Upgrade to Python 3.12 / Snakemake 8 #355
Merged
Conversation
This file contains 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
…ove pyrunner test strategy
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
jsbrittain
added a commit
that referenced
this pull request
Sep 17, 2024
* Upgrade to Python 3.12 / Snakemake 8; migrate from poetry to uv; improve pyrunner test strategy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add ruff to dev-dependencies * Remove redundant import * Revert docs build to Python 3.11 * Update test-repo to use grapevne-helper * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove absolute paths from test workflows * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add setuptools to github actions * Remove absolute path from pyinstaller test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Migrate install_miniforge script to .venv from poetry * Separate file and folder copying when packaging modules * Modify Dockerfile for Snakemake v8 and install grapevne-py * Fix bug that prevented email alerts from being sent * Remove sources from docs build * Setup conda using github action for postbuild tests * Switch payload-shell to payload-run for Windows testing * Disable workflow checks on Windows where modules connect together (known bug) * Update nightly and publish workflows to support action-based conda install * Update nightly and publish workflows to support action-based conda install * Reject non-native binaries introduced by PuLP * Remove .venv from build * Revert and update nightly_build github action * Disable colima/docker install on macos-12 as both very slow and inconsistent * Migrate to grapevne-py installer * Update grapevne_helper in tests --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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.
builder,runner,pyrunner(inelectron-app))pyrunnertest strategy to support packaged routines,postcalls, andpyinstaller(bundled) workflowsGithub actions for building and publishing have also been updated. Postbuild checks are available as CI to this PR. Nightly checks have been run on the local repo (https://github.com/jsbrittain/GRAPEVNE/actions/runs/10852170943), and publish checks have been run on the local repo (https://github.com/jsbrittain/GRAPEVNE/actions/runs/10851936860). note that windows builds still report a false-negative during upload; this is fine.
Resolves #189 #146
note: by upgrading to Snakemake 8 some previous modules will be made incompatible; this can be resolved by adopting grapevne helper in those scripts.