Add uv process directive for Python package management#7023
Open
evanroyrees wants to merge 2 commits intonextflow-io:masterfrom
Open
Add uv process directive for Python package management#7023evanroyrees wants to merge 2 commits intonextflow-io:masterfrom
evanroyrees wants to merge 2 commits intonextflow-io:masterfrom
Conversation
Add a new `uv` process directive that allows Nextflow processes to declare Python dependencies managed by the uv package manager, following the same pattern as the existing `conda` and `spack` directives. The directive accepts package names, requirements.txt files, pyproject.toml files, or paths to existing virtual environments. Nextflow automatically creates, caches, and activates uv virtual environments for each unique set of dependencies. Includes CLI options (-with-uv / -without-uv), configuration scope (uv.enabled, uv.cacheDir, uv.pythonVersion, etc.), environment variables (NXF_UV_ENABLED, NXF_UV_CACHEDIR), lineage tracking, task hash integration, tests, and documentation. Signed-off-by: Evan Rees <evanroyrees@gmail.com> Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add the missing `uv` positional argument to all lineage model TaskRun constructor calls in tests that were missed in the initial commit (LinObserverTest, CmdLineageTest). Signed-off-by: Evan Rees <evanroyrees@gmail.com> Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
✅ Deploy Preview for nextflow-docs-staging canceled.
|
b6edfb1 to
bfd069f
Compare
Member
|
Thanks for the contribution, but I think we're going to hold off on adding new directives for each Python package manager. Instead we're looking into a generic |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Add a new
uvprocess directive for managing Python dependencies via the uv package manager, following the existingcondaandspackdirective patterns.Supports inline packages and requirements files:
Changes
UvConfig/UvCache— config scope and environment creation/cachingTaskBean,TaskRun,BashWrapperBuilder)-with-uv/-without-uv), config builder, launcher arg normalizationNXF_UV_ENABLED,NXF_UV_CACHEDIR)docs/uv.md)Signed-off-by: Evan Rees evanroyrees@gmail.com