Fix website build and remove build cache across workflows

eberrigan commented 5 months ago

Description

All actions updated to latest versions in all of the github workflows.
Cache steps are removed from all workflows.
pip install lxml[html_clean] is added as a step in the website build since this module is required and it is a separate project now.
This will accompany another pre-release with the published conda packages which will have --label dev.

Types of changes

[ ] Bugfix
[ ] New feature
[ ] Refactor / Code style update (no logical changes)
[X] Build / CI changes
[ ] Documentation Update
[ ] Other (explain)

Does this address any currently open issues?

This is a follow-up to #1776 where the conda builds were updated. Now we just need to upload the corrected conda packages to anaconda using the github workflows.
Cache in github workflow is not behaving as expected: environment in conda packages is not resolving because of ndx-pose being installed via conda-forge. ndx-pose is a new conda package so it cannot use the cache when making the environment.
If dependencies change, it should not use the cache anyways, but this will be the case unless the CACHE_NUMBER is increased when dependencies change.
1785 cannot pass tests since the website build is out of date.
Pre-releases v1.4.1a0 and v1.4.0a0 did not result in published conda packages since the environment was not able to resolve using the cache.

Outside contributors checklist

[ ] Review the guidelines for contributing to this repository
[ ] Read and sign the CLA and add yourself to the authors list
[X] Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
[X] Add tests that prove your fix is effective or that your feature works
[x] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

:heart:

coderabbitai[bot] commented 5 months ago

Walkthrough

The recent updates primarily focus on refining the GitHub Actions workflows for building manuals, continuous integration, and website deployment. Key changes include updating branch triggers, replacing caching mechanisms with direct checkouts, and upgrading action versions for better performance and compatibility.

Changes

File Path	Change Summary
`.github/workflows/build_manual.yml`	- Updated branch trigger to `elizabeth/Fix-website-build-and-remove-build-cache-across-workflows` - Replaced conda package caching with `actions/checkout@v4` - Removed `CACHE_NUMBER` configuration
`.github/workflows/build_ci.yml`	- Updated `actions/checkout` to `v4` - Updated `setup-python` to `v5` - Updated upload/download artifact actions to `v4`
`.github/workflows/website.yml`	- Updated branch triggers to `fakebranch` and `elizabeth/Fix-website-build-and-remove-build-cache-across-workflows` - Updated `setup-miniconda` to `v3.0.3` - Updated `actions-gh-pages` to `v4`

Poem

In the land of code, where workflows play,
Branches shift and actions sway,
Cache is gone, checkout's here,
Updates flow without a fear.
Miniconda steps anew,
Pages deploy with a brighter hue.
Hopping forward, swift and keen,
Our builds are now a smoother scene.

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codecov[bot] commented 5 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 74.03%. Comparing base (7ed1229) to head (77f9911). Report is 10 commits behind head on develop.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #1786 +/- ## =========================================== + Coverage 73.30% 74.03% +0.72% =========================================== Files 134 135 +1 Lines 24087 24500 +413 =========================================== + Hits 17658 18138 +480 + Misses 6429 6362 -67 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

talmolab / sleap