fixes#36339
We were missing a rule that enforced a match between
the `node_compiler` and the compiler used to satisfy
a requirement.
Fix compiler with custom, made up version too
* gcc: fix for apple-clang conflict
* Update var/spack/repos/builtin/packages/gcc/package.py
Use variant by @adamjstewart
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Specs that define 'new' versions in the require: section need to generate
associated facts to indicate that those versions are valid.
* add test to verify success with unknown versions.
Since environment-modules has support for autoloading since 4.2,
and Spack-builds of it enable it by default, use the same autoload
default for tcl as lmod.
* add opppy-0_1_6 and opppy-0_1_7 releases to the spack recipes
* update urls
* remove sphinx from the dependency list
* cleanup OPPPY versions to capture OPPPY-0_1_1 tag descrepency
* one more attempt at fixing the url for opppy-0_1_1 (simpler fix)
---------
Co-authored-by: Cleveland <cleveland@lanl.gov>
Co-authored-by: clevelam <clevelam@users.noreply.github.com>
* update python package
* change package inheritance
* small update
* enable cpp tests
* small update
* Add flaky package
* Restructure PennyLane deps and order
* Change Lightning defaults and add libomp support for MacOS
* Replace explicit git url with PyPI
* Add Flaky support
* Update PennyLane and PennyLane Lightning support
* fix format
* update packages versioning
* Add patching and default updates for lightning package
* Format
* fix patch version
* update py-flaky package
* update py-pennylane-lightning package
* update py-pennylane package
* remove explicity python dependence
* Remove redundant lines from patch-file
* Update SHA for new patch
* Initial commit for PLLKokkos.
* Comment verbose variant.
* Update develop commit version and restore verbose option.
* Add backends.
* Add mesa package dep (libxml2). Fix rocm install for py-pennylane-lightning-kokkos.
* Restore sycl backend.
* Revert mesa package.
* Make py-pe-li-kokkos into CudaPackage, ROCmPackage.
* Do not force kokkos+wrapper when +cuda
* Few mods following comments on py-pll.
* Update versions of py-pennylane*.
* Remove py-pennylane-lightning patch.
* Remove redundant preferred=True.
* Fix lint in py-pennylane-lightning-kokkos.
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Ninja and pip not required at runtime. Set lower bound on PL/PLL versions.
* Remove v0.29.0 from pennylane.
* Add AmintorDusko as maintainer.
---------
Co-authored-by: AmintorDusko <amintor_dusko@hotmail.com>
Co-authored-by: Lee J. O'Riordan <lee@xanadu.ai>
Co-authored-by: Amintor Dusko <87949283+AmintorDusko@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The xcb-utils have been migrated to the gitlab.freedesktop.org, from the
previous separate location. That means that a URL change is needed to
pick up newer version
([ref](https://lists.freedesktop.org/archives/xcb/2022-October/011422.html)).
This replaces the `homepage` and `url` with the latest (to an `xz`
file), adds a `url_for_version` function to resolve past versions, and
add the latest versions. Because of the `url_for_version` I don't think
we can use the `xorg_mirror_path` approach here.
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
netcdf-cxx and netcdf-c now build with CMake rather than Autotools.
netcdf-c can still optionally build with Autotools (but defaults to
CMake). With some additional patches to the CMake files, netcdf-c
can use CMake to build on Windows.
* abinit: add version 9.8.3
* require hdf5 up to 1.8 and libxc up to version 5
* abinit: constrained versions of libxc and hdf5
* fixed bad syntax for format
* fixed error looking for fftw in spec.
* Changed to look for fftw-api in spec.
* Update var/spack/repos/builtin/packages/abinit/package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Xorg apps: updated versions to current latest
This updates all xorg apps to the latest versions, adding updated
requirements where needed.
No major version increases in any packages.
Minor version increases in some packages (build changes, if any, are
indicated below):
- rgb
- xauth
- xcalc
- xclock
- xeyes: xi >= 1.7, x11-xcb xcb-present >= 1.9 xcb-xfixes xcb-damage
- xfontsel
- xfs: xfont2 >= 2.0.1
- xinit
- xpr
- xrdb
Bugfix version increases in many packages, with no expected impact on
dependencies or interfaces.
Summary of dependency changes:
- xeyes:
- depends_on("libxi@1.7:", when="@1.2:")
- depends_on("libxcb@1.9:", when="@1.2:")
- xfs:
- depends_on("libxfont@1.4.5:", when="@:1.1")
- depends_on("libxfont2@2.0.1:", when="@1.2:")
* setxkbmap: depends_on libxrandr when @1.3.3:
* constype: new version
Add support for building with CMake and make it the default build
system on all platforms. By doing this, lz4 can now be built on
Windows. The makefile-based build remains as an option.
* wayland: new versions, new build system (meson)
* wayland-protocols: new version, new build system (meson)
* [@spackbot] updating style on behalf of wdconinc
* wayland-protocols: added maintainer
* wayland: added maintainer
* wayland-protocols: no need to import build systems, per flake8
* wayland: no need to import build system, per flake8
* Update var/spack/repos/builtin/packages/wayland/package.py
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
If you have a "require:" section in your packages config, and you
use it to specify a list of requirements, the list elements can
now include strings (before this, each element in the list had to
be a `one_of` or `any_of` specification, which is awkward if you
wanted to apply just one spec with no alternatives).
* py-pdf2image: new package
* py-pdf2image: 1.16.3 source now available on pypi
* Update var/spack/repos/builtin/packages/py-pdf2image/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Example one:
```
spack install --add x y z
```
is equivalent to
```
spack add x y z
spack concretize
spack install --only-concrete
```
where `--only-concrete` installs without modifying spack.yaml/spack.lock
Example two:
```
spack install
```
concretizes current spack.yaml if outdated and installs all specs.
Example three:
```
spack install x y z
```
concretizes current spack.yaml if outdated and installs *only* concrete
specs in the environment that match abstract specs `x`, `y`, or `z`.
* update versions and arch flags
* style update
* more style issues
* fix hashes and testing problem
* return the old versions, but they are really bad
* fix style
---------
Co-authored-by: Gerald Ragghianti <gerald@ragghianti.com>
The `ignore` parameter was only used for `spack activate/deactivate`, and it isn't used
by Spack Environments which have their own handling of file conflicts. We should remove it.
Everything that handles `ignore=` was removed in #29317 and included in 0.19, when we
removed `spack activate` and `spack deactivate` in favor of environments. So all of these
usages removed here were already being ignored by Spack.
Adapt tcl modulefile template to call "module load" on autoload
dependency without testing if this dependency is already loaded or not.
The is-loaded test is not necessary, as module commands know how to cope
with an already loaded module. With environment-modules 4.2+ (released
in 2018) it is also important to have this "module load" command even if
dependency is already loaded in order to record that the modulefile
declares such dependency. This is important if you want to keep a
consistent environment when a dependent module is unloaded.
The "Autoloading" verbose message is also removed as recent module
commands will report such information to the user (depending on the
verbosity configured for the module command).
Such change has been test successfully with Modules 3.2 (EL7), 4.5 (EL8)
and 5.2 (latest) and also with Lmod 7 and 8 (as it is mentionned in
Spack docs that Lmod can be used along with tcl modules). Dependencies
are correctly loaded or unloaded, whether they are loaded/unloaded or
not.
This change fixes Tcl quoting issue introduced in #32853.
Fixes#19155.
* py-setuptools-git-versioning: new package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-hepunits: new versions 2.2.0, 2.2.1, 2.3.0, 2.3.1
Python 2 support dropped in 2.2 series.
Ref: https://github.com/scikit-hep/hepunits/compare/v2.1.1...v2.3.1
* py-hepunits: py-hatchling as of version 2.3
* [@spackbot] updating style on behalf of wdconinc
* py-hepunits: only depends_on toml through 2.1.1
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
In the Windows filesystem logic for creating a symlink, we intend to
fall back to a copy when the symlink cannot be created (for some
configuration settings on Windows it is not possible for the user
to create a symlink). It turns out we were overly-broad in which
exceptions lead to this fallback, and the subsequent copy would
also fail: at least one case where this occurred is when we
attempted to create a symlink that already existed.
The updated logic expressly avoids falling back to a copy when the
file/symlink already exists.
* Bazel: limit parallelism
* Patch packages that don't directly invoke bazel
* Style fixes
* flag comes after build, not bazel
* flag comes after build, not bazel
* command is only attribute if specific package
* ASP-based solver: use satisfies instead of intersects
They are semantically equivalent for concrete versions,
but the GitVersion.intersects implementation is buggy
* Mitigation for git version bug
fixes#36134
This commit works around the issue in #36134, by using
GitVersion.satisfies instead of GitVersion.intersects
There are still underlying issues when trying to infer the
"reference version" when no explicit one is given, but:
1. They are not reproducible with our synthetic repo
2. They occur only when the `git.<xxx>` form of Git version
is used
Here we just work around the user facing issue and ensure
the tests are correct with our synthetic repository.
* py-pytorch-lightning: add v2.0.0
* py-lightning-utilities: add v0.8.0
* Update all PyTorch packages
* Open-CE does not yet have patches for PyTorch 2 on ppc64le
For `spack install --test=all gromacs`
* remove the `test` target from the `check()` call and just use
the `check` target, in accordance with usual GROMACS test protocol
* build the test binaries explicitly during the build phase
Additional minor updates are necessary. This change
updates the package structure to the newer format with a
separate Builder class so we can override `check()`.
However, note that additional modernization should be
undertaken with care.
This PR does 2 unrelated things:
1. It changes the encoding of the compilers
2. It tweaks the heuristic for the solves in a0d8817907
Both were initially motivated by trying to get a performance gain but, while 2 showed significant speed-ups[^1], 1 instead didn't. I kept it anyhow, since I think the code related to compilers is more consolidated with the new encoding and we might get some performance improvement out of it if we can base our errors on the `node_compiler(Package, CompilerID)` atoms instead of `attrs`.
[^1]: In general the changes in the heuristic brought a ~10% speed-up on the tests I did. I'll post detailed results below.
Add a warning about compilers.yaml that is triggered if there are multiple compilers with the same spec, os and
target (since they can't be selected by users with the spec syntax only).
* [openmpi] 5.0.0.rc10 onwards needs munge
This is the error you will see when munge is missing from `PKG_CONFIG_PATH`:
```
configure:63942: checking for pmix pkg-config cflags
configure:63956: check_package_pkgconfig_run_results=Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63959: $? = 1
configure:63966: pkg-config output: Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63972: result: error
configure:63974: error: An error occurred retrieving pmix cppflags from pkg-config
```
* Use same PKG_CONFIG_PATH defaults for ompi+pmix+prrte
The issue I tried to fix in https://github.com/spack/spack/pull/36105 comes from
different default search paths in different `pkg-config` executables used in
`openmpi` and `pmix` package. As these tools (`openmpi`, `pmix`, and `prrte`)
all use the same mechanisms to detect dependencies, the `pkg-config` environment
they use should also be equal.
Since GPG clear-sign cannot deal with lines longer than 19995 characters
and doesn't even error but simply truncates those linese (don't ask me
why...), we have to be careful not to hit that line limit when reducing
the filesize.
So, instead this PR sets the indent level to 0 and drops the whitespace
after `: `, which still reduces file size by 50% or so.
Per feedback from the UCX community, we rarely do update
releases to anything but the current and one previous main
release stream.
Update comments in the UCX spack file to reflect this.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* py-pyshacl: patch dependency typo
* py-pyshacl: satisfy flake8
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Adds builders appropriate for building these packages on Windows.
It is intended that builds on other platforms are unaffected (e.g.
they build with Autotools as before on Linux).
* py-pint: new versions
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-antspyx: new package
Also adds required dependencies.
Requires options to ITK to enable the right support libraries, and
patches to remove tune the setup and provide resources rather than
downloading libraries/"submodules" on the fly.
* Fix patch URL
* Style fixes.
* bump version and re-include `git clone ...` as resource
... and use colors in disambiguate message for clarity.
This commit avoids the loop:
```
for root in roots:
for dep in deps(root):
...
```
instead it ensures each node is visited once and only once.
Also adds a small optimization when searching for concrete specs, since
we can assume uniqueness of dag hash, so it's fine to early exit.
This adds a new mode for `concretizer:reuse` called `dependencies`,
which only reuses dependencies. Currently, `spack install foo` will
reuse older versions of `foo`, which might be surprising to users.
* update mda dependencies
* apply black
* mdanalysis draft
* update
* small fixes
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ci: version bump for ghcr.io/spack/e4s-amazonlinux-2
This new image comes with GnuPG v2.4.0
* py-cython: upperbounds for Python versions
* fix py-gevent nonsense
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* CI configuration boilerplate reduction and refactor
Configuration:
- New notation for list concatenation (prepend/append)
- New notation for string concatenation (prepend/append)
- Break out configuration files for: ci.yaml, cdash.yaml, view.yaml
- Spack CI section refactored to improve self-consistency and
composability
- Scripts are now lists of lists and/or lists of strings
- Job attributes are now listed under precedence ordered list that are
composed/merged using Spack config merge rules.
- "service-jobs" are identified explicitly rather than as a batch
CI:
- Consolidate common, platform, and architecture configurations for all CI stacks into composable configuration files
- Make padding consistent across all stacks (256)
- Merge all package -> runner mappings to be consistent across all
stacks
Unit Test:
- Refactor CI module unit-tests for refactor configuration
Docs:
- Add docs for new notations in configuration.rst
- Rewrite docs on CI pipelines to be consistent with refactored CI
workflow
* Script verbose environ, dev bootstrap
* Port #35409
By setting the traversal depth to 1, only specs matching the changed
package and direct dependents of those (and of course all dependencies
of that set) are removed from pruning candidacy.
* py-deap: newer version can use newer setuptools
* Update var/spack/repos/builtin/packages/py-deap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The overlapping dependency version ranges caused the concretizer to pick
version 7.1 even though version 8.0 is available:
```
==> Error: No version for 'cubelib' satisfies '@4.7.1' and '@4.8'
```
Moreover, Score-P 8.0 requires libbfd:
```
configure: error: bfd.h required
```
* Provide openmp from rocm-open-extras when tensile uses openmp
* Correcting audit check failure in rocm-openmp-extras dependency
* Fixing style check error
* rocm-openmp-extras required instead of llvm-amdgpu both varient
When untouched spec pruning is enabled, specs possibly affected
by a change cannot be pruned from a pipeline.
Previously spack looked at all specs matching changed package
names, and traversed dependents of each, all the way to the
environment root, to compute the set of environment specs
possibly affected by a change (and thus, not candidates for
pruning).
With this PR, when untouched spec pruning is enabled, a new
environment variable can control how far towards the root spack
traverses to compute the set of specs possibly affected by a
change. SPACK_UNTOUCHED_PRUNING_DEPENDENT_DEPTH can be set
to any numeric value before the "spack ci generate" command
is called to control this traversal depth parameter. Setting
it to "0" traverses only touched specs, setting it to "1"
traverses only touched specs and their direct dependents, and
so on. Omitting the variable results in the previous behavior
of traversing all the way to the root. Setting it to a negative
value means no traversal is done, and always yields an empty
set of possibly affected specs (which would result in the max
pruning possible).
Currently `spack buildcache create` creates compressed tarballs that
differ between each invocation, thanks to:
1. The gzip header containing mtime set to time.time()
2. The generated buildinfo file which has a different mtime every time.
To avoid this, you have to explicitly construct GZipFile yourself, since
the Python API doesn't expose the mtime arg, and we have to manually
create the tarinfo object for the buildinfo metadata file.
Normalize mode: regular files & hardlinks executable by user, dirs, symlinks: set 0o755 permissions in tarfile; other files use 0o644
* "new py-thop package"
* [@spackbot] updating style on behalf of Sangu-Mbekelu
* Update package.py
modified the url and dependencies
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* py-openmesh: new package
* Update var/spack/repos/builtin/packages/py-openmesh/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit formalizes `satisfies(lhs, rhs, strict=True/False)`
and splits it into two functions: `satisfies(lhs, rhs)` and
`intersects(lhs, rhs)`.
- `satisfies(lhs, rhs)` means: all concrete specs matching the
left hand side also match the right hand side
- `intersects(lhs, rhs)` means: there exist concrete specs
matching both lhs and rhs.
`intersects` now has the property that it's commutative,
which previously was not guaranteed.
For abstract specs, `intersects(lhs, rhs)` implies that
`constrain(lhs, rhs)` works.
What's *not* done in this PR is ensuring that
`intersects(concrete, abstract)` returns false when the
abstract spec has additional properties not present in the
concrete spec, but `constrain(concrete, abstract)` will
raise an error.
To accomplish this, some semantics have changed, as well
as bugfixes to ArchSpec:
- GitVersion is now interpreted as a more constrained
version
- Compiler flags are interpreted as strings since their
order is important
- Abstract specs respect variant type (bool / multivalued)
* New package: py-imbalanced-learn
* Fix typo
* [@spackbot] updating style on behalf of meyersbs
* Update var/spack/repos/builtin/packages/py-imbalanced-learn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update/fix py-meldmd; update openmm
* Restrict filter_file based on openmm version
* Updates based on Adam's feedback
* [@spackbot] updating style on behalf of meyersbs
* Break up long filter_file
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Cray fortran compiler names fortran modules in uppercase by
default. Compile with the "-ef" flag to produce the lowercase
name that singularity-eos is expecting.
Two fixes:
1. `-Wl,a,b,c,d` is a comma separated list of linker arguments, we
incorrectly assume key/value pairs, which runs into issues with for
example `-Wl,--enable-new-dtags,-rpath,/x`
2. `-Xlinker,xxx` is not a think, so it shouldn't be parsed.
* httpie: add v3.2.1
* Add additional 3.2.1 dependencies to httpie
* Add version condition to dependency
* Reorder dependencies for efficiency
* Update var/spack/repos/builtin/packages/httpie/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* awscli: add v1.27.84
* Add botocore dependency to awscli
* Update var/spack/repos/builtin/packages/awscli/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-botocore@1.29.84 dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update mda dependencies
* apply black
* Update var/spack/repos/builtin/packages/py-gsd/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove numpy upper bound
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gsd/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update proj
* re-add autotools support
* style
* Setup env in builders
* Drop direct windows conflict for older versions
* Default to CMake
Add new style class definiton
* Proj: setup_run_environment in package not builder
* Proj: move run env changes to pkg, rm cmake arg
* Set PROJ_LIB during build
* Style
* Rm redundant configure arg
Currently, if two compilers with the same spec differ on the flags, the concretizer will:
1. mix both sets of flags for the spec in the ASP program
2. error noting that the set of flags from the compiler (both of them) doesn't match the set from the lower priority compiler
This PR fixes both -- only flags from the highest priority compiler with a given spec are considered.
* py-elasticsearch: new versions
Also add py-elastic-transport as a new dependency
* py-elasticsearch: py-urllib3 is no longer a dependency
* Update var/spack/repos/builtin/packages/py-elasticsearch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`mypy` only understands `sys.platform == "win32"`, not indirect assignments of that
value to things like `is_windows`. If we don't use the accepted platform checks, `mypy`
registers many Windows-only symbols as not present on Linux, when it should skip the
checks for platform-specific code.
* add 2.14.2 py-astroid version
* add py-pylint 2.26.2
* fix black
* fix py-dill depends_on
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix py-astroid minor versionning
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* modify typing_extensions depends_on
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Start using paths found in extra_rpaths in compilers.yaml when building
* running black and changing maintainer list
* changing import order to pass isort
---------
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
Update `spack.util.environment` to remove legacy idioms.
* Remove kwargs from method signature and use a class for traces
* Uppercase a few global variables
* spack.util.environment: add type-hints
* Improve docstrings
* Fixed most style issues reported by pylint
* py-ipdb: updating versions
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* py-ipdb: fixing versions problem and deleting 10.1 which is too old for Python > 3.6
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: removed useless dependencies
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: missing @
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e3sm-scorpio: add e3sm-scorpio package
This is the Scorpio package from the e3sm.org site.
* fixed style errors
* removed unneeded dependency on cmake
Use correct `shlib_symbol_version` for Julia 1.8, work around issue where libuv-julia's git checkout has arbitrary mtime, causing make to regenerate configure scripts, sometimes.
* Add a `py-gmxapi` package.
This package provides the Python package for the GROMACS
public API. The Python package is not strongly coupled to
a specific GROMACS _version_, but its compiled extension module
is strongly coupled to a specific GROMACS _installation_.
* Update conflict info.
In order to allow `^gromacs@2022.1` while rejecting `^gromacs@2022`,
we need to compare to `gromacs@2022.0`.
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review.
* Simplify build system structure.
* Update dependencies for completeness.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Per code review, pretend gmxapi <0.4 doesn't exist, for simplicity.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
a shared library /lib64/libcxi.so, which seems to also appear on other
non-slingshot systems. This patch also checks to make sure that there
is a Cray programming enviornment in /opt/cray/pe in addition to the
shared library.
* py-pygments 2.12; fix py-docutils, again
`2.12` is the latest for which our style hack works, beyond that we need
our own package to make a plugin.
Old docutils needs old setuptools
* py-setuptools is always a dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update the range
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Intel OneAPI's extreme pickiness continues to bring out
buggy/noncompliant code.
This patch fixes an error in the configure.in embedded 'c' test code
and also in a file with an initialized, but unused, variable.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Updates to release 0.6.
* Dep updates
* Dep version fix
* Another version fix
* Fix typo
* UFL version fix
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fenics-ffcx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Some updates following review
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* More updates
* More updates
* build/run updates
* Small fix
* Fix version number.
* specify lower bounds for python dependencies
* address style issues
* address style issues
* address PR comments
* amend setuptools dependency to be of type build only
* amend setuptools dependency to be of type run and build for ffcx and ufl
* add build dependency to ensure import tests pass
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
* py-dask-mpi: new package with dependencies
* py-hatch-jupyter-builder is not needed after all
* skip_modules seems cleaner
* Update var/spack/repos/builtin/packages/py-jupyter-server-proxy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-simpervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Flags `-fallow-argument-mismatch -fallow-invalid-boz` set in `FFLAGS`/`FCFLAGS`
environment variables don't really have effect in older versions of WRF, we need
to force them in the compiler wrappers.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
With the last merge request for OOMMF [1], the intention was to have version
20b0_20220930 as the preferred version, and provide 20b0_20220930-vanilla as an
additional version for the unlikely case anybody needed that.
I made the (wrong) assumption that the `version` listed first in the `package.py` file
would be the preferred version. This merge request is to correct that by
explicitly tagging the preferred version with `preferred=True`.
[1] https://github.com/spack/spack/pull/33072/files
If the docbook packages
- docbook-xml
- docbook-xsl
are installed in a spack environment view the catalog files will be in
conflict in the view directory. This PR resolves that by adding an
appropriate prefix to each catalog name so that they are unique in the
view. The resulting XML_CATALOG_FILES environment variable will then be
able to point to both of them.
1. add version 2023.03.01
2. add variant 'python' that supports unwinding python source
3. clean up some things with the cray variant
4. require the latest libmonitor
5. fix sha256 checksum for url patch
6. delete rocm 5.3 from older versions
* cleaned up style, linked to external htslib
* removed htslib/bcfrools/samtools deps, use bundled libs instead
the pysam package includes the necessary libs to link to, so it wasn't even using linked libs when building
* fixed style
* revert to using external htslib
currently uses bundled samtools and bcftools, and there is no way to use external versions for those dependencies
* added libs property to htslibs package
added support for lib64
* added htslib name
* onednn: add variant to use Arm Compute Library on aarch64
* Update cmake version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Shorten macro definition
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update cpu/gpu_runtime variants
* Update acl variant when 1.7+
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of annop-w
* Add dependencies for new runtimes
* Fix dependency package name to oneapi-level-zero
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: new version 1.10.*, 2.0.*
Lots of changes in 2.0.*, see https://github.com/scikit-hep/awkward/releases. This will need some extra testing.
* py-awkward: hatchling
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* py-scikit-build-core: new and improved py-scikit-build
* py-awkward-cpp: new package
* py-awkward: add depends_on py-awkward-cpp
* py-awkward: depends_on py-packaging
* py-awkward-cpp: new versions pinned by py-awkward
* py-scikit-build-core: additional depends_on
* py-awkward: branch master deprecated
* py-pytest-subprocess: new package
* py-pytest: new version 7.2.1
* py-scikit-build-core: add tests dependencies
* [@spackbot] updating style on behalf of wdconinc
* py-scikit-build-core: two more test dependencies
* py-pytest: depends_on py-exceptiongroup
* py-awkward: add pytest support
* py-pytest: suggestions from review
* py-scikit-build-core: suggestions from review
* Update var/spack/repos/builtin/packages/py-awkward-cpp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: depends_on pyyaml when @:1, order old deps last
* [@spackbot] updating style on behalf of wdconinc
* py-awkward: move some opt deps to test, order test deps
* py-awkward: remove test dependencies
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
if dump file existed it was not truncating the file, resulting in
a file with unaltered filesize, with the new content at the beginning,
"padded" with the tail of the old content, since the new content was
not enough to overwrite it.
`colify` is an old module in Spack that still uses `**kwargs` liberally.
We should be more explicit. Doing this eliminates the need for many
checks (can't pass the wrong arg if it isn't allowed) and makes the
function documentation more clear.
Fixes a bug introduced in 44ed0de8c0
where the push method of binary_distribution now takes named args
include_root and include_depedencies, to avoid the **kwarg hole.
But the call site wasn't update and we passed a dict of keys/values instead
of arguments, which resulted in a call like this:
```
push(include_root={"include_root": True, "include_dependencies": False})
```
This commit fixes that, and adds a test to see if we push the correct packages.
This error shows up a lot, typically it's harmless because an error
happened before the source build even started, in which case we don't
have build logs to copy. So, warn instead of error, cause it distracts
from the actual CI error.
Currently we attempt to setup the build environment even when
dependencies are not installed, which typically results in error while
searching for libraries or executables in a dependency's prefix.
With this change, we get a more user friendly error:
```
$ spack build-env perl
==> Error: Not all dependencies of perl are installed, cannot setup build environment:
- qpj6dw5 perl@5.36.0%apple-clang@14.0.0+cpanm+open+shared+threads build_system=generic arch=darwin-ventura-m1
- jq2plbe ^berkeley-db@18.1.40%apple-clang@14.0.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=darwin-ventura-m1
...
$ echo $?
1
```
* Allow users to specify root env dir
Environments managed by spack have some advantages over anonymous Environments
but they are tucked away inside spack's directory tree. This PR gives
users the ability to specify where the environments should live.
See #32823
This is also taken as an opportunity to ensure that all references are to "managed environments",
rather than "named environments". Prior to this PR some references to the latter persisted.
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* Update exago w/ 1.5.1 and small updates to hiop.
* Fix styling.
* Add RAJA back to ExaGO package.
* Update RAJA requirement for ExaGO and HiOp.
* Update last RAJA requirement in HiOp.
* Add new sphinx rtd theme release 1.2.0
The new release helps with supporting more recent version of docutils
* set docutils officially supported version
* add jquery dependency for sphinx-rtd-theme
* add conflict with jquery version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* correct dependency
* fix version dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* set sphinx version
* fix sha256
* add version for flit-core
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The call:
```
x.satisfies(y[, strict=False])
```
is commutative, and tests non-empty intersection, whereas:
```
x.satsifies(y, strict=True)
```
is not commutative, and tests set-inclusion.
There are 2 fast paths. When strict=False both self and other need to
be concrete, when strict=True we can optimize when other is concrete.
a) It's used by site administrators, so it's niche
b) If it's used by site administrators, they likely need to modify the config anyhow, so the default config only serves as an example to get started
c) it's too arbitrary to enable tcl, but disable lmod
Spack generally ignores file-file projection clashes in environment
views, but would eventually error when linking the `.spack` directory
for two specs of the same package.
This leads to obscure errors where users have no clue what the issue is
and how to fix it. On top of that, the error comes very late, since it
happens when the .spack dir contents are linked (which happens after
everything else)
This PR improves that by doing a quick check ahead of time if clashes
are going to be anticipated (by simply checking for clashes in the
projection of each spec's .spack metadir). If there are clashes, a
human-readable error is thrown which shows two of the conflicting specs,
and tells users to user unify:true, view:false, or set up custom
projections.
* add pytng
* black
* add setuptools
* fix
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pytng/package.py
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Kokkos when compiled by spack without +wrapper could potentially capture the spack compiler wrappers, resulting in cmake configs and kokkos_launch_compiler trying to run the spack compiler wrapper after installation.
The checksum exception was not detailed enough and not reraised when using cache only, resulting in useless error messages.
Now it dumps the file path, expected
hash, computed hash, and the downloaded file summary.
Batch scripts in general will not function without carriage return line
endings on Windows. We rely on these scripts to support cmd, so we
should not allow these scripts to be converted to lf.
Note: Windows 11 supports lf line endings due to the use of Windows
Terminal. Once support for Windows 10 is dropped, this change can be
reverted.
When running many concurrent spack install processes that need to write
to the db, Spack regularly times out. This is because writing to the DB
after another process has written to it requires deserialization of the
db, mutating it in memory, and serializing it again, which takes some
time. On top of that, I believe there's a 1 second retry when a write
lock cannot be obtained, so I think this means only 3 processes can
really write to the DB at the same time before timing out.
* Style: black 23, skip magic trailing commas
* isort should use same line length as black
* Fix unused import
* Update version of black used in CI
* Update new packages
* Update new packages
* Update package.py
Initial new stuff
* Update package.py
* Update package.py
* Update package.py
* fix targets
* non-llvm backends
* ooops
* fix style
* Somehow that was not caught?
Somehow that was not caught?
* style
* Last fix
make capitalization consistent with Halide not LLVM...
* py-cmake-format: new version, new variants
* Update var/spack/repos/builtin/packages/py-cmake-format/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cufflinks: new package version with 0.17.3
* Update var/spack/repos/builtin/packages/py-cufflinks/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Specs that did not contribute any files to an env view caused a problem
where zip(specs, files grouped by prefix) got "out of sync", causing the
wrong merge map to be passed to a package's `add_files_to_view`, which
specifically caused an issue where *sometimes* bin/python ended up as a
symlink instead of a copy.
One such example is kokkos + kokkos-nvcc-wrapper, as the latter package
only provides the file bin/nvcc_wrapper, which is also added to view by
kokkos, causing kokkos-nvcc-wrapper to contribute 0 files.
The test feels a bit contrived, but it captures the problem... pkg a is
added first and has 0 files to contribute, pkg b adds a single file, and
we check if pkg b receives a merge map (and a does not).
* pfunit: add v4.6.3
* pfunit: use CMakePackage methods to define arguments
* pfunit: deprecate v3.X, make a variant conditional
* pfunit: simplify setting up environment variables
Reading the docs it seems only v3
needs F90_VENDOR to be set
* pfunit: fix option names
The names set before were unused
* pfunit: shared libraries seem not to be supported
See https://github.com/Goddard-Fortran-Ecosystem/pFUnit/issues/308#issuecomment-874725759
* Add py-mlflow and its dependencies
* mlflow: fix syntax error in package.py
* py-mlflow: cleanup
Process review remarks, add missing dependencies, add skinny variant
* Apply suggestions from code review
* Fix flake8 issues
* More formatting fixes
* Fix py-waitress dependency version
* py-mlflow: platform-specific dependency
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Process review remarks
* Fix typo in dependency version
* py-shap: fix dependencies
* py-arrow: fix dependencies
* py-slicer: remove py-setuptools explicit version
* py-pyarrow: dataset variant and pass options through environment
It appears there are some issues when using `pip install` instead of
`python setup.py` - this setup_build_environment should fix that.
* py-pyarrow: review remark
* Decouple setup_build_environment from install_options
* py-pyarrow: style
* Bump licenses to 2023
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
`spack gc` removes build deps of explicitly installed specs, but somehow
if you take one of the specs that `spack gc` would remove, and feed it
to `spack uninstall /<hash>` by hash, it complains about all the
dependents that still rely on it.
This resolves the inconsistency by only following run/link type deps in
spack uninstall.
That way you can finally do `spack uninstall cmake` without having to
remove all packages built with cmake.
Default package requirements might contain
variants that are not defined in each package,
so we shouldn't verify them when emitting facts
for the ASP solver.
Account for group when enforcing requirements
packages:all : don't emit facts for requirement conditions
that can't apply to current spec
* Update package.py
Several libraries are need to be present at run time so that the code can be run in parallel.
I have added them as dependencies and to LD_LIBRARY_PATH. Orca comes as a binary so the libraries cannot be added as RPATH at compilation time.
Also, orca 5.0.3 was compiled against 4.1.1, not 4.1.2.
* fortls
* Update var/spack/repos/builtin/packages/py-fortls/package.py
* review
* Update var/spack/repos/builtin/packages/py-fortls/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fixes
* review
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new py-amplpy package
* [@spackbot] updating style on behalf of sm2939
* Update package.py
* Rename var/spack/repos/builtin/py-amplpy/package.py to var/spack/repos/builtin/packages/py-amplpy/package.py
* Edited file to change copyright year/dependencies and changed the directory of the file
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
#35098 added the correct extraction of toolset version for the MSVC
compiler. This updates the associated method in MSBuilder to retrieve
the (now correct) property.
Meme 4.5.0 has the first occurrence of the string
```
use XML::Simple
```
I found this by doing a binary search manually extracting tarballs until `grep` came up empty.
* new ampltools package
* [@spackbot] updating style on behalf of sm2939
* Update and rename var/spack/repos/builtin/py-ampltools/package.py to var/spack/repos/builtin/packages/py-ampltools/package.py
Edited file to change copyright year/dependencies and edited directory
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* Add Score-P 8.0 and Cube 4.7/4.8 packages.
* Score-P 8.0 requires 4.8, not 4.7, Cube packages
* Add maintainer
* Add CUDA and HIP variants. Add version checks for CUDA (Score-P 8 requires CUDA 7), ROCm (variant only valid as of Score-P 8), and MPI (Score-P 7 requires at least version 2.2 of the MPI standard).
* Deprecate everything pre-7.0.
* Fix HIP dependencies and enable CUDA and HIP variants for configure.
* Deprecate OTF2 pre-2.3 and Cube pre-4.6
* Add "fake" mpi compiler wrappers to msmpi: msmpi doesn't actually
provide wrappers, so this just assigns the wrappers to be whatever
compiler that a dependent is using. Packages referencing the
wrappers would otherwise break. This is assumed to be workable
because build scripts will need to assemble appropriate information
to pass to the compiler anyway
* Fix msmpi detection stanza ('executable' is not the correct name of
the property)
* Fix compiler pkg dereference
* add initial package.
* Update package.py
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* Hopefully this will be fine.
* Update package.py
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/tiramisu/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cvise: new package
* cvise: colordiff as optional dependency
* cvise: remove old versions and correctly name master version
* cvise: update license date
* cvise: use maintainers directive
* Remove @olupton as maintainer
After live discussion: it's been too long since he did anything with this package.
* add halide package.
* some style changes.
* small fix
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
add comment to requirements.txt
* Update package.py
Fix version order.
* Update package.py
style
* Update package.py
Removed unneeded vars.
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/halide/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Fix some deps
* Update package.py
* Fix finding llvm cmake info
* Update package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR enables the successful execution of the spack binary cache
tutorial on Windows. It assumes gnupg and file are available (they
can be installed with choco).
* Fix handling of args with quotes in spack.bat
* `file` utility can be installed on Windows (e.g. with choco): update
error message accordingly
I don't know if this is new in version 7.0, but to build `info`, which is a required executable at the end of the recipe, it is necessary to have a terminal library, otherwise you get
```
[...]
checking for tgetent in -ltinfo... no
checking for tgetent in -lncurses... no
checking for tgetent in -lcurses... no
checking for tgetent in -ltermlib... no
checking for tgetent in -ltermcap... no
checking for tgetent in -lterminfo... no
configure: WARNING: info needs a terminal library, one of: tinfo ncurses curses termlib termcap terminfo
[...]
configure: WARNING: Could not find a terminal library among tinfo ncurses curses termlib termcap terminfo
configure: WARNING: The programs from `info' directory will not be built.
```
then compilation runs, `info` is not built and installation fails according to Spack because the required executable is missing.
* Support packages for using scitokens on OSG
The Open Science Grid (OSG) encourages scitokens to provide
certain services (e.g. writing to xrootd). Spack already
supports this through scitokens-cpp and xrootd +scitokens-cpp.
This adds py-htgettoken, a python utility to get a scitoken
from a vault through web authentication. To support htgettoken,
this also adds py-gssapi.
This also adds the OSG CA cert collection which is typically
at /etc/grid-security but pointed to in user installations by
the X509_CERTS_DIR variable.
This allows userspace through spack for functionality that
otherwise depends on installing the RPMs provided by OSG.
* fine, I'll fix style myself then
* fix maintainers
* py-gssapi: version before depends_on
* remove list_url
* add documentation on reason for git describe version numbers
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* better BEARER_TOKEN definition
* import os
* remove older version that don't build with setuptools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
At least with ZSH, prefix inspections containing `./bin` result in a
`$PREFIX/./bin` and result in strange `$PATH` handling.
I.e., `module load git` will prepend `/path/to/git/./bin`, `which git`
will find the right executable, but `git --version` will print the
system one. Normalize the relative path to avoid this behavior.
See also spack/spack#31867.
* changes to enable LLVM_ENABLE_RUNTIMES for libcxx and libcxxabi
* remove version update for 5.3.0 as it is done thru PR #33320 to enable
ci and reviews
* initial commit for rocm-5.4.0 release
* update the versions for more packages for 5.4.0 release
* update the gallium patch for mesa for libllvm-15 for ROCm-5.4.0 release
* update rocm-openmp-extras and rocwmma recipes for 5.4.0 release
* fix build error for rocfft for 5.4.0
* address review comments for rocfft for 5.4.0 change
* undo the removal of the older patch file
* bump up the version for hipfft for 5.4.0
* fix the failure after the merge with develop
* add recipes updates for 5.4.0 for migraphx.miopen-hip,miopen-opencl
* address the review comments on the mesa patch.update the rdc package for
5.4.0 release
* fix style errors
* acts: new versions 21.1.1, 22.0.1, 23.0.0
New versions:
- [major 23.0.0](https://github.com/acts-project/acts/compare/v22.0.0...v23.0.0):
- new option `ACTS_BUILD_PLUGIN_GEANT4` -> enabled with existing variant `geant4`
- new option `ACTS_BUILD_EXAMPLES_BINARIES`:
- it is my understanding that the binaries for examples are deprecated (in favor of python examples); warnings to this effect have been printed for a few versions, and now the building of binaries is disabled by default,
- rather than introducing a variant to enable deprecated behavior for only one or two versions, I propose that we just follow the default and keep this disabled.
- [bugfix 22.0.1](https://github.com/acts-project/acts/compare/v22.0.0...v22.0.1) (no build system changes)
- [bugfix 21.1.1](https://github.com/acts-project/acts/compare/v21.1.0...v21.1.1) (no build system changes)
* acts: correct 23.0.0 sha
Co-authored-by: Hadrien G. <knights_of_ni@gmx.com>
As of 2.4.113, the flag for man-pages is now a feature,
so true/false is now enabled/disabled. Other similarly
changed options are not used in the spack recipe (i.e.
experimental kms drivers).
* qt: new versions 6.4.0, 6.4.1
- New libpsl vendored dependency in qt-base.
- New embree and tinyexr dependency in qt-quick3d.
We need to figure out a better way to deal with these vendored
dependencies in src/3rdparty. Removing them was a way to make sure
they are not used unintentionally. Many of these dependencies cannot
be overridden with a QT_FEATURE_system_* flag and are included directly
in cpp files. Many change versions from release to release, so even if
they use system (ie spack managed) versions we need to support this in
the depends_on lines.
What we can rely on?
- src/3rdparty is where vendored stuff is stored
- not much else...
Possible ways to deal with this:
- Change vendor_deps_to_keep to dict with versions, eg
```
vendor_deps_to_keep = {
"xatlas": "@6:",
"embree": "@6.4:",
"tinyexr": "@6.4:",
}
```
- Similarly introduce system_deps_to_use:
```
system_deps_to_use = {
"assimp@5.2:": "@6:",
}
```
and derive depends_on and QT_FEATURE_system_* from this dict.
* qt-*: new version 6.4.2, invert vendored pkgs logic
* qt-base: fix vendor_deps_to_avoid typo
* qt-*: move lots into QtPackage base layer
* py-minkowskiengine: new package (sparse tensor autodiff by Nvidia)
This python package (with cuda support) provides torch support for sparse
tensors. The `pybind11` headers are not found without the patch to `setup.py`.
* [@spackbot] updating style on behalf of wdconinc
* py-minkowskiengine: depends_on numpy, pybind11 type=link; no patch
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
The fastqc script was using the system perl. This PR sets the script to
use the spack built/provided perl. This PR also removes the code that
adds the java path. That should be handled by module loading as far as I
know.
* Add HDF5 version 1.13.3.
* Remove maintainers no longer with The HDFGroup.
* Add version hdf5-vol-async@1.4
* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.
* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.
* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.
* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.
* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.
* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.
* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.
* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.
* Don't guard ParaView patch on HDF5 variant
ParaView always needsd HDF5 and ignores the variant.
* py-h5py: Newer versions of HDF5 introduce breaking API changes
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
* Add trilinos-solvers variant to nalu-wind package.
This allows nalu-wind to be built against a trilinos installation
which doesn't have amesos2, belos, ifpack2, or muelu enabled, if
the nalu-wind user provides the spec 'nalu-wind@master~trilinos-solvers'
Support for these solver-packages remains on by default.
* Fixed a style issue reported by CI.
* Incorporate change in wording suggested from review comments.
... to clarify that at least one, or both, of hypre and/or
trilinos-solvers must be enabled. The error condition is if
both are disabled.
* That style checker is picky...
* It really did want a trailing comma...
* py-jinja2-cli: new package
* Update var/spack/repos/builtin/packages/py-jinja2-cli/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-docker@5:
* [@spackbot] updating style on behalf of spoutn1k
* Ignore `tls` variant
* Update var/spack/repos/builtin/packages/py-docker/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* `py-docker`: `py-paramiko` version fix
---------
Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The gfx906:xnack- and gfx908:xnack- targets were introduced in ROCm 4.1
and replaced gfx906 and gfx908 as default build targets, but the library
can still be built for gfx906 and gfx908 if requested.
* e4s: restore builds builds
* gitlab ci: allow UO to build protected binaries for signing
* use newer image; comment out failing builds
* gitlab-ci: Some tweaks for e4s power builds
- fix tags (no longer require generate jobs to run on aws)
- fix resource requests for generation jobs resource requests
- remove SPACK_SIGNING_KEY from protected power build jobs
- update UO signing key path
- change the CDash build group to reflect stack name
- retry pipeline generation jobs *always*
* correct double packages: section
* gitlab-ci:script: modernize
* remove new gnu make, not for ppc64le
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
* Added e4s-cl package
* Version order change
* Added e4s-cl dependencies
* Added python-sotools dependency
* [@spackbot] updating style on behalf of spoutn1k
* Add missing versions to py- packages
* Fix style
* [@spackbot] updating style on behalf of spoutn1k
* Update var/spack/repos/builtin/packages/e4s-cl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/e4s-cl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-python-sotools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add docker removing patch for e4s-cl
Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nexusforge: add with dependencies
* py-pyshacl, py-sseclient: more style
* py-hjson, py-nexus-sdk, py-nexusforge, py-puremagic: more style
* py-pyshacl: license update
* py-nexusforge, py-prettytable, py-pyshacl: review remarks
* py-nexusforge: make the variant mean something
Too hasty to commit...
* py-ipyparallel: add 8.4.1, which builds with py-hatchling
* py-ipyparallel: copyright and redundant py-setuptools dependency
* py-ipyparallel: py-packaging was dropped after 8.0.0
fixes#34879
This commit adds a new maintainer directive,
which by default extend the list of maintainers
for a given package.
The directive is backward compatible with the current
practice of having a "maintainers" list declared at
the class level.
Move the relocation of binary text in its own class
Drop threaded text replacement, since the current bottleneck
is decompression. It would be better to parallellize over packages,
instead of over files per package.
A small improvement with separate classes for text replacement is that we
now compile the regex in the constructor; previously it was compiled per
binary to be relocated.
The regex doesn't actually work because dollar signs and parentheses have to be
escaped. Also, compiling with OpenMPI requires defining the macro
`MPI2SUPPORT`.
This commit makes explicit the format version of the spec file
we are reading from.
Before there were different functions capable of reading some
part of the spec file at multiple format versions. The decision
was implicit, since checks were based on the structure of the
JSON without ever checking a format version number.
The refactor makes also explicit which spec file format is used
by which database and lockfile format, since the information is
stored in global mappings.
To ensure we don't change the hash of old specs, JSON representations
of specs have been added as data. A unit tests checks that we read
the correct hash in, and that the hash stays the same when we
re-serialize the spec using the most recent format version.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
```
File ".../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/site-packages/h5py/_hl/base.py", line 19, in <module>
from collections import (Mapping, MutableMapping, KeysView,
ImportError: cannot import name 'Mapping' from 'collections' (.../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/collections/__init__.py)
```
Fixed in https://github.com/h5py/h5py/pull/1069 which was first merged
in v2.9.
* py-flatten-dict: require poetry to build.
The sources seem to contain a bundled, auto-generated `setup.py`.
Building with `pip` insist on using Poetry as mentioned in
`pyproject.toml`, so require it as a build dependency.
* Update var/spack/repos/builtin/packages/py-flatten-dict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-flatten-dict/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Currently we print "sha256 checksum failed for [file]. Expected X but
got Y".
This PR extends that message with file size and contents info:
"... but got Y. File size = 123456 bytes. Contents = b'abc...def'"
That way we can immediately see if the file was downloaded only
partially, or if we downloaded a text page instead of a binary, etc.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
py-scipy 1.6 and older come with pre cython-ized files that
use the _PyGen_Send symbol that was removed from python 3.10.0.161,
so do not build these old versions with python 3.10.1 and later
Parts of libgcrypt should not be optimized with -O1/2/3, so it's best to
let the build system do that; the build system cannot know the compiler
wrapper would inject optimization flags
When running unit-test the test/ci.py module is leaving
garbage (help.sh, test.sh files) in the current working
directory.
This commit changes the current working directory to a
temporary path before those files are created.
* freeimage: fails to compile with c++17, use c++14
Only `opencascade` when a (non-default) variant depends on `freeimage`, which seems to have gone unmaintained. There are c++17 standard violations [[1]]( https://en.cppreference.com/w/cpp/language/except_spec) in the code, so we can at most expect c++14. Since some compilers default to c++17 (gcc-12) we need to be explicit.
* freeimage: install directly in prefix
* freeimage: fix inverted patch
* environments: don't rewrite relative view path, expand path on cli ahead of time
Currently if you have a spack.yaml that specifies a view by relative
path, Spack expands it to an absolute path on `spack -e . install` and
persists that to disk.
This is rather annoying when you have a `spack.yaml` file inside a git
repo, cause you want to use relative paths to make it relocatable, but
you constantly have to undo the changes made to spack.yaml by Spack.
So, as an alternative:
1. Always stick to paths as they are provided in spack.yaml, never
replace them with a canonicalized version
2. Turn relative paths on the command line into absolute paths before
storing to spack.yaml. This way you can do `spack env create --dir
./env --with-view ./view` and both `./env` and `./view` are resolved
to the current working dir, as expected (not `./env/view`). This
corresponds to the old behavior of `spack env create`.
* create --with-view always takes a value
All packages with explicit Windows support can be found with
`spack list --tags=windows`.
This also removes the documentation which explicitly lists
supported packages on Windows (which is currently out of date and
is now unnecessary with the added tags).
Note that if a package does not appear in this list, it *may*
still build on Windows, but it likely means that no explicit
attempt has been made to support it.
* nextflow recipe: added latest stable version
* tower-cli recipe: added latest release
* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli
* recipes nf-tower-agent and nf-tower-cli: small fix
* nf-core-tools recipe: added most py- dependencies
* nf-core-tools: recipe without galaxy-tool-util (for testing)
* fixed typos in py-yacman recipe
* fixed typos in py-pytest-workflow recipe
* fixed typo in nf-core-tools recipe
* fixed typos in py-yacman recipe
* fixes in recipes for py-questionary and py-url-normalize
* fixes to py-yacman recipe
* style fixes to py- packages that are dependencies to nf-core-tools
* fix in py-requests-cache recipe
* added missing dep in py-requests-cache recipe
* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper
* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util
* nf-core-tools: new version with extra dependency
* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps
* nextflow and nf-core-tools packages: added my self as maintainer
* style fixes
* style fix for nf-core-tools recipe
* added license to py-logmuse recipe
* audit fixes
* style fix after audit fix
* py-galaxy-tool-util: added deps 1st bunch
* audit/style fixes, including adding missing dep package
* more audit/style fixes
* more more audit/style fixes
* moooore audit fixes
* py-galaxy-tool-util: dependencies 2nd chunk
* silly audit fix
* py-galaxy-util deps: 3rd bunch - first 20 done
* fixes
* style fix
* py-galaxy-tool-util: 4th bunch of deps
* stashing dep recipe backbones for py-galaxy-tool-util
* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util
* nf-core-tools: adding also py-galaxy-util, as wheel
* fix
* nextflow: added latest bugfix version
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* nf-core-tools pr: 1st bunch of review edits
* nf-core-tools: 2nd bunch of review edits
* adding back tower-agent and tower-cli as deprecated
* nf-core-tools: 3rd bunch of review edits
* small style fix
* prepping py-galaxy-tool-util for further work
* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar
* audit fixes
* updates to py-galaxy-tool-util and its deps, still 2 to work on
* one style fix
* updated recipe for py-galaxy-util
* updated recipe for py-pulsar-galaxy-lib
* typo fix
* shasum fixes
* updated py-sqlalchemy from develop
* added newest versions (today) for nf-tower-agent and nf-tower-cli
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adding 2nd bunch of nf-core deps from update/nextflow-tools
* adding 3rd bunch of nf-core deps from update/nextflow-tools
* 4th chunk of nf-core deps from update/nextflow-tools
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pebble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gunicorn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-parsley/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-gxformat2: added comment
* py-lagom: now using github tarballs
* fix for py-lagom
* adding missing deps to py-fastapi-utils
* another fix to py-lagom
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-lagom/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-supervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fixes from PR review
* adding missing deps, from PR review
* py-galaxy2cwl from github tarball, as per PR review
* fix to py-tuswsgi, as per PR review
* nf-tools: edits from PR review
* adding 3x more galaxy deps
* fix
* fixing circular dep of py-poetry-plugin-export with py-poetry
* added newest nf-core-tools version
* Update var/spack/repos/builtin/packages/py-galaxy-util/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix in py-poetry-plugin-export
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`.
We no longer set `CPATH` and other destructive environment variables (like
`LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python.
Also, the way `python` sets `CPATH` causes issues. Because it does a header search to
find directories containing headers, if you bootstrap `mypy` or other style tools on a
fresh Ubuntu image with *no* python devel headers installed, you'll get an error like
this when trying to load the thing you just installed:
```console
[root@980de539843d /]# spack -b load py-mypy
==> Error: Unable to locate python headers in any of these locations:
/usr/include/python3.6m
/usr/include/3.6
/usr/Headers
```
The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work,
so we're failing unnecessarily here.
- [x] remove `setup_run_environment()` from `python/package.py`
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes
more sense to call the flag `--make-prefix` and alias the old flag
`--make-target-prefix` to it.
1. add variant cray-static, older crays build hpcprof-mpi static,
newer ones build dynamic.
2. move URL patches from github to gitlab.
3. add workaround for a bug where a file is mistakenly overwritten.
4. add conflict for hpcprof-mpi at 2022.10.01.
* [@spackbot] updating style on behalf of mwkrentel
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
Normally when using external packages in concretization, Spack ignores
all dependencies of the external. #33777 updated this logic to attach
a Python Spec to external Python extensions (most py-* packages), but
as implemented there were a couple issues:
* this did not account for concretization groups and could generate
multiple different python specs for a single DAG
* in some cases this created a fake Python spec with insufficient
details to be usable (concretization/installation of the
extension would fail)
This PR addresses both of these issues:
* For environment specs that are concretized together, external python
extensions in those specs will all be assigned the same Python spec
* If Spack needs to "invent" a Python spec, then it will have all the
needed details (e.g. compiler/architecture)
* npm: Add latest version, update build
The `npm` package had gotten a bit long in the tooth and only suported the last version
for which running `configure` / `make` / `make install` actually worked.
- [x] Update the package to support npm@9, in which `npm install .` works properly and
installation is easier.
- [x] Update the package so that `npm@6:8` also install successfullly. The incantation
that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node
bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install`
or `npm pack` will fail when run straight from the install directory. So now we just
manually copies things over.
This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least
for me).
udpates the `npm` build to support versions 6-9 and fixes the install for all of
them on macos.
* update for review
With the new variable [prefix/]SPACK_PACKAGE_IDS you can conveniently execute
things after each successful install.
For example push just-built packages to a buildcache
```
SPACK ?= spack
export SPACK_COLOR = always
MAKEFLAGS += -Orecurse
MY_BUILDCACHE := $(CURDIR)/cache
.PHONY: all clean
all: push
ifeq (,$(filter clean,$(MAKECMDGOALS)))
include env.mk
endif
# the relevant part: push has *all* example/push/<pkg identifier> as prereqs
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
$(SPACK) -e . buildcache update-index --directory $(MY_BUILDCACHE)
$(info Pushed everything, yay!)
# and each example/push/<pkg identifier> has the install target as prereq,
# and the body can use target local $(HASH) and $(SPEC) variables to do
# things, such as pushing to a build cache
example/push/%: example/install/%
@mkdir -p $(dir $@)
$(SPACK) -e . buildcache create --allow-root --only=package --unsigned --directory $(MY_BUILDCACHE) /$(HASH) # push $(SPEC)
@touch $@
spack.lock: spack.yaml
$(SPACK) -e . concretize -f
env.mk: spack.lock
$(SPACK) -e . env depfile -o $@ --make-target-prefix example
clean:
rm -rf spack.lock env.mk example/
``
* [armpl-gcc] Make pkg-config files available
ARMpl pkgconfig files are located in a non-default location and do not have the
.pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
In the past we checked remote binary mirrors for existence of a spec
before attempting to download it. That changed to only checking local
copies of index.jsons (if available) to prioritize certain mirrors where
we expect to find a tarball. That was faster for CI since fetching
index.json and loading it just to order mirrors takes more time than
just attempting to fetch tarballs -- and also if we have a direct hit
there's no point to look at other mirrors.
Long story short: the info message only makes sense in the old version
of Spack, so it's better to remove it.
* py-sphinx-immaterial: new package
This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on
the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear
and readable. We *might* consider switching to it for Spack's docs.
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add note about node.js requirements
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Forward lookup of "test_log_file" and "test_failures"
refers #34531closes#34487fixes#34440
* Add unit test
* py-libensemble: fix tests
* Support stand-alone tests with cached files as install-time tests
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Ensure `spack mirror add <name> <url/path>` without further arguments translates to `<name>: <url>` key value pairs in mirrors.yaml. If --s3-* flags are provided, only store the provided ones.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs.
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* Add new file for MVAPICH 3.0a release
Creating this as a new package since it requires some new configuration
options and because we are moving to the name "MVAPICH" and droping the
2 (following a similar move by MPICH).
Co-authored-by: Nat Shineman <shineman.5@osu.edu>
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
* OpenCV: checksum for 4.5.5, make contrib optional
* [@spackbot] updating style on behalf of iarspider
* Add conflicts for contrib modules
* Fix typo
* Implement changes from review
* Update var/spack/repos/builtin/packages/opencv/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)"
This reverts commit 891a63cae6.
* fix to py-python-multipart, as per PR review
* py-macs2: add version 2.2.7.1 and support python@3.10:
The tarball from PyPi includes the Cythonized C files. The tarball from
github does not. Remove the Cythonized C files from the source so that
they are rebuilt with the Spack Python/Cython combination. This is
necessary for python-3.10 but make sense for other combinations as well.
* Edits based on review
- set python version constraint on version 2.2.4
- removed all python-2 versions and related constraints.
* Add package file for xtb and py-xtb
* Retain maintainers from PythonPackage
* Update package files
- use extends("python") instead of tampering with PYTHONPATH
- use PyPI for downloading sdist of py-xtb
- add simple-dftd3 0.7.0
- add dftd4 3.5.0
- remove --wrap-mode=nodownload from toml-f
* Remove logic for download URL
With this change we get the invariant that `mirror.fetch_url` and
`mirror.push_url` return valid URLs, even when the backing config
file is actually using (relative) paths with potentially `$spack` and
`$env` like variables.
Secondly it avoids expanding mirror path / URLs too early,
so if I say `spack mirror add name ./path`, it stays `./path` in my
config. When it's retrieved through MirrorCollection() we
exand it to say `file://<env dir>/path` if `./path` was set in an
environment scope.
Thirdly, the interface is simplified for the relevant buildcache
commands, so it's more like `git push`:
```
spack buildcache create [mirror] [specs...]
```
`mirror` is either a mirror name, a path, or a URL.
Resolving the relevant mirror goes as follows:
- If it contains either / or \ it is used as an anonymous mirror with
path or url.
- Otherwise, it's interpreted as a named mirror, which must exist.
This helps to guard against typos, e.g. typing `my-mirror` when there
is no such named mirror now errors with:
```
$ spack -e . buildcache create my-mirror
==> Error: no mirror named "my-mirror". Did you mean ./my-mirror?
```
instead of creating a directory in the current working directory. I
think this is reasonable, as the alternative (requiring that a local dir
exists) feels a bit pendantic in the general case -- spack is happy to
create the build cache dir when needed, saving a `mkdir`.
The old (now deprecated) format will still be available in Spack 0.20,
but is scheduled to be removed in 0.21:
```
spack buildcache create (--directory | --mirror-url | --mirror-name) [specs...]
```
This PR also touches `tmp_scope` in tests, because it didn't really
work for me, since spack fixes the possible --scope values once and
for all across tests, so tests failed when run out of order.
Packages that use docbook-xml may specify a specific entity version.
When this is specified as a version constraint in the package recipe it
will cause problems when using `unify = True` in a Spack environment, as
there could be multiple versions of docbook-xml in the spec. In
practice, any entity version should work with any other version and
everything should work with the latest version. This PR maps all Spack
docbook-xml entity versions to the docbook-xml version in the spec.
Ideally, the version in the spec would be the latest version. With this
PR, even if a package specifies an older entity version, it will map
to the entity version (latest) in the spec. This means that there can be one
docbook-xml version in a Spack environment spec and packages requesting
older entity versions will still work.
To help facilitate this, docbook-xml version constraints for packages
that have them have been removed. Those packages are dbus and gtk-doc.
What's in AOCL 4.0:
1. amdblis
LPGEMM variants with post-ops support
AMD "Zen4" support for BLIS
2. amdlibflame
Upgrade to LAPACK 3.10.1 specification
Improvements in a few more variants of SVD and Eigen Value routines
Multithread support enabled for selected APIs
3. amdfftw
AVX-512 enablement of DFT kernels
AVX-512 optimization of copy and transpose routines
5. amdlibm
Black & Scholes support (logf, expf, erff, both scalar and vector)
AVX-512 variants of vector functions
6. aocl-sparse
New Iterative Solver APIs
AVX-512 support for SPMV API
7. amdscalapack
Upgrade to Netlib ScaLAPACK 2.2.0
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Sometimes I just want to know how many packages of a certain type there are.
- [x] add `--count` option to `spack list` that output the number of packages that
*would* be listed.
```console
> spack list --count
6864
> spack list --count py-
2040
> spack list --count r-
1162
```
* Add packages
* Style
* Respond to comments
* Change conflct dep type
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* paraview: add `rocm` variant
This conflicts with CUDA and requires at least ParaView 5.11.0. More
dependencies are also needed.
* E4S: Add ParaView for ROCm and CUDA stacks
* DAV SDK: Update ParaView version and GPU variants
* Verify using hipcc vs amdclang++ for newer hip
Co-authored-by: Ben Boeckel <ben.boeckel@kitware.com>
* adding 1st version of py-strawberryfields
* py-strawberryfields: minor edit
* added backbone for 4x new SF dependencies
* edits to SF and its 4x new deps
* added all deps for SF
* added one version to py-lark-parser
* py-quantum-xir with tarball from github
* Update var/spack/repos/builtin/packages/py-strawberryfields/package.py
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* updated version for py-quantum-xir : pypy fixed
* py-pennylane: added pythonpackage.maintainers, too
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Currently, all of the replacements in `spack.util.path.replacements()` get evaluated for
each replacement. This makes it easy to get bootstrap issues, because config is used
very early on in Spack.
Right now, if I run `test_autotools_gnuconfig_replacement_no_gnuconfig` on my M1 mac, I
get the circular reference error below. This fixes the issue by making all of the path
replacements lazy lambdas.
As a bonus, this cleans up the way we do substitution for `$env` -- it's consistent with
other substitutions now.
- [x] make all path `replacements()` lazy
- [x] clean up handling of `$env`
```console
> spack unit-test -k test_autotools_gnuconfig_replacement_no_gnuconfig
...
==> [2022-12-31-15:44:21.771459] Error: AttributeError:
The 'autotools-config-replacement' package cannot find an attribute while trying to build from sources. This might be due to a change in Spack's package format to support multiple build-systems for a single package. You can fix this by updating the build recipe, and you can also report the issue as a bug. More information at https://spack.readthedocs.io/en/latest/packaging_guide.html#installation-procedure
/Users/gamblin2/src/spack/lib/spack/spack/package_base.py:1332, in prefix:
1330 @property
1331 def prefix(self):
>> 1332 """Get the prefix into which this package should be installed."""
1333 return self.spec.prefix
Traceback (most recent call last):
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 1030, in _setup_pkg_and_run
kwargs["env_modifications"] = setup_package(
^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 757, in setup_package
set_module_variables_for_package(pkg)
File "/Users/gamblin2/src/spack/lib/spack/spack/build_environment.py", line 596, in set_module_variables_for_package
m.std_cmake_args = spack.build_systems.cmake.CMakeBuilder.std_args(pkg)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/build_systems/cmake.py", line 241, in std_args
define("CMAKE_INSTALL_PREFIX", pkg.prefix),
^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/package_base.py", line 1333, in prefix
return self.spec.prefix
^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1710, in prefix
self.prefix = spack.store.layout.path_for_spec(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 336, in path_for_spec
path = self.relative_path_for_spec(spec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/directory_layout.py", line 106, in relative_path_for_spec
projection = spack.projections.get_projection(self.projections, spec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/projections.py", line 13, in get_projection
if spec.satisfies(spec_like, strict=True):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 3642, in satisfies
if not self.virtual and other.virtual:
^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/spec.py", line 1622, in virtual
return spack.repo.path.is_virtual(self.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 890, in is_virtual
return have_name and pkg_name in self.provider_index
^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 770, in provider_index
self._provider_index.merge(repo.provider_index)
^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 1096, in provider_index
return self.index["providers"]
~~~~~~~~~~^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 592, in __getitem__
self._build_all_indexes()
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 607, in _build_all_indexes
self.indexes[name] = self._build_index(name, indexer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/spack/repo.py", line 616, in _build_index
index_mtime = self.cache.mtime(cache_filename)
^^^^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 826, in __getattr__
return getattr(self.instance, name)
^^^^^^^^^^^^^
File "/Users/gamblin2/src/spack/lib/spack/llnl/util/lang.py", line 825, in __getattr__
raise AttributeError()
AttributeError
```
* Added support for libfabric to find an external installation and
identify variants supported.
* Change the fabrics definition to only include CXI when on a cray
system with a libfabric-based slingshot network.
* Added a conflict when trying to build the CXI fabric value since it is
only available as closed source at this time.
#33128 Introduces a dependency on re2c into the Ninja build recipe.
This is problematic on Windows as we use CMake to build re2c, and
Ninja to drive the CMake build. This PR resolves this issue by
adding a variant to toggle the use of re2c with ninja.
* Added a more robust check for an external version of the library.
Included a guard to identify when the library gives no discernible
version information and then to substitute with "unknown_ver"
identifier.
* gaudi: new versions 36.8, 36.9
As of 36.8, the tests use catch2 ([commit](https://gitlab.cern.ch/gaudi/Gaudi/- /commit/f2cafb5c9d04c9d497d49182258aa3a0440622c0)).
* gaudi: still depends_on fmt@:8
* unifyfs: new release v1.0.1
Add 1.0.1 release
Add new variant for new configure time option
Co-authored-by: CamStan <CamStan@users.noreply.github.com>
Now that the `tix` variant is conditional, it should also be detected
condititionally, otherwise the spec is invalid and cannot be used during
concretization.
ShellCheck is installed with a downloaded binary instead of being
compiled from source, and there should be comments to point out this
unorthodox approach.
autoconf 2.70 uses use warnings instead of -w so that PERL=/usr/bin/env perl can be passed, but we want to fix absolute paths anyhow through sbang upon install. So, we stick to patching the one perl script that's used during the build.
Gitlab does not merge lists when a job extends two other definitions
that include the same list (e.g. tags). Also, it merges dictionaries
as long as the keys are distinct, but just takes the last mentioned
value when there are key collisions.
This change makes sure that when different tags are needed by a
pipeline, the ones we want are actually provided. It also changes
the example stack to better follow this pattern so we do not lead
developers astray in the future.
Since we dropped support for Python 2.7, we can embrace using keyword only arguments
for many functions in Spack that use **kwargs in the function signature. Here this is done
for the llnl.util.filesystem module.
There were a couple of bugs lurking in the code related to typo-like errors when retrieving
from kwargs. Those have been fixed as well.
* Update xsbench to version 20
XSBench version 20 has implementations for new
architectures and accelerators.
* Added CUDA support for XSBench
* Fixed style issues
The code in FileCache for write_transaction attempts to delete the temporary file when an exception occurs under the context by calling shutil.rmtree. However, rmtree only operates on directories while the rest of FileCache uses normal files. This causes an empty file to be written to the cache key when unneeded.
Use os.remove instead which operates on normal files.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* cernlib: depends_on freetype, libnsl, libxcrypt, openssl; and patch
In addition to #34448, cernlib depends on these additional packages.
This also applies a patch to the current release in which crypto is
specified wbere libcrypt (in libxcrypt) is actually needed. Because
the upstream git repository is behind a CERN login, we cannot patch
by gitlab URL link.
* [@spackbot] updating style on behalf of wdconinc
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* update the version for 5.3.0 release
* update the rocwmma for 5.3.0 release
* fix the +hip variant
* update the version for rocm-openmp-extras package for 5.3.0 release
* update the hipsolver and hipfft as per review comments
* address review comments
* revert changes to mivisionx with regard to change added for clangrt
* fix for the petsc failure
Spack was running an external detection of Python during each invocation
of the setup script for Windows CMD/PWSH, which has dramatic performance
implications each time the script is invoked, and is completely
unneccesary. Remove this operation.
Windows CMD prompt does not automatically support ASCI color control
characters on the console from Python. Enable this behavior by
accessing the current console and allowing the interpreation of ASCI
control characters from Python via the win32 API.
* adding 2nd bunch of nf-core deps from update/nextflow-tools
* adding 3rd bunch of nf-core deps from update/nextflow-tools
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pebble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gunicorn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-parsley/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-gxformat2: added comment
* py-lagom: now using github tarballs
* fix for py-lagom
* adding missing deps to py-fastapi-utils
* another fix to py-lagom
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-lagom/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-supervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit allows (remote) spec.json files to be clearsigned and gzipped.
The idea is to reduce the number of requests and number of bytes transferred
* added recipes for py-qutip and py-qutip-qip
* small fix
* updated qutip 2x versions
* py-qutip-qip: tarball url from github
* style fix in py-qutip-qip
* Update var/spack/repos/builtin/packages/py-qutip-qip/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-qutip-qip/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-qutip-qip/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-qutip/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-qutip/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* draft for py-pennylane recipe
* first draft for py-strawberryfields recipe
* minimal fix
* small fixes
* accounting for circular dep in py-pennylane and py-pennylane-lightning
* removing py-strawberryfields from this branch
* updated versions for py-pennylane 2x
* needs cmake
* py-pennylane-lightning using github tarball
* Update var/spack/repos/builtin/packages/py-autoray/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pennylane-lightning/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Intel compiler isn't able to deal with noinline member functions of template classses defined in headers. As such it outputs
```
warning #2196: routine is both "inline" and "noinline"
```
cmake bootstrap will fail due to the word 'warning'.
See spack/var/spack/repos/builtin/packages/protobuf/intel-v2.patch for reference.
The issue does not appear with intel@2021.7.0 or later:
```
$~: compiler=/shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-12.2.0/intel-oneapi-compilers-2022.2.0-uqvb2553zy5toeapvoopacndd27x6p5m/compiler/2022.2.0/linux/bin/intel64/icpc
$~: $compiler unique.c
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
```
This is a clean version of https://github.com/spack/spack/pull/34167
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
* package/libproxy: fix py3 install
* improve readability
* fix bug
* also add extend
* make flake happy
* [@spackbot] updating style on behalf of Sinan81
* Update var/spack/repos/builtin/packages/libproxy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* python dependency implied by extends const.
* disable python variant by default
* add run_env, add py conflict
* Update var/spack/repos/builtin/packages/libproxy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* set env for macos as well
* generalize lib dir detection
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add_new_package: py-file-magic
* re-order depends...
* Update var/spack/repos/builtin/packages/py-file-magic/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of Sinan81
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
* Add py-svgpath and dependency
* Update copyright expiration
* [@spackbot] updating style on behalf of heerener
* Process review remarks
* Update var/spack/repos/builtin/packages/py-trimesh/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix style issue
* py-trimesh: cleanup and optional dependencies
* Fix formatting issue
* py-trimesh: complete dependency list for easy variant
Two new packages: py-mapbox-earcut and py-pycollada
* Some more missing dependencies
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-kb-python + dependencies
- py-loompy
- py-ngs-tools
- py-numpy-groupies
* Update var/spack/repos/builtin/packages/py-kb-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-shortuuid: add version 1.0.11
* Update var/spack/repos/builtin/packages/py-shortuuid/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update packages config to indicate that MSVC is the preferred compiler
* Update packages config to indicate that msmpi is the preferred MPI provider
* Fix msmpi external detection
Spack imports `pytest`, which *can* import `numpy`. Recent versions of `numpy` require
Python 3.8 or higher, and they use 3.8 type annotations in their type stubs (`.pyi`
files). At the same time, we tell `mypy` to target Python 3.7, as we still support older
versions of Python.
What all this means is that if you run `mypy` on `spack`, `mypy` will follow all the
static import statements, and it ends up giving you this error when it finds numpy stuff
that is newer than the target Python version:
```
==> Running mypy checks
src/spack/var/spack/environments/default/.spack-env/._view/4g7jd4ibkg4gopv4rosq3kn2vsxrxm2f/lib/python3.11/site-packages/numpy/__init__.pyi:638: error: Positional-only parameters are only supported in Python 3.8 and greater [syntax]
Found 1 error in 1 file (errors prevented further checking)
mypy found errors
```
We can fix this by telling `mypy` to skip all imports of `numpy` in `pyproject.toml`:
```toml
[[tool.mypy.overrides]]
module = 'numpy'
follow_imports = 'skip'
follow_imports_for_stubs = true
```
- [x] don't follow imports from `numpy` in `mypy`
- [x] get rid of old rule not to follow `jinja2` imports, as we now require Python 3
The code in Spack to generate install and test reports currently suffers from unneeded complexity. For
instance, we have classes in Spack core packages, like `spack.reporters.CDash`, that need an
`argparse.Namespace` to be initialized and have "hard-coded" string literals on which they branch to
change their behavior:
```python
if do_fn.__name__ == "do_test" and skip_externals:
package["result"] = "skipped"
else:
package["result"] = "success"
package["stdout"] = fetch_log(pkg, do_fn, self.dir)
package["installed_from_binary_cache"] = pkg.installed_from_binary_cache
if do_fn.__name__ == "_install_task" and installed_already:
return
```
This PR attempt to polish the major issues encountered in both `spack.report` and `spack.reporters`.
Details:
- [x] `spack.reporters` is now a package that contains both the base class `Reporter` and all
the derived classes (`JUnit` and `CDash`)
- [x] Classes derived from `spack.reporters.Reporter` don't take an `argparse.Namespace` anymore
as argument to `__init__`. The rationale is that code for commands should be built upon Spack
core classes, not vice-versa.
- [x] An `argparse.Action` has been coded to create the correct `Reporter` object based on command
line arguments
- [x] The context managers to generate reports from either `spack install` or from `spack test` have
been greatly simplified, and have been made less "dynamic" in nature. In particular, the `collect_info`
class has been deleted in favor of two more specific context managers. This allows for a simpler
structure of the code, and less knowledge required to client code (in particular on which method to patch)
- [x] The `InfoCollector` class has been turned into a simple hierarchy, so to avoid conditional statements
within methods that assume a knowledge of the context in which the method is called.
On systems with remote groups, the primary user group may be remote and may not exist on
the local system (i.e., it might just be a number). On the CLI, it looks like this:
```console
> touch foo
> l foo
-rw-r--r-- 1 gamblin2 57095 0 Dec 29 22:24 foo
> chmod 2000 foo
chmod: changing permissions of 'foo': Operation not permitted
```
Here, the local machine doesn't know about per-user groups, so they appear as gids in
`ls` output. `57095` is also `gamblin2`'s uid, but the local machine doesn't know that
`gamblin2` is in the `57095` group.
Unfortunately, it seems that Python's `os.chmod()` just fails silently, setting
permissions to `0o0000` instead of `0o2000`. We can avoid this by ensuring that the file
has a group the user is known to be a member of.
- [x] Add `ensure_known_group()` in the permissions tests.
- [x] Call `ensure_known_group()` on tempfile in `test_chmod_real_entries_ignores_suid_sgid`.
There are a number of places in our docstrings where we write "list of X" as the type, even though napoleon doesn't actually support this. It ends up causing warnings when generating docs.
Now that we require Python 3, we don't have to rely on type hints in docs -- we can just use Python type hints and omit the types of args and return values from docstrings.
We should probably do this for all types in docstrings eventually, but this PR focuses on the ones that generate warnings during doc builds.
Some `mypy` annoyances we should consider in the future:
1. Adding some of these type annotations gets you:
```
note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked]
```
because they are in unannotated functions (like constructors where we don't really need any annotations).
You can silence these with `disable_error_code = "annotation-unchecked"` in `pyproject.toml`
2. Right now we support running `mypy` in Python `3.6`. That means we have to support `mypy` `.971`, which does not support `disable_error_code = "annotation-unchecked"`, so I just filter `[annotation-unchecked]` lines out in `spack style`.
3. I would rather just turn on `check_untyped_defs` and get more `mypy` coverage everywhere, but that will require about 1,000 fixes. We should probably do that eventually.
4. We could also consider only running `mypy` on newer python versions. This is not easy to do while supporting `3.6`, because you have to use `if TYPE_CHECKING` for a lot of things to ensure that 3.6 still parses correctly. If we only supported `3.7` and above we could use [`from __future__ import annotations`](https://mypy.readthedocs.io/en/stable/runtime_troubles.html#future-annotations-import-pep-563), but we have to support 3.6 for now. Sigh.
- [x] Convert a number of docstring types to Python type hints
- [x] Get rid of "list of" wherever it appears
Based on the following lines in the top level `CMakeLists.txt` (I can't deep link since gitlab.cern.ch not public), `cernlib` needs an explicit dependency on `libxaw` and `libxt`:
```cmake
find_package(X11 REQUIRED)
message(STATUS "CERNLIB: X11_Xt_LIB=${X11_Xt_LIB} X11_Xaw_LIB=${X11_Xaw_LIB} X11_LIBRARIES=${X11_LIBRARIES}")
```
Per https://github.com/spack/spack/issues/34192, apptainer does not support `--without-conmon`, so we introduce a base class `config_options` property that can be overridden in the `apptainer` package.
`texinfo` depends on `gettext`, and it builds a perl module that uses gettext via XS
module FFI. Unfortunately, the XS modules build asks perl to tell it what compiler to
use instead of respecting the one passed to configure.
Without this change, the build fails with this error:
```
parsetexi/api.c:33:10: fatal error: 'libintl.h' file not found
^~~~~~~~~~~
```
We need the gettext dependency and the spack wrappers to ensure XS builds properly.
- [x] Add needed `gettext` dependency to `texinfo`
- [x] Override XS compiler with `PERL_EXT_CC`
Co-authored-by: Paul Kuberry <pakuber@sandia.gov>
Local `git` tests will fail with `fatal: transport 'file' not allowed` when using git 2.38.1 or higher, due to a fix for `CVE-2022-39253`.
This was fixed in CI in #33429, but that doesn't help the issue for anyone's local environment. Instead of fixing this with git config in CI, we should ensure that the tests run anywhere.
- [x] Introduce `spack.util.git`.
- [x] Use `spack.util.git.get_git()` to get a git executable, instead of `which("git")` everywhere.
- [x] Make all `git` tests use a `git` fixture that goes through `spack.util.git.get_git()`.
- [x] Add `-c protocol.file.allow=always` to all `git` invocations under `pytest`.
- [x] Revert changes from #33429, which are no longer needed.
`spack graph` has been reworked to use:
- Jinja templates
- builder objects to construct the template context when DOT graphs are requested.
This allowed to add a new colored output for DOT graphs that highlights both
the dependency types and the nodes that are needed at runtime for a given spec.
`spack solve` is supposed to show you times you can compare. setup, ground, solve, etc.
all in a list. You're also supposed to be able to compare easily across runs. With
`pretty_seconds()` (introduced in #33900), it's easy to miss the units, e.g., spot the
bottleneck here:
```console
> spack solve --timers tcl
setup 22.125ms
load 16.083ms
ground 8.298ms
solve 848.055us
total 58.615ms
```
It's easier to see what matters if these are all in the same units, e.g.:
```
> spack solve --timers tcl
setup 0.0147s
load 0.0130s
ground 0.0078s
solve 0.0008s
total 0.0463s
```
And the units won't fluctuate from run to run as you make changes.
-[x] make `spack solve` timings consistent like before
* py-pytest-datadir: Init at 1.4.1
* py-pytest-data-dir: Fix missing dep
Co-authored-by: "Adam J. Stewart" <ajstewart426@gmail.com>
Co-authored-by: "Adam J. Stewart" <ajstewart426@gmail.com>
* ML CI: Linux x86_64
* Update comments
* Rename again
* Rename comments
* Update to match other arches
* No compiler
* Compiler was wrong anyway
* Faster TF
Avoid text decoding and encoding when combining log files, instead
combine in binary mode.
Also do a buffered copy which is sometimes faster for large log files.
Currently, the Spack docs show documentation for submodules *before* documentation for
submodules on package doc pages. This means that if you put docs in `__init__.py` in
some package, the docs in there will be shown *after* the docs for all submodules of the
package instead of at the top as an intro to the package. See, e.g.,
[the lockfile docs](https://spack.readthedocs.io/en/latest/spack.environment.html#module-spack.environment),
which should be at the
[top of that page](https://spack.readthedocs.io/en/latest/spack.environment.html).
- [x] add the `--module-first` option to sphinx so that it generates module docs at top of page.
* librsvg: add 2.40.21, which does not require rust and has some security backports
https://download.gnome.org/sources/librsvg/2.40/librsvg-2.40.21.news
* librsvg: prevent finding broken gtkdoc binaries when ~doc is selected.
On my CentOS7 hosts, ./configure finds e.g. /bin/gtkdoc-rebase even when
~doc is selected. These tools use Python2, and fail with an error:
"ImportError: No module named site"
So prevent ./configure from finding these broken tools when not building
the +doc variant.
without this patch, build of paraview has a meltdown when reaching 3rd party catalyst and other packages
with these types of errors:
335 /tmp/foo/spack-stage/spack-stage-paraview-5.10.1-gscoqxhhakjyyfirdefuhmi2bzw4scho/spack-src/VTK/ThirdParty/fmt/vtkfmt/vtkfmt/format.h:1732:11: error: cannot capture a bi
t-field by reference
336 if (sign) *it++ = static_cast<Char>(data::signs[sign]);
337 ^
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
The sticky property will prevent clingo from changing the amdgpu_target
to work around conflicts. This is the same behaviour as was adopted for
cuda_arch in 055c9d125d.
Replace the filter_file for older configure with rocm 5.3 with an
upstream patch. Further, the patch is no longer needed for develop or
later releases.
Implement an alternative strategy to do index.json invalidation.
The current approach of pairs of index.json / index.json.hash is
problematic because it leads to races.
The standard solution for cache invalidation is etags, which are
supported by both http and s3 protocols, which allows one to do
conditional fetches.
This PR implements that for the http/https schemes. It should also work
for s3 schemes, but that requires other prs to be merged.
Also it improves unit tests for index.json fetches.
* py-scikit-image: add 0.19.3
* Update var/spack/repos/builtin/packages/py-scikit-image/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* LLVM: replace libelf dependency with elf
I didn't test this extensively, but in CMS LLVM builds just fine with elfutils.
* [@spackbot] updating style on behalf of iarspider
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
* exiv2: add new versions
* babl: new package required to build GIMP
* gegl: new package required to build GIMP
* gexiv2: new package required to build GIMP
* libmypaint: new package required to build GIMP
* mypaint-brushes: new package required to build GIMP
* vala: new package required to build GIMP
* GIMP: new package definition for building GIMP-2.10 from source
* libjxl: update for 0.7.0
* libwmf: a library for reading vector images in Windows Metafile Format (WMF)
* libde265: an open source implementation of the h.265 video codec
* libwebp: add new versions
* GIMP: additional variants for building GIMP-2.10 from source
* libde265: remove boilerplate
* fixes for style precheck
* updates based on feedback
* fixes for style precheck
Update the depends_on("perl") to depends_on("perl+threads").
This and #34074 is needed to properly handle e.g. the perl-Thread-Queue
rpm package:
It may not be installed on RedHat-based hosts, which can lead to automake
build failures when `spack external find perl` or `spack external find --all`
was used to use the system-provided perl install.
* nextflow recipe: added latest stable version
* tower-cli recipe: added latest release
* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli
* recipes nf-tower-agent and nf-tower-cli: small fix
* nf-core-tools recipe: added most py- dependencies
* nf-core-tools: recipe without galaxy-tool-util (for testing)
* fixed typos in py-yacman recipe
* fixed typos in py-pytest-workflow recipe
* fixed typo in nf-core-tools recipe
* fixed typos in py-yacman recipe
* fixes in recipes for py-questionary and py-url-normalize
* fixes to py-yacman recipe
* style fixes to py- packages that are dependencies to nf-core-tools
* fix in py-requests-cache recipe
* added missing dep in py-requests-cache recipe
* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper
* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util
* nf-core-tools: new version with extra dependency
* commit to merge packages on focus from update/nextflow-tools
* nf-core: commenting galaxy dep for this pr
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed nf-core-tools from this branch, will be back at the end
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Interim fix for #34559
Spack's MSVC compiler definition uses ifx as the Fortran compiler.
Prior to #33385, the Spack MSVC compiler definition required the
executable to be called "ifx.exe"; #33385 replaced this with just
"ifx", which inadvertently led to ifx falsely indicating the
presence of MSVC on non-Windows systems (which leads to future
errors when attempting to query/use those compiler objects).
This commit applies a short-term fix by updating MSVC Fortran
version detection to always indicate a failure on non-Windows.
fixes#34518
Fix an issue due to the MRO chain of the package wrapper
during build. Before this PR we were always returning
False when the builder object was created before the
run_tests method was monkey patched.
openPMD, a metadata standard on top of backends like ADIOS2 and HDF5,
is implemented in ParaView 5.9+ via a Python3 module.
Simplify Conflicts & Variant
Add to ECP Data Vis SDK
This reverts commit 8035eeb36d.
And also removes logic around an additional HEAD request to prevent
a more expensive GET request on wrong content-type. Since large files
are typically an attachment and only downloaded when reading the
stream, it's not an optimization that helps much, and in fact the logic
was broken since the GET request was done unconditionally.
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