deps(python): bump snakemake from 7.32.4 to 8.0.1 in /dependencies/python

[dependabot]

Bumps snakemake from 7.32.4 to 8.0.1.

Release notes

Sourced from snakemake's releases.

v8.0.1

8.0.1 (2023-12-21)

Bug Fixes

• remove bash completion entrypoint (no longer supported, was too slow to be usable anyway) (922b53a)

Documentation

• fix cli options rendering (264c1a9)
• fixes in migration guide (f8adefa)

v8.0.0

8.0.0 (2023-12-20)

⚠ BREAKING CHANGES

Snakemake 8 marks the beginning of decomposing Snakemake into a framework of plugins. This enables the democratization of method development within the Snakemake ecosystem. We start with plugins for storage and execution backends. In the future, there will be plugins for the scheduling, metadata, software deployment, reporting, and many more. This way, it will be possible to easily launch and explore new developments in workflow management and reproducible data analysis without the need to get your work merged into the main codebase of Snakemake and also without the need to develop a new workflow management system as a proof of concept.

In detail, Snakemake 8 introduces the following changes. Unfortunately it was unavoidable to break some usages (we apologize). Nevertheless, we tried to ensure that every removed or modified feature has been replaced with an equivalent reimplementation, as outlined in our migration docs. While Snakemake 8 has an even more thorough testing framework than any release before, and while it has been quite heavily tested in practice by us, you might initially experience bugs and glitches for which we want to apologize beforehand. We think that the massive codebase improvements are worth it in the long run, and hope that everything goes well. As always, any pull requests with test cases and pointers to bugs are more than welcome.

Detailed breaking changes

• removed the long time ago deprecated support for dynamic, version, and subworkflow (see the migration docs)
• migrated old remote providers into storage plugins (see the migration docs)
• migrated execution backends into plugins, including a change in the respective command line interfaces (see the migration docs)
• deprecates --use-conda and --use-singularity in favor of --software-deployment-method conda or --software-deployment-method apptainer and --software-deployment-method conda apptainer (see the migration docs)
• profile support is now versioned, such that different profiles can be written for different minimum Snakemake versions (see the migration docs)
• redesigned Snakemake API. It now uses a modern, dataclass based approach (see the migration docs)

Features

• add ability to inject conda environments into running Snakefile (#2479) (6140e29)
• add functionality for deploying sources if no shared FS is assumed (#2486) (76eac3c)
• add option to control software deployment mode (shared or non shared FS) (#2525) (04ec2c0)
• allow detailed configuration of shared FS usage (#2528) (0d34be9)
• allow environment variables in string values of profile (e.g. paths may now contain elements like $USER). (58dc70c)
• allow python expressions in --set-resources (#2521) (022a31e)
• allow to set latency_wait in executor test suite (c0bca0b)
• automatically upload workflow sources to default storage provider if no shared FS is used (a450c49)

... (truncated)

Changelog

Sourced from snakemake's changelog.

8.0.1 (2023-12-21)

Bug Fixes

• remove bash completion entrypoint (no longer supported, was too slow to be usable anyway) (922b53a)

Documentation

• fix cli options rendering (264c1a9)
• fixes in migration guide (f8adefa)

8.0.0 (2023-12-20)

⚠ BREAKING CHANGES

Snakemake 8 marks the beginning of decomposing Snakemake into a framework of plugins. This enables the democratization of method development within the Snakemake ecosystem. We start with plugins for storage and execution backends. In the future, there will be plugins for the scheduling, metadata, software deployment, reporting, and many more. This way, it will be possible to easily launch and explore new developments in workflow management and reproducible data analysis without the need to get your work merged into the main codebase of Snakemake and also without the need to develop a new workflow management system as a proof of concept.

In detail, Snakemake 8 introduces the following changes. Unfortunately it was unavoidable to break some usages (we apologize). Nevertheless, we tried to ensure that every removed or modified feature has been replaced with an equivalent reimplementation, as outlined in our migration docs. While Snakemake 8 has an even more thorough testing framework than any release before, and while it has been quite heavily tested in practice by us, you might initially experience bugs and glitches for which we want to apologize beforehand. We think that the massive codebase improvements are worth it in the long run, and hope that everything goes well. As always, any pull requests with test cases and pointers to bugs are more than welcome.

Detailed breaking changes

• removed the long time ago deprecated support for dynamic, version, and subworkflow (see the migration docs)
• migrated old remote providers into storage plugins (see the migration docs)
• migrated execution backends into plugins, including a change in the respective command line interfaces (see the migration docs)
• deprecates --use-conda and --use-singularity in favor of --software-deployment-method conda or --software-deployment-method apptainer and --software-deployment-method conda apptainer (see the migration docs)
• profile support is now versioned, such that different profiles can be written for different minimum Snakemake versions (see the migration docs)
• redesigned Snakemake API. It now uses a modern, dataclass based approach (see the migration docs)

Features

• add ability to inject conda environments into running Snakefile (#2479) (6140e29)
• add functionality for deploying sources if no shared FS is assumed (#2486) (76eac3c)
• add option to control software deployment mode (shared or non shared FS) (#2525) (04ec2c0)
• allow detailed configuration of shared FS usage (#2528) (0d34be9)
• allow environment variables in string values of profile (e.g. paths may now contain elements like $USER). (58dc70c)
• allow python expressions in --set-resources (#2521) (022a31e)
• allow to set latency_wait in executor test suite (c0bca0b)
• automatically upload workflow sources to default storage provider if no shared FS is used (a450c49)
• Faster ci test setup (#2489) (4798e8a)
• implement precommand (#2482) (ff0f979)

... (truncated)

Commits

• 6a0b521 chore(main): release 8.0.1 (#2550)
• f8adefa docs: fixes in migration guide
• 264c1a9 docs: fix cli options rendering
• e939074 Merge branch 'main' of github.com:snakemake/snakemake
• 922b53a fix: remove bash completion entrypoint (no longer supported, was too slow to ...
• f155ed2 chore(main): release 8.0.0 (#2535)
• faa2230 Merge branch 'main' of github.com:snakemake/snakemake
• d87b355 simplify docker image
• 5230abc Fix command in short.rst (#2506)
• ca91661 fix: allow pepfile and pepschema to take pathlib (#2546)
• Additional commits viewable in compare view

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Checking migration notes first