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A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
29,222 Commits 246 Branches 186 Tags 666 MiB
Python 97.3%
Shell 2.1%
C 0.2%
f2f3d03d00
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Marco De La Pierre f2f3d03d00
Add nf-core-tools, and three remainder deps (#34466) 
* nextflow recipe: added latest stable version

* tower-cli recipe: added latest release

* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli

* recipes nf-tower-agent and nf-tower-cli: small fix

* nf-core-tools recipe: added most py- dependencies

* nf-core-tools: recipe without galaxy-tool-util (for testing)

* fixed typos in py-yacman recipe

* fixed typos in py-pytest-workflow recipe

* fixed typo in nf-core-tools recipe

* fixed typos in py-yacman recipe

* fixes in recipes for py-questionary and py-url-normalize

* fixes to py-yacman recipe

* style fixes to py- packages that are dependencies to nf-core-tools

* fix in py-requests-cache recipe

* added missing dep in py-requests-cache recipe

* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper

* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util

* nf-core-tools: new version with extra dependency

* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps

* nextflow and nf-core-tools packages: added my self as maintainer

* style fixes

* style fix for nf-core-tools recipe

* added license to py-logmuse recipe

* audit fixes

* style fix after audit fix

* py-galaxy-tool-util: added deps 1st bunch

* audit/style fixes, including adding missing dep package

* more audit/style fixes

* more more audit/style fixes

* moooore audit fixes

* py-galaxy-tool-util: dependencies 2nd chunk

* silly audit fix

* py-galaxy-util deps: 3rd bunch - first 20 done

* fixes

* style fix

* py-galaxy-tool-util: 4th bunch of deps

* stashing dep recipe backbones for py-galaxy-tool-util

* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util

* nf-core-tools: adding also py-galaxy-util, as wheel

* fix

* nextflow: added latest bugfix version

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* nf-core-tools pr: 1st bunch of review edits

* nf-core-tools: 2nd bunch of review edits

* adding back tower-agent and tower-cli as deprecated

* nf-core-tools: 3rd bunch of review edits

* small style fix

* prepping py-galaxy-tool-util for further work

* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar

* audit fixes

* updates to py-galaxy-tool-util and its deps, still 2 to work on

* one style fix

* updated recipe for py-galaxy-util

* updated recipe for py-pulsar-galaxy-lib

* typo fix

* shasum fixes

* updated py-sqlalchemy from develop

* added newest versions (today) for nf-tower-agent and nf-tower-cli

* Update var/spack/repos/builtin/packages/py-requests-cache/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-requests-cache/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* adding 2nd bunch of nf-core deps from update/nextflow-tools

* adding 3rd bunch of nf-core deps from update/nextflow-tools

* 4th chunk of nf-core deps from update/nextflow-tools

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pebble/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-gunicorn/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-starlette/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-parsley/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-paste/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-gxformat2: added comment

* py-lagom: now using github tarballs

* fix for py-lagom

* adding missing deps to py-fastapi-utils

* another fix to py-lagom

* Update var/spack/repos/builtin/packages/py-dnspython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-lagom/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-supervisor/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fixes from PR review

* adding missing deps, from PR review

* py-galaxy2cwl from github tarball, as per PR review

* fix to py-tuswsgi, as per PR review

* nf-tools: edits from PR review

* adding 3x more galaxy deps

* fix

* fixing circular dep of py-poetry-plugin-export with py-poetry

* added newest nf-core-tools version

* Update var/spack/repos/builtin/packages/py-galaxy-util/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fix in py-poetry-plugin-export

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-20 04:05:26 -08:00
.github build(deps): bump actions/checkout from 3.2.0 to 3.3.0 (#34829) 2023-01-17 10:02:31 +01:00
bin license year bump (#34921) 2023-01-18 14:30:17 -08:00
etc/spack/defaults Doc: config.yaml mention $env (#34905) 2023-01-17 10:06:00 +01:00
lib/spack Add type hints to DependencySpec (#35021) 2023-01-20 09:53:57 +01:00
share/spack e4s: ecp-data-vis-sdk +rocm: remove redundant amdgpu_target specification (#35022) 2023-01-20 00:18:41 +00:00
var/spack Add nf-core-tools, and three remainder deps (#34466) 2023-01-20 04:05:26 -08:00
.codecov.yml codecov: allow coverage offsets for more base commit flexibility (#25293) 2021-08-06 01:33:12 -07:00
.dockerignore Docker: ignore var/spack/cache (source caches) when creating container (#23329) 2021-05-17 11:28:58 +02:00
.flake8 Make GHA tests parallel by using xdist (#32361) 2022-09-07 20:12:57 +02:00
.git-blame-ignore-revs black: fix .git-blame-ignore-revs commit 2022-07-31 15:06:38 -07:00
.gitattributes
.gitignore Windows Support: Testing Suite integration 2022-03-17 09:01:01 -07:00
.mailmap Update mailmap (#22739) 2021-04-06 10:32:35 +02:00
.readthedocs.yml More strict ReadTheDocs tests (#26580) 2021-10-08 09:27:17 +02:00
CHANGELOG.md Update CHANGELOG.md for v0.19.0 2022-11-14 08:22:29 -06:00
CITATION.cff Add citation information to GitHub (#27518) 2021-11-30 01:37:50 -07:00
COPYRIGHT unparser: implement operator precedence algorithm for unparser 2022-01-12 06:14:18 -08:00
LICENSE-APACHE
LICENSE-MIT license year bump (#34921) 2023-01-18 14:30:17 -08:00
NOTICE
pyproject.toml Use "vendoring" to manage 3rd party dependencies 2023-01-04 09:43:04 -08:00
pytest.ini Be strict on the markers used in unit tests (#33884) 2022-12-13 09:21:57 +01:00
README.md Github Discussions can be used for Q&A (#33364) 2022-10-17 08:38:25 -07:00
SECURITY.md Update SECURITY.md for v0.19 2022-11-14 08:22:29 -06:00

README.md

Spack Spack

Unit Tests Bootstrapping codecov Containers Read the Docs Code style: black Slack

Spack is a multi-platform package manager that builds and installs multiple versions and configurations of software. It works on Linux, macOS, and many supercomputers. Spack is non-destructive: installing a new version of a package does not break existing installations, so many configurations of the same package can coexist.

Spack offers a simple "spec" syntax that allows users to specify versions and configuration options. Package files are written in pure Python, and specs allow package authors to write a single script for many different builds of the same package. With Spack, you can build your software all the ways you want to.

See the Feature Overview for examples and highlights.

To install spack and your first package, make sure you have Python. Then:

$ git clone -c feature.manyFiles=true https://github.com/spack/spack.git
$ cd spack/bin
$ ./spack install zlib

Documentation

Full documentation is available, or run spack help or spack help --all.

For a cheat sheet on Spack syntax, run spack help --spec.

Tutorial

We maintain a hands-on tutorial. It covers basic to advanced usage, packaging, developer features, and large HPC deployments. You can do all of the exercises on your own laptop using a Docker container.

Feel free to use these materials to teach users at your organization about Spack.

Community

Spack is an open source project. Questions, discussion, and contributions are welcome. Contributions can be anything from new packages to bugfixes, documentation, or even new core features.

Resources:

Contributing

Contributing to Spack is relatively easy. Just send us a pull request. When you send your request, make develop the destination branch on the Spack repository.

Your PR must pass Spack's unit tests and documentation tests, and must be PEP 8 compliant. We enforce these guidelines with our CI process. To run these tests locally, and for helpful tips on git, see our Contribution Guide.

Spack's develop branch has the latest contributions. Pull requests should target develop, and users who want the latest package versions, features, etc. can use develop.

Releases

For multi-user site deployments or other use cases that need very stable software installations, we recommend using Spack's stable releases.

Each Spack release series also has a corresponding branch, e.g. releases/v0.14 has 0.14.x versions of Spack, and releases/v0.13 has 0.13.x versions. We backport important bug fixes to these branches but we do not advance the package versions or make other changes that would change the way Spack concretizes dependencies within a release branch. So, you can base your Spack deployment on a release branch and git pull to get fixes, without the package churn that comes with develop.

The latest release is always available with the releases/latest tag.

See the docs on releases for more details.

Code of Conduct

Please note that Spack has a Code of Conduct. By participating in the Spack community, you agree to abide by its rules.

Authors

Many thanks go to Spack's contributors.

Spack was created by Todd Gamblin, tgamblin@llnl.gov.

Citing Spack

If you are referencing Spack in a publication, please cite the following paper:

On GitHub, you can copy this citation in APA or BibTeX format via the "Cite this repository" button. Or, see the comments in CITATION.cff for the raw BibTeX.

License

Spack is distributed under the terms of both the MIT license and the Apache License (Version 2.0). Users may choose either license, at their option.

All new contributions must be made under both the MIT and Apache-2.0 licenses.

See LICENSE-MIT, LICENSE-APACHE, COPYRIGHT, and NOTICE for details.

SPDX-License-Identifier: (Apache-2.0 OR MIT)

LLNL-CODE-811652