* tximeta: add package
Signed-off-by: Pablo <pablo.aledo@seqera.io>
* [@spackbot] updating style on behalf of pabloaledo
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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.
