* Nalu: updating Trilinos recipe a bit
Basic changes to build/install nalu properly using Spack.
Some more changes would be nice for instance adding an
option to build against Trilinos master or develop. Adding
a dependency on googletest to avoid the annoying build
failures in the unit-tests.
* Nalu: adding release 1.6.0
Nalu v1.6.0 can build cleanly against Trilinos 14.0.0 with the
proposed changes. The only other combo is master / master but
than one is "floating" as these branch evolve over time. When a
new Nalu comes out we might want to add another fixed version to
keep this recipes up to date!
the autotools build system does something funky which causes a link line
where gccs default link dirs are explicitly added and end up before the
-L from spack's libunwind, so that ultimately it links against system
libunwind.
the cmake build system does better.
* upgrade new versions
* style fix
* update jaxlib deps (not cuda and bazel yet)
* update jaxlib cuda versions
* update jaxlib cuda versions
* update jaxlib cuda versions
* chore: style fix
* Update package.py
* Update package.py
* fix: typo
* docs: add source for cuda version
* py-jaxlib 0.4.14 also doesn't build on ppc64le
* Add 0.4.26
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ParaView: Update version 5.12.0
Add 5.12.0 release
Update default to 5.12.0
* Add patch for building ParaView 5.12 with kits
* Drop VTKm from neoverse
* For avx build, the start address of values_ buffer in KernelParameters
is not a correct as it is computed based on 16-byte alignment.
* Style check error fix
* updating package.py for py-celery, py-kombu, py-amq
* added more py-kombu package versions
* fix copyrights and stype on py-kombu/package.py
* removed extra spaces
* added py-billiard 4.2.0 and added back the license('BSD-3-Clause')
* removed extra spaces in py-celery/package.py
* fixed py-amqp 2.4.0 sha; fixed py-celery's dependency of py-click (when version restrictions)
* more clean up on specifying version bounds
* Relax compiler and target mismatches
The mismatch occurs on an edge. Previously it was assigned
the parent priority, now it is assigned the child priority.
This should make reuse from buildcaches or store more likely,
since most mismatches will be counted with "reused" priority.
* Optimize version badness for runtimes at very low priority
We don't want to e.g. switch other attributes because we
cannot reuse an old installed runtime.
* Optimize runtime attributes at very low priority
This is such that the version of the runtime would
not influence whether we should reuse a spec.
Compiler mismatches are considered for runtimes,
to avoid situations where compiling foo%gcc@9
brings in gcc-runtime%gcc@13 if gcc@13 is among
the available compilers
* Exclude specs without runtimes from reuse
This should ensure that we do not reuse specs that
could be broken, as they expect the compiler to be
installed in a specific place.
The installer runs `get_dependent_ids`, which follows edges outside the
subdag that's being installed, so it returns a superset of the actual
dependents.
That's generally fine, except that it calls `s.package` on every
dependent, which triggers a package class to be instantiated, which is a
lot of work.
Instead, compute the package id from the spec, since that's all that's
used anyways and does not trigger *lots* of slow and redundant
instantiations of package objects.
If ONEAPI_ROOT is not set as an environment variable, the current approach will raise an error.
Instead we can compute the OneAPI_ROOT from the compiler paths like we do with vcvarsall.
The installation mechanism used on Linux to install py-pip (using pip
from the downloaded wheel to install the wheel) does not work on Windows.
This updates the installation of py-pip on Windows to download and
use a zipapp of a specific pip version in order to install the wheel
pip version that is requested.
`dpcpp` is deprecated by intel and has been superseded by `oneapi` compilers for a very long time.
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* SEACAS, EXODUSII: New version; deprecate older versions; better variant descriptions
* [@spackbot] updating style on behalf of gsjaardema
* Fix long lines reported by flake8
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Add release 2.8.0
* Changing C compiler to hipcc
* Final release version
* Adding new cmake definition for rocm support
* Enabling rocm version support
* Update sha256
* Updating website URL
* Removing unnecessary C compiler spec
* Adding rocm-core dependency
* fixing rocm-core version
* fixing rocm-core version
* fixing style
* bugfix
* Add systemd
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* gobject-introspection: Correct glib versions
- The meson.build requirement that the glib version
is >= the gobject-introspective version is not in place
until v1.76.1.
- Prior to that, the requirement was glib >= 2.58.0.
- Bug introduced in acbf0d99c4, PR #42222.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* util-linux: add v2.39.3
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-natsort: add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: default systemd support to true
- Make the dependency sticky to force a failure
if systemd compilation fails, or force
the user to disable the option.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: Add initial multi-architecture support
- Restrict arch conflicts to 3.0.1
- Disable cpuid at configure time on non-x86_64 platforms.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* geopm-service: update docstrings
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-geopmdpy
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-runtime recipe
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
This PR allows the user to specify a path to a custom cert file (or directory) in
Spack's config:
```yaml
# This is where custom certs for proxy/firewall are stored.
# It can be a path or environment variable. To match ssl env configuration
# the default is the environment variable SSL_CERT_FILE
ssl_certs: $SSL_CERT_FILE
```
`config:ssl_certs` can be a path to a file or a directory, or it can be and environment
variable that resolves to one of those. When it posts to something valid, Spack will
update the ssl context to include custom certs, and fetching via `urllib` and `curl`
will trust the provided certs.
This should resolve many issues with fetching behind corporate firewalls.
---------
Co-authored-by: psakievich <psakievich@users.noreply.github.com>
Co-authored-by: Alec Scott <alec@bcs.sh>
After #41373, where we stopped considering the source directory to be the stage for develop builds,
we resumed *deleting* the stage even after a successful build.
We don't want this for develop builds because developers need to iterate; we should keep the artifacts
unless they explicitly run `spack clean`.
Now:
- [x] Build artifacts for develop packages are not removed after a successful install
- [x] They are also not removed before an install starts, i.e. develop packages always
reuse prior artifacts, if available.
- [x] They can be deleted in any other context, e.g. by running `spack clean --stage`
Prior FleCSI releases relied on commits on the control-replication branch (cr)
of Legion. That branch has now been merged into master and is part of the
24.03.0 Legion release.
* (py-)onnx: new version 1.14.{0,1}, 1.15.0
Notes on `onnx`:
- The C++ standard was changed to 14 in 1.15, so no more filter_file is needed. (The C++ standard has since changed to 17 in master.)
Notes on `py-onnx`:
- `py-pybind11` was an unlisted requirement in CMakeLists.txt since 1.3 or so (before earliest spack package).
* py-onnx: depends_on pybind11 with type link, not run
* py-onnx: depends_on py-setuptools@64:
Users requested an option to filter between local/upstream results in `spack find` output.
```
# default behavior, same as without --install-tree argument
$ spack find --install-tree all
# show only local results
$ spack find --install-tree local
# show results from all upstreams
$ spack find --install-tree upstream
# show results from a particular upstream or the local install_tree
$ spack find --install-tree /path/to/install/tree/root
```
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
* sundials: add new version
* note previous default
* update when clause for removed options
---------
Co-authored-by: David J. Gardner <gardner48@llnl.gov>
* SEACAS: Update package.py to handle new SEACAS project name
The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.
The refactor also changes several:
"-DSome_CMAKE_Option:BOOL=ON"
to
define("Some_CMAKE_Option", True)
* exodusii -- refactor and bring up-to-date
* Add missed patch file
* [@spackbot] updating style on behalf of gsjaardema
* Apply seacas windows patch here also.
* Update url so old checksums valid; redo new checksums
---------
Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>
* Initial commit to bump rocprofiler-dev to 6.0 and add aqlprofile recipe
* bump to 6.0.2 and extracting binaries from deb pkg
* fixes for hpctoolkit build errors
* add yum and zyp aqlprofile packages
* fix style issues
* Allow compilers to function across compatible OS's
* Add documentation in the default yaml
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* py-libsonata: new package starting at 0.1.25
* align spack version with the git branch
* Fix min required versions / use spack packages instead of submodules
* Create devcontainer.json
* Ensure codespace can be setup for current branch
* fix: find compilers in site scope
* fix: use cloud_pipelines ubuntu20.04 image
* fix: spack config --scope site add
* fix: use develop, not develop-root mirror
This adds a dependency on pkg-config which in turn builds pkg-config
on pipelines using %onapi/%cce: update the pkg-config build to disable
specific warnings-as-errors from these compilers.
Co-authored-by: Reid Priedhorsky <1682574+reidpr@users.noreply.github.com>
* Add macos-14 as a runner (Apple M1)
* Mark a test xfail
We need to check later if this test needs modifications
on Apple Silicon chips.
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Co-authored-by: alalazo <alalazo@users.noreply.github.com>
* buildcache sync: manifest-glob with arbitrary destination
The current implementation of the --manifest-glob is a bit restrictive
requiring the destination to be known by the generation stage of CI.
This allows specifying an arbitrary destination mirror URL.
* Add unit test for buildcache sync with manifest
* Fix test and arguments for manifest-glob with override destination
* Add testing path for unused mirror argument
* Remove a few compilers from static test data
These compilers were used only in a bunch of tests, so
they are added only there.
* Remove clang@3.3 from unit test configuration
* Parametrize compilers.yaml
* Remove specially named gcc from static data
The compilers are used in two tests
* Remove apple-clang and macOS compilers from static data
The compiler was used only in multimethod tests
* Remove clang@3.5 (compiler seems to be unused)
* Remove gcc@4.4.0 (compiler seems to be unused)
* Exclude x86_64 tests on other architectures
* Mark two tests as for clingo only
* Update version syntax in compilers.yaml
* Parametrize tcl tests on architectures
* Parametrize lmod tests on architectures
* Substitute gcc@4.5.0 with gcc@4.8.0 so it can be used on aarch64
* Fix a few issues with aarch64 and unit-tests
It's now possible to add config on the command line with `spack -c <CONFIG_VARS> ...`, but the new `command_line` scope isn't reflected in the help output for `--scope`:
```bash
> spack help config
...
--scope {defaults,system,site,user}[/PLATFORM] or env:ENVIRONMENT
configuration scope to read/modify
...
```
This PR adds:
- A new runtime for `%oneapi` compilers, called `intel-oneapi-runtime`
- Information to both `gcc-runtime` and `intel-oneapi-runtime`, to ensure
that we don't mix compilers using different soname for either `libgfortran`
or `libifcore`
To do so, the following internal mechanisms have been implemented:
- Possibility to inject virtual dependencies from the `runtime_constraints`
callback on packages
Information has been added to `gcc-runtime` to provide the correct soname
under different conditions on its `%gcc`.
Rules injected into the solver looks like:
```prolog
% Add a dependency on 'gfortran@5' for nodes compiled with gcc@=13.2.0 and using the 'fortran' language
attr("dependency_holds", node(ID, Package), "gfortran", "link") :-
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("virtual_node", node(RuntimeID, "gfortran")) :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
attr("node_version_satisfies", node(RuntimeID, "gfortran"), "5") :-
attr("depends_on", node(ID, Package), ProviderNode, "link"),
provider(ProviderNode, node(RuntimeID, "gfortran")),
attr("node", node(ID, Package)),
attr("node_compiler", node(ID, Package), "gcc"),
attr("node_compiler_version", node(ID, Package), "gcc", "13.2.0"),
not external(node(ID, Package)),
not runtime(Package),
attr("language", node(ID, Package), "fortran").
```
The default url couldn't be the one with v0.0.0-aws since spack was
replacing v0.0.0-aws with v<version_number> for example, deleting the
-aws suffix. I used the url_for_version method to specify this suffix.
This adds support for prereleases. Alpha, beta and release candidate
suffixes are ordered in the intuitive way:
```
1.2.0-alpha < 1.2.0-alpha.1 < 1.2.0-beta.2 < 1.2.0-rc.3 < 1.2.0 < 1.2.0-xyz
```
Alpha, beta and rc prereleases are defined as follows: split the version
string into components like before (on delimiters and string boundaries).
If there's a string component `alpha`, `beta` or `rc` followed by an optional
numeric component at the end, then the version is prerelease.
So `1.2.0-alpha.1 == 1.2.0alpha1 == 1.2.0.alpha1` are all the same, as usual.
The strings `alpha`, `beta` and `rc` are chosen because they match semver,
they are sufficiently long to be unambiguous, and and all contain at least
one non-hex character so distinguish them from shasum/digest type suffixes.
The comparison key is now stored as `(release_tuple, prerelease_tuple)`, so in
the above example:
```
((1,2,0),(ALPHA,)) < ((1,2,0),(ALPHA,1)) < ((1,2,0),(BETA,2)) < ((1,2,0),(RC,3)) < ((1,2,0),(FINAL,)) < ((1,2,0,"xyz"), (FINAL,))
```
The version ranges `@1.2.0:` and `@:1.1` do *not* include prereleases of
`1.2.0`.
So for packaging, if the `1.2.0alpha` and `1.2.0` versions have the same constraints on
dependencies, it's best to write
```python
depends_on("x@1:", when="@1.2.0alpha:")
```
However, `@1.2:` does include `1.2.0alpha`. This is because Spack considers
`1.2 < 1.2.0` as distinct versions, with `1.2 < 1.2.0alpha < 1.2.0` as a consequence.
Alternatively, the above `depends_on` statement can thus be written
```python
depends_on("x@1:", when="@1.2:")
```
which can be useful too. A short-hand to include prereleases, but you
can still be explicit to exclude the prerelease by specifying the patch version
number.
### Concretization
Concretization uses a different version order than `<`. Prereleases are ordered
between final releases and develop versions. That way, users should not
have to set `preferred=True` on every final release if they add just one
prerelease to a package. The concretizer is unlikely to pick a prerelease when
final releases are possible.
### Limitations
1. You can't express a range that includes all alpha release but excludes all beta
releases. Only alternative is good old repeated nines: `@:1.2.0alpha99`.
2. The Python ecosystem defaults to `a`, `b`, `rc` strings, so translation of Python versions to
Spack versions requires expansion to `alpha`, `beta`, `rc`. It's mildly annoying, because
this means we may need to compute URLs differently (not done in this commit).
### Hash
Care is taken not to break hashes of versions that do not have a prerelease
suffix.
Generate CI scripts as powershell on Windows. This is intended to
output exactly the same bash scripts as before on Linux.
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
As the cmake build is triggered by scikit build, the usual spack option
for enabling tests had no effect and the heavy test suite ran all the time.
Used https://github.com/scikit-build/cmake-python-distributions/issues/172#issuecomment-890322263
to implement how to pass options to the actual `cmake` build.
I also excluded some tests that failed for me on alma9 (gcc 11.4.1),
so the rest of the test suite can be run.
Enable OpenBLAS's built-in CPU capability detection and kernel selection.
This allows run-time selection of the "best" kernels for the running CPU, rather
than what is specified at build time. For example, it allows OpenBLAS to use
AVX512 kernels when running on ZEN4, and built targeting the "ZEN" architecture.
Co-authored-by: Branden Moore <branden.moore@amd.com>
* Changes to re-enable aws-pcluster pipelines
- Use compilers from pre-installed spack store such that compiler path relocation works when downloading from buildcache.
- Install gcc from hash so there is no risk of building gcc from source in pipleine.
- `packages.yam` files are now part of the pipelines.
- No more eternal `postinstall.sh`. The necessary steps are in `setup=pcluster.sh` and will be version controlled within this repo.
- Re-enable pipelines.
* Add and
* Debugging output & mv skylake -> skylake_avx512
* Explicilty check for packages
* Handle case with no intel compiler
* compatibility when using setup-pcluster.sh on a pre-installed cluster.
* Disable palace as parser cannot read require clause at the moment
* ifort cannot build superlu in buildcache
`ifort` is unable to handle such long file names as used when cmake compiles
test programs inside build cache.
* Fix spack commit for intel compiler installation
* Need to fetch other commits before using them
* fix style
* Add TODO
* Update packages.yaml to not use 'compiler:', 'target:' or 'provider:'
Synchronize with changes in https://github.com/spack/spack-configs/blob/main/AWS/parallelcluster/
* Use Intel compiler from later version (orig commit no longer found)
* Use envsubst to deal with quoted newlines
This is cleaner than the `eval` command used.
* Need to fetch tags for checkout on version number
* Intel compiler needs to be from version that has compatible DB
* Install intel compiler with commit that has DB ver 7
* Decouple the intel compiler installation from current commit
- Use a completely different spack installation such that this current pipeline
commit remains untouched.
- Make the script suceed even if the compiler installation fails (e.g. because
the Database version has been updated)
- Make the install targets fall back to gcc in case the compiler did not install
correctly.
* Use generic target for x86_64_vX
There is no way to provision a skylake/icelake/zen runner. They are all in the
same pools under x86_64_v3 and x86_64_v4.
* Find the intel compiler in the current spack installation
* Remove SPACK_TARGET_ARCH
* Fix virtual package index & use package.yaml for intel compiler
* Use only one stack & pipeline per generic architecture
* Fix yaml format
* Cleanup typos
* Include fix for ifx.cfg to get the right gcc toolchain when linking
* [removeme] Adding timeout to debug hang in make (palace)
* Revert "[removeme] Adding timeout to debug hang in make (palace)"
This reverts commit fee8a01580489a4ea364368459e9353b46d0d7e2.
* palace x86_64_v4 gets stuck when compiling try newer oneapi
* Update comment
* Use the latest container image
* Update gcc_hashes to match new container
* Use only one tag providing tags per extends call
Also removed an unnecessary tag.
* Move generic setup script out of individual stack
* Cleanup from last commit
* Enable checking signature for packages available on the container
* Remove commented packages / Add comment for palace
* Enable openmpi@5 which needs pmix>3
* don't look for intel compiler on aarch64
* py-python-lsp-server: add v1.10.0
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-wheel from package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Running a `spack-python` script like this:
```python
import spack
import multiprocessing
def echo(args):
print(args)
if __name__ == "__main__":
pool = multiprocessing.Pool(2)
pool.map(echo, range(10))
```
will fail in `develop` with an error like this:
```console
_pickle.PicklingError: Can't pickle <function echo at 0x104865820>: attribute lookup echo on __main__ failed
```
Python expects to be able to look up the method `echo` in `sys.path["__main__"]` in
subprocesses spawned by `multiprocessing`, but because we use `InteractiveConsole` to
run `spack python`, the executed file isn't considered to be the `__main__` module, and
lookups in subprocesses fail. We tried to fake this by setting `__name__` to `__main__`
in the `spack python` command, but that doesn't fix the fact that no `__main__` module
exists.
Another annoyance with `InteractiveConsole` is that `__file__` is not defined in the
main script scope, so you can't use it in your scripts.
We can use the [runpy.run_path()](https://docs.python.org/3/library/runpy.html#runpy.run_path) function,
which has been around since Python 3.2, to fix this.
- [x] Use `runpy` module to launch non-interactive `spack python` invocations
- [x] Only use `InteractiveConsole` for interactive `spack python`
Often in containers, the files we use to detect whether a cray system supports new features are not available.
Given that the cray containers only support the newer versions, and that these versions have been
around for a while at this point and few sites don't support them, this PR changes the logic for
detecting cray systems so that:
1. Don't even consider whether something is the `cray` platform if `opt/cray` is not in `MODULEPATH`
2. Only use the `cray` platform if we can read files in /opt/cray/pe and positively detect an older version
3. Otherwise, assume we're *not* on a cray (includes newer Cray PE's, which we treat as Linux)
Compilation with the old flags fails on PowerPC (power8le) due to syntax
errors in the output from the preprocessor. Compilation with the
extended set of flags works both on PowerPC and x86_64.
The correct set of flags was suggested from the berkeleygw developers:
https://groups.google.com/a/berkeleygw.org/g/help/c/ewi3RZgOyeE/m/jSIoe45PAgAJ
Uses spack-provided compiler prefix to call cpp when compiling berkeleygw with gcc.
Adds variants to turn off tests
Add variants for some missing TPL options
Add the variables required to build in ~shared
* Add pamgen to Trilinos as a variant to support SEACAS
This adds the ability to turn off and on pamgen as needed
through the variant interface for the Trilinos package.py.
Add changes for seacas package.py to build the appropriate
Trilinos variants.
Add zlib-api as depends_on instead of zlib directly for SEACAS
package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Add variant typescript for py-jupyter-server@:1, which then requires npm/node. Patch the build system for ~typescript so that it doesn't find any npm/node installations and attempts to build the typescript extension even though it shouldn't
* Fix formatting in var/spack/repos/builtin/packages/py-jupyter-server/package.py
* Constrain typescript variant to py-jupyter-server versions 1.10.2:1
* with when not needed if variant doesn't exist for other versions
This should fix issue #43192
Basically, had issue where a make variable was set to the output
of a shell function which included cd commands, and then the value
of that variable used as a makefile target.
The cd commands in the shell function caused assorted informational
messages (e.g. "Entering directory ...") which got included in the
return of the shell function, corrupting the value of the variable.
The presence of colons in the corrupted value caused make to issue
"multiple target" erros.
This fix adds --no-print-directory flags to the calls to the
make function in the package's build method, which resolves the
issue above.
It is admittedly a crude fix, and will remove *all* informational
messages re directory changes, thereby potentially making it more
difficult to diagnose/debug future issues building this package.
However, I do not see a way for to turn off these messages in a
more surgical manner.
* mgard: don't restrict protobuf version more than necessary
successfully built:
mgard@2022-11-18 ^protobuf@3.{4,21,25}
mgard@2023-01-10 ^protobuf@3.{4,25}
mgard@2023-03-31 ^protobuf@3.{4,25}
compile failures:
mgard@2022-11-18 ^protobuf@3.3
mgard@2023-01-10 ^protobuf@3.3
mgard@2023-03-31 ^protobuf@3.3
* mgard: add conflicts to address CI errors
* mgard: conflict between cuda and abseil@20240116.1
compiling mgard+cuda with gcc@12.3.0 and nvcc from cuda@12.3.0 against
protobuf pulling in abseil-cpp@20240116.1 results in the errors reported
here: https://github.com/abseil/abseil-cpp/issues/1629
* py-shacl: new version, update dependencies
Also updates the dependencies py-prettytable and py-rdflib.
* review comments
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-poetry-core: add required 1.8.1
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`jinja2` can be a costly import, and right now it happens at startup every time we run
Spack. This slows down `spack --print-shell-vars` a bit, which is needed by `setup-env.*sh`.
Patch allowing Clingo to build with VS22 has landed both in Spack
and Clingo upstream, update Spack's bootstrap constraints to handle
this.
Additionally, properly scope the patch application in the clingo
package to handle upstream patch.
Currently (outside of this PR) when you `spack develop` a path, this path is treated as the staging
directory (this means that for example all build artifacts are placed in the develop path).
This PR creates a separate staging directory for all `spack develop`ed builds. It looks like
```
# the stage root
/the-stage-root-for-all-spack-builds/
spack-stage-<hash>
# Spack packages inheriting CMakePackage put their build artifacts here
spack-build-<hash>/
```
Unlike non-develop builds, there is no `spack-src` directory, `source_path` is the provided `dev_path`.
Instead, separately, in the `dev_path`, we have:
```
/dev/path/for/foo/
build-{arch}-<hash> -> /the-stage-root-for-all-spack-builds/spack-stage-<hash>/
```
The main benefit of this is that build artifacts for out-of-source builds that are relative to
`Stage.path` are easily identified (and you can delete them with `spack clean`).
Other behavior added here:
- [x] A symlink is made from the `dev_path` to the stage directory. This symlink name incorporates
spec details, so that multiple Spack environments that develop the same path will not conflict
with one another
- [x] `spack cd` and `spack location` have added a `-c` shorthand for `--source-dir`
Spack builds can still change the develop path (in particular to keep track of applied patches),
and for in-source builds, this doesn't change much (although logs would not be written into
the develop path). Packages inheriting from `CMakePackage` should get this benefit
automatically though.
Add current versions of the 17 and 18 releases
Stop making it nearly impossible to compose this correctly with code built with gcc
Build for compatibility by default like we do in every other llvm package
The `patch()` directive can now be invoked with `reverse=True` to apply a patch in reverse.
This is useful for reverting commits that caused errors in projects, even if only the forward
patch is available, e.g. via a GitHub commit patch URL.
`patch(..., reverse=True)` runs `patch -R` behind the scenes. This is a POSIX option so we
can expect it to be available on the `patch` command.
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
set the FC variable to the MPI Fortran compiler and also set the F90 variable
to the same compiler for versions 9.8 and up. FC needs to be set because the
configure script still uses FC.
* unmaintained packages: add new versions
* Fix parallel and numactl
* Revert numactl changes
* rollback lua-sol2 version
* Update alluxio version format
* py-psyclone and py-fparser new releases added
* py-fparser: add missing releases for py-psyclone
* py-psyclone: actioned @adamjstewart comments
* py-psyclone: removed py-pytest-pylint
* py-pytest-pylint: added package @ latest version
* py-pytest-pylint: reformatted
* Update var/spack/repos/builtin/packages/py-psyclone/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pytest-pylint: added build deps and runtime dep versions
* py-pytest-pylint: removed version from setuptools
* py-psyclone: add py-pytest-pylint test dep and alphabetize deps
* Update var/spack/repos/builtin/packages/py-pytest-pylint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-psyclone: deps ordered
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
fixes#43097
Before this PR the behavior of mixins used together with
builders was to mask completely the callbacks defined from
the class coming later in the MRO.
Here we fix the behavior by accumulating all callbacks,
and de-duplicating them later.
* package/qgis: add new version
* improve Qsci.pro
* improve
* fix undefined symbol qsciprinter error
* add import test
* fix bug
* add version 3.36
* [@spackbot] updating style on behalf of Sinan81
* fix long line
* only run import test when +python
* first attempt at stand-alone test
* add TODO
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Sinan81 <Sinan@world>
* proj: correct CMake arg for shared build with proj older than 7.0.0
* Actually use new CMake arg
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This adds Spack packages for these Perl distributons:
- Bio::DB::EUtilities and its dependencies:
- Bio::ASN1::EntrezGene
- Bio::Cluster
- Bio::Variation
* Properly specify Curl builder interface for static vs shared curl
with NMake system to ensure all built curls export expected
symbols.
* Symlinks curl library build artifact to more idiomatic name for
FindCurl.cmake implementations and other NMake consumers.
* Deprecating py-pylint@2.3 as it cannot build with python@3.8:
* Style fix
* Removed versions because can't build with python@3.7
---------
Co-authored-by: Gava, Francesco <francesco.gava@mclaren.com>
* py_cheap_repr: add initial package.py
* Update var/spack/repos/builtin/packages/py-cheap-repr/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cheap-repr: use pypi link instead
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Added new versions @1.5.1 and @1.4.1 (sfcgal moved from github to gitlab)
Placed restrictions on what versions of cgal are supported for different
cfcgal versions. These restrictions are based on what was found in the
version history at https://gitlab.com/sfcgal/SFCGAL/-/blob/v1.5.1/NEWS?ref_type=tags
as well as the CMakeLists.txt for different versions.
@1.4 and @1.5 seem to require a specific version of cgal based on CMakeLists.txt
Earlier versions (@1.3.8:1.3.10) claim to support cgal@4.3: (but Spack recipe
claims did not work until @4.7, so sticking with that as minimum). CMakeList.txt
suggests they support cgal@5 as well, but version history suggests otherwise.
* Expanding the duckdb package to fix the version number (required for external extensions to work) being pulled from git and have variants for the built-in extensions at build-time. This also changes the build system from CMakePackage to Makefile package (as advised from upstream).
* - Reorganized and cleaned up variants
- Updated the patch to work for 0.10.0+
- Removed (or made non-default) some unecessary variants
- Added ninja as the default generator
- Set up some shared library dependencies;
* enable tensorflow-2.11 support for ROCm
* add latest sha for mesa and limit the patches to older version.similar
changes in #37910 to enable gitlab-ci pass
* address review commemts
Remove dependency on `importlib_metadata` and `pkg_resources`, which can be problematic if the version in PYTHONPATH is incompatible with the interpreter Spack is running under.
* Kokkos Kernels: adding missing TPLs and pre-conditions
Adding variants and dependencies for rocBLAS and rocSPARSE.
Also adding a "when=" close to the TPL variants that prevents
enabling the TPLs in versions of the library when it was not
yet available.
* Kokkos Kernels: remove comment for better format
* Kokkos Kernels: fix issue with unpacking wrong number of args
After changing the tpls dictionary we need to update the unpacking
logic to catch the right number of outputs out of it!
* Kokkos Kernels: updating doc string for tpls var and using f-string
Improving comment a bit and switching to f-string for more readability.
When setup to do more testing will try to use f-string in the CMake
options generation part of the package.
* Style change
* sst-core now effectively depends on ncurses
* use --with-curses
* sst-core: update comment about ncurses
* should have curses for build, link, and run
Closes#43052.
Maybe moving the argument to the `find` subcommand is a good idea, but I
just wanted to get the docs fix out.
Co-authored-by: Patrice Peterson <patrice.peterson@itz.uni-halle.de>
This PR adds the ability to load spack extensions through `importlib.metadata` entry
points, in addition to the regular configuration variable.
It requires Python 3.8 or greater to be properly supported.
#42878 adds a post install filter of the netCDFConfig.cmake file
that replaces a valid CMake target on Windows with an invalid one.
Don't do this replacement on Windows.
* Updates for migraphx 6.0.0 & 6.0.2
* Style check error and audit check error fix
* Adding patch for half-include-directory
* The parameter GPU_TARGETS is used from 5.7 in migraphx
* Adding rocmlir dependency in migraphx and 6.0 updates in rocmlir
* Applying upcoming changes to make CK JIT optional and enable
compilation on Windows in order to build without ck dependency
* mpfr: missing dependency for version 4.0.1
mpfr 4.0.1 (like 4.0.2) needs autoconf-archive where it takes the
AX_PHREAD macro from
* autoconf-archive is also required for mpfr@4.0.0
New changes have been made to nvptx-tools that address dropping support
for sm_30 in later CUDA versions (12.0+).
Also refactor gcc to make nvptx-tools a dependency instead of a resource.
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Adds CHI::Driver::Memcached.
Modified perl-chi to make the tests work. Testing modules in perl-chi
were not loaded when testing CHI::Driver::Memcached, so added the "run"
type to these.
* ASP-based solver: improve reusing nodes with gcc-runtime
This PR skips emitting dependency constraints on "gcc-runtime",
for concrete specs that are considered for reuse.
Instead, an appropriate version of gcc-runtime is recomputed
considering also the concrete nodes from reused specs.
This ensures that root nodes in a DAG have always a runtime
that is at a version greater or equal than their dependencies.
* Add unit-test for view with multiple runtimes
* Select latest version of runtimes in views
* Construct result keeping track of latest
* Keep ordering stable, just in case
1) support for version @3.0
Unfortunately, download seems to require registration now
so using manual_download mechanism for @3:
2) copying from hdf-eos5 patch from @vanderwb to enable
use of Spack compiler wrappers instead of h4cc
3) Patching an issue in hdf-eos2 configure script. The
script will test for jpeg, libz libraries, succeed and
append HAVE_LIBJPEG=1, etc to confdefs.h, and then abort
because HAVE_LIBJPEG not set in running environment.
4) Add some LDFLAGS to build environment. Otherwise
seems to fail to build test script due to rpc dependence
in HDF4.
Adds Net::Server::SS::PreFork and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Server::Starter
- Net::Server
- HTTP::Server::Simple
Adds Catalyst::Action::RenderView and its dependencies.
Installed OK with build-time tests. Added dependencies:
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
- Catalyst::Action::RenderView
* package/imagemagick add new version, improve
* confimed that build fails when libsm is missing on linux
---------
Co-authored-by: Sinan81 <Sinan@world>
* perl-chi and deps: new packages
Adds CHI and its dependencies.
Installed OK with build-time tests. Added dependencies:
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
- CHI
* Add license
* legion: Add 23.09.0 and 23.12.0, remove control_replication.
The branch control_replication has been merged to master and should no
longer be used.
* flecsi: Switch to Legion master branch.
Legion control_replication has been merged to master.
* Fix Legion 23.09.0 and 23.12.0 build for ROCm 6.
* Add ncvis and opengl option for wxwidgets
* Style fixes for ncvis
* Replace in with satisfies for opengl constraint
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* when built with cmake, libogg does not build with a shared libary by default. This resolves that
* spack style fixes
* Clean up imports
* enforce +pic when +shared
* Execute `args.help` after setting main options so that extension commands will show with `spack -h`
---------
Co-authored-by: psakievich <psakiev@sandia.gov>
* Update package.py
1. add one compiler type named 'musl'
2. add a variant name 'multilib'
3. add a variant name 'cmodel'
* Added one compiler type named 'musl'.
Added a variant named 'multilib'.
Added a variant named 'cmodel'.
Added several versions.
* aarch64 is not supported.
The deps were added in #40945 to make it work on macOS 11, because the
old configure scripts only detect macOS 10. Apparently people reported the
autoreconf script caused issues, later fixed in #41057. However, also
with that fix, things are incorrect, cause people now report:
```
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.7
libtool: and run autoconf again.
```
HOWEVER, all this is unnecessary, because the underlying issue was
already fixed long ago, it's just that it regressed at some point, but
it's back in place since #41205.
This adds Readonly::XS. Since this module can not be used by itself, the
Spack package comes with a test override. This anticipates that the perl
builder will one day have a generic standalone module usage test.
This should fix issue #40780
We explicitly cast self.spec["python"].command to str in the filter_file
call in _fix_dtrace_shebang to avoid the error
==> Error: TypeError: expected str, bytes or os.PathLike object, not Executable
Not sure why the error is appearing (is it only for specific python versions, etc?),
but the fix should be quite safe.
* e4s: new packages: glvis, laghos
* gl: require: osmesa
* be explicit: glvis ^llvm so that llvm-amdgpu not chosen
* glvis fails on oneapi stack due to issue 42839
Spack merges ranges and concrete versions if they have non-empty
intersection. That is not enough for adjacent version ranges.
This commit ensures that disjoint ranges in version lists are simplified
if their union is not disjoint:
```python
"@1.0:2.0,2.1,2.2:3,4:6" # simplifies to "@1.0:6"
```
Libraries for openexr are named libOpenEXR*.so, etc., so the default libs
handler in spec does not find them.
Add a custom libs property to address this.
Partial fix for #42273
Co-authored-by: payerle <payerle@users.noreply.github.com>
for various reasons had to advance dependency of 5.0.2 to at least
pmix 4.2.4. 5.0.1 and 5.0.0 can also build with 4.2.4 pmix or newer.
related to #42651
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Refactoring `SpackSolverSetup` is a bit easier with type annotations, so I started
adding some. This adds annotations for the (many) instance variables on
`SpackSolverSetup` as well as a few other places.
This also refactors `condition()` to reduce redundancy and to allow
`_get_condition_id()` to be called independently of the larger condition
function.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* py-ipyvuetify: new package
* Limit py-jupyter-packing version to 0.7.x
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-jupyterlab version and type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix py-ipyvue version range to exclude 2
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rm py-wheel, already considered for PythonPackage
* fix: pynpm only required for build, reorder dependencies as in the pyproject.toml
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* snakemake: add Snakemake 8 with dependencies
* snakemake: add missing description
* Whitespace
* Whitespace
* Whitespace
* Whitespace
* py-conda-inject: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-azure-batch: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-cluster-generic: add constraint for Python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake: add upper bound for Python
* py-snakemake-executor-plugin-drmaa: specify dependency type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-googlebatch: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-executor-plugin-tes: correct dependency version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-snakemake-storage-plugin-s3: reorder
* snakemake: remove newly added variants
* snakemake: remove newly added variants
* snakemake: remove newly added variant
* snakemake: update version
* snakemake: update version
* snakemake: whitespace
* py-snakemake-storage-plugin-s3: update version
* snakemake: use newer version
* snakemake: whitespace
* snakemake: update interfaces
* py-snakemake-storage-plugin-gcs: link issue
* snakemake: update versions
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* package/libspatialite: add conflict, new version
* depends on new version of freexl
* fix bug
* remove manual download stuff
* improve style
* first depracate
* [@spackbot] updating style on behalf of Sinan81
* get rid of conflict, reorder deps
* remove manual download
---------
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
* Allow awscli-v2 to be installed without examples/ dir
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/awscli-v2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The CMake-based build is anticipated to work in all cases where the
Autotools-based build did, and to address all prior issues with less
maintenance of the package. In detail:
* Fixes#42735 (CMake's find_package helps with linking to proper
netcdf-c)
* Replaces older Autotools-based build
* All preexisting variants are handled
* Record hdf5 as an explicit dependency (was missing before)
* Add +tests option
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
* proj: apply stdint.h patch in version 8
* Update var/spack/repos/builtin/packages/proj/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Some builds on Windows break when encountering paths with spaces. This
reencodes some paths in Windows 8.3 filename format (when on Windows):
this serves as an equivalent identifier for the file, but in a form that
does not have spaces.
8.3 filenames are also truncated in length, which could be helpful, but
that is not the primary intended purpose of using this format.
Overall
* nmake/msbuild packages do this generally for the install prefix
* curl/perl require additional modifications (as written now, each package
may require calls to `windows_sfn` to work when the Spack
root/install/staging prefixes contain spaces)
Some items for follow-up:
* Spack itself does not create paths with spaces "on top" of whatever
the user configures or where it is placed (e.g. the Spack root, the
staging directory, etc.), so it might be possible to edit some of these
paths once and avoid a proliferation of individual `windows_sfn`
calls in individual packages.
* This approach may result in the insertion of 8.3-style paths into
build artifacts (on Windows), handling this may require additional
bookkeeping (e.g. when relocating).
* Move spec_list into its own file, instead of __init__.py
* Remove spack.schema.spack
This module was introduced in #33960 It's almost an exact duplicate of
spack.schema.env, and is not used anywhere.
* Fix typo
* adds the spack recipe for py-jwcrypto
* split long line to fix E501
* Specify versions for py-cryptography and py-typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adds the spack recipe for reacton python package
* Fix versions for ipywidgets and typing-extensions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-find-libpython: new package
* Update var/spack/repos/builtin/packages/py-find-libpython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add spack recipe for ipyvue
* Specify version for ipywidgets
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
fix bug.
* Update var/spack/repos/builtin/packages/pdal/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ansible: add v2.16.3
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add specific python version requirements from setup.cfg
* Add additional ranges for py-setuptools
* Update var/spack/repos/builtin/packages/py-ansible/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Compiling version 2.2.4 fails (on a Debian system with only a minimum set of packages installed) with an error because `INT_MAX` is undeclared:
```
263 gd_gd2.c: In function '_gd2GetHeader':
>> 264 gd_gd2.c:212:54: error: 'INT_MAX' undeclared (first use in this function)
265 212 | if (*ncx <= 0 || *ncy <= 0 || *ncx > INT_MAX / *ncy) {
266 | ^~~~~~~
267 gd_gd2.c:87:1: note: 'INT_MAX' is defined in header '<limits.h>'; did you forget to '#include <limits.h>'?
```
* pythia6: deal with dead pythiasix.hepforge.org
* pythia6: rm main81.f from CMakeLists.txt
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Any package `X` used as `depends_on("x", type="build")` will have
`X.setup_run_environment(env)` called, because it has to be able to
"run" in the build environment.
So there is no point in calling `setup_run_environment` from
`setup_dependent_build_environment`.
Also it's redundant to call `setup_run_environment` in
`setup_dependent_run_environment`, cause (a) the latter is called _for
every parent edge_ instead of once per node, and (b) it's only called
after `setup_run_environment` is called anyways. Better to call
`setup_run_environment` once and only once.
fftw object was originally created with spec["fftw:openmp"], but
referencing spec["fftw"] overwrites the 'last_query' in the spec object,
so later use of fftw.libs was not returing FFTW OpenMP libs.
Also allow the post-install fixup to support amdfftw as well as fftw.
Co-authored-by: Branden Moore <branden.moore@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
* new builtin package: py-biobb-model
* Update var/spack/repos/builtin/packages/py-biobb-model/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add package py-jacobi
* fix: add description
* fix: add description
* fix: add description
* [@spackbot] updating style on behalf of jonas-eschle
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/py-jacobi/package.py
I don't think that numpy is used in "build"? But not important
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: jonas-eschle <jonas-eschle@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-google-cloud-storage: add new versions
* py-google-api-core: add new versions
* py-proto-plus: add new package
* py-google-api-core: add grpc variant
* py-google-api-core: add grpc variant
* py-google-api-core: add missing prefix
* py-google-cloud-batch: add new package
* py-google-cloud-logging: add new package
* py-google-cloud-appengine-logging: add new package
* py-google-cloud-audit-log: add new package
* py-grpc-google-iam-v1: add new package
* py-proto-plus: remove obvious dependency
* Whitespace
* Whitespace
* py-google-cloud-audit-log: correct conflict
* py-proto-plus: correct dependency type
* Whitespace
* py-google-auth: add new version
* py-google-resumable-media: add new version
* py-google-cloud-storage: constrain version of dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-grpcio-status: use newer version
* py-google-resumable-media: add upper bound of dependency
* Add types of dependencies.
* py-grpcio: add new version
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-smote-variants: Added package py-smote-variants
Also added py-minisom and py-metric-learn as dependencies
* py-metric-learn: Added build dependency on setuptools
* py-smote-variants: Added a dependency on py-pytest-runner
As well as a comment about why statistics isn't included
* [@spackbot] updating style on behalf of alex391
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-charm4py: needs Cython<3.0
* Update var/spack/repos/builtin/packages/py-charm4py/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Kokkos Ecosystem: update for release 4.2.01
Will rebase this on top of develop once Kokkos Core PR merges.
* Kokkos Ecosystem: update license statement to reflect current license
* helics: Add version 3.5.0
* helics: define CMAKE_CXX_STANDARD=20 when GCC>=13 is used to compile
---------
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Ryan Mast <mast9@llnl.gov>
* Add support for clang in oneapi packages with OpenMP
* Add fallback search for libomp in OneApi package with OpenMP threading
* Add requires for the compiler when using threads=openmp in intel-oneapi-mkl
* Cosmetic changes to messages in oneapi.py
* Update error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Update another error message in oneapi.py
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* Inline helper error function in oneapi.py
* Update one more error message in oneapi.py
* Wrap long line in oneapi.py
---------
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
* allow packages to request no submodules be updated when self.submodules is a
callable function
* Extend the test added in Allow more fine-grained control over what submodules are
updated: part 2 #27293 to include this case
* Update the type signature for the submodules arg of version() in directives.py
---------
Co-authored-by: tjfulle <tjfulle@users.noreply.github.com>
* cmake: Enable CMAKE_EXPORT_COMPILE_COMMANDS
Enabling this option causes CMake to generate a compile_commands.json file
containing a compilation database that can be used to drive third-party tools.
CMAKE_EXPORT_COMPILE_COMMANDS only exists for CMake >= 3.5
Exporting compilation databases is only supported for Makefile and Ninja
generators, so check these conditions as well.
CMAKE_EXPORT_COMPILE_COMMANDS is only enabled in supported configurations
* khmer: new package @2.1.1
* rationalising patch
* adding dep, modifying patch
* Update var/spack/repos/builtin/packages/khmer/package.py
Indeed!
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* possvm: new package @1.2
* black!
* appeasing flake8
* Updating commit ID
* Adding graphing dep
* Update var/spack/repos/builtin/packages/py-markov-clustering/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pysftp: add new package
* py-pysftp: correct version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adds the spack recipe for building the pynpm python package
* fix license header
* Update var/spack/repos/builtin/packages/py-pynpm/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-fastremap: new package @1.14.1
* py-pyqtgraph: new package @0.13.3
* py-roifile: new package @2024.1.10
* py-superqt: new package @0.6.1
* cellpose: new package @2.2.3
* Appeasing black ...
* Dropping the cuda variant
* Update var/spack/repos/builtin/packages/py-fastremap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding python version dependency
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-roifile/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-superqt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding missing dep & conflict
* Appeasing black
* Adding missing py- prefix for dep
* Switching over to py-pyqt6
* Switching over to py-pyqt6
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-structure-checking
* Update var/spack/repos/builtin/packages/py-biobb-structure-checking/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* dependencies are also build dependencies
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-io
* Update var/spack/repos/builtin/packages/py-biobb-io/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new builtin package: py-biobb-gromacs
* Update var/spack/repos/builtin/packages/py-biobb-gromacs/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added setuptools dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Bump up the version for rocm-6.0.2 release
* extend the patches that were created for apps for rocm-6.0.0 and rocm-6.0.2 releases
(but apply hipfft patch for only 6.0.0)
* gitlab: remove requests for unreferenced packages
The packages removed in this commit are not built by any of
our current GitLab CI stacks.
* gitlab: update memory requests for "huge" packages
* gitlab: reduce memory requests for overprovisioned packages
* gitlab: more memory for py-torch (again)
* gitlab: update memory but keep CPU the same
This fixes bugs, performance issues, and removes no longer necessary code.
Short version:
1. Creating views from Python extensions would error if the Spack `opt` dir itself was in some symlinked directory. Use of `realpath` would expand those, and keying into `merge_map` would fail.
2. Creating views from Python extensions (and Python itself, potentially) could fail if the `bin/` dir contains symlinks pointing outside the package prefix -- Spack keyed into `merge_map[target_of_symlink]` incorrectly.
3. In the `python` package the `remove_files_from_view` function was broken after a breaking API change two years ago (#24355). However, the entire function body was redundant anyways, so solved it by removing it.
4. Notions of "global view" (i.e. python extensions being linked into Python's own prefix instead of into a view) are completely outdated, and removed. It used to be supported but was removed years ago.
5. Views for Python extension would _always_ copy non-symlinks in `./bin/*`, which is a big mistake, since all we care about is rewriting shebangs of scripts; we don't want to copy binaries. Now we first check if the file is executable, and then read two bytes to check if it has a shebang, and only if so, copy the entire file and patch up shebangs.
The bug fixes for (1) and (2) basically consist of getting rid of `realpath` entirely, and instead simply keep track of file identifiers of files that are copied/modified in the view. Only after patching up regular files do we iterate over symlinks and check if they target one of those. If so, retarget it to the modified file in the view.
--with-ch4-max-vcis=default is no longer accepted by MPICH configure
since the 4.1 release. Just omit the option from the +vci variant, since
configure will select the default value in its absence.
Problem: Older versions of the flux-core package require czmq and
jsonschema, but these dependencies have been dropped in recent
versions.
Add `when=` arguments to drop these requirements for the appropriate
versions of flux-core.
* fix wrong versioning
use doc version and not the one extrapolated from the path (i.e. 0.2.0.1)
* nvpl-lapack requires nvpl-blas
propagate matching variants to nvpl-blas dependency
Co-authored-by: albestro <albestro@users.noreply.github.com>
* rct: update packages (RE, RG, RP, RS, RU) with new versions
* rct: updated style
* rct: 1.46 release
* rct: RP 1.46.1 (hotfix applied)
* rct: deprecated old versions
* Update var/spack/repos/builtin/packages/py-radical-entk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-pilot/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-radical-saga/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* rct: brought back dependencies for deprecated versions
* rct: RP hotfix release 1.46.2
* rct: new stack release 1.47.0
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ucsf-pyem: updating to commit e92cd4d
* py-pyfftw: updating to @0.13:1
* py-ucsf-pyem: correcting install of scripts
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Upper limits
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* updates from github review
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add new package libsixel
* reorder to group variants and dependencies together
* Switch to using source from fork
The original developer of libsixel, Hayaki Saito (@saitoha), disappeared
in early 2020 and has not updated the repository or been seen since.
However, a fork of the project has been created at libsixel/libsixel,
and that fork has been getting much more regular updates. In this commit
I switch the package to using the better-maintained, now apparently
canonical fork of the project.
That project switched the build system from autotools to Meson, so much
of the build arguments code needed to be rewritten. The newest official
release also contained an error in meson.build which would break on
newer versions of Meson. That error only applied to the libjpeg and
libpng variants, though, so I switched the default to use libgd which
has broader format support anyway.
* blacken
* broke description into multiple lines
* allow libjpeg, etc to be loaded automatically
* apply patch to all compilers as per spack/issues/42007
* [@spackbot] updating style on behalf of Chrismarsh
* Resolve flake8 style issue from spackbot
* fix flake8 trailing whitespace
---------
Co-authored-by: Chrismarsh <Chrismarsh@users.noreply.github.com>
These 7 hooks were not used.
- Six of them related to install phases were unused after `spack`
`monitor` was removed, and the code seems to have bit rotten as there
were reports they were not (always?) triggered when they should.
- The post environment one was made redundant after spack install for
environment started following the common code path for generating
module files in #42147.
It should not be a breaking change to remove, since users cannot define
hooks in extensions, they would have to fork Spack.
If we ever _were_ to make those hooks extendable outside of core Spack,
it would also be better to start with fewer rather than more, cause
everything you expose gets relied upon...
Removing those also allows us to rethink what hooks we really need, and
in particular it seems like we need a hook that runs post install also when
the spec is inserted into the database.
The lack of a rule to avoid enforcing requirements on multi-valued variants, when the condition activating the environment was not met, resulted in multiple optimal solutions. The fix is to prevent imposing a requirement if the when= rule activating it is not met.
The section was highly outdated as it referred to old defaults, and
failed to mention `hide_implicits: true`.
This commit restructures it, moves some deeply nested sections a level
up, and promotes `hide_implicits: true` + `autoload: direct` before
talking about `exclude`.
It is useful to enable/disable stacks in order to handle turning
specific stacks on/off based on runner availability, stack stability,
testing requirements, etc.
The disabled stack list takes precedence over the enable stack list. The
assumption is that stacks that are disabled are so due to some
functionality missing or broken for that stack.
The enable stack list implicitly disables all stacks not listed in the
enable list.
* Registry queries can fail due to simultaneous access from other
processes. Wrap some of these accesses and retry when this may
be the cause (the generated exceptions don't allow pinpointing
this as the reason, but we add logic to identify cases which
are definitely unrecoverable, and retry if it is not one of
these).
* Add make recursion optioal for most registry search functions;
disable recursive search in case where it was originally always
recursive.
* py-pythran: apply patch to fix compilation with GCC 13
* Update var/spack/repos/builtin/packages/py-pythran/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix ipyrad numpy depedencies
ipyrad versions through 0.9.90 use np.int, which is deprecated in numpy 1.20.
* fix whitespace
* Correct numpy dependency restrictions
Fix two separate problems:
1. We want to always visit parents before children while creating views
(when it comes to ignoring conflicts, the first instance generated in
the view is chosen, and we want the parent instance to have precedence).
Our preorder traversal does not guarantee that, but our topological-
order traversal does.
2. For copy style views with packages x depending on y, where
<x-prefix>/foo is a symlink to <y-prefix>/foo, we want to guarantee
that:
* A conflict is not registered
* <y-prefix>/foo is chosen (otherwise, the "foo" symlink would become
self-referential if relocated relative to the view root)
Note that
* This is an exception to [1] (in this case the dependency instance
overrides the dependent)
* Prior to this change, if "foo" was ignored as a conflict, it was
possible to create this self-referential symlink
Add tests for each of these cases
* Sqlite requires the user to provide a command line arg (DYNAMIC_SHELL)
to export shared symbols to import lib from .def
* Add other options recommended by Sqlite docs:
https://github.com/sqlite/sqlite/blob/master/doc/compile-for-windows.md
* Some of these options mean we can restore variants that were
disabled for Windows (fts, functions, rtree).
* Updated with generic test functions
* Added level_zero test
As the compiler is not installed by TAU, it should be loaded first and run with --dirty. Will check if there is a way to make it work without --dirty.
* Update var/spack/repos/builtin/packages/tau/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
The main script body is over-written for power. Putting thet timing
aggregation in the after script allows it to be called on all of the
current pipelines.
* Update package.py
Add support for OpenSubdiv 3.5.x
* Fixed Dependencies
I was getting errors about cmake not being able to find `xf86vm`, and adding a dependency on `libxxf86vm` fixes it.
Sometimes the logs are too long and the copy & paste command is not
shown. In that case I'd like to just copy the failing GitLab job URL in
my browser to `spack reproduce-build <url>`.
Currently, the `SpackSolverSetup` and the `PyclingoDriver` are more coupled than necessary:
1. The driver object needs a setup object to be injected during a solve,
2. And the setup object will get a reference back to the driver
This design is necessary because we use the low-level `clingo.backend` interface to setup our problem. This interface though is meant to bypass the grounder and add symbols directly in the grounded table, which is a feature we don't currently use.
The PR simplifies the encoding by having the setup object returning the problem-specific facts / rules as a list of strings, and the driver ingesting them using the [clingo.Control.add](https://potassco.org/clingo/python-api/5.6/clingo/control.html#clingo.control.Control.add) method. This removes any use of the low level interface.
Using this encoding makes it easy to hash the output of the setup phase, since it is returned as a string.
* py-nbconvert: avoid install-time downloads
* install css files as resources for py-nbconvert
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* py-nbconvert: update dependencies for 7.14.1
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update resources & remove style.min.css file
* Update package.py
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This "breaks" the deprecated schema by allowing unknown attributes
to the attributes section of the job types. The breaking change here is
that deprecated stacks will no longer ignore attributes that are unknown
but rather assume the new CI schema behavior of injecting them into the
generated CI configuration. This change is required to secure
authentication in Spack CI.
Improve naming, so it's clear file "extensions" are not taken in the
`PurePath(path).suffix` sense as the original function name suggests,
but rather that the files are opened and their magic bytes are
classified.
Add type hints.
Fix a bug where `stream.read(num_bytes)` was run on the compressed
stream instead of the uncompressed stream, which can potentially break
detection of tar.bz2 files.
Ensure that when peeking into streams for magic bytes, they are reset to
their original position upon return.
Use new API in `spack logs`.
Relocation of `PT_INTERP` in ELF files already happens to work from long to short path, thanks to generic binary relocation (i.e. find and replace). This PR improves it:
1. Adds logic to grow `PT_INTERP` strings through patchelf (which is only useful if the interpreter and rpath paths are the _only_ paths in the binary that need to be relocated)
2. Makes shrinking `PT_INTERP` cleaner. Before this PR when you would use Spack-built glibc as link dep, and relocate
executables using its dynamic linker, you'd end up with
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /////////////////////////////////////////////////path/to/glibc/lib/ld-linux.so
```
With this PR you get something sensible:
```
$ file exe
exe: ELF 64-bit LSD pie executable, ..., interpreter /path/to/glibc/lib/ld-linux.so
```
When Spack cannot modify the interpreter or rpath strings in-place, it errors out without modifying the file, and leaves both tasks to patchelf instead.
Also add type hints to `elf.py`.
Certain versions of ifx (the majority of those available) have an issue
where they are not compatible with TMP directories with dot chars
This precludes their use with CMake.
Remap TMP to point to the stage directory rather than whatever the TMP
default is
* Add fenics development version and ufl-legacy
* Make sure python and setuptools are added to ufl-legacy and add version 2022.3.0 as well
* Run black and add maintainer to fenics package
* Fix typo
* Use Fiat version 2019.1.0
* Run black
* Add back master branch of fiat
* Remove master from the list of dolfin versions and add one extra line of each deps instead
* Run black
* Do not specify python version in ufl-legacy
* Remove python dependency from ufl-legacy
* Remove python dependency from ffc
* Add special case for master in ffc
* Run black
* Remove master from loop in ffc
* Run black again
* geopm: Mark all as deprecated
- This recipe will be removed in a future release.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-sphinx-emoji
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add py-dasbus
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-pygobject: Add v3.46.0
- Previous versions error during build phase.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-sphinx-tabs: Add new versions
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* Add geopm-service
- Previous geopm package is now 2 packages:
geopm-service and geopm-runtime.
- The GEOPM service is designed as a systemd/dbus
service providing a userspace interface to
privileged hardware telemetry and configurations.
- Installing via spack will enable some userspace
testing, but generally most users will want to
install the GEOPM service via the system package
manager as root to get full functionality.
- This recipe will enable the creation of the fully
userspace geopm-runtime recipe which will replace
the old geopm recipe.
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
---------
Signed-off-by: Brad Geltz <brad.geltz@intel.com>
* py-textual: New package py-textual
* py-textual: Depend on py-mdit-py-plugins
* py-textual: Added dependency on python@3.8:3
* py-textual: Added a comment about why there is a dependency on
py-mdit-py-plugins
* py-textual: Ran black
---------
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* add pytest-aiohttp
* black
* py-setuptools -> py-setuptools-scm
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
VTK struggles to consume some Spack-derived packages on Windows:
Patch VTK to allow a smoother integration
Also add install for examples as they are not part of the install
interface.
gl2ps tries to build static and shared libs simultaneously with
the same target name on the generator side. This causes a name
clash issue for Ninja on Windows (where the extension is .lib
in both cases).
Add a variant on Windows to force building only one of shared
or static, and patch the CMake build to enable use of this
variant.
* gitlab: remove commented-out duplicate entries
* gitlab: reclassify some packages from "huge" to "large"
Our observed max memory usage for these packages is as follows:
hipblas: 7.7G
qt: 6.6G
visit: 9.7G
All of these should fit within a "large" request (currently 12G).
* gitlab: remove pango from list of huge packages
This package is not currently built by any of our CI stacks.
* gitlab: update requests for high memory packages
Refine resource requests for memory-intensive packages based on
max memory usage data.
- Adds perl-sql-translator and its missing deps:
- Adds perl-import-into
- Adds perl-package-variant
- Adds perl-strictures
Built with build-time tests and comes with a simple run-time test.
Add the empty deptype `spack.deptypes.NONE`.
Test the case `traverse_nodes(deptype=spack.deptypes.NONE)` to not
traverse dependencies, only de-duplicate.
Use the construct in environment views that otherwise would branch on
whether deps are enabled or not.
* ensure umpire~cuda~rocm when ~cuda~rocm
* MDAnalysis: add v2.7.0
* Apply suggestions from code review
* license
* review changes
* add gsd and py-cmake versions
* Update package.py
* py-cmake
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix and reorder
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add py-vl-convert-python
* code format
* Update package.py
add homepage
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove old versions, add todo
* Update var/spack/repos/builtin/packages/py-vl-convert-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove blank line
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: py-metrics
* [py-metrics] cleaned up extra comment
* Updated copyright and ran black
* py-pathspec: Added version 0.5.5
---------
Co-authored-by: vehrc <vehrc@rit.edu>
Co-authored-by: Jen Herting <jen@herting.cc>
Co-authored-by: Alex C Leute <aclrc@rit.edu>
* py-frozendict: patch up for Python 3.11
See also Marco-Sulla/python-frozendict#68, rely on a pure Python
implementation when 3.11+ is used.
* mention related Github issue
* new builtin package: biobb-common
* removed whitespace for the style test
* replaced ' by " for the style test
* changed import line for the style test
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update var/spack/repos/builtin/packages/biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed test
* using pypi instead of git
I hope this is declared the right way.
I tried to test it locally but I am having problems with a dependency (openblas) thus I can not even try if this works.
* upgraded version
* Added py prefix
* removed biopython version restriction
* directory with new py-prefixed name
* Delete old non-prefixed package
* Update var/spack/repos/builtin/packages/py-biobb-common/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update tarball urls, add new versions and update maintainers
* remove unnecessary variant like cross-compile
* use self.define and self.define_from_variant
* improve regex / bug that matches with -DMPICH_SKIP_MPICXX=1
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Previously, for abstract specs like:
```
foo ^[virtuals=a] bar ^[virtuals=b] bar
```
the second requirement was silently discarded on concretization. Now they're merged, and the abstract spec is equivalent to:
```
foo ^[virtuals=a,b] bar
```
* Added countdown repo
* Added fixed version of COUNTDOWN
* Style fixes
* Changed mantainer syntax
* Variants listed in alphabetical order by name
* Added conflicts and some reordering
* Fixed conflicts syntax
* Style fixes
* [@spackbot] updating style on behalf of danielecesarini
---------
Co-authored-by: danielecesarini <danielecesarini@users.noreply.github.com>
CMake may write and read from `~/.cmake` through `export(...)` and read `find_package(...)` respectively. We don't want this as it may influence the build in a non-deterministic way, so disable it for all versions of `cmake`.
* Trilinos: Add AMD to SuiteSparse TPL list
When Trilinos is built with SuiteSparse support, it should enable AMD as
one of the TPLs. It was previously enabling only UMFPACK. The Xyce
package uses AMD (but not UMFPACK).
* Xyce: Add 7.8 release and various improvements
In addition to adding the latest Xyce release (7.8), all the earlier
releases were deprecated, with the exception of 7.7.
The Trilinos specification was updated to remove unneeded packages,
explicitly enable all needed packages, and specify additional
do-not-build packages.
The serial build is now the default, with MPI still being an option.
I also epanded the explanation for one of the patches; and, finally, I
took the opportunity to update the Xyce description to better match the
current Xyce README description.
Fixes a bug where Spack did not generate module files of non-roots during
spack install with an active environment.
The reason being that Environment.new_installs only contained roots.
This PR:
Drops special casing of automatic module generation in post-install hooks
When `use_view`, compute environment variable modifications like always, and
applies a view projection to them afterwards, like we do for spack env activate.
This ensures we don't have to delay module generation until after the view is
created.
Fixes another bug in use_view where prefixes of dependencies would not be
projected -- previously Spack would only temporarily set the current spec's prefix.
Removes the one and only use of the post_env_write hook (but doesn't drop it to
make this backportable w/o changes)
Previously `std_args` was called on non-roots in a build context, which is redundant, and also leads to issues when `std_args` expects build deps of the `pkg` to be installed.
HPCToolkit `develop` now can optionally be built via Meson. This PR adds the `build_system=(autotools|meson)` variant and splits the build-system-dependent pieces into `AutotoolsBuilder` and `MesonBuilder`. The default is to build with `autotools`.
As of writing, the Meson is simply a wrapper around the original Autotools build, hence the build requires a native file listing install prefixes of all dependencies (which are internally mapped to `--with-{pkg}={prefix}` arguments for `./configure`). This is an unconventional but temporary state of affairs until the build system is fully ported to Meson and conventional dependency acquisition techniques like `pkg-config` and `cmake` are practically available.
* Environments: fix environment config
* Don't change the lockfile manifest path
* Update activate's comments to tie the manifest to the configuration
* Add spec_list override method
* Remove type checking from 'activate' since already have built-in check
* Refactor global methods tied to the manifest to be in its class
* Restore Environment's 'env_subdir_path' and pass its config_stage_dir to EnvironmentManifestFile
* Restore global env_subdir_path for use by Environment and EnvironmentManifestFile
The CUDA target should be specified at build time, otherwise
by default `autodock-gpu` will be built for compute capabilities
52, 60, 61, 70, which may cause errors on unsopported cards.
Currently requirements allow to express "strong preferences" and "conflicts" from
configuration using a convoluted syntax:
```yaml
packages:
zlib-ng:
require:
# conflict on %clang
- one_of: ["%clang", "@:"]
# Strong preference for +shared
- any_of: ["+shared", "@:"]
```
This PR adds syntactic sugar so that the same can be written as:
```yaml
packages:
zlib-ng:
conflict:
- "%clang"
prefer:
- "+shared"
```
Preferences written in this way are "stronger" that the ones documented at:
- https://spack.readthedocs.io/en/latest/packages_yaml.html#package-preferences
`spack install` early exit behavior was sometimes convenient, except
that it had and has bugs:
1. prior bug: we didn't mark env roots of already installed specs as
explicit in the db
2. current bug: `spack install --overwrite` is ignored
So this PR simplifies by letting the installer do its thing even if
everything is supposedly installed.
* Bump up the version for ROCm-6.0.0
* Adding patch files
* Style check failure fix
* Style check fixes
* Style check error fixes
* Patch to remove hipblas client file installation in 6.0
* Patch need to be applied on all 5.7 relases
* 6.0 update for math libs and other packages, new github url etc
* Correct package-audit failures
* Correcting shasum for rocfft patch and limiting patch in rocblas
* Reverting updates in rocprofiler-dev due to ci-gitlab failure
* Fixes for ci-gitlab failure due to disabling hip backward compatibilit
* Adding patch file to Change HIP_PLATFORM from HCC to AMD and NVCC to NVIDIA
* Use the gcnArchName inplace of gcnArch as gcnArch is deprecated from rocm-6.0.0
* Patches to fix magma and blaspp build error with rocm 6.0.0
* Patch for mfem and arborx for rocm 6.0
* Style check error fix
* Correcting style check errors
* Uodating dependent version
* Update for petsc to build with rocm 6.0
Need reverting-operator-mixup-fix-for-slate.patch for rocm 6.0
* Reverting the change in url for 2.7.4-rocm-enhanced
* hip-tensor 6.0.0 update
This commit ensures that CMake packages that also have Python as a build/link dep get a couple defines for the Python path so that CMake's builtin `FindPython3`, `FindPython`, `FindPythonInterp` modules can locate Python correctly.
The main problem with those CMake modules is that they first search for Python versions known at the time of release, meaning that old CMake maybe find older system Python 3.8 even though Python 3.11 comes first in `CMAKE_PREFIX_PATH` and `PATH`.
Package maintainers can opt out of this by overriding the `find_python_hints = False` attribute in the package class.
* Add nglview package
* Use slightly older version
* py-nglview: Correct py-versioneer version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nglview: Correct version of py-jupyter-packaging dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-versioneer-518 package
* py-versioneer-518: Correct version
* py-nglview: Numpy is needed during build for the tests
* py-nglview: dependency needed for tests
* py-nglview: Correct dependency types
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e4s ci: use latest intel/hpckit 2024 based image
* use latest container image: ecpe4s/ubuntu22.04-runner-amd64-oneapi-2024.0.0:2023.12.01
* comment out failing specs
* update to use patched container
* remove generalized package preference for intel-oneapi-mkl@2023
* change packages commented out
* VecGeom: new version 1.2.7 and fix URLs
* vecgeom: remove deprecated ancient RC version with incorrect hash
* geant4: remove support for @10.3+vecgeom
The piece of code that is removed in this PR predates environment views.
Spack would symlink build logs in `<env>/.spack-env/logs/*`, but this is
redundant because:
1. Views already add `<prefix>/.spack` (and there's logic there to avoid
clashes)
2. The code was broken anyways: it would only symlink the logs of
environment roots, not their deps, even if they were just built.
If users disable views, I'm pretty sure they're not waiting for
`.spack-env/logs` either. So, imo we can delete this code, and it was
probably overlooked in the past.
For a requirement like
```
packages:
foo:
require:
- "+debug"
```
(not `one_of:`, `any_of:`, or `spec:`)
`spack config change` would ignore the string. This was particularly evident if toggling a variant for a previously unmentioned package:
```
$ spack config change packages:foo:require:+debug
$ spack config change packages:foo:require:~debug
```
This fixes that and adds a test for it.
```
$ curl 'https://thepeg.hepforge.org/downloads/?f=ThePEG-2.3.0.tar.bz2' | sha256sum
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1904k 0 1904k 0 0 1075k 0 --:--:-- 0:00:01 --:--:-- 1074k
ac35979ae89c29608ca92c156a49ff68aace7a5a12a0c92f0a01a833d2d34572 -
```
* Reduce the size on disk for logs
This PR does two things:
1. Store a compressed `spack-build-out.txt.gz`
2. Get rid of phase logs, as they are duplicates of
`spack-build-out.txt`
The logs are not compressed in the stage dir, so on build failure the
workflow for users is no different.
It's just that on install the logs are rarely used, and if needed, users
can easily `gzip -d` or `zgrep` them.
In the case of GCC installs, the compressed logs are <5% of the original
size, which is typically dozens of MBs.
* get rid of "backwards compat" of file names in stage dirs
Sbangs don't exist on Native Windows, and the hook is causing errors
due to the file comparison + behavior of os.rename on Windows. Skip
the hook on Windows.
New patch 7.5.3p5, new bugfix 7.7.2, new minor 7.8.0.
Only possible impact on spack is the potential addition of a variant to select the memory manager in 7.8.0, see [diff](https://github.com/Open-Cascade-SAS/OCCT/compare/V7_7_2...V7_8_0). Not adding a variant at this time.
Like `spack change` for specs in environments, this can e.g. replace `examplespec+debug` with `examplespec~debug` in a `require:` section.
Example behavior for a config like:
```
packages:
foo:
require:
- spec: +debug
```
* `spack config change packages:foo:require:~debug` replaces `+debug` with `~debug`
* `spack config change packages:foo:require:@1.1` adds a requirement to the list
* `spack config change packages:bar:require:~debug` adds a requirement
As observed in #40944, when using `spack config add <path>`, the `path` might
contain keys that are enclosed in quotes.
This was broken in https://github.com/spack/spack/pull/39831, which assumed that
only the value (if present, the final element of the path) would use quotes.
This preserves the primary intended behavior of #39931 (allowing ":" in values when
using `spack config add`) while also allowing quotes on keys.
This has complicated the function `process_config_path`, but:
* It is not used outside of `config.py`
* The docstring has been updated to account for this
* Created an object to formalize the DSL, added a test for that, and
refactored parsing to make use of regular expressions as well.
* Updated the parsing and also updated the `config_path_dsl` test with an explicit check.
At a higher level, split the parsing to check if something is either a key or not:
* in the first case, it is covered by a regex
* in the second, it may be a YAML value, but in that case it would have to be the last
entry of x:y:z, so in that case I attempt to use the YAML handling logic to parse it as such
- Use MakefilePackage and simplified package.py
- Deprecate old versions - they did not build for me with OCaml 4.13.1
that is currently in Spack. Also, the changes from the previous
versions seem to be quite significant.
Spack packages may not have a public download option, and can implement
`download_instr` to inform users how to obtain the artifacts needed to
build. `spack checksum` however did not account for this and would print
out a confusing error message when invoked on such packages ("Could not
find any remote versions").
This PR updates the error message to output the manual download instructions
if `spack checksum` is invoked on a package with `manual_download = True`.
Currently when you repeatedly create a bootstrap mirror that includes
`clingo-bootstrap@spack` you get different tarballs every time.
This is a general problem with mirroring checkouts from version control
as tarballs. I think it's best to create tarballs ourselves, since that way we
have more control over its contents.
This PR ensures normalized tarballs like we do for build caches:
- normalize file permissions (in fact that was already inspired by git, so
should be good)
- normalized file creation/modification time (timestamp 0)
- uid / guid = 0, no usernames
- normalized gzip header
- dir entries are ordered by `(is_dir, name)` where strings are not locale aware ;)
- POSIX says st_mode of symlinks is unspecified, so work around it and
force mode to `0o755`
R embeds an absolute path to the `which` executable in the sources for
`Sys.which`. This gets ultimately stored as serialized byte code in some
custom database format, which uses compression for entries.
As a result, Spack cannot relocate `<prefix which>/bin/which` when
installing from a build cache.
The patch works around this by making R create a symlink to `which` in
its own prefix, have the R sources call that, so that relocation works
again.
See https://github.com/r-devel/r-svn/pull/151
Explicitly requested namespaces are annotated during
the setup phase, and used to retrieve the correct package
class.
An attribute for the namespace has been added for each node.
Currently, a single namespace per package is allowed
during concretization.
* add new versions of py-altair
* fix year
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-altair/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* reorder dependencies
* remove rc
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
@@ -73,9 +73,12 @@ are six configuration scopes. From lowest to highest:
Spack instance per project) or for site-wide settings on a multi-user
machine (e.g., for a common Spack instance).
#.**plugin**: Read from a Python project's entry points. Settings here affect
all instances of Spack running with the same Python installation. This scope takes higher precedence than site, system, and default scopes.
#.**user**: Stored in the home directory: ``~/.spack/``. These settings
affect all instances of Spack and take higher precedence than site,
system, or defaults scopes.
system, plugin, or defaults scopes.
#.**custom**: Stored in a custom directory specified by ``--config-scope``.
If multiple scopes are listed on the command line, they are ordered
@@ -196,6 +199,45 @@ with MPICH. You can create different configuration scopes for use with
mpi: [mpich]
.._plugin-scopes:
^^^^^^^^^^^^^
Plugin scopes
^^^^^^^^^^^^^
..note::
Python version >= 3.8 is required to enable plugin configuration.
Spack can be made aware of configuration scopes that are installed as part of a python package. To do so, register a function that returns the scope's path to the ``"spack.config"`` entry point. Consider the Python package ``my_package`` that includes Spack configurations:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ ├── __init__.py
│ │ └── spack/
│ │ │ └── config.yaml
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make ``my_package``'s ``spack/`` configurations visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.config"]
my_package="my_package:get_config_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
@@ -111,3 +111,39 @@ The corresponding unit tests can be run giving the appropriate options to ``spac
(5 durations < 0.005s hidden. Use -vv to show these durations.)
=========================================== 5 passed in 5.06s ============================================
---------------------------------------
Registering Extensions via Entry Points
---------------------------------------
..note::
Python version >= 3.8 is required to register extensions via entry points.
Spack can be made aware of extensions that are installed as part of a python package. To do so, register a function that returns the extension path, or paths, to the ``"spack.extensions"`` entry point. Consider the Python package ``my_package`` that includes a Spack extension:
..code-block::console
my-package/
├── src
│ ├── my_package
│ │ └── __init__.py
│ └── spack-scripting/ # the spack extensions
└── pyproject.toml
adding the following to ``my_package``'s ``pyproject.toml`` will make the ``spack-scripting`` extension visible to Spack when ``my_package`` is installed:
..code-block::toml
[project.entry_points."spack.extenions"]
my_package="my_package:get_extension_path"
The function ``my_package.get_extension_path`` in ``my_package/__init__.py`` might look like
suffix not recognized as a pre-release is treated as an ordinary
string component, so ``1.2 < 1.2-mysuffix``.
The order on versions is defined as follows. A version string is split
into a list of components based on delimiters such as``.``, ``-`` etc.
Lists are then ordered lexicographically, where components are ordered
as follows:
Finally, there are a few special string components that are considered
"infinity versions". They include ``develop``,``main``, ``master``,
``head``, ``trunk``, and ``stable``. For example: ``1.2 < develop``.
These are useful for specifying the most recent development version of
a package (often a moving target like a git branch), without assigning
a specific version number. Infinity versions are not automatically used when determining the latest version of a package unless explicitly required by another package or user.
More formally, the order on versions is defined as follows. A version
string is split into a list of components based on delimiters such as
``.`` and ``-`` and string boundaries. The components are split into
the **release** and a possible **pre-release** (if the last component
is numeric and the second to last is a string ``alpha``, ``beta`` or ``rc``).
The release components are ordered lexicographically, with comparsion
between different types of components as follows:
#. The following special strings are considered larger than any other
numeric or non-numeric version component, and satisfy the following
@@ -925,6 +949,9 @@ as follows:
#. All other non-numeric components are less than numeric components,
and are ordered alphabetically.
Finally, if the release components are equal, the pre-release components
are used to break the tie, in the obvious way.
The logic behind this sort order is two-fold:
#. Non-numeric versions are usually used for special cases while
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