Currently, Windows SDK detection will only pick up SDK versions
related to the current version of Windows Spack is running on.
However, in some circumstances, we want to detect other version
of the SDK, for example, for compiling on Windows 11 for Windows
10 to ensure an API is compatible with Win10.
* Make use of `prefix` in the Cray manifest schema (prepend it to
the relative CC etc.) - this was a Spack error.
* Warn people when wrong-looking compilers are found in the manifest
(i.e. non-existent CC path).
* Bypass compilers that we fail to add (don't allow a single bad
compiler to terminate the entire read-cray-manifest action).
* Refactor Cray manifest tests: module-level variables have been
replaced with fixtures, specifically using the `test_platform`
fixture, which allows the unit tests to run with the new
concretizer.
* Add unit test to check case where adding a compiler raises an
exception (check that this doesn't prevent processing the
rest of the manifest).
If you `spack install x ^y` where `y` is a pure build dep of `x`, and
then uninstall `y`, and then `spack install --overwrite x ^y`, the build
fails because `y` is not re-installed.
Same can happen when you install a develop spec, run `spack gc`,
modify sources, and install again; develop specs rely on overwrite
install to work correctly.
-- Performaing formatting changes
-- Formatting file to conform with spack style
-- Adding updates from review
-- Removing old release candidates from the specification
-- Adding external conduit support for Catalyst
-- Adding Catalyst to `CMAKE_PREFIX_PATH` for the test to find
This PR adds a new audit sub-command to check that detection of relevant packages
is performed correctly in a few scenarios mocking real use-cases. The data for each
package being tested is in a YAML file called detection_test.yaml alongside the
corresponding package.py file.
This is to allow encoding detection tests for compilers and other widely used tools,
in preparation for compilers as dependencies.
Add versions 2020.08.1 and branch 2023.08.stable. Note: the version
numbers are a little different. Here, 2023.08.1 means release no. 1
from the release/2023.08 branch.
Modifications:
- [x] Move `spack.util.string` to `llnl.string`
- [x] Remove dependency of `llnl` on `spack.error`
- [x] Move path of `spack.util.path` to `llnl.path`
- [x] Move `spack.util.environment.get_host_*` to `spack.spec`
This resolves an interesting circular dependency between gcc and glibc:
1. glibc < 2.17 depends on libgcc.a and libgcc_eh.a
2. libgcc_eh.a is only built when gcc is configured with
--enable-shared
3. but building shared libraries requires crt*.o and libc.so
Backport AT_RANDOM auxval changes to avoid dealing with wrong inline
assembly (fallback code fails on ubuntu 23.04)
Update Trilinos and dependencies to build a limited version of Trilinos
on Windows.
* Support trilinos~mpi~shared on Windows
* superlu: force CMake build on Windows
* boost: update to build on Windows (proper option formatting and
build tool names)
* pcre, openblas: add CMake-based build (keep prior build system
as default on platforms other than Windows)
* openblas: add patch when using Intel Fortran compiler (currently
this is included as part of the hybrid %msvc compiler in Spack)
Co-authored-by: John Parent <john.parent@kitware.com>
As reported in #40159, a shared library build of ffmpeg 6.0 fails with the linker that was added with XCode 15:
ld: building exports trie: duplicate symbol '_av_ac3_parse_header'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Forcing the old linker with -Wl,-ld_classic works around this.
VTK's (and therefore Paraview's) FindFreetype module required patching to
handle static import libraries from Freetype. However it did not cover
shared libraries. This adds support for importing shared freetype into the VTK build
* Rename var/spack/repos/builtin/packages/python/cray-rpath-3.1.patch as var/spack/repos/builtin/packages/python/rpath-non-gcc.patch and apply unconditionally
* Update var/spack/repos/builtin/packages/python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-numcodecs: drop upperbound, add new version, avoid native compilation
* py-numcodecs: add entrypoints
* Remove another upperbound on python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The fix for the compile issue was improved by Bernhard Kaindl.
He also added to fix two classes of other build fails:
- add missing openssl dependency version limit to older openssh versions
- add missing -fcommon for new compilers building old openssh versions
Co-authored-by: snehring <snehring@iastate.edu>
* e4s cray rhel stack: expand to full spec list
* comment out gasnet; require %gcc for unzip
* require openblas@0.3.20 to get around %cce error; follow up with issue report
* comment out failing specs;
* comment out axom and xyce due to errors
* improve clarity of failing specs
* msvc.py: don't import distutils
Introduced in #27021, makes Spack forward incompatible with Python.
The module was already deprecated at the time of the PR.
* update spack package
* py-gpy: drop cython induced python upperbound
* py-gpy: bump scipy
* py-fn-py: python bounds for old version, new version w/o
* py-statsmodels: force recythonization
* py-gpy: clarifying comment about cython build type
* py-aiofiles: Add version 0.7.0 required by py-cylc-flow
* py-aiofiles: update from review
* depends on py-setuptools before 0.6
* depends on py-poetry-core after 0.7
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
* py-aiofiles: Taking reviewing into account; add a upper version constraint for Python.
* py-aiofiles: update from review, set lower version of python
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-fenics-dolfinx: add upper bound on Python version
* Small fix
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Fixes#39622
Add a timeout to compiler detection and allow Spack to proceed when
this timeout occurs.
In all cases, the timeout is 120 seconds: it is assumed any compiler
invocation we do for the purposes of verifying it would resolve in
that amount of time.
Also refine executables that are tested as being possible MSVC
instances, and limit where we try to detect MSVC. In more detail:
* Compiler detection should timeout after a certain period of time.
Because compiler detection executes arbitrary executables on the
system, we could encounter a program that just hangs, or even a
compiler that hangs on a license key or similar. A timeout
prevents this from hanging Spack.
* Prevents things like cl-.* from being detected as potential MSVC
installs. cl is always just cl in all cases that Spack supports.
Change the MSVC class to indicate this.
* Prevent compilers unsupported on certain platforms from being
detected there (i.e. don't look for MSVC on systems other than
Windows).
The first point alone is sufficient to address #39622, but the
next two reduce the likelihood of timeouts (which is useful since
those slow down the user even if they are survivable).
Put back normalization of the "virtuals" input as a sorted tuple.
Without this we might get edges that differ just for the order of
virtuals, or that have lists, which are not hashable.
Add unit-tests to prevent regressions.
By default, do not let deprecated versions enter the solve.
Previously you could concretize to something deprecated, only to get errors on install.
With this commit, we get errors on concretization, so the issue is caught earlier.
* initial commit to add composable kernel package
* change dependencies to type build and add amdgpu_target variant
* fix spacing
* fix styling
* remove rocmmlir from miopen-hip recipe
* enable miopen with ck after 5.5.1
* fix typo
Fix permissions for configure file in var/spack/repos/builtin/packages/hdf-eos2/package.py, fix dependencies to match what hdf provides, update compiler flags for apple-clang
* [chore] py-aniso8601: Add version 3.0.2 required by py-graphene
* py-aniso8601: Add version 7.0.0 and constraints on python version
* py-aniso8601: fix style
* [fix] py-aniso8601: remove version 3.0.2 which depends on removed version of python; set the minimal version of python to 3.7
* py-aniso8601: remove version constraint on python
* Add Scine QCMaquis recipe to builtin packages
* Format scine-qcmaquis recipe using black
* Remove import os from scine-qcmaquis recipe
* Reduce length of symmetries line in scine-qcmaquis
* Add myself as a maintainer of the scine-qcmaquis recipe
* Update Scine-QCMaquis recipe following the review
PR URL: https://github.com/spack/spack/pull/39709
Changes:
- Updated Symmetries variant to us multi feature
- Added dependency to boost+chrono since it was undocumented
- Use define_from_variant to setup CMake args
- Make version 3.1.2 be preferred since 3.1.3 build is broken
* Change build_tests boolean condition
---------
Co-authored-by: Adam Grofe <adamgrofe@microsoft.com>
PythonExtension is a base class for PythonPackage, and
is meant to be used for any package that is a Python
extension but is not built using "python_pip".
The "update_external_dependency" method in the base
class calls another method that is defined in the derived
class.
Push "get_external_python_for_prefix" up in the hierarchy
to make method calls consistent.
* Add OIDC tokens to gitlab-ci jobs
This should allow us to start issuing just-in-time generated
credentials for CI jobs that need to modify binary mirrors. The "aud"
claim of the token describes what the token is allowed to do. The
claim is verified against a set of rules on the IAM role using signed
information from GitLab. See spack-infrastructure for the claim
verification logic.
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
This commit replaces the internal representation of deptypes with `int`, which is more compact
and faster to operate with.
Double loops like:
```
any(x in ys for x in xs)
```
are replaced by constant operations bool(xs & ys), where xs and ys are dependency types.
Global constants are exposed for convenience in `spack.deptypes`
Currently the configuration of the pipeline is such that
there are multiple "optimal" solutions. This is due to
the pipeline making ~lld the default for LLVM, but leaving
+libomptarget from package.py
Since LLVM recipe has a:
conflicts("~lld", "+libomptarget")
clingo is forced to change one of the two defaults, and
the penalty for doing so is the same for each. Hence, it
is random whether we'll get +libomptarget+lld
or ~libomptarget~lld.
This fixes it by changing also the default for libomptarget.
* scorep version 8.1 added
* configure finds cudart and cupti in the nvhpcsdk suite
* style fixed
* changes to find libcuda.so in cuda directory
---------
Co-authored-by: Laura Bellentani <lbellen1@login01.leonardo.local>
* cp2k: patch several old versions to help newer compilers
* cp2k: use -O2 optimization for AOCC compiler
* cp2k: do not support old AOCC compilers
* cp2k: simplify when clause due to conflicting out old compilers
* cp2k: give a more meaningful message for confilcts
Co-authored-by: Ning Li <ning.li@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
* libfirefly: Add cmake package for v2.1.0 and master (git) versions
* Separate git URL from version declaration
Co-authored-by: Alec Scott <alec@bcs.sh>
Currently, the concretizer emits facts for all versions known to Spack, including deprecated versions, and has a specific optimization objective to minimize their use.
This commit simplifies how deprecated versions are handled by considering possible versions for a spec only if they appear in a spec literal, or if the `config:deprecated:true` is set directly or through the `--deprecated` flag. The optimization objective has also been removed, in favor of just ordering versions and having deprecated ones last.
This results in:
a) no delayed errors on install, but concretization errors when deprecated versions would be the only option. This is in particular relevant for CI where it's better to get errors early
b) a slight concretization speed-up due to fewer facts
c) a simplification of the logic program.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* unifyfs: drop upperbound on deprecated openssl
The package uses deprecated MD5 functions from OpenSSL, which causes
warnings, but (a) Spack by default disables -Werror, and (b) those
functions will continue to exist in OpenSSL 3.
* unifyfs: enable parallel build, only make check sequential
* unifyfs: order class methods by install phases
* py-maestrowf: add new version 1.1.9, deprecate development releases
* py-maestrowf: drop py-cryptography in 1.1.9
* py-maestrowf: drop py-cryptography dependency entirely, since it is not a direct dependency
* py-merlin: new version, ensure openssl 3 compat
* py-merlin: drop py-coloredlogs@10: lowerbound
* py-maestrowf: add py-rich, reorder deps
* py-celery: explain why upperbound is in spack but not in requirements.txt
* openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0
- 2.5.9 is the latest version compatible with OpenScenGraph
- improved compatibility with GCC 13
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* openexr: drop unsupported debug variant
--disable/enable-debug is not supported by ./configure in 1.3, 1.7, 2.0, 2.2 and 2.3
* openexr: transform into multi-build system package
simplifies package considerably, as nothing special seems to be required
* openexr: pkg-config is also used by @3
* openexr: use system libdeflate instead of internal
if no libdeflate is found, openexr would download and build its own starting with 3.2.0
* openexr: disable tests
would download lots of data during cmake and make build times noticably longer
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Make the state of the Python Front End (PFE) and Python data reader
support sticky so that the concretizer does not arbitrarily disable
them.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* package_qscintilla_build_with_qt6
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* improve
* fix Qsci.abi3.so install
* simplify, fix, tidy
* fix style
* fix style
* fix style
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* improve
* improve style
* fix style
* make black happy
* add ver 2.14.1
* update
* make black happy
* Update var/spack/repos/builtin/packages/qscintilla/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* improve
---------
Co-authored-by: Sinan81 <Sinan@world>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* simple build of py-openai
* added variants to py-openai
* py-pandas-stubs is a dependency for py-openai
* fixed format and flake8 errors for py-openai
* black format error for py-pandas-stubs
* [@spackbot] updating style on behalf of sidpbury
* made style and format changes to py-openai
* made style and format changes to py-pandas-stubs
* py-types-pytz is a dependency for py-openai
* [@spackbot] updating style on behalf of sidpbury
* updated py-openpyxl for ver 3.0.7 and 3.1.2
* Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ajs requested changes for py-openai
* updated py-openpyxl for supported python
* [@spackbot] updating style on behalf of sidpbury
* updated py-openpyxl
* removed requirement.txt dependencies in py-openpyxl
* removed python depends on from openpyxl
* updated package to support newer versions
* updated version of py-pygit2
* py-fairscale is a new package in support of torch
* py-pgzip is a dependency for py-fairscale
* switch fairscale pypi, added extra variant for convenience
* removed python dependency
* changed multiple requirement versions
* changes for upstream py-fairscale
* changes for upsteam py-pygit2
* Update package.py
* Update package.py
* sorted out some of the dependency versions
* removed version 1.12.2 because dependency could not be met
* updated py-cached-property dependency
* suggested changes from adamjstewart
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ensure umpire~cuda~rocm when ~cuda~rocm
* update mdanalysis
* 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>
* py-hatchling: add 1.18.0
* py-pipdeptree: add new package
* py-hatchling: add Python 3.8 dependency
* Apply suggestion from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* glibc: add missing deps, drop < 2.17
Building glibc 2.17 requires linking libgcc_{s,eh}.a, which themselves
depend on whatever glibc the current gcc uses for its runtime libraries.
Newer gcc depends on gnu extensions of libdl it seems, so that means you
simply cannot build old glibc with gcc-using-new-glibc.
The relevant fix in glibc is this commit:
commit 95f5a9a866695da4e038aa4e6ccbbfd5d9cf63b7
Author: Joseph Myers <joseph@codesourcery.com>
Date: Tue Jul 3 19:14:59 2012 +0000
Avoid use of libgcc_s and libgcc_eh when building glibc.
See also references to that commit in the glibc mailing list.
* update the gmake bound
* add --without-selinux
SIRIUS was introduced in version 7 of cp2k but could be used
in practice in version 9 (input format and functionalities).
SIRIUS with version 6 and below are marked as a dependency
conflict until CP2K version 9.
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Instead of pointing to the image on DockerHub, which rate limits us and
causes pipeline failures durying busy times, use the version at ghcr.
And we might as well use the ghcr version everywhere else too.
NMake makefiles are still called makefiles. The corresponding builder
variable was called "nmakefile", which is a bit unintuitive and lead
to a few easy-to-make, hard-to-notice mistakes when creating packages.
This commit renames the builder property to be "makefile"
Extensionless archives requiring two-stage decompression and extraction
require intermediate archives to be renamed after decompression/extraction
to prevent collision. Prior behavior attempted to cleanup the intermediate
archive with the original name, this PR ensures the renamed folder is
cleaned instead.
Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
Co-authored-by: John Parent <john.parent@kitware.com>
Smart alias completion introduced in #39499 wasn't as smart as it needed to be, and
would complete any invalid command prefix and some env names with alias names.
- [x] don't complete aliases if there are no potential completions
e.g., don't convert `spack isnotacommand` -> `spack concretize`
- [x] don't complete with an aliases if we're not looking at a top-level subcommand.
* Perform external spec detection with multiple workers
The logic to perform external spec detection has been refactored
into classes. These classes use the GoF "template" pattern to account
for the small differences between searching for "executables" and
for "libraries", while unifying the larger part of the algorithm.
A ProcessPoolExecutor is used to parallelize the work.
* Speed-up external find by tagging detectable packages automatically
Querying packages by tag is much faster than inspecting the repository,
since tags are cached. This commit adds a "detectable" tag to every
package that implements the detection protocol, and external detection
uses it to search for packages.
* Pass package names instead of package classes to workers
The slowest part of the search is importing the Python modules
associated with candidate packages. The import is done serially
before we distribute the work to the pool of executors.
This commit pushes the import of the Python module to the job
performed by the workers, and passes just the name of the packages
to the executors.
In this way imports can be done in parallel.
* Rework unit-tests for Windows
Some unit tests were doing a full e2e run of a command
just to check a input handling. Make the test more
focused by just stressing a specific function.
Mark as xfailed 2 tests on Windows, that will be fixed
by a PR in the queue. The tests are failing because we
monkeypatch internals in the parent process, but the
monkeypatching is not done in the "spawned" child
process.
* Write timing information for installs from cache
* CI: aggregate and upload install_times.json to artifacts
* CI: Don't change root directory for artifact generation
* Flat event based timer variation
Event based timer allows for easily starting and stopping timers without
wiping sub-timer data. It also requires less branching logic when
tracking time.
The json output is non-hierarchical in this version and hierarchy is
less rigidly enforced between starting and stopping.
* Add and write timers for top level install
* Update completion
* remove unused subtimer api
* Fix unit tests
* Suppress timing summary option
* Save timers summaries to user_data artifacts
* Remove completion from fish
* Move spack python to script section
* Write timer correctly for non-cache installs
* Re-add hash to timer file
* Fish completion updates
* Fix null timer yield value
* fix type hints
* Remove timer-summary-file option
* Add "." in front of non-package timer name
---------
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* seacas: Set TPL_ENABLE_Pthread=ON when +thread_safe
This should fix#39702
Basically, following suggestion of error message and setting
TPL_ENABLE_Pthread to the value of the boolean spack variant thread_safe
* seacas: Fix style issue
Add space after comment #
* cgns: Add -fPIC to Fortan/C compilation flags
This should fix#39699
* cgns: Add -fPIC compilation flags when +fortran
Incorporating suggestions of @aumuell with addition of making +pic required when +fortran
* r-sets: Add r-sets.
* r-sets: Fix R dependency for first version.
* r-sets: Remove package versions for which a compatible version of R cannot be installed.
The spiral-software package had a number of extensions, but does not
work unless they actually exist in the spiral software prefix (creating
a view is not sufficient). With the removal of "spack activate"
(different from "spack env activate"), a new approach is needed to
support optional components of `spiral-software` . This commit updates
the spiral-software package to copy the dependency installations into
its own prefix.
This commit also adds versions for `fftx` and `spiral-software`, as
well as an optional `spiral-software-jit` package.
This is a fixed version of b72a268
* That commit would discard the final key component (so if you set
"config:install_tree:root", it would discard "root" and just set
install tree).
* When setting key:"value", with the quotes, that commit would
discard the quotes, which would confuse the system if adding a
value like "{example}" (the "{" character indicates a dictionary).
This commit retains the quotes.
* adding bacio to g2 dependencies
* edited documentation
* added version 3.4.6
* starting with 3.4.6, can use any version of jasper
* adding w3emc dependency for versions up to 3.4.5
* removed t-brown as maintainer at his request
* Add hpx-kokkos 0.4.0
* Make git global package property in hpx-kokkos instead of having it version-specific
* Add variant for choosing future type in hpx-kokkos
* Add support for testing hpx-kokkos
These commands are currently broken on powershell (Windows) due to
improper use of the InvokeCommand commandlet and a lack of direct
support for the `--pwsh` argument in `spack load`, `spack unload`,
and `spack env deactivate`.
If you wanted to set a configuration option like
`config:install_tree:root` to "C:/path/to/config.yaml", Spack had
trouble parsing this because of the ":" in the value. This adds
logic to allow using quotes to enclose the value, so you can add
`config:install_tree:root:"C:/path/to/config.yaml"`.
Configuration keys should never contain a quote character, so the
presence of any quote is taken to mean that the rest of the string
is specifying the value.
* add a possibility to control default cuda version
* fix stype
* style fix
* resolve comment
* resolve comment
* Fix style in nvhpc package.py
---------
Co-authored-by: antonk <antonk@cscs.ch>
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Setting the undocumented variable SPACK_CONCRETIZER_REQUIRE_CHECKSUM
now causes the solver to avoid accounting for versions that are not checksummed.
This feature is used in CI to avoid spurious concretization against e.g. develop branches.
* The flang project does not support exceptions enabled in the core llvm
library (and developer guidelines explicitly state they should not be
used). For this reason, when the flang variant is selected,
LLVM_ENABLE_EH needs to be disabled. In the current main branch of
llvm (and thus future releases), enabling flang and setting
LLVM_ENABLE_EH will cause the overall build to fail.
* Update var/spack/repos/builtin/packages/llvm/package.py
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* fix syntax
---------
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
Currently, OneAPI's setvars scripts effectively disregard any arguments
we're passing to the MSVC vcvars env setup script, and additionally,
completely ignore the requested version of OneAPI, defaulting to whatever
the latest installed on the system is.
This leads to a scenario where we have improperly constructed Windows
native development environments, with potentially multiple versions of
MSVC and OneAPI being loaded or called in the same env. Obviously this is
far from ideal and leads to some fairly inscrutable errors such as
overlapping header files between MSVC and OneAPI and a different version
of OneAPI being called than the env was setup for.
This PR solves this issue by creating a structured invocation of each
relevant script in an order that ensures the correct values are set in
the resultant build env.
The order needs to be:
1. MSVC vcvarsall
2. The compiler specific env.bat script for the relevant version of
the oneapi compiler we're looking for. The root setvars scripts seems
to respect this as well, although it is less explicit
3. The root oneapi setvars script, which sets up everything else the
oneapi env needs and seems to respect previous env invocations.
`compgen -W` does not behave the same way in zsh as it does in bash; it seems not to
actually generate the completions we want.
- [x] add a zsh equivalent and `_compgen_w` to abstract it away
- [x] use `_compgen_w` instead of `compgen -W`
Bash completion is now smarter about handling aliases. In particular, if all completions
for some input command are aliased to the same thing, we'll just complete with that thing.
If you've already *typed* the full alias for a command, we'll complete the alias.
So, for example, here there's more than one real command involved, so all aliases are
shown:
```console
$ spack con
concretise concretize config containerise containerize
```
Here, there are two possibilities: `concretise` and `concretize`, but both map to
`concretize` so we just complete that:
```console
$ spack conc
concretize
```
And here, the user has already typed `concretis`, so we just go with it as there is only
one option:
```console
spack concretis
concretise
```
From a user:
> Aargh.
> ```
> ==> Error: concretise is not a recognized Spack command or extension command; check with `spack commands`.
> ```
To make things easier for our friends in the UK, this adds `concretise` and
`containerise` aliases for the `spack concretize` and `spack containerize` commands.
- [x] add aliases
- [x] update completions
Switch from makefile to CMake-based build. CMake support is currently
in a specific branch of the amg2023 repo, so add this branch as a
version in the package.
Set BL_USE_PARTICLES to 1, which should case boxlib build to include Particles classes
according to CMakeLists.txt.
This seems to fix#18172
The aforementioned error seems to occur in cmake phase while processing
CMakeLists.txt in Src/C_ParticleLib, and appears to be due to the
variable containing the list of src files for the add_library() call
being empty unless BL_USE_PARTICLES is set to 1.
Use full length commit sha instead of short prefixes, to improve
reproducibility (future clashes) and guard against compromised repos and
man in the middle attacks.
Abbreviated commit shas are expanded to full length, to guard against future
clashes on short hash. It also guards against compromised repos and
man in the middle attacks, where attackers can easily fabricate a malicious
commit with a shasum prefix collision.
Versions with just tags now also get a commit sha, which can later be used to
check for retagged commits.
* VTK: Add patch for python 3.8 support
* CI: Re-enable VisIt in CI
* Configure spec matrix for stack with VisIt
* Add pugixml dep for 8.2.0
* Make VTK and ParaView consistent on proj dep
* OpenMPI 3: provides MP support by default
* Add details on proj dep in ParaView
* Add python 3.8 to test mock repo
* Patches to get VisIt VTK interface
* CI: Disable VisIt with GUI in DAV
GitHub's beta private security issue reporting feature is enabled on the Spack repo now,
so we can change `SECURITY.md` to recommend using it instead of `maintainers@spack.io`.
- [x] Update `SECURITY.md` to direct people to the GitHub security tab.
- [x] Update working in `SECURITY.md` to say "last two major releases" with a link to
the releases page, instead of explicitly listing release names. This way we don't have
to update it (which we keep forgetting to do).
This reapplies 66f7540, which adds supports for hardlinks/junctions on
Windows systems where developer mode is not enabled.
The commit was reverted on account of multiple issues:
* Checks added to prevent dangling symlinks were interfering with
existing CI builds on Linux (i.e. builds that otherwise succeed were
failing for creating dangling symlinks).
* The logic also updated symlinking to perform redirection of relative
paths, which lead to malformed symlinks.
This commit fixes these issues.
There are other ways to enforce cray-pmi being loaded in environments
that use cray-mpich. This avoids breaking environments where this was
already the case and avoids forcing them to declare an external.
* AOCC and AOCL spack recipes for 4.1 release
* Fix broken checksum
* remove blank line
* Add missing `@when` for 4.1 only function
---------
Co-authored-by: vijay kallesh <Vijay-teekinavar.Kallesh@amd.com>
* Create a smartsim package
* rm ss 0.4.2
* no py upper bound, add build dep
* add setup_build_env
* add comment to find ml deps lower bounds
* Apply suggestions from code review
Correct dep versions, use `python_purelib`
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove the cuda/rocm vars
* point editors to bin deps version constraints
* Apply suggestions from code review
Loosen `py-smartredis` constraint, enforce `setup.cfg` py version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* style
* rm rai lower bound
* lower bound setuptools
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add magma variant to strumpack
* clarify conflicts to be excuive to rocm/cuda, without it +magma+cuda fails as it is ~rocm
modified: var/spack/repos/builtin/packages/strumpack/package.py
* add missing depends_on for magma variant
#35042 introduced lazy hash parsing, but didn't remove a
few attributes from the parser that were needed only for
concrete specs
This commit removes them, since they are effectively
dead code.
Clone is a hard dependency as of HTTP-Message v6.44. This causes
problems in packages like Roary which depend on perl-http-message:
$ spack load roary
$ roary
Use of uninitialized value in require at /var/scratch/spack/opt/spack/linux-centos8-x86_64_v3/gcc-8.5.0/perl-http-message-6.44-lzp5th4jddd3gojkjfli4hljgem2nl26/lib/perl5/HTTP/Headers.pm line 8.
Can't locate Clone.pm in @INC (you may need to install the Clone module) (@INC contains: /home/aorth/lib ...
See: https://github.com/libwww-perl/HTTP-Message/blob/master/Changes
While spack does not yet provide binutils 2.41, they might still be
installed. However, building ffmpeg on x86_64 fails with multiple errors like
this:
./libavcodec/x86/mathops.h:125: Error: operand type mismatch for `shr'
also reported here: https://trac.ffmpeg.org/ticket/10405
Add amg2023 package
Consolidate existing amg and amg2013 packages (they reference the
same code) under the amg2013 name to minimize confusion between
amg2023 and amg2013.
Co-authored-by: Riyaz Haque <haque1@llnl.gov>
The heuristic for duplicate nodes contains a few typos, and
apparently slows down the solve for specs that have a lot of
sub-optimal choices to be taken.
This is likely because with a lot of sub-optimal choices, the
low priority, flawed heuristic is being used by clingo.
Here I split the heuristic, so complex rules that matter only
if we allow multiple nodes from the same package are used
only in that case.
* use full cuda_arch list
* update compiler requirement
* update boost requirements
* propagate +kokkos to legion in non-GPU cases
* add missing graphviz dependency for +doc
Spack installs the hsa-rocr-dev and rocprofiler packages into different
directories. However, PAPI typically expects those to be under the same
directory and locates such directory through the PAPI_ROCM_ROOT env
variable.
The PAPI rocm component also allows users to override PAPI_ROCM_ROOT to
locate directly the librocprofiler64.so through the HSA_TOOLS_LIB env
variable that acts directly onto the HSA runtime tools mechanism.
Hence, in order to account for the decoupling of hsa and rocprofiler,
this patch sets HSA_TOOLS_LIB to librocprofiler64.so full path.
* Update pennylane-lightning.
* Update Lightning-Kokkos to v0.31
* Constrain scipy version.
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix PLK kokkos dep versioning.
* Move kokkos ver outised backend loop and reformat.
* Update package.py
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Since #34821 we are annotating virtual dependencies on
DAG edges, and reconstructing virtuals in memory when
we read a concrete spec from previous formats.
Therefore, we can remove a TODO in asp.py, and rely on
"virtual_on_edge" facts to be imposed.
Add support for PGO and LTO for gcc, clang and apple-clang, and add a
patch to allow mimalloc as an allocator in operator new/delete, give
reduces clingo runtime by about 30%.
Previous changes to this file stopped directly processing CL args to
stop batch `for` from interpolating batch reserved characters needed in
arguments like URLS. In doing so, we relied on `for` for an easy
"split" operation, however this incorrectly splits paths with spaces in
certain cases. Processing everything ourselves with manual looping via
`goto` statements allows for full control over CL parsing and handling
of both paths with spaces and reserved characters.
* WarpX 23.08
Update WarpX and related Python packages to the lastest releases.
* fix style
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
In the HPC package manager, we want the fastest `zlib` implementation by default. `zlib-ng` is up to 4x faster than stock `zlib`, and it can do things like take advantage of AVX-512 instructions. This PR makes `zlib-ng` the default `zlib-api` provider (`zlib-api` was introduced earlier, in #37372).
As far as I can see, the only issues you can encounter are:
1. Build issues with packages that heavily rely on `zlib` internals. In Gitlab CI only one out of hundreds of packages had that issue (it extended zlib with deflate stuff, and used its own copy of zlib sources).
2. Packages that like to detect `zlib-ng` separately and rely on `zlib-ng` internals. The only issue I've found with this among the hundreds of packages built in CI is `perl` trying to report more specific zlib-ng version details, and relied on some internals that got refactored. But yeah... that warrants a patch / conflict and is nothing special.
At runtime, you cannot really have any issues, given that zlib and zlib-ng export the exact same symbols (and zlib-ng tests this in their CI).
You can't really have issues with externals when using zlib-ng either. The only type of issue is when system zlib is rather new, and not marked as external; if another external uses new symbols, and Spack builds an older zlib/zlib-ng, then the external might not find the new symbols. But this is a configuration issue, and it's not an issue caused by zlib-ng, as the same would happen with older Spack zlib.
* zlib-api: use zlib-ng +compat by default
* make a trivial change to zlib-ng to trigger a rebuild
* add `haampie` as maintainer
Computing str(spec) is faster than computing hash(spec), and
since all the abstract specs we deal with come from user configuration
they cannot cover DAG structures that are not captured by str() but
are captured by hash()
Delay lookup for abstract hashes until concretization time, instead of
until Spec comparison. This has a few advantages:
1. `satisfies` / `intersects` etc don't always know where to resolve the
abstract hash (in some cases it's wrong to look in the current env,
db, buildcache, ...). Better to let the call site dictate it.
2. Allows search by abstract hash without triggering a database lookup,
causing quadratic complexity issues (accidental nested loop during
search)
3. Simplifies queries against the buildcache, they can now use Spec
instances instead of strings.
The rules are straightforward:
1. a satisfies b when b's hash is prefix of a's hash
2. a intersects b when either a's or b's hash is a prefix of b's or a's
hash respectively
The median length of this list of 1. For reasons I don't know, `.sort()`
still like to call the key function.
This saves ~9% of total database read time, and the number of calls
goes from 5305 -> 1715.
* Do not impose provider conditions, if the node is not a provider
fixes#39455
When a node can be a provider of a spec, but is not selected as
a provider, we should not be imposing provider conditions on the
virtual.
* Adjust the integrity constraint, by using the correct atom
* Add "only_clingo", "only_original" and "not_on_windows" markers
* Modify tests to use the "not_on_windows" marker
* Mark tests that run only with clingo
* Mark tests that run only with the original concretizer
* Fixed HeFFTe package spec to not do the smoke test prior to 2.2.0, where it breaks
* Convert test return to 'raise SkipTest'
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
To avoid paying the cost of setup and of a full grounding again,
move cycle detection into a separate program and check first if
the solution has cycles.
If it has, ground only the integrity constraint preventing cycles
and solve again.
The "concretizer" section has been extended with a "duplicates:strategy"
attribute, that can take three values:
- "none": only 1 node per package
- "minimal": allow multiple nodes opf specific packages
- "full": allow full duplication for a build tool
This refactor introduces extra indices for triggers and
effect of a condition, so that the corresponding clauses
are evaluated once for every condition they apply to.
All the solution modes we use imply that we have to solve for all
the literals, except for "when possible".
Here we remove a minimization on the number of literals not
solved, and emit directly a fact when a literal *has* to be
solved.
Introduce the concept of "condition sets", i.e. the set of packages on which
a package can require / impose conditions. This currently maps to the link/run
sub-dag of each package + its direct build dependencies.
Parametrize the "condition" and "requirement" logic to multiple nodes.
So far the encoding has a single ID per package, i.e. all the
facts will be node(0, Package). This will prepare the stage for
extending this logic and having multiple nodes from the same
package in a DAG.
Each fact that is deduced from package rules, and start with
a bare package atom, is transformed into a "facts" atom containing
a nested function.
For instance we transformed
version_declared(Package, ...) -> facts(Package, version_declared(...))
This allows us to clearly mark facts that represent a rule on the package,
and will be of help later when we'll have to distinguish the cases where
the atom "Package" is being used referred to package rules and not to a
node in the DAG.
Windows executable paths can have spaces in them, which was leading to
errors when constructing Executable objects: the parser was intended
to handle cases where users could provide an executable along with one
or more space-delimited arguments.
* Executable now assumes that it is constructed with a string argument
that represents the path to the executable, but no additional arguments.
* Invocations of Executable.__init__ that depended on this have been
updated (this includes the core, tests, and one instance of builtin
repository package).
* The error handling for failed invocations of Executable.__call__ now
includes a check for whether the executable name/path contains a
space, to help users debug cases where they (now incorrectly)
concatenate the path and the arguments.
* The module-level skip for tests in `cmd.install` on Windows is removed.
A few classes of errors still persist:
* Cdash tests are not working on Windows
* Tests for failed installs are also not working (this will require
investigating bugs in output redirection)
* Environments are not yet supported on Windows
overall though, this enables testing of most basic uses of "spack install"
* Git repositories cached for version lookups were using a layout that
mimicked the URL as much as possible. This was useful for listing the
cache directory and understanding what was present at a glance, but
the paths were overly long on Windows. On all systems, the layout is
now a single directory based on a hash of the Git URL and is shortened
(which ensures a consistent and acceptable length, and also avoids
special characters).
* In particular, this removes util.url.parse_git_url and its associated
test, which were used exclusively for generating the git cache layout
* Bootstrapping is now enabled for unit tests on Windows
Change the shebang in mkinc from /usr/bin/perl to /usr/bin/env perl for
portability to systems that don't necessarily have perl in /usr/bin.
Also adds perl as a build-time dependency.
#36770 added git as a dependency to `setuptools-scm`. This in turn makes `git` a
transitive dependency for our bootstrapping process.
Since `git` may take a long time to build, and is found on most systems, try to
detect it as an external.
* WarpX 23.07
Update WarpX and related Python packages to the lastest releases.
* py-picmistandard: refresh hashes
Keeping even a single `git` version in here confuses the fetcher.
Remove broken old versions.
* Remove `py-warpx` versions with broken PICMI
* py-cryptography: does not run-depend on py-setuptools-rust
* py-cryptography: depens_on py-setuptools-rust when @3.4.2:
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cryptography: re-add depends_on type=run for narrow range
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This makes the name of the global variable representing
the repository currently in use uppercase. Doing so is advised
by pylint rules, and helps to identify where the global is used.
* fix(sgpp): Fix installation phase scons args
* fix(sgpp): Workaround for distutils deprecation
The distutils deprecation warning in Python 3.10 - 3.11 caused
problems within the SGpp SConfigure checks by causing failures
when looking for Python.h. This commit works around this by adding a
patch that simply disables the warning. It also puts limits on the
python dependency version until distutils is removed from SGpp.
* fix(sgpp): cleanup and simplify
* fix(sgpp): Fix style
`cmake+qt` depends on `qt`, which depends on `libmng`, which is a CMake
package, and has been for 4 years. Nobody ever complained about
`cmake+qt` not concretizing... so why pay the solve cost.
Before:
```
setup 3.779s
load 0.018s
ground 2.625s
solve 4.511s
total 11.236s
```
After:
```
setup 3.734s
load 0.018s
ground 0.468s
solve 0.560s
total 5.080s
```
* Prefix conflict messages with package name
This patch prefixes all conflict messages with the package name to
alleviate what was otherwise a very manual process. Note that this patch
is a one line change but has a fairly outsized impact.
* same for requires directive
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* AMReX: 23.06+ Multi-Dim Support
This updated the Spack package to allow to install AMReX, modules of
AMReX in E4S deployments and dependent packages with support for
multiple dimensions. Due to an upstream change in AMReX, we do not
longer need to ship three, binary incompatible package variants.
* [E4S] oneAPI AMReX < 23.06 Variant
Work-around the auto-concretization to the multi-dim of `dimensions`,
which only in 23.06+ became a multi-variant.
* e4s cray rhel ci: temporarily disable amrex build until spurious ci failure can be resolved
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
The package won't compile with newer compilers because warnings
are converted to errors. Hence, disable such conversion.
Co-authored-by: Cristian Di Pietrantonio <cdipietrantonio@pawsey.org.au>
With the previous version of the recipe I would get linking errors due
to missing `-lfftw3f`.
Co-authored-by: Cristian Di Pietrantonio <cdipietrantonio@pawsey.org.au>
* Ensure that all variants have a description
* Update mock packages too
* Fix test invocations
* Black fix
* mgard: update variant descriptions
* flake8 fix
* black fix
* Add to audit tests
* Relax type hints
* Older Python support
* Undo all changes to mock packages
* Flake8 fix
This adds the latest C-Blosc2 release, the first to add CMake
CONFIG install files for easier downstream usage of the installed
library and CMake targets.
* include tests for h5bench
* update to new test format
* update path
* improve description and detect MPI runner
* fix test name
* Include new release
* update with corrections
* include SLURM dependency and reduce test to one process
* fixes on filters
* fix on oversubscribe
* suggested fixes
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Refactor gitlab ci configs so that mac and cray jobs can reuse as much higher level
configuration as possible.
* CI: remove redundant sections
* CI: Include base linux CI configs in cray stacks
Relocation and runner mapping is consistent between cray and linux runners.
* Export user cache path in before script
* CI: add GPG root for mac runners
* Disable user configs
Metal runners share a ~ directory
* Disable user config and add configs in activate env
This PR extracts two responsibilities from the `Database` class:
1. Managing locks for prefixes during an installation
2. Marking installation failures
and pushes them into their own class (`SpecLocker` and `FailureMarker`). These responsibilities are also pushed up into the `Store`, leaving to `Database` only the duty to manage `index.json` files.
`SpecLocker` classes no longer share a global list of locks, but locks are per instance. Their identifier is simply `(dag hash, package name)`, and not the spec prefix path, to avoid circular dependencies across Store / Database / Spec.
* Fixed the LD_LIBRARY_PATH to use the lib64 directory.
* On AMD systems the llvm/lib directory is not properly put into the LD_LIBRARY_PATH.
* Added both lib and lib64 paths for libfabric.
* Split the prepend statements.
* Add support to export the LD_LIBRARY_PATH for the libfabric package
and subsequent module files.
Fix the AWS OFI RCCL package so that it prepends the enviornment
variables.
* Fixed comment
* Create a spack package for smartredis python client
* make py-SR deps versions match docs
* tie SR v0.4.0 to redis-plus-plus v1.3.5
* looser extension lib deps for concretization
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Address reviewer feedback
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0
* Update var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* vecgeom: new version 1.2.5
* Mark previous versions as deprecated
* [@spackbot] updating style on behalf of sethrj
* vecgeom: fix 1.2.4 checksum for change to git describe
FastPackageChecker.modified_since should use a default number < 0
When the repo cache does not exist, Spack uses mtime 0. This causes the repo
cache not to be generated when the repo has mtime 0.
Some popular package managers such as spack use 0 mtime normalization for
reproducible tarballs. So when installing spack with spack from a buildcache, the
repo cache doesn't generate
Also add some typehints
* Inform mypy that tty.die is noreturn
* avoid temporary allocation in env
* update spack buildcache save-specfile
* fix spack buildcache check/download/get-buildcache-name
- ensure that required args and mutually exclusive ones are marked as
such in argparse for better error messages
- deprecate --spec-file everywhere
- use disambiguate for better error messages
* py-paralleltask: new package @0.2.2
* adding hidden dependency
* nextdenovo: new package @2.5.2
* style
* Update var/spack/repos/builtin/packages/py-paralleltask/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-melissa-core: add new versions and py-iterative-stats dependency
* Enhance dependency specification
* Fix dependency specification
* Fix comment alignment
* Improve dependency specification style
* Enhance dependencies
* Fix mpi4py, py-cloudpickle and py-python-hostlist dependencies
* Update var/spack/repos/builtin/packages/py-melissa-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-melissa-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-melissa-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Set develop version as preferred
* Update var/spack/repos/builtin/packages/py-melissa-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* libEnsemble: add v0.10.2
* Make setuptools build only dep
* Update var/spack/repos/builtin/packages/py-libensemble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* tximeta: add package
Signed-off-by: Pablo <pablo.aledo@seqera.io>
* [@spackbot] updating style on behalf of pabloaledo
---------
Signed-off-by: Pablo <pablo.aledo@seqera.io>
* CI: Refactor ci reproducer
* Autostart container
* Reproducer paths match CI paths
* Generate start scripts for docker and reproducer
* CI: Add interactive and gpg options to reproduce-build
* Interactive will determine if the docker container persists
after running reproduction.
* GPG path/url allow downloading GPG keys needed for binary
cache download validation. This is important for running
reproducer for protected CI jobs.
* Add exit_on_failure option to CI scripts
* CI: Add runtime option for reproducer
- Run `mkdirp` on `spec.prefix`
- Extract directly into `spec.prefix`
1. No need for `$store/tmp.xxx` where we extract the tarball directly, pray that it has one subdir `<name>-<version>-<hash>`, and then `rm -rf` the package prefix followed by `mv`.
2. No need to clean up this temp dir in `spack clean`.
3. Instead figure out package directory prefix from the tarball contents, and strip the tarinfo entries accordingly (kinda like tar --strip-components but more strict)
- Set package dir permissions
- Don't error during error handling when files cannot removed
- No need to "enrich" spec.json with this tarball-toplevel-path
After this PR, we can in fact tarball packages relative to `/` instead of `spec.prefix/..`, which makes it possible to use Spack tarballs as container layers, where relocation is impossible, and rootfs tarballs are expected.
`spack buildcache list` did not have a way to display the namespace of
packages in the buildcache. This PR adds that functionality.
For consistency's sake, it moves the `-N/--namespace` arg definition to
the `common/arguments.py` and modifies `find`, `solve`, `spec` to use
the common definition.
Previously, `find` was using `--namespace` (singular) to control whether
to display the namespace (it doesn't restrict the search to that
namespace). The other commands were using `--namespaces` (plural). For
backwards compatibility and for consistency with `--deps`, `--tags`,
etc, the plural `--namespaces` was chosen. The argument parser ensures
that `find --namespace` will continue to behave as before.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* dcmtk: checksum 3.6.7
compiles on macos
* dcmtk: support pic configuration
* [@spackbot] updating style on behalf of aumuell
* dcmtk: use define_from_variant for shorter code
* dcmtk: refine conflict
it appears that dcmtk < 3.6.7 only fails on macos/aarch64:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/include/xmmintrin.h:14:2:
error: "This header is only meant to be used on x86 and x64 architecture"
---------
Co-authored-by: aumuell <aumuell@users.noreply.github.com>
* py-gevent: add 23.7.0 and py-greenlet: add 3.0.0a1
* Update var/spack/repos/builtin/packages/py-gevent/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove version 1.3.a2
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* simple build of py-openai
* added variants to py-openai
* py-pandas-stubs is a dependency for py-openai
* fixed format and flake8 errors for py-openai
* black format error for py-pandas-stubs
* [@spackbot] updating style on behalf of sidpbury
* made style and format changes to py-openai
* made style and format changes to py-pandas-stubs
* py-types-pytz is a dependency for py-openai
* [@spackbot] updating style on behalf of sidpbury
* updated py-openpyxl for ver 3.0.7 and 3.1.2
* Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ajs requested changes for py-openai
* updated py-openpyxl for supported python
* [@spackbot] updating style on behalf of sidpbury
* updated py-openpyxl
* removed requirement.txt dependencies in py-openpyxl
* removed python depends on from openpyxl
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix Python package.py for Debian and derivatives to find the system Python library location
When bootstrapping from source, find_library() does not contain any paths that work for Debian and derivatives. fixes#36666
* Update to pass styling
* Update to styling
* Update python package.py with fake config value for LIBPL
* Update python package.py libpl config_vars entry to follow double quote standard
* styling update
* Add rewrite of spack checksum to include --verify and better add versions to package.py files
* Fix formatting and remove unused import
* Update checksum unit-tests to correctly test multiple versions and add to package
* Remove references to latest in stage.py
* Update bash-completion scripts to fix unit tests failures
* Fix docs generation
* Remove unused url_dict argument from methods
* Reduce chance of redundant remote_versions work
* Add print() before tty.die() to increase error readablity
* Update version regular expression to allow for multi-line versions
* Add a few unit tests to improve test coverage
* Update command completion
* Add type hints to added functions and fix a few py-lint suggestions
* Add @no_type_check to prevent mypy from failing on pkg.versions
* Add type hints to format.py and fix unit test
* Black format lib/spack/spack/package_base.py
* Attempt ignoring type errors
* Add optional dict type hint and declare versions in PackageBase
* Refactor util/format.py to allow for url_dict as an optional parameter
* Directly reference PackageBase class instead of using TypeVar
* Fix comment typo
---------
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
* py-cupy updates: add +rocm and +all
* rocm deps are link only
* set parallelism for both +rocm and +cuda
* add missing deps; remove unnecessary deps; uncomment maintainers; get hipcc properly
* py-rdflib: add 6.3.2
* Update var/spack/repos/builtin/packages/py-rdflib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove python dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add recipe for py-hostlist
* Fix style
* Fix style
* Add homepage, fix version url and remove unnecessary dependency
* Fix version and remove url
* Rename package and fix git link
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
* sourmash: new package @4.8.2
* sourmash: new package @4.8.2
* py-bitarray: add 2.7.6, 2.7.4
* Update var/spack/repos/builtin/packages/py-bitstring/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update setuptools dependency
* Adding missing deps
* Update var/spack/repos/builtin/packages/sourmash/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Correcting maturin dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/sourmash/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/sourmash/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/sourmash/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding dependency types
* Add `@0.14.17` as the last pre-`@1:` release
* Switch to use `python_platlib`
* Update package.py
* Update var/spack/repos/builtin/packages/py-screed/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding optional hip test
* Modifications to run every samples test
* Skipping test directories without a Makefile
* fix styling and cleaning code
* fix styling and changed method of itterating through sample folders
* changed to new syntax for standalone tests
* Updates for changes in syntax
Currently lm-sensors defaults to the compiler specified in the Makefile
(gcc) rather than the one specified in the spec. This patch appends the
CC flag to the make invocation with the spec compiler to fix this
behavior.
* initial commit for rocm-5.5.0 release
* fix the hipsparse build error for 5.5.0
* fix build error for amrex .add hiprand as a dependency
* modify the patch for rocprofiler-dev
* add hiprand for +rocm build
* initial commit for rocm-5.5.1 release
* bump up the version for rocm-5.5.1 release.
* bump up the version for rocmlir.miopen to use this backend only till 5.5
* add new recipe py-barectf and add it as dependency for rocprofiler-dev
* revert the changes for rocprofiler-dev for 5.5.0/1 for now as it depends
on hsa-amdaqlprofile.so which is a closed source and no spack recipe is
available for now.
* add rocm-core as dependency for rocm packages from 5.5.0 onwards
* avoid download of the gtest for building unit tests
* feature (packages): implement `odgi` package
This commit re-implements odgi package (superseded by #38741)
* fix (packages): remove redundant `requires()` from odgi package
This commit removes redundant use of `requires()` for gcc version in the `odgi` package
libelf fails to build with clang16+ due to Wimplicit-int and
Wimplicit-function-declarations becoming errors by default. This breaks
the configuration stage, so no build takes place. This patch fixes this
by passing -Wno-error=implicit-int and
-Wno-error=implicit-function-declarations as cflags.
gcoff uses the register keyword in a couple different places which
causes errors when building with c++17, which is the default in clang
16. This patch adds the -Wno-register flag to ignore these errors when
when building with clang 16.
Clang 16's change to erroring out by default on implicit function
declarations and implicit integers causes the build script for unzip to
break. Since this project hasn't had a release since 2010, we need to
patch it downstream/pass additional flags to get the build to succeed.
With the release of clang 16, clang now treats implicit function
declarations and implicit integers as errors rather than warnings,
causing the build to fail. This patch adds flags to prevent build
failures.
The sanitization function is completely bogus as it tries to replace /
on unix after ... splitting on it. The way it's implemented is very
questionable: the input is a file name, not a path. It doesn't make
sense to interpret the input as a path and then make the components
valid -- you'll interpret / in a filename as a dir separator.
It also fails to deal with path components that contain just unsupported
characters (resulting in empty component).
The correct way to deal with this is to have a function that takes a
potential file name and replaces unsupported characters.
I'm not going to fix the other issues on Windows, such as reserved file
names, but left a note, and hope that @johnwparent can fix that
separately.
(Obviously we wouldn't have this problem at all if we just fixed the
filename in a safe way instead of trying to derive something from
the url; we could use the content digest when available for example)
* py-jaxlib: add conflict for missing cuda cuda_arch specification
* Update var/spack/repos/builtin/packages/py-jaxlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-jaxlib: conflict missing cuda_arch value when with cuda
* Update var/spack/repos/builtin/packages/py-jaxlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* commands: provide more information to Command
* fish: Add script to generate fish completion
* fish: auto prepend `spack` command to avoid duplication
* fish: impove completion generation code readability
* commands: replace match-case with if-else
* fish: fix optspec variable name prefix
* fish: fix return value in get_optspecs
* fish: fix return value in get_optspecs
* format: split long line and trim trailing space
* bugfix: replace f-string with interpolation
* fish: compete more specs and some fixes
* fish: complete hash spec starts with /
* fish: improve compatibility
* style: trim trailing whitespace
* commands: add fish to update args and update tests
* commands: add fish completion file
* style: merge imports
* fish: source completion in setup-env
* fish: caret only completes dependencies
* fish: make sure we always get same order of output
* fish: spack activate
only show installed packages that have extensions
* fish: update completion file
* fish: make dict keys sorted
* Blacken code
* Fix bad merge
* Undo style changes to setup-env.fish
* Fix unit tests
* Style fix
* Compatible with fish_indent
* Use list for stability of order
* Sort one more place
* Sort more things
* Sorting unneeded
* Unsort
* Print difference
* Style fix
* Help messages need quotes
* Arguments to -a must be quoted
* Update types
* Update types
* Update types
* Add type hints
* Change order of positionals
* Always expand help
* Remove shared base class
* Fix type hints
* Remove platform-specific choices
* First line of help only
* Remove unused maps
* Remove suppress
* Remove debugging comments
* Better quoting
* Fish completions have no double dash
* Remove test for deleted class
* Fix grammar in header file
* Use single quotes in most places
* Better support for remainder nargs
* No magic strings
* * and + can also complete multiple
* lower case, no period
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* tinygltf: new versions and release branch
for each minor release available, the newest patch release has been added
---------
Co-authored-by: aumuell <aumuell@users.noreply.github.com>
- drop use_xcode = True, as this would lead to an attempt install Xcode (#34064)
- don't automatically build Qt Location with +opengl, as this is
still broken
This built sucessfully with qt@5.15.10+opengl+dbus+phonon on ventura/arm without
Xcode installed (only command line tools) - I did not check with Xcode installed.
The user store is lazily evaluated. The change
in #38975 made it such that the first evaluation
was happening in the middle of swapping to user
configuration.
Ensure we construct the user store before that.
Use curly braces instead of quotes to enclose value or text in Tcl
modulefile. Within curly braces Tcl special characters like [, ] or $
are treated verbatim whereas they are evaluated within quotes.
Curly braces is Tcl recommended way to enclose verbatim content [1].
Note: if curly braces charaters are used within content, they must be
balanced. This point has been checked against current repository and no
unbalanced curly braces has been spotted.
Fixes#24243
[1] https://wiki.tcl-lang.org/page/Tcl+Minimal+Escaping+Style
* Fetching patches wouldn't result in acquiring a stage lock during install
* The installer would acquire a stage lock *after* fetching instead of
before, leading to races
* The name of the stage for patches was random, so on build failure
(where stage dirs are not removed), these directories would continue
to exist after a second successful install.
* There was this redundant "composite fetch" object -- there's already
a composite stage. Remove this.
* For some reason we do *double* shasum validation of patches, before
and after compression -- that's just too much? I removed it.
Spack heuristically adds `<install prefix>/lib` and `<install prefix>/lib64` as rpath entries, as it doesn't know what the install dir is going to be ahead of the build. This PR cleans up non-existing, absolute paths[^1], which
1. avoids redundant stat calls at runtime
2. drops redundant rpaths in `patchelf`, making it relocatable -- you don't need patchelf recursively then.
[^1]: It also removes relative paths not starting with `$` (so, `$ORIGIN/../lib` is retained -- we _could_ interpolate `$ORIGIN`, but that's hard to get right when symlinks have to be taken into account). Relative paths _are_ supported in glibc, but are relative to _the current working directory_, which is madness, and it would be better to drop those paths.
A LazyReference object is a reference to an attribute of a
lazily evaluated singleton. Its only purpose is to let developers
use shorter names to refer to such attribute.
This class does more harm than good, as it obfuscates the fact
that we are using the attribute of a global object. Also, it can easily
go out of sync with the singleton it refers to if, for instance, the
singleton is updated but the references are not.
This commit removes the LazyReference class entirely, and access
the attributes explicitly passing through the global value to which
they are attached.
Without the package name being present in the conflict messages, it is
significantly more difficult to debug concretization failures in
environments that contain many packages.
mesa-glu still has a couple instances of the register keyword which
causes build failures with clang on my platform. This patch removes the
register keyword which doesn't have any impact on correctness.
gperf still uses the register keyword in one place which makes
compilation fail with c++17. This patch adds in a patch file to remove
the usage of the reigster keyword so that it compiles properly.
In late 2021 elfutils was patched to make it build with clang, and these
patches ended up in version 0.186. This commit updates the conflicts to
specify this so elfutils can be built with clang.
These tests now work without any changes to core. Furthermore, it is
surprising that they had to be disabled (at least, as long as the
installer.py tests are run on Windows: these tests are more-basic
and their functionality would have been exercised automatically).
* py-poetry-core: add 1.6.1 and fix url
* Update var/spack/repos/builtin/packages/py-poetry-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Re-add python upper bound for older versions
* Update var/spack/repos/builtin/packages/py-poetry-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
In Clang 15, -Wint-conversion became an error instead of a warning,
breaking the fftw build for clang versions > 15. This patch fixes fftw
builds with clang 15+ by passing -Wno-error=int-conversion as a cflag.
Without --allow-root spack cannot push binaries that contain paths in
binaries. This flag is almost always needed, so there is no point of
requiring users to spell it out.
Even without --allow-root, rpaths would still have to be patched, so the
flag is not there to guarantee binaries are not modified on install.
This commit makes --allow-root the default, and drops the code
required for it. It also deprecates `spack buildcache preview`, since
the command made sense only with --allow-root.
As a side effect, Spack no longer depends on binutils for relocation
Add support for conflict directives in Lua modulefile like done for Tcl
modulefile.
Note that conflicts are correctly honored on Lmod and Environment
Modules <4.2 only if mutually expressed on both modulefiles that
conflict with each other.
Migrate conflict code from Tcl-specific classes to the common part. Add
tests for Lmod and split the conflict test case in two.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* When using system tools to unpack a .gz file, the input file needs a
different name than the output file. Normally, we generate this new
name by stripping off the .gz extension off of the file name.
This was not sufficient if the file name did not have an extension,
so we temporarily rename the file in that case.
* When using system tar utility to untar on Windows, we were (erroneously)
skipping the actual untar step if the filename was lacking a .tar
extension
* For foo.txz, we were not changing the extension of the decompressed file
(i.e. we would decompress foo.txz to foo.txz). This did not cause any
problems, but is confusing, so has been updated such that the output
filename reflects its decompressed state (i.e. foo.tar).
* Added test for strip_compression_extension
* Update test_native_unpacking to test each archive type with and without
an extension as part of the file name (i.e. we test "foo.tar.gz", but
also make sure we decompress properly if it is named "foo").
* py-pyside: fix build for version 1.2.2
* Remove check for python version
* Fix style
* Remove unnecessary patch
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-markupsafe conflict
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Move python check removal below suprocess patch
* Remove preference of 1.2.2
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* soapdenovo2: strip optimization flags from injected flags
* soapdenovo2: add maintainer
* soapdenovo2: only append on cflags
* soapdenovo2: clean up some wording and implementation
Running `spack test run <python package>` resulted in the error
```
'str' object is not callable
```
because the python executable was not set correctly.
* qt-base: always link to GSS framework on macOS
On macos, the code in src/network/kernel/qauthenticator.cpp
unconditionally includes the header from the GSS framework, so we should
link against it.
This applies two patches from the dev branch. They are to be cherry-picked
into the 6.5 (probably released with 6.5.2) and 6.6 branches, but they
apply against 6.3.2 as well.
* qt-base: disable libproxy on macOS
src/network/CMakeLists.txt disables it on MACOS anyway. And as it is not
found without pkg-config, building with +network would break because of
the feature being explicitly enabled.
* qt-base: don't depend on pkgconfig on macOS
On macOS, usage of pkg-config is disabled by unsetting
PKG_CONFIG_EXECUTABLE, unless the feature pkg-config is requested explicitly.
* qt-base: don't depend on at-spi2-core on macOS
Does not build on macOS and seems to be targeted at linux. Qt6 on
homebrew does not depend on it, either.
* qt-base: fix long lines
* qt-base: restrict use of pkgconfig to linux
yes, probably not needed on windows, either
Co-authored-by: Alec Scott <alec@bcs.sh>
* qt-base: disable libproxy on Windows as well
according to src/network/CMakeLists.txt it's only used on Unix
* qt-base: improvements based on reviewer suggestions
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* legion: Add 23.06.0, variants for UCX, max nodes, update CUDA version.
* legion: Make newer CUDA versions dependent on newer Legion.
* legion: Update CUDA arch list so that we can stop tracking manually.
* Added py-eprosima-fastdds package
* Fixed python extension and dependency version
* Added build type for swig
* Added minimum cmake support
* Added py-test dependency
* Added suggestion on python extension
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added suggestion on build type for cmake
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Lock objects can now be instantiated independently,
without being tied to the global configuration. The
same is true for database and store objects.
The database __init__ method has been simplified to
take a single lock configuration object. Some common
lock configurations (e.g. NO_LOCK or NO_TIMEOUT) have
been named and are provided as globals.
The use_store context manager keeps the configuration
consistent by pushing and popping an internal scope.
It can also be tuned by passing extra data to set up
e.g. upstreams or anything else that might be related
to the store.
Not having the package name in the conflict messages can make debugging
conflicts exceedingly hard when trying to concretize an environment with
a sufficient number of packages. This patch adds the package name to all
of the conflict messages so that it is easy to tell just from the
message which package is causing conflicts.
* py-jinja2: add conflict for py-markupsafe@2.0.2
* Update var/spack/repos/builtin/packages/py-jinja2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-shiboken: fix build by restricting dependencies
* Update var/spack/repos/builtin/packages/py-shiboken/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove conflict
* Remove py-markupsafe conflict
* Update var/spack/repos/builtin/packages/py-shiboken/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add a phist patch to avoid trying to compile SSE code if that is not available.
* phist: make the avoid-sse patch more robust because compiler on ARM system still tried to compile SSE code
* Bugfix: spack.yaml concretizer:unify needs to be read and used
* Optional: add environment test to ensure configuration scheme is used
* Activate environment in unit tests
A more proper solution would be to keep
an environment instance configuration as
an attribute, but that is a bigger refactor
* Delay evaluation of Environment.unify
* Slightly simplify unit tests
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update TensorFlow ecosystem
* Re-add +cpp
* Do not use system protobuf
* Let bazel auto-detect macOS SDK version
* Unnecessary duplicated dep
* Remove unused import
Allow the following formats:
```yaml
mirrors:
name: <url>
```
```yaml
mirrors:
name:
url: s3://xyz
access_pair: [x, y]
```
```yaml
mirrors:
name:
fetch: http://xyz
push:
url: s3://xyz
access_pair: [x, y]
```
And reserve two new properties to indicate the mirror type (e.g.
mirror.spack.io is a source mirror, not a binary cache)
```yaml
mirrors:
spack-public:
source: true
binary: false
url: https://mirror.spack.io
```
A few packages have version directives evaluated
within if statements, conditional on the value of
`platform.platform()`.
Sometimes there are no cases for e.g. platform=darwin and that
causes a lot of spurious failures with version existence
audits.
This PR allows expressing conditions to skip version
existence checks in audits and avoid these spurious reports.
### Rationale
While working on #29549, I noticed a lot of inconsistencies in our argparse help messages. This is important for fish where these help messages end up as descriptions in the tab completion menu. See https://github.com/spack/spack/pull/29549#issuecomment-1627596477 for some examples of longer or more stylized help messages.
### Implementation
This PR makes the following changes:
- [x] help messages start with a lowercase letter.
- [x] Help messages do not end with a period
- [x] the first line of a help message is short and simple
longer text is separated by an empty line
- [x] "help messages do not use triple quotes"
"""(except docstrings)"""
- [x] Parentheses not needed for string concatenation inside function call
- [x] Remove "..." "..." string concatenation leftover from black reformatting
- [x] Remove Sphinx argument docs from help messages
The first 2 choices aren't very controversial, and are designed to match the syntax of the `--help` flag automatically added by argparse. The 3rd choice is more up for debate, and is designed to match our package/module docstrings. The 4th choice is designed to avoid excessive newline characters and indentation. We may actually want to go even further and disallow docstrings altogether.
### Alternatives
Choice 3 in particular has a lot of alternatives. My goal is solely to ensure that fish tab completion looks reasonable. Alternatives include:
1. Get rid of long help messages, only allow short simple messages
2. Move longer help messages to epilog
3. Separate by 2 newline characters instead of 1
4. Separate by period instead of newline. First sentence goes into tab completion description
The number of commands with long help text is actually rather small, and is mostly relegated to `spack ci` and `spack buildcache`. So 1 isn't actually as ridiculous as it sounds.
Let me know if there are any other standardizations or alternatives you would like to suggest.
* ci: run spack list in power ci
Let's see if Spack itself is the bottleneck in CI...
* rebuild curl in CI
* more of the same please!
* drop the profiler
* undo rebuildme test in ci variant
* add comment for posterity
* enable profiling
* trigger CI
* See how it goes now that perf regressions are fixed on develop
* try shorter poll intervals
* Revert "try shorter poll intervals"
This reverts commit d60c34ad3eceead0c13a5277cf8e783fd42b7458.
* Remove spec.format call in Database._get_matching_spec_key
* once more in ci please
* undo irrelevant changes
* run spack list in before script
* test in ci
* -:
* Undo CI testing
The spdlog project precisely states/depends which fmt version should
be used for compatibility. Latest version 1.11.0 depends explictly on
fmt 9.1.0. Without fixed version micromamba build fails when using spack
install micromamba on e.g. Rockylinux 8.5.
The 'bison' executable requires libtextstyle to run. I think this was
usually satisfied because gettext is often installed with the OS, or
brought in accidentally via perl/m4.
Looks like the libtextstyle library dependency started in Bison 3.4
Refactor `TermTitle` into `InstallStatus` and use it to show progress
information both in the terminal title as well as inline. This also
turns on the terminal title status by default.
The inline output will look like the following after this change:
```
==> Installing m4-1.4.19-w2fxrpuz64zdq63woprqfxxzc3tzu7p3 [4/4]
```
* llvm: fix build with libcxx=none
* ispc: checksum 1.20.0
* ispc: ensure that it does not crash immediately
this would happen if linked to the wrong libc++
* ispc: fix build on macos
find ncurses instead of curses and link against tinfo in order to avoid
unresolved references to _del_curterm, _set_curterm, _setupterm, and
_tigetnum
* ispc: enable arm targets, if building on arm
* ispc: remove double cmake argument
I forgot to remove the constant -DARM_ENABLED=FALSE when adding
-DARM_ENABLED with a value depending on target architecture
* ispc: fix linux build
since 1.20, linux build uses TBB as default tasking system and thus
needs to depend on it
* ispc: try to fix link error on linux
link against both curses (as before) and tinfo (added because of macos)
* ispc: update for recent llvm changes
libcxx=none instead of ~libcxx
`mypy` will check *all* imported packages, even optional dependencies outside your
project, and this can cause issues if you are targeting python versions *older* than the
one you're running in. `mypy` will report issues in the latest versions of dependencies
as errors even if installing on some older python would have installed an older version
of the dependency.
We saw this problem before with `numpy` in #34732. We've started seeing it with IPython
in #38704. This fixes the issue by exempting `IPython` and a number of other imports of
Spack's from `mypy` checking.
* Setting library path as lib similar to other rocm packages.
* Fix style check failure
* Restricting changes to 5.4.3 and above
* Including comgr change
* initial commit for adding hip-examples package
* adding test to hip-examples
* fixed compile error on add4
* change standalone test to use new syntax
Spack-installed Perl always has opcode support, but external Perl
installations might not. This commit adds a +opcode variant and
updates the external detection logic to check for opcode support.
The postgresql package is updated to require perl+opcode (in
combination with the above, this helps detect when an external
Perl instance is sufficient for a Spack build of postgreqsql, or
if Spack needs to build its own Perl).
* Update cp2k recipe to use cmake or the current build system
Offers the possibility to build cp2k with the new cmake build system. commands like this are now supported
spack install cp2k@master build_system=cmake +.....
the recipe supports the following optional functionalities
- superlu, cosma, sirius, spglib, metis, spglib, libxc, libint, cuda/rocm, mkl/openblas/sci (and others), mpi, openmp, dbcsr
- dbcsr is built separately using the currently available recipe.
Two PRs need to be merged to be fully functional (cosma update in spack + one PR in cp2k github).
* Fix indentation
* Fix indentation
* Update libvori
* More typos
* Simplify BLAS/LAPACK
* Simplify BLAS/LAPACK
* Add A100 gpu value
* Fix typo
* Add the enable_regtests option
if -DCP2K_ENABLE_REGTESTS=ON (+enable_regtests with spack) then the location of the binary executables will be in the cp2k root directory under exe/build-cmake-*. This option is needed to run the regtests afterwards.
* Minor update
* more fixes
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* small changes
* Remove any reference to nvidia architecture in the rocm list
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Final reformating
* Update py-fypp
---------
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
People frequently ask us how to pipe `spack find` output to other commands, and we tell
them to do things like this:
```console
$ spack find --format "/{hash}" | spack uninstall -ay
```
Sometimes users don't know about hash references and come up with potentially ambiguous
formulations like this:
```console
spack find --format {name}@{version}%{compiler} | spack uninstall -ay
```
Since this is a common enough thing to want to do, and to make it more obvious how, this
PR adds a `-H` / `--hashes` as a shortcut, so you can now just do:
```console
spack find -H | spack uninstall -ay
```
* Added packages bitstruct, callmonitor, and PYnvtx
* Revert "Added packages bitstruct, callmonitor, and PYnvtx"
This reverts commit 76d25aa76b.
* py-bitstruct: This module is intended to have a similar interface as the python struct module, but working on bits instead of primitive data types (char, int, …)
* Update package.py
To pass the style prechecks
* PyNVTX: new package
* Delete package.py
Accidentally added this package.
* Update var/spack/repos/builtin/packages/py-bitstruct/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* openssl: prefer 3.x
This PR is not intended to be merged immediately, but it would be good
to see what packages fail to build in CI so that we can get proper
version constraints on openssl (before all packages update and support
both openssl 1 and 3)
* Disable assembly for 3.x %oneapi
* cmake: depend on spack curl, to deal with curl - openssl compat
* also make zlib external
* remove overly strict & unsafe requirement on py-cryptographty patch version number
* update openssl compat bounds in py-cryptography
* smaller diff
* Make libssh2 an autotools/cmake package
* fix weird upperbound in libssh2 as there is not openssl v2
* libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output
* Actually fix the issue in libssh2: its pc file looks broken
`"%s" % spec` formats the spec with deps included, which produces sometimes KBs
of data and is slow to run in pure Python. It can delay otherwise very short-lived
read/write locks on the database.
Discovered in #38762 where profile output showed about 2 seconds is spent in
`spec.format`, which is significant overhead when using multiprocessing to install
from binary cache in parallel (installation often takes <5s for small packages). With
this change, `spec.format` no longer shows up in profile output.
(This line hasn't changed since Spack v0.9 ;p)
* move format() call to custom NoSuchSpecError exception
* add a comment saying why, so we can eventually change `Spec.__str__`
* qt-base: new version 6.5.0
* qt-declarative: new version 6.5.0
* qt-quick3d: new version 6.5.0
* qt-quicktimeline: new version 6.5.0
* qt-shadertools: new version 6.5.0
* qt-*: new version 6.5.1
* qt-base: new version 6.5.1
* py-pyarrow: enable parquet variant by default
* Disable parquet variant by default
* Add conflict to enable parquet when dataset is active
* Disable dataset variant by default
* initial commit of nanobind package
* style fixes
* Update package.py
Typo
* addressed PR comments
* add v1.4.0
* Update var/spack/repos/builtin/packages/py-nanobind/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-astropy: fix import tests and restrict py-pip version
* Fix --install-option name in comments
* Rename variant and fix variant dependencies
* Remove parquet variant from py-pyarrow
1. Fix O(n^2) iteration in `_get_overwrite_specs`
2. Early exit `get_by_hash` on full hash
3. Fix O(n^2) double lookup in `all_matching_specs` with hashes
4. Fix some legibility issues
* mlpack: new package
mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers.
* mlpack: upstream merged patch to allow python installation in spack
* Added v5.0.0 of PyAMG. This required v7.1.0 of setuptools_scm due to a bug in 7.0.5.
* Added comment about version requirement.
* Loosened dependency based on build experiments.
* Updated tomli deps.
* Update var/spack/repos/builtin/packages/py-setuptools-scm/package.py
Dependence for 7.0 only.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyamg/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Swapped lines.
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pip: add 23.1.2
* Restrict py-pip version for py-protobuf
* Restrict py-pip version for straightforward packages
* Restrict py-pip version for nrm
* Fix --install-option name in comments
* Simplify py-pip restriction for py-scs
* nrm: fix wrong comment
* py-spglib: add 2.0.2
* Update var/spack/repos/builtin/packages/py-spglib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-setuptools as run dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add maintainers
* Updated cosma archive checksum and costa version
- updated cosma version (in the cosma build system)
- updated costa version
- use the default generic url for downloading packages
- do not build tiled-mm when the cpu only version is needed
Signed-off-by: Dr. Mathieu Taillefumier <mathieu.taillefumier@free.fr>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
NAMD users expect the Tcl scripting interface to be enabled as it is used in many examples and tutorials in addition to being required for features such as multi-copy algorithms.
* When installing a package Spack will attempt to set group permissions on
the install prefix even when the configuration does not specify a group.
Co-authored-by: David Gomez <dvdgomez@users.noreply.github.com>
From the configure.ac file:
> H5VL_log is built on top of MPI. Configure option --without-mpi or
> --with-mpi=no should not be used. Abort.
This currently fails to build in the oneAPI pipeline on `develop`
* py-userpath: new package
* pipx: new package
* Update var/spack/repos/builtin/packages/pipx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* pipx: Remove incorrect dependency on py-platformdirs
* Update var/spack/repos/builtin/packages/pipx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-userpath: Remove version requirements to match upstream
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR removes deprecated versions for all packages that I'm maintaining. In future Spack releases, I'm planning to do this on a much larger scale, but we can hold off until we have better reproducibility.
I'm hoping that this will improve the maintainability of these packages. If any other maintainers of these recipes would like to retain any of these deprecated versions, or add new versions, speak now or forever hold your peace 😄
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
Windows runtime library loading searches PATH, and therefore bin/ is
the appropriate place to put .dll files. Prior to this change, XZ was
installing both .dll and .lib files to the lib/ directory.
Move the logic checking which mirrors have the specs we need closer
to where that information is needed. Also update the staging summary
to contain a brief description of why we scheduled or pruned each
job. If a spec was found on any mirrors, regardless of whether
we scheduled a job for it, print those mirrors.
* Change maintainer, add new version and deprecate old one
* Fix style issue
* Revert deprecation
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
PowerShell requires explicit shell and env support in Spack.
This is due to the distinct differences in shell interactions between
cmd and pwsh. Add a doskey in pwsh piping 'spack' commands to a
powershell script similar to the sh function 'spack'. Add
support for PowerShell-specific shell interactions from Spack
(set/unset shell variables).
* py-ruamel-yaml: add 0.17.32 and py-ruamel-yaml-clib: add 0.2.7
* Update var/spack/repos/builtin/packages/py-ruamel-yaml/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix style
* Fix python dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* HDF5: is_enabled helper (ON)
Slightly generalize the `is_enabled` helper in the HDF5 package.
`ON` is the most typical CMake bool option passed, besides many
other possible `true` values, and should be included as a possible
check to the config.
* Simplify
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Support hardlinks/junctions on Windows systems without developer
mode enabled
* Generally, use of llnl.util.symlink.symlink is preferred over
os.symlink since it handles this automatically
* Generally an error is now reported if a user attempts to create a
symlink to a file that does not exist (this was previously allowed
on Linux/Mac).
* One exception to this: when Spack installs files from the source
into their final prefix, dangling symlinks are allowed (on
Linux/Mac - Windows does not allow this in any circumstance).
The intent behind this is to avoid generating failures for
installations on Linux/Mac that were succeeding before.
* Because Windows is strict about forbidding dangling symlinks,
`traverse_tree` has been updated to skip creating symlinks if they
would point to a file that is ignored. This check is not
transitive (i.e., a symlink to a symlink to an ignored file would
not be caught appropriately)
* Relocate function: resolve_link_target_relative_to_the_link
(this is not otherwise modified)
Co-authored-by: jamessmillie <smillie@txcorp.com>
Update list of excluded variables in `from_sourcing_file` function to
cover all variables specific to Environment Modules or Lmod. Add
specifically variables relative to the definition of `module()`, `ml()`
and `_module_raw()` Bash functions.
Fixes#13504
* Add new versions of Qthreads
* Add version URLs explicitly as it has recently changed
* Use function to extrapolate version URL for older versions
* Fix url formatter
llvm @13-15 is required for ispc, but fails to build with GCC 13.
14.0.6 and 15.0.7 built successfully with upstream patch, 13.0.1
still fails. Thus upstream patch is applied to 14 and 15 only.
Update `env.set` command and underlying `SetEnv` object to add the `raw`
boolean attribute. `raw` is optional and set to False by default. When
set to True, value format is skipped for object when generating
environment modifications.
With this change it is now possible to define environment variable
whose value contains variable reference syntax (like `{foo}` or `{}`)
that should be set as-is.
Fixes#29578
By default, `find_package(Python)` searches from highest version to lowest version, identifying the highest version that satisfies the requirements. This means that `/usr/bin/python3.11` will be found before `$(spack location -i python)/bin/python3.10`, even when other packages have been built with the `python` in spack.
This ensures that the `python` dependency is explicitly the `python` version that is used.
* libEnsemble: add v0.10.0
* Make new deps required
* Fixes to deps
* Update var/spack/repos/builtin/packages/py-libensemble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix build, run
* Reorder required deps
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pytest: add 7.3.2
* [@spackbot] updating style on behalf of manuelakuhn
* Swap py-importlib-metadata dependency order
* Restrict python version for older versions
* Add recipe for iterative-stats
* Fix branch name and remove comment
* Add git link
* Add package maintainer
* Enforce multiple requested changes
* Update var/spack/repos/builtin/packages/py-iterative-stats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update checksum
* Fix openturns dependency specification
* Add python variant spec to openturns
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add rust v1.70.0 and simplify package logic by moving bootstrap to dedicated package
* Fix formatting of rust-bootstrap package file
* Re-enable Rust as extendable
* Add nightly version to rust and rust-bootstrap
* Manually inject openssl certs into environment
* Add master and beta versions to rust
* Add additional documentation for using rust development releases
* Remove @AndrewGaspar as maintainer
* py-notebook: add 6.5.4
* [@spackbot] updating style on behalf of manuelakuhn
* Update var/spack/repos/builtin/packages/py-notebook/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix version of py-nbclassic dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
It installs the LFortran runtime library and
LFortran can compile codes to binaries. The interactive mode does not
work yet with LLVM > 11, that has to be fixed upstream.
Co-authored-by: Wileam Y. Phan <50928756+wyphan@users.noreply.github.com>
No changes to the build system, no changes to `package.py` needed.
Changelog: https://github.com/qt/qtbase/compare/v5.15.9-lts-lgpl...v5.15.10-lts-lgpl
Main change taking up space:
- bundled 3rdparty/pcre2 updated from 10.39 to 10.40 (spack now includes 10.42, and we don't put specific version requirements in `package.py`)
* py-networkx: add 3.1
* Update var/spack/repos/builtin/packages/py-networkx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add default variant
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pycairo: add 1.24.0
* Change python dependency to 3.8
* Remove upper bound for python dependency
* Update var/spack/repos/builtin/packages/py-pycairo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add darshan 3.4.3 releases
* darshan-runtime 3.4.3
* darshan-util 3.4.3
* py-darshan 3.4.3.0
- add py-humanize as new dependency
* py-darshan has strict darshan-util version reqs
darshan-util version required is based on the first 3 parts of
the py-darshan version string
* remove support for python3.6
* py-humanize dependency for 3.4.3+ versions
* only enforce scipy dependency for 3.4.0.1
* drop optional lxml dependency
* drop matplotlib pinning
* importlib-resources not a dep in python-3.7+
* drop unnecessary numpy pin
* add build dep for pytest-runner
* fix typo in pytest-runner package name
* pip setuptools to match pydarsan setup.py
* spack style fix
* py-gsutil: add 5.24, fix and add dependencies
* Update var/spack/repos/builtin/packages/py-httplib2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add httplib2@0.20.4 and pin it in py-gsutil
* Add py-cryptography conflict
* Update var/spack/repos/builtin/packages/py-httplib2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pyopenssl: fix py-cryptography conflict
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update mda and mdatests
* black
* 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>
* polish
* Update var/spack/repos/builtin/packages/py-mdanalysistests/package.py
* fixes
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`FFLAGS` and `FCFLAGS` are being ignored by WRF build system. Not only in version
`3.9.1.1`, but also `4.x`.
Also, I see no reason to explicitly add `-w` and `-O2` to compile lines when
using `gcc@10:`. Tested for version `3.9.1.1`, `4.2.2`, & `4.5.0`.
Tagging original authors of this part @MichaelLaufer and @giordano in case they
want to chime in.
* ncbi-rmblastn: patching to support building with %gcc@13:
* ncbi-rmblastn: patching to build with %gcc@13:
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* py-pre-commit: add 3.3.3
* Update var/spack/repos/builtin/packages/py-pre-commit/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Spack flags supplied by users should supersede flags from package build systems and
other places in Spack. However, Spack currently adds user-supplied flags to the
beginning of the compile line, which means that in some cases build system flags will
supersede user-supplied ones.
The right place to add a flag to ensure it has highest precedence for the compiler really
depends on the type of flag. For example, search paths like `-L` and `-I` are examined
in order, so adding them first is highest precedence. Compilers take the *last* occurrence
of optimization flags like `-O2`, so those should be placed *after* other such flags. Shim
libraries with `-l` should go *before* other libraries on the command line, so we want
user-supplied libs to go first, etc.
`lib/spack/env/cc` already knows how to split arguments into categories like `libs_list`,
`rpath_dirs_list`, etc., so we can leverage that functionality to merge user flags into
the arg list correctly.
The general rules for injected flags are:
1. All `-L`, `-I`, `-isystem`, `-l`, and `*-rpath` flags from `spack_flags_*` to appear
before their regular counterparts.
2. All other flags ordered with the ones from flags after their regular counterparts,
i.e. `other_flags` before `spack_flags_other_flags`
- [x] Generalize argument categorization into its own function in the `cc` shell script
- [x] Apply the same splitting logic to injected flags and flags from the original compile line.
- [x] Use the resulting flag lists to merge user- and build-system-supplied flags by category.
- [x] Add tests.
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
Co-authored-by: iermolae <igor.ermolaev@intel.com>
* py-vermin: add latest version 1.5.2
* Removed obsolete dep and setuptools is only for build-time
- setuptools are not used as runtime
- py27 isn't strictly necessary
The `unparser` that Spack uses for package hashing had several tweaks to ensure compatibility
with Python 2.7:
1. Currently, the unparser automatically moves `*` and `**` args to the end to preserve
compatibility with `python@:3.4`
2. `print a, b, c` statements and single-tuple `print((a, b, c))` function calls were
remapped to `print(a, b, c)` in the unparsed output for consistency across versions.
(1) is causing issues in our tests because a recent patch to the Python source code
(https://github.com/python/cpython/pull/102953/files#diff-7972dffec6674d5f09410c71766ac6caacb95b9bccbf032061806ae304519c9bR813-R823)
has a `**` arg before an named argument, and we round-trip the core python source code
as a test of our unparser. This isn't actually a break with our consistent unpausing -- it's still
consistent, the python source just doesn't unparse to the same thing anymore. It does makes
it harder to test, so it's not worth maintaining the Python2-specific stuff anymore.
Since we only support `python@3.6:`, this PR removes (1) and (2) from the unparser, but keeps
one last tweak for unicode AST inconsistencies, as it's still needed for Python 3.5-3.7.
This fixes the CI error we've been seeing on `python@3.11.4` and `python@3.10.12`. Again, that
bug exists only in the test system and doesn't affect our canonical hashing of Python code.
* WarpX 23.06
Update WarpX and related Python packages to the lastest releases.
WarpX 23.06 introduces multi-dimension support in a single package,
which will ease deployment in E4S et al. that can ship now a single,
full-feature module/package that is NOT incompatible with itself
anymore.
* e4s ci stacks: multiple specs for each dim variant no longer required
* [@spackbot] updating style on behalf of ax3l
* WarpX: Update CMake CLI and Test/Check
* Add Missing `build-directory`
* [@spackbot] updating style on behalf of ax3l
* Remove `build_directory` again
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: ax3l <ax3l@users.noreply.github.com>
* star: add 2.7.10
* star: fix building for non-avx2 arch processors
* convert to MakefilePackage, second take at fixing for aarch64
* style
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* DependencySpec: add virtuals attribute on edges
This works for both the new and the old concretizer. Also,
added type hints to involved functions.
* Improve virtual reconstruction from old format
* Reconstruct virtuals when reading from Cray manifest
* Reconstruct virtual information on test dependencies
* openradioss-starter,engine: new package
* openradioss-engine: change version name develop to main
* openradioss-starter: change version name develop to main
Update Tcl modulefile template to use the `depends-on` command to
autoload modules if Lmod is the current module tool.
Autoloading modules with `module load` command in Tcl modulefile does
not work well for Lmod at some extend. An attempt to unload then load
designated module is performed each time such command is encountered. It
may lead to a load storm that may not end correctly with large number of
module dependencies.
`depends-on` command should be used for Lmod instead of `module load`,
as it checks if module is already loaded, and does not attempt to reload
this module.
Lua modulefile template already uses `depends_on` command to autoload
dependencies. Thus it is already considered that to use Lmod with Spack,
it must support `depends_on` command (version 7.6+).
Environment Modules copes well with `module load` command to autoload
dependencies (version 3.2+). `depends-on` command is supported starting
version 5.1 (as an alias of `prereq-all` command) which was relased last
year.
This change introduces a test to determine if current module tool that
evaluates modulefile is Lmod. If so, autoload dependencies are defined
with `depends-on` command. Otherwise `module load` command is used.
Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set
by Lmod starting version 5.1.
Fixes#36764
When interpreting local paths as relative URL endpoints, they were
formatted as Windows paths on Windows (i.e. with '\'). URLs should
always be POSIX-style.
Update modulefile templates to append a trailing delimiter to MANPATH
environment variable, if the modulefile sets it.
With a trailing delimiter at ends of MANPATH's value, man will search
the system man pages after searching the specific paths set.
Using append-path/append_path to add this element, the module tool
ensures it is appended only once. When modulefile is unloaded, the
number of append attempt is decreased, thus the trailing delimiter is
removed only if this number equals 0.
Disclaimer: no path element should be appended to MANPATH by generated
modulefiles. It should always be prepended to ensure this variable's
value ends with the trailing delimiter.
Fixes#11355.
* opencascade: new variants
OpenCascade has several major modules and not every
application needs all of them. This adds variants for
the various modules.
It also uodatws the 3rdparty dependency treatment.
* [@spackbot] updating style on behalf of wdconinc
* Update var/spack/repos/builtin/packages/opencascade/package.py
* opencascade: remove variant foundation_classes (always true)
* [@spackbot] updating style on behalf of wdconinc
* Update var/spack/repos/builtin/packages/opencascade/package.py
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Deprecate R packages for spatial analysis
* [@spackbot] updating style on behalf of adamjstewart
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
No changes to build system required. Changelog: https://github.com/xiaoyeli/superlu/compare/v5.3.0...v6.0.0
Since this new version adds "64-bit indexing support", and since at least one dependent package (`armadillo`) requires "32-bit integers" (faa6cbf895), the previous version remains preferred.
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* New version for openCARP packages
* Update carputils dependencies
* Update types of openCARP dependencies
* Add type "run" to setuptools dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add package py-common as carputils dependency
* Add setuptools dependency for py-common
* Remove spaces on blank line
* Restrict type of dependency setuptools to "build"
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: openCARP consortium <info@opencarp.org>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [gromacs] Fix intel (classic) libstdc++ path
Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or
`--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good
g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`:
cb6b311c39/cmake/FindLibStdCpp.cmake (L97)
Spack installed intel compilers already define a g++ for std libs. But in
`icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not
only have less chance of mixing g++ versions, but also don't need to explicitly
add `gcc` as dependency to `gromacs`.
* Fix format
* Use a variant
As there is no way to check if a file exists at depends_on stage
* Fix format
* New name and fail if variant is used with other compiler
* Line too long.
The pcluster image has am internal buildcache without an index.
Also, we need to force reuse to avoid rebuilding GCC, since the default is
to only reuse dependencies - and that is subject to changes in the GCC
recipe.
* bedtools2: patching to build with gcc@13
* bedtools2: patching to build with gcc@13
* Update var/spack/repos/builtin/packages/bedtools2/package.py
Yep, sure. Makes sense.
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
* ensmallen: new package
ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Improve lib/spack/spack/test/cmd/compiler.py
* Use "tmp_path" in the "mock_executable" fixture
* Return a pathlib.Path from mock_executable
* Fix mock_executable fixture on Windows
"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication
* Remove wrong compiler cache, fix compiler removal
fixes#37996
_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.
Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
* e4s oneapi ci: use official intel oneapi-derived runner image
* update oneapi image
* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
* Guard for define in netcdf 4.9.0 and later.
This code is already available in ParaView 5.11.0 so no patching
needed there.
* Add latest needed version (even if not in spack).
---------
Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
* llvm: add new versions and set default for libomptarget according to os
modified: var/spack/repos/builtin/packages/llvm/package.py
* Incorporate reviewer suggestions
Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
---------
Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
* e4s cray ci stack
* e4s ci: add cray
* add zen4 tag
* WIP: new defintions just for cray
* updates
* remove ci signing job overrride, not necessary
* echo $PATH and show modules loaded
* add mirror
* add external def for cray-libsci
* comment out quantum-espresso
* use /etc/protected-runner as key path
* cray ci stack: do not remove tags: [spack, public]
* make cray stack composable
* generate job should run on public tagged runner, override default config:install_tree:root
* CI: Use relative path in default script
* CI: Use relative includes paths for shell runners
* Use concrete_env_dir for relpath
* ml-darwin-aarch64-mps: jax has bazel codesign issue
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES.
The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none`
when cuda_arch=none (incorrect check on the value of a multi-valued
variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates
the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES
is only set if cuda_arch is not none (which seems to be the pattern used
in other packages).
This does the same for HIP (although in general ROCmPackage disallows
amdgpu_target=none when +rocm).
* fastqc: add 0.12.1
* fastqc: add 0.12.1
* Update var/spack/repos/builtin/packages/fastqc/package.py
Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good.
Co-authored-by: Alec Scott <alec@bcs.sh>
* Update package.py
Style fiddles to make the bot contented.
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
* py-htseq: add 0.12.3, switching over to new GitHub repo
* py-htseq: add 0.12.3, switching over to new GitHub repo
Style fixes
* py-htseq: add 2.0.3, switch to PyPI
* py-htseq: add 2.0.3, switch to PyPI
* Update package.py
* Update var/spack/repos/builtin/packages/py-htseq/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Removing SWIG
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* llvm: replace +omp_as_runtime with omp=runtime
* llvm: fetch 'libomp-libflags-as-list.patch' from upstream repo
* llvm: replace 'llvm14-hwloc-ompd.patch' with the official fix from upstream repo
* llvm: fix-up for the black reformatting
* llvm: fetch 'constexpr_longdouble.patch' from upstream repo
* llvm: optionally build libcxx as a runtime
* llvm: fetch 'llvm5-sanitizer-ustat.patch' from upstream repo
* llvm: update 'sanitizer-ipc_perm_mode.patch'
* llvm: refactor compiler conflicts when libcxx=project
* llvm: fetch 'llvm_python_path.patch' from upstream repo
* llvm: update comments and condition for 'xray_buffer_queue-cstddef.patch'
* llvm: optionally build compiler-rt as a runtime
* llvm: fetch 'lldb_external_ncurses-10.patch' from upstream repo
* llvm: fetch 'llvm_py37.patch' from upstream repo
* llvm: rename variant 'internal_unwind' to 'libunwind'
* llvm: optionally build libunwind as a runtime
* llvm: extend the list of maintainers
* llvm: allow for explicit '~clang~flang~libomptarget~lldb~omp_debug~z3'
* llvm: fetch 'llvm5-lld-ELF-Symbols.patch' from FreeBSD port repo
* llvm: fetch most of 'missing-includes.patch' from upstream repo and reuse 'llvm-gcc11.patch'
* llvm: regroup patches for missing include directives and drop compiler constraints for them
* llvm: fetch 'llvm-gcc11.patch' from upstream repo
* llvm: fetch 'no_cyclades.patch' from upstream repo
* llvm: update comments and condition for 'no_cyclades9.patch'
* llvm: rename variant 'omp' to 'openmp'
* llvm: constrain and rename variant 'omp_tsan' to 'libomp_tsan'
* llvm: rename variant 'omp_debug' to 'libomptarget_debug'
* llvm: do not apply same patch twice
* llvm: constrain and document the '*-thread.patch' patches
* llvm: document the '~lld+libomptarget' conflict
* llvm: update comments for the 'D133513.diff' patch
* py-future: add 0.18.3
* Update var/spack/repos/builtin/packages/py-future/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding libpsm3 package
* Make changes suggested by flake8
* Make one more flake8-suggested change, blank line after 'import os'
* Change to standard header to pass flake8 tests
* Update doc string, remove unnecessary comments
* Reviewer-recommende changes
* Alphabetize variants
* Use helper functions
* Change quotes to pass spack style check
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
- Add pkgconfig dependency from 1.23.0 onward.
- Add conflict of old versions with new gcc due to missing includes.
- Deprecate uneven minor versions because they are not regarded as stable.
- Add maintainer
* [xsdk-examples] Initial commit for v0.4.0
* [xsdk-examples] v0.4.0 depends on xsdk@0.8.0
* add in missing xsdk dependencies
* [xsdk-examples] remove repeated 'depends_on' directive
* [xsdk-examples] simplify and extend a bit the package
[mfem] process more optional dependencies of HiOp
[strumpack, superlu-dist] add a workaround for an issue on Mac
* [mfem] fix the handling of the hiop dependency
* [@spackbot] updating style on behalf of v-dobrev
* [xsdk-examples] enable 'heffte' and 'tasmanian' if enabled in 'xsdk'
* [xsdk-examples] Add PUMI dependency
* [xsdk-examples] Add preCICE dependency
* [xsdk-examples] add +rocm
* heffte: add in a backport fix for building xsdk-examples with cuda
* [xsdk] Remove the explicit requirement for deal.II to be built +hdf5
* ENABLE_ROCM -> ENABLE_HIP
* [hiop] Workaround for CMake not finding Cray's BLAS (libsci)
[xsdk-examples] Set CUDA/HIP architectures; sync cuda/rocm variants with xsdk
* [@spackbot] updating style on behalf of v-dobrev
* [exago] Workaround for CMake not finding Cray's LAPACK/BLAS, libsci
[mfem] Tweaks for running tests under Flux and PBS
* [slate] Pass CUDA/HIP architectures to CMake
* [heffte] For newer CMake versions, set CMAKE_CUDA_ARCHITECTURES
* [hypre] Patch v2.26.0 to fix sequential compilation in 'src/seq_mv'
* [xsdk-examples] Some tweaks in dependencies and compilers used
* [xsdk] Make the 'trilinos' variant sticky
[xsdk-examples] Tweak dependencies
* [slate] Fix copy-paste error
* [xsdk-examples] Workaround for CMakePackage not having the legacy
property 'build_directory'
* [xsdk-examples] Replace the testing branch used temporarily for v0.4.0 with
the official release
---------
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
* Add CMake options for building with CUDA/HIP support to
CachedCMakePackages (intended to reduce duplication across packages
building with +hip/+cuda and using CachedCMakePackage)
* Define generic variables like CMAKE_PREFIX_PATH for
CachedCMakePackages (so that a user may invoke "cmake" themselves
without needing to setthem on the command line).
* Make `lbann` a CachedCMakePackage.
Co-authored-by: Chris White <white238@llnl.gov>
fa7719a changed syntax for specifying exact versions, which are
required for some compiler specs (including those read as part
of parsing a Cray manifest). This fixes that and also makes a
couple other improvements to manifest parsing.
* Instantiate compiler specs with exact versions (fixes#37893)
* fix slingshot network detection (CPE 22.10+ has libcxi.so
in /usr/lib64)
* "spack external find": add arg to ignore default dir for cray
manifests
This will build flux-security separately to have a flux-imp
that can be defined in a flux broker.toml. Note that the user
that wants a multi-user setup is recommended to create a view,
and then a system/broker.toml in flux config directory that
points to it.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Sphinx is used to build Open MPI manpages, etc. as part of the make dist
process to create release tarballs. There should be no need/use to do
this within Spack. Also some sites have older Sphinx installs which
aren't compatible with the needs of the Open MPI documentation.
For example, attempts to install openmpi@main fail at NERSC owing to
such a situation.
Since Spack normally is used to build from release tarballs, in which
the docs have already been installed, this should present no issues.
This configuration option will be ignored for older than 5.0.0 Open MPI releases.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
This option is needed for DFT FE - or more accurately the check needs to
be checked off for a number of platforms or else the code doesn't work.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Change default naming scheme for tcl modules for a more user-friendly
experience.
Change from flat projection to "per software name" projection.
Flat naming scheme restrains module selection capabilities. The
`{name}/{version}...` scheme make possible to use user-friendly
mechanisms:
* implicit defaults (`module load git`)
* extended default (`module load git/2`)
* advanced version specifiers (`module load git@2:`)
* py-cutadapt: add 4.4, 4.3, 4.2 versions
* Update var/spack/repos/builtin/packages/py-cutadapt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cutadapt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update PennyLane ecosystem for 0.30 release
* Update package dep versions
* Fix formatting
* Update dep versions
* Remove PL hard pin and rely on PLQ to define version
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
* Convert pybind11 from build to link dep, and PL ver limit
---------
Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
Note the win-sdk package is not installable and reports an error
which instructs the user how to add it. Without this fix, a
(more confusing) error occurs before this message can be generated.
"spack build-env" was not generating proper environment variable
definitions on Windows; this commit updates the generated commands
to succeed with batch/PowerShell.
Add a nightly job to attempt building all Paraview dependencies and
upload the results to cdash. This check doesn't affect the reported
build/test status of Spack. We are using this to monitor the state of
Windows support while working on more-robust checks (eventually the
Windows build will have to succeed to merge PRs to Spack).
* Dyninst: add standalone test
* Add docstring with description
* Don't use join_path for builtin path objects
* Whitespace
* Update format of docstring
Some requirements for @main version of environment-modules were missing:
* python (to build ChangeLog documentation file)
* py-sphinx@1.0: (to build man-pages, etc)
Also adding gzip, which is now required to build ChangeLog.gz (which is
now shipped instead of ChangeLog).
Other versions are not requiring these tools (as documentation is
pre-built in dist tarball).
* [devito] Move to version 4.8.1
* Fix: Adding patch file
* Update var/spack/repos/builtin/packages/py-devito/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-devito/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Addressing @adamjstewart comments
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add macOS ML CI stacks
* torchmeta is no longer maintained and requires ancient PyTorch
* Add MXNet
* update darwin aarch64 stacks
* add darwin-aarch64 scoped config.yaml
* remove unnecessary cleanup job
* fix specifications
* fix labels
* fix labels
* fix indent on tags specification
* no tags for trigger jobs
* try overriding tags in stack spack.yaml
* do not use CI_STACK_CONFIG_SCOPES
* incorporate config:install_tree:root: overrides and compiler defs
* copy relevant ci-scoped config settings directly into stack spack.yaml
* remove build-job-remove
* spack ci generate: add debug flag
* include cdash config directly in stack spack.yaml
* customize build-job script section to avoid absolute paths
* add any-job specification
* tags: use aarch64-macos instead of aarch64
* generate tags: use aarch64-macos instead of aarch64
* do not add morepadding
* use shared mirror; comment out known failures
* remove any-job
* nproc || true
* comment out specs failing due to bazel from cache codesign issue
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* py-babel: add 2.12.1
* Update var/spack/repos/builtin/packages/py-babel/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When attempting to build paraview@5.10.1 using a recent Intel
compiler (Classic or OneAPI) or the IBM XL compiler, the build
fails if the version of protobuf used is > 3.18
* [pcluster pipeline] Use local buildcache instead of upstream spack
Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.
* gcc needs to be installed via postinstall to get correct deps
* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1
* Force gitlab to pull the new container
* Revert "Force gitlab to pull the new container"
This reverts commit 3af5f4cd88.
Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml
* Gitlab keeps picking up wrong container. Renaming
* Update containers once more after failed build
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
* add version 1.78.0 to bioconductor package r-acgh
* add version 2.56.0 to bioconductor package r-acme
* add version 1.70.0 to bioconductor package r-adsplit
* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
* add version 2.50.0 to bioconductor package r-agimicrorna
* add version 1.32.0 to bioconductor package r-aims
* add version 1.32.0 to bioconductor package r-aldex2
* add version 1.38.0 to bioconductor package r-allelicimbalance
* add version 1.26.0 to bioconductor package r-alpine
* add version 2.62.0 to bioconductor package r-altcdfenvs
* add version 2.24.0 to bioconductor package r-anaquin
* add version 1.28.0 to bioconductor package r-aneufinder
* add version 1.28.0 to bioconductor package r-aneufinderdata
* add version 1.72.0 to bioconductor package r-annaffy
* add version 1.78.0 to bioconductor package r-annotate
* add version 1.62.0 to bioconductor package r-annotationdbi
* add version 1.24.0 to bioconductor package r-annotationfilter
* add version 1.42.0 to bioconductor package r-annotationforge
* add version 3.8.0 to bioconductor package r-annotationhub
* add version 3.30.0 to bioconductor package r-aroma-light
* add version 1.32.0 to bioconductor package r-bamsignals
* add version 2.16.0 to bioconductor package r-beachmat
* add version 2.60.0 to bioconductor package r-biobase
* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
* add version 1.10.0 to bioconductor package r-biocio
* add version 1.18.0 to bioconductor package r-biocneighbors
* add version 1.34.0 to bioconductor package r-biocparallel
* add version 1.16.0 to bioconductor package r-biocsingular
* add version 2.28.0 to bioconductor package r-biocstyle
* add version 3.17.1 to bioconductor package r-biocversion
* add version 2.56.0 to bioconductor package r-biomart
* add version 1.28.0 to bioconductor package r-biomformat
* add version 2.68.0 to bioconductor package r-biostrings
* add version 1.48.0 to bioconductor package r-biovizbase
* add version 1.10.0 to bioconductor package r-bluster
* add version 1.68.0 to bioconductor package r-bsgenome
* add version 1.36.0 to bioconductor package r-bsseq
* add version 1.42.0 to bioconductor package r-bumphunter
* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
* add version 1.36.0 to bioconductor package r-cner
* add version 1.32.0 to bioconductor package r-codex
* add version 2.16.0 to bioconductor package r-complexheatmap
* add version 1.74.0 to bioconductor package r-ctc
* add version 2.28.0 to bioconductor package r-decipher
* add version 0.26.0 to bioconductor package r-delayedarray
* add version 1.22.0 to bioconductor package r-delayedmatrixstats
* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
* add version 1.74.0 to bioconductor package r-dnacopy
* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
* add version 2.24.0 to bioconductor package r-ensembldb
* add version 1.46.0 to bioconductor package r-exomecopy
* add version 2.8.0 to bioconductor package r-experimenthub
* add version 1.26.0 to bioconductor package r-fgsea
* add version 2.72.0 to bioconductor package r-gcrma
* add version 1.36.0 to bioconductor package r-gdsfmt
* add version 1.82.0 to bioconductor package r-genefilter
* add version 1.36.0 to bioconductor package r-genelendatabase
* add version 1.72.0 to bioconductor package r-genemeta
* add version 1.78.0 to bioconductor package r-geneplotter
* add version 1.22.0 to bioconductor package r-genie3
* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
* add version 1.36.0 to bioconductor package r-genomicalignments
* add version 1.52.0 to bioconductor package r-genomicfeatures
* add version 1.52.0 to bioconductor package r-genomicranges
* add version 2.68.0 to bioconductor package r-geoquery
* add version 1.48.0 to bioconductor package r-ggbio
* add version 3.8.0 to bioconductor package r-ggtree
* add version 2.10.0 to bioconductor package r-glimma
* add version 1.12.0 to bioconductor package r-glmgampoi
* add version 5.54.0 to bioconductor package r-globaltest
* update r-go-db
* add version 1.20.0 to bioconductor package r-gofuncr
* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
* add version 2.66.0 to bioconductor package r-gostats
* add version 1.78.0 to bioconductor package r-graph
* add version 1.62.0 to bioconductor package r-gseabase
* add version 1.32.0 to bioconductor package r-gtrellis
* add version 1.44.0 to bioconductor package r-gviz
* add version 1.28.0 to bioconductor package r-hdf5array
* add version 1.72.0 to bioconductor package r-hypergraph
* add version 1.36.0 to bioconductor package r-illumina450probevariants-db
* add version 0.42.0 to bioconductor package r-illuminaio
* add version 1.74.0 to bioconductor package r-impute
* add version 1.38.0 to bioconductor package r-interactivedisplaybase
* add version 2.34.0 to bioconductor package r-iranges
* add version 1.60.0 to bioconductor package r-kegggraph
* add version 1.40.0 to bioconductor package r-keggrest
* add version 3.56.0 to bioconductor package r-limma
* add version 2.52.0 to bioconductor package r-lumi
* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
* add version 1.8.0 to bioconductor package r-metapod
* add version 2.46.0 to bioconductor package r-methylumi
* add version 1.46.0 to bioconductor package r-minfi
* add version 1.34.0 to bioconductor package r-missmethyl
* add version 1.80.0 to bioconductor package r-mlinterfaces
* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
* add version 2.32.0 to bioconductor package r-qvalue
* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
* add version 1.12.0 to bioconductor package r-rhdf5filters
* add version 1.22.0 to bioconductor package r-rhdf5lib
* add version 1.76.0 to bioconductor package r-roc
* add version 1.28.0 to bioconductor package r-rots
* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
* add version 1.28.0 to bioconductor package r-scater
* add version 1.14.0 to bioconductor package r-scdblfinder
* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
* add version 1.22.0 to bioconductor package r-tmixclust
* add version 2.52.0 to bioconductor package r-topgo
* add version 1.24.0 to bioconductor package r-treeio
* add version 1.28.0 to bioconductor package r-tximport
* add version 1.28.0 to bioconductor package r-tximportdata
* add version 1.46.0 to bioconductor package r-variantannotation
* add version 3.68.0 to bioconductor package r-vsn
* add version 2.6.0 to bioconductor package r-watermelon
* add version 2.46.0 to bioconductor package r-xde
* add version 1.58.0 to bioconductor package r-xmapbridge
* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
This reverts commit 1702071c6d.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
This reverts commit 58a7df2387.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
This reverts commit 0a1f59de6c.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
This reverts commit cd49fb8e4c.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
This reverts commit 6e9a951cbe.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
macOS doesn't have `getrandom`, and 1.10.2 fails to compile because of this.
There's an upstream fix at https://dev.gnupg.org/T6442 that will be in the next
`libgcrypt` release, but the patch is available now.
Clone `spack-configs <https://github.com/spack/spack-configs>`_ repo and activate Intel oneAPI CPU environment::
git clone https://github.com/spack/spack-configs
spack env activate spack-configs/INTEL/CPU
spack concretize -f
`Intel oneAPI CPU environment <https://github.com/spack/spack-configs/blob/main/INTEL/CPU/spack.yaml>`_ contains applications tested and validated by Intel, this list is constantly extended. And currently it supports:
and software development kits (e.g., `EcpDataVisSdk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/ecp-data-vis-sdk/package.py>`_).
These versioned packages primarily consist of dependencies on the associated
software packages. They can include :ref:`variants <variants>` to ensure
common build options are consistently applied to dependencies. Known build
failures, such as not building on a platform or when certain compilers or
variants are used, can be flagged with :ref:`conflicts <packaging_conflicts>`.
Build requirements, such as only building with specific compilers, can similarly
be flagged with :ref:`requires <packaging_conflicts>`.
The ``spack create --template bundle`` command will create a skeleton
``BundlePackage````package.py`` for you:
..code-block::console
$ spack create --template bundle --name coolsdk
Now you can fill in the basic package documentation, version(s), and software
package dependencies along with any other relevant customizations.
..note::
Remember that bundle packages have no software of their own so there
is nothing to download.
^^^^^^^^^^^^^^^^^^^^^^^^^
Non-downloadable software
^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -610,7 +646,16 @@ add a line like this in the package class:
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