Fix conda builds - Githubissues

eberrigan commented 6 months ago

Description

conda package tests removed from stage on .conda/meta.yml since conda solver is taking too long.
conda package tests are now a stage in build_manual.yml and build.yml since we are able to use the libmamba conda-solver in the miniconda set-up.
Now during the build conda package stage for each OS, the BUILD_PATH is saved as a GITHUB_ENV so it can be used in the next stage.
The BUILD_PATH is used to create an environment with the conda package for each OS.
SLEAP is imported and the version of SLEAP is printed to confirm the environment is working for each OS.
The mac environment has changed to ensure python 3.9 is used every time: conda-forge::python >=3.9.0, <3.10.0.
qudida and alubmentations are now longer needed in the mac build.sh since they are installed using conda-forge.

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 following up pull request #1744 where we moved the conda package tests to the CI because importing sleap during the conda build was either taking forever or failing for macs--see pull request #1734.
After moving the tests to build_manual.yaml by creating a conda environment with the built conda packages, it became clear that the mac build was failing for a different reason then taking forever to resolve with a conda solver.
The mac build was being allowed to use python 3.10 so it was not building correctly due to the packages being in python 3.9 folders.
This is also following up dependency updates and fixes such as the TensorFlow conda package https://github.com/talmolab/sleap/pull/1726 and the pypi build https://github.com/talmolab/sleap/pull/1724.

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
[ ] Add tests that prove your fix is effective or that your feature works
[ ] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

:heart:

coderabbitai[bot] commented 6 months ago

Walkthrough

The recent updates focus on enhancing build and test workflows using conda and pip. Changes include reorganizing test configurations, updating Python versions, refining installation commands, and improving GitHub Actions workflows for multi-OS testing. Detailed comments address dependency issues for future maintenance.

Changes

Files/Paths	Change Summaries
`.conda/meta.yaml`, `.conda_mac/condarc.yaml`	Moved `sleap` test config to build workflow; removed unused comment.
`.conda_mac/build.sh`	Removed specific flags from `pip install` command.
`.conda_mac/meta.yaml`	Updated Python version requirement, commented out test imports.
`.github/workflows/build_manual.yml`	Adjusted branch triggers, build and test steps for multiple OS.
`requirements.txt`	Added detailed comment on `imgstore` version issue.
`.github/workflows/build.yml`, `.github/workflows/build_ci.yml`	Added test steps for various OS; switched to testing with built wheels.

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Python versions aligned, dependencies now clear,
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codecov[bot] commented 6 months ago

Codecov Report

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

Project coverage is 74.11%. Comparing base (7ed1229) to head (d084f74). Report is 6 commits behind head on develop.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #1776 +/- ## =========================================== + Coverage 73.30% 74.11% +0.80% =========================================== Files 134 134 Lines 24087 24462 +375 =========================================== + Hits 17658 18131 +473 + Misses 6429 6331 -98 ```

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

talmolab / sleap

Fix conda builds #1776