-core-tools packages: added my self as maintainer
* style fixes
* style fix for nf-core-tools recipe
* added license to py-logmuse recipe
* audit fixes
* style fix after audit fix
* py-galaxy-tool-util: added deps 1st bunch
* audit/style fixes, including adding missing dep package
* more audit/style fixes
* more more audit/style fixes
* moooore audit fixes
* py-galaxy-tool-util: dependencies 2nd chunk
* silly audit fix
* py-galaxy-util deps: 3rd bunch - first 20 done
* fixes
* style fix
* py-galaxy-tool-util: 4th bunch of deps
* stashing dep recipe backbones for py-galaxy-tool-util
* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util
* nf-core-tools: adding also py-galaxy-util, as wheel
* fix
* nextflow: added latest bugfix version
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* nf-core-tools pr: 1st bunch of review edits
* nf-core-tools: 2nd bunch of review edits
* adding back tower-agent and tower-cli as deprecated
* nf-core-tools: 3rd bunch of review edits
* small style fix
* prepping py-galaxy-tool-util for further work
* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar
* audit fixes
* updates to py-galaxy-tool-util and its deps, still 2 to work on
* one style fix
* updated recipe for py-galaxy-util
* updated recipe for py-pulsar-galaxy-lib
* typo fix
* shasum fixes
* updated py-sqlalchemy from develop
* added newest versions (today) for nf-tower-agent and nf-tower-cli
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adding 2nd bunch of nf-core deps from update/nextflow-tools
* adding 3rd bunch of nf-core deps from update/nextflow-tools
* 4th chunk of nf-core deps from update/nextflow-tools
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pebble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gunicorn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-parsley/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-gxformat2: added comment
* py-lagom: now using github tarballs
* fix for py-lagom
* adding missing deps to py-fastapi-utils
* another fix to py-lagom
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-lagom/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-supervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fixes from PR review
* adding missing deps, from PR review
* py-galaxy2cwl from github tarball, as per PR review
* fix to py-tuswsgi, as per PR review
* nf-tools: edits from PR review
* adding 3x more galaxy deps
* fix
* fixing circular dep of py-poetry-plugin-export with py-poetry
* added newest nf-core-tools version
* Update var/spack/repos/builtin/packages/py-galaxy-util/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix in py-poetry-plugin-export
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`.
We no longer set `CPATH` and other destructive environment variables (like
`LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python.
Also, the way `python` sets `CPATH` causes issues. Because it does a header search to
find directories containing headers, if you bootstrap `mypy` or other style tools on a
fresh Ubuntu image with *no* python devel headers installed, you'll get an error like
this when trying to load the thing you just installed:
```console
[root@980de539843d /]# spack -b load py-mypy
==> Error: Unable to locate python headers in any of these locations:
/usr/include/python3.6m
/usr/include/3.6
/usr/Headers
```
The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work,
so we're failing unnecessarily here.
- [x] remove `setup_run_environment()` from `python/package.py`
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes
more sense to call the flag `--make-prefix` and alias the old flag
`--make-target-prefix` to it.
1. add variant cray-static, older crays build hpcprof-mpi static,
newer ones build dynamic.
2. move URL patches from github to gitlab.
3. add workaround for a bug where a file is mistakenly overwritten.
4. add conflict for hpcprof-mpi at 2022.10.01.
* [@spackbot] updating style on behalf of mwkrentel
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
Normally when using external packages in concretization, Spack ignores
all dependencies of the external. #33777 updated this logic to attach
a Python Spec to external Python extensions (most py-* packages), but
as implemented there were a couple issues:
* this did not account for concretization groups and could generate
multiple different python specs for a single DAG
* in some cases this created a fake Python spec with insufficient
details to be usable (concretization/installation of the
extension would fail)
This PR addresses both of these issues:
* For environment specs that are concretized together, external python
extensions in those specs will all be assigned the same Python spec
* If Spack needs to "invent" a Python spec, then it will have all the
needed details (e.g. compiler/architecture)
* npm: Add latest version, update build
The `npm` package had gotten a bit long in the tooth and only suported the last version
for which running `configure` / `make` / `make install` actually worked.
- [x] Update the package to support npm@9, in which `npm install .` works properly and
installation is easier.
- [x] Update the package so that `npm@6:8` also install successfullly. The incantation
that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node
bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install`
or `npm pack` will fail when run straight from the install directory. So now we just
manually copies things over.
This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least
for me).
udpates the `npm` build to support versions 6-9 and fixes the install for all of
them on macos.
* update for review
With the new variable [prefix/]SPACK_PACKAGE_IDS you can conveniently execute
things after each successful install.
For example push just-built packages to a buildcache
```
SPACK ?= spack
export SPACK_COLOR = always
MAKEFLAGS += -Orecurse
MY_BUILDCACHE := $(CURDIR)/cache
.PHONY: all clean
all: push
ifeq (,$(filter clean,$(MAKECMDGOALS)))
include env.mk
endif
# the relevant part: push has *all* example/push/<pkg identifier> as prereqs
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
$(SPACK) -e . buildcache update-index --directory $(MY_BUILDCACHE)
$(info Pushed everything, yay!)
# and each example/push/<pkg identifier> has the install target as prereq,
# and the body can use target local $(HASH) and $(SPEC) variables to do
# things, such as pushing to a build cache
example/push/%: example/install/%
@mkdir -p $(dir $@)
$(SPACK) -e . buildcache create --allow-root --only=package --unsigned --directory $(MY_BUILDCACHE) /$(HASH) # push $(SPEC)
@touch $@
spack.lock: spack.yaml
$(SPACK) -e . concretize -f
env.mk: spack.lock
$(SPACK) -e . env depfile -o $@ --make-target-prefix example
clean:
rm -rf spack.lock env.mk example/
``
* [armpl-gcc] Make pkg-config files available
ARMpl pkgconfig files are located in a non-default location and do not have the
.pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
In the past we checked remote binary mirrors for existence of a spec
before attempting to download it. That changed to only checking local
copies of index.jsons (if available) to prioritize certain mirrors where
we expect to find a tarball. That was faster for CI since fetching
index.json and loading it just to order mirrors takes more time than
just attempting to fetch tarballs -- and also if we have a direct hit
there's no point to look at other mirrors.
Long story short: the info message only makes sense in the old version
of Spack, so it's better to remove it.
* py-sphinx-immaterial: new package
This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on
the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear
and readable. We *might* consider switching to it for Spack's docs.
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add note about node.js requirements
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Forward lookup of "test_log_file" and "test_failures"
refers #34531closes#34487fixes#34440
* Add unit test
* py-libensemble: fix tests
* Support stand-alone tests with cached files as install-time tests
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Ensure `spack mirror add <name> <url/path>` without further arguments translates to `<name>: <url>` key value pairs in mirrors.yaml. If --s3-* flags are provided, only store the provided ones.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs.
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* Add new file for MVAPICH 3.0a release
Creating this as a new package since it requires some new configuration
options and because we are moving to the name "MVAPICH" and droping the
2 (following a similar move by MPICH).
Co-authored-by: Nat Shineman <shineman.5@osu.edu>
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
* OpenCV: checksum for 4.5.5, make contrib optional
* [@spackbot] updating style on behalf of iarspider
* Add conflicts for contrib modules
* Fix typo
* Implement changes from review
* Update var/spack/repos/builtin/packages/opencv/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)"
This reverts commit 891a63cae6.
* fix to py-python-multipart, as per PR review
* py-macs2: add version 2.2.7.1 and support python@3.10:
The tarball from PyPi includes the Cythonized C files. The tarball from
github does not. Remove the Cythonized C files from the source so that
they are rebuilt with the Spack Python/Cython combination. This is
necessary for python-3.10 but make sense for other combinations as well.
* Edits based on review
- set python version constraint on version 2.2.4
- removed all python-2 versions and related constraints.
* Add package file for xtb and py-xtb
* Retain maintainers from PythonPackage
* Update package files
- use extends("python") instead of tampering with PYTHONPATH
- use PyPI for downloading sdist of py-xtb
- add simple-dftd3 0.7.0
- add dftd4 3.5.0
- remove --wrap-mode=nodownload from toml-f
* Remove logic for download URL
With this change we get the invariant that `mirror.fetch_url` and
`mirror.push_url` return valid URLs, even when the backing config
file is actually using (relative) paths with potentially `$spack` and
`$env` like variables.
Secondly it avoids expanding mirror path / URLs too early,
so if I say `spack mirror add name ./path`, it stays `./path` in my
config. When it's retrieved through MirrorCollection() we
exand it to say `file://<env dir>/path` if `./path` was set in an
environment scope.
Thirdly, the interface is simplified for the relevant buildcache
commands, so it's more like `git push`:
```
spack buildcache create [mirror] [specs...]
```
`mirror` is either a mirror name, a path, or a URL.
Resolving the relevant mirror goes as follows:
- If it contains either / or \ it is used as an anonymous mirror with
path or url.
- Otherwise, it's interpreted as a named mirror, which must exist.
This helps to guard against typos, e.g. typing `my-mirror` when there
is no such named mirror now errors with:
```
$ spack -e . buildcache create my-mirror
==> Error: no mirror named "my-mirror". Did you mean ./my-mirror?
```
instead of creating a directory in the current working directory. I
think this is reasonable, as the alternative (requiring that a local dir
exists) feels a bit pendantic in the general case -- spack is happy to
create the build cache dir when needed, saving a `mkdir`.
The old (now deprecated) format will still be available in Spack 0.20,
but is scheduled to be removed in 0.21:
```
spack buildcache create (--directory | --mirror-url | --mirror-name) [specs...]
```
This PR also touches `tmp_scope` in tests, because it didn't really
work for me, since spack fixes the possible --scope values once and
for all across tests, so tests failed when run out of order.
Packages that use docbook-xml may specify a specific entity version.
When this is specified as a version constraint in the package recipe it
will cause problems when using `unify = True` in a Spack environment, as
there could be multiple versions of docbook-xml in the spec. In
practice, any entity version should work with any other version and
everything should work with the latest version. This PR maps all Spack
docbook-xml entity versions to the docbook-xml version in the spec.
Ideally, the version in the spec would be the latest version. With this
PR, even if a package specifies an older entity version, it will map
to the entity version (latest) in the spec. This means that there can be one
docbook-xml version in a Spack environment spec and packages requesting
older entity versions will still work.
To help facilitate this, docbook-xml version constraints for packages
that have them have been removed. Those packages are dbus and gtk-doc.
What's in AOCL 4.0:
1. amdblis
LPGEMM variants with post-ops support
AMD "Zen4" support for BLIS
2. amdlibflame
Upgrade to LAPACK 3.10.1 specification
Improvements in a few more variants of SVD and Eigen Value routines
Multithread support enabled for selected APIs
3. amdfftw
AVX-512 enablement of DFT kernels
AVX-512 optimization of copy and transpose routines
5. amdlibm
Black & Scholes support (logf, expf, erff, both scalar and vector)
AVX-512 variants of vector functions
6. aocl-sparse
New Iterative Solver APIs
AVX-512 support for SPMV API
7. amdscalapack
Upgrade to Netlib ScaLAPACK 2.2.0
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Sometimes I just want to know how many packages of a certain type there are.
- [x] add `--count` option to `spack list` that output the number of packages that
*would* be listed.
```console
> spack list --count
6864
> spack list --count py-
2040
> spack list --count r-
1162
```
* Add packages
* Style
* Respond to comments
* Change conflct dep type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* paraview: add `rocm` variant
This conflicts with CUDA and requires at least ParaView 5.11.0. More
dependencies are also needed.
* E4S: Add ParaView for ROCm and CUDA stacks
* DAV SDK: Update ParaView version and GPU variants
* Verify using hipcc vs amdclang++ for newer hip
Co-authored-by: Ben Boeckel <ben.boeckel@kitware.com>
* adding 1st version of py-strawberryfields
* py-strawberryfields: minor edit
* added backbone for 4x new SF dependencies
* edits to SF and its 4x new deps
* added all deps for SF
* added one version to py-lark-parser
* py-quantum-xir with tarball from github
* Update var/spack/repos/builtin/packages/py-strawberryfields/package.py
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* updated version for py-quantum-xir : pypy fixed
* py-pennylane: added pythonpackage.maintainers, too
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Currently, all of the replacements in `spack.util.path.replacements()` get evaluated for
each replacement. This makes it easy to get bootstrap issues, because config is used
very early on in Spack.
Right now, if I run `test_autotools_gnuconfig_replacement_no_gnuconfig` on my M1 mac, I
get the circular reference error below. This fixes the issue by making all of the path
replacements lazy lambdas.
As a bonus, this cleans up the way we do substitution for `$env` -- it's consistent with
other substitutions now.
- [x] make all path `replacements()` lazy
- [x] clean up handling of `$env`
```console
> spack unit-test -k test_autotools_gnuconfig_replacement_no_gnuconfig
...
==> [2022-12-31-15:44:21.771459] Error: AttributeError:
The 'autotools-config-replacement' package cannot find an attribute while trying to build from sources. This might be due to a change in Spack's package format to support multiple build-systems for a single package. You can fix this by updating the build recipe, and you can also report the issue as a bug. More information at https://spack.readthedocs.io/en/latest/packaging_guide.html#installation-procedure
/Users/gamblin2/src/spack/lib/spack/spack/package_base.py:1332, in prefix:
1330 @property
1331 def prefix(self):
>> 1332 """Get the prefix into which this package should be installed."""
1333 return self.spec.prefix
Traceback (most recent call last):
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 1030, in _setup_pkg_and_run
kwargs["env_modifications"] = setup_package(
^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 757, in setup_package
set_module_variables_for_package(pkg)
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 596, in set_module_variables_for_package
m.std_cmake_args = spack.build_systems.cmake.CMakeBuilder.std_args(pkg)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/build_systems/cmake.py", line 241, in std_args
define("CMAKE_INSTALL_PREFIX", pkg.prefix),
^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/package_base.py", line 1333, in prefix
return self.spec.prefix
^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1710, in prefix
self.prefix = spack.store.layout.path_for_spec(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 336, in path_for_spec
path = self.relative_path_for_spec(spec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 106, in relative_path_for_spec
projection = spack.projections.get_projection(self.projections, spec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/projections.py", line 13, in get_projection
if spec.satisfies(spec_like, strict=True):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 3642, in satisfies
if not self.virtual and other.virtual:
^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1622, in virtual
return spack.repo.path.is_virtual(self.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 890, in is_virtual
return have_name and pkg_name in self.provider_index
^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 770, in provider_index
self._provider_index.merge(repo.provider_index)
^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 1096, in provider_index
return self.index["providers"]
~~~~~~~~~~^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 592, in __getitem__
self._build_all_indexes()
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 607, in _build_all_indexes
self.indexes[name] = self._build_index(name, indexer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 616, in _build_index
index_mtime = self.cache.mtime(cache_filename)
^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 826, in __getattr__
return getattr(self.instance, name)
^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 825, in __getattr__
raise AttributeError()
AttributeError
```
* Added support for libfabric to find an external installation and
identify variants supported.
* Change the fabrics definition to only include CXI when on a cray
system with a libfabric-based slingshot network.
* Added a conflict when trying to build the CXI fabric value since it is
only available as closed source at this time.
#33128 Introduces a dependency on re2c into the Ninja build recipe.
This is problematic on Windows as we use CMake to build re2c, and
Ninja to drive the CMake build. This PR resolves this issue by
adding a variant to toggle the use of re2c with ninja.
Thanks for taking the time to report this build failure. To proceed with the report please:
1. Title the issue `Installation issue: <name-of-the-package>`.
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
- type:textarea
id:reproduce
@@ -29,7 +29,9 @@ body:
description:|
Please post the error message from spack inside the `<details>` tag below:
value:|
<details><summary>Error message</summary><pre>
<details><summary>Error message</summary>
<pre>
...
</pre></details>
validations:
@@ -53,7 +55,7 @@ body:
Please upload the following files:
* **`spack-build-out.txt`**
* **`spack-build-env.txt`**
They should be present in the stage directory of the failing build. Also upload any `config.log` or similar file if one exists.
description:Suggest adding a feature that is not yet in Spack
labels:[feature]
body:
@@ -29,13 +29,11 @@ body:
attributes:
label:General information
options:
- label:I have run `spack --version` and reported the version of Spack
required:true
- label:I have searched the issues of this repo and believe this is not a duplicate
required:true
- type:markdown
attributes:
value:|
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on [our Slack](https://slack.spack.io/) first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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)
@@ -942,7 +942,7 @@ first ``libelf`` above, you would run:
$ spack load /qmm4kso
To see which packages that you have loaded to your enviornment you would
To see which packages that you have loaded to your environment you would
use ``spack find --loaded``.
..code-block::console
@@ -1103,16 +1103,31 @@ Below are more details about the specifiers that you can add to specs.
Version specifier
^^^^^^^^^^^^^^^^^
A version specifier comes somewhere after a package name and starts
with ``@``. It can be a single version, e.g. ``@1.0``, ``@3``, or
``@1.2a7``. Or, it can be a range of versions, such as ``@1.0:1.5``
(all versions between ``1.0`` and ``1.5``, inclusive). Version ranges
can be open, e.g. ``:3`` means any version up to and including ``3``.
This would include ``3.4`` and ``3.4.2``. ``4.2:`` means any version
above and including ``4.2``. Finally, a version specifier can be a
set of arbitrary versions, such as ``@1.0,1.5,1.7`` (``1.0``, ``1.5``,
or ``1.7``). When you supply such a specifier to ``spack install``,
it constrains the set of versions that Spack will install.
A version specifier ``pkg@<specifier>`` comes after a package name
and starts with ``@``. It can be something abstract that matches
multiple known versions, or a specific version. During concretization,
Spack will pick the optimal version within the spec's constraints
according to policies set for the particular Spack installation.
The version specifier can be *a specific version*, such as ``@=1.0.0`` or
``@=1.2a7``. Or, it can be *a range of versions*, such as ``@1.0:1.5``.
Version ranges are inclusive, so this example includes both ``1.0``
and any ``1.5.x`` version. Version ranges can be unbounded, e.g. ``@:3``
means any version up to and including ``3``. This would include ``3.4``
and ``3.4.2``. Similarly, ``@4.2:`` means any version above and including
``4.2``. As a short-hand, ``@3`` is equivalent to the range ``@3:3`` and
includes any version with major version ``3``.
Notice that you can distinguish between the specific version ``@=3.2`` and
the range ``@3.2``. This is useful for packages that follow a versioning
scheme that omits the zero patch version number: ``3.2``, ``3.2.1``,
``3.2.2``, etc. In general it is preferable to use the range syntax
``@3.2``, since ranges also match versions with one-off suffixes, such as
``3.2-custom``.
A version specifier can also be a list of ranges and specific versions,
separated by commas. For example, ``@1.0:1.5,=1.7.1`` matches any version
in the range ``1.0:1.5`` and the specific version ``1.7.1``.
For packages with a ``git`` attribute, ``git`` references
may be specified instead of a numerical version i.e. branches, tags
@@ -1121,36 +1136,35 @@ reference provided. Acceptable syntaxes for this are:
..code-block::sh
# branches and tags
foo@git.develop # use the develop branch
foo@git.0.19 # use the 0.19 tag
# commit hashes
foo@abcdef1234abcdef1234abcdef1234abcdef1234 # 40 character hashes are automatically treated as git commits
foo@git.abcdef1234abcdef1234abcdef1234abcdef1234
Spack versions from git reference either have an associated version supplied by the user,
or infer a relationship to known versions from the structure of the git repository. If an
associated version is supplied by the user, Spack treats the git version as equivalent to that
version for all version comparisons in the package logic (e.g. ``depends_on('foo', when='@1.5')``).
# branches and tags
foo@git.develop # use the develop branch
foo@git.0.19 # use the 0.19 tag
The associated version can be assigned with ``[git ref]=[version]`` syntax, with the caveat that the specified version is known to Spack from either the package definition, or in the configuration preferences (i.e. ``packages.yaml``).
Spack always needs to associate a Spack version with the git reference,
which is used for version comparison. This Spack version is heuristically
taken from the closest valid git tag among ancestors of the git ref.
Once a Spack version is associated with a git ref, it always printed with
the git ref. For example, if the commit ``@git.abcdefg`` is tagged
``0.19``, then the spec will be shown as ``@git.abcdefg=0.19``.
If the git ref is not exactly a tag, then the distance to the nearest tag
is also part of the resolved version. ``@git.abcdefg=0.19.git.8`` means
that the commit is 8 commits away from the ``0.19`` tag.
In cases where Spack cannot resolve a sensible version from a git ref,
users can specify the Spack version to use for the git ref. This is done
by appending ``=`` and the Spack version to the git ref. For example:
..code-block::sh
foo@git.my_ref=3.2 # use the my_ref tag or branch, but treat it as version 3.2 for version comparisons
foo@git.abcdef1234abcdef1234abcdef1234abcdef1234=develop # use the given commit, but treat it as develop for version comparisons
If an associated version is not supplied then the tags in the git repo are used to determine
the most recent previous version known to Spack. Details about how versions are compared
and how Spack determines if one version is less than another are discussed in the developer guide.
If the version spec is not provided, then Spack will choose one
according to policies set for the particular spack installation. If
the spec is ambiguous, i.e. it could match multiple versions, Spack
will choose a version within the spec's constraints according to
policies set for the particular Spack installation.
Details about how versions are compared and how Spack determines if
one version is less than another are discussed in the developer guide.
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