replace `conda:` parameter with `conda_packages:` by zacharyburnett · Pull Request #391 · OpenAstronomy/github-actions-workflows

zacharyburnett · 2026-05-05T13:22:57Z

alternative to #361

replace the conda: parameter (which invoked the now-archived tox-conda) with conda_packages:.

If the user populates conda_packages then the workflow sets up a Mamba environment that tox runs within.

To migrate from tox-conda, copy conda_deps from tox.ini to conda_packages in the test workflow, and then also remember to list any non-Python Conda packages in allowlist_externals:

allowlist_externals =
    hstcal

this will require a major version bump

zacharyburnett · 2026-06-03T18:18:20Z

@pllim this should hopefully be a good way forward instead of using tox-conda; please let me know your thoughts. I don't think this should go into 3.0.0 at the moment, probably 4.0.0 eventually

pllim · 2026-06-03T18:22:16Z

Ooo thanks! Is there a way to test with this branch over at https://github.com/spacetelescope/wfc3tools ?

zacharyburnett · 2026-06-03T18:25:03Z

Yes! Just make a PR that changes this line:
https://github.com/spacetelescope/wfc3tools/blob/f0eaea52a6f233c9238d45b2dcfc42a1f326a395/.github/workflows/tests.yml#L25

-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@2835f0cacddf3f8de198db9afdb5354a5cebe0ef  # v2.6.3
+    uses: zacharyburnett/github-actions-workflows/.github/workflows/tox.yml@install_conda_packages_directly

zacharyburnett · 2026-06-03T18:28:17Z

here: spacetelescope/wfc3tools#119

zacharyburnett · 2026-06-03T18:46:49Z

actually @Cadair if we can squeeze another PR into the 3.0.0 release, this one seems to be working well

zacharyburnett · 2026-06-03T18:49:32Z

wait no never mind, I still need to use matrix.conda_packages instead of inputs.conda_packages

zacharyburnett · 2026-06-03T19:09:09Z

ok, fixed

zacharyburnett · 2026-06-03T19:11:25Z

tested at https://github.com/spacetelescope/wfc3tools/actions/runs/26904804618

Cadair · 2026-06-03T19:17:46Z

This let's you install binaries for use in tox but not libraries right? You couldn't import a package installed like this?

Cadair · 2026-06-03T19:39:57Z

        type: string
-      conda:
-        description: Whether to test with conda (deprecated)
+      conda_packages:


Given how this is separate from tox, I wonder if it would be best folded into libraries like the system package managers?

Oh that's a good idea!

actually on second thought, maybe we should keep them separate; the conda environment is distinct from the runner and platform, and you can install both

I'm still not entirely sure what the limits of this functionality are so hard to judge. Can you use this to install C libraries and have them picked up inside tox?

yes, anything in the conda environment is exposed to tox via allowlist_externals

allowlist_externals is for command line tools only no?

oh yes you're right. The only usage of it I've seen is for testing wfc3tools with hstcal

I'm not sure if C libraries will be exposed, but I assume they should be since Conda modifies that path

I'll have to experiment. I still think that this is still a good match for libraries? There's not any meaningful difference between using conda like this and homebrew?

I guess I don't really understand how the libraries installer works, so I'm fine with pushing this PR off to 4.0 if you think it can be better

I've completely failed to write a test which checks to see if you can load a c library installed with conda or apt inside the tox env. Feel free to have a play if you want.

I think this functionality should be in libraries, I think it's the sensible place for it to be. Note, that with your current implementation I haven't been able to install a conda package on a per-env basis, you can see this in my broken test commit.

Cadair · 2026-06-03T19:45:23Z

I'm in no mad rush for 3.0 fwiw, so happy to get this in.

codecov-commenter · 2026-06-03T19:55:06Z

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 66.66%. Comparing base (e113052) to head (7747782).
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #391   +/-   ##
=======================================
  Coverage   66.66%   66.66%           
=======================================
  Files           2        2           
  Lines           6        6           
=======================================
  Hits            4        4           
  Misses          2        2

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

for more information, see https://pre-commit.ci

Cadair · 2026-06-08T14:31:27Z

muffled screaming

zacharyburnett · 2026-06-09T14:41:25Z

for some reason the clib test with conda_packages: specified

  - linux: libraries-clibrary
    conda_packages: libffcall

isn't actually picking up the conda packages and is just setting up Python with setup-python instead:
https://github.com/OpenAstronomy/github-actions-workflows/actions/runs/27213866684/job/80350042102?pr=391

zacharyburnett force-pushed the install_conda_packages_directly branch 2 times, most recently from c0c196b to e374ea0 Compare May 5, 2026 13:25

zacharyburnett changed the title ~~instead of using tox-conda, install Conda packages directly with micromamba~~ replace conda: parameter with conda_packages: May 5, 2026

zacharyburnett marked this pull request as ready for review May 5, 2026 13:25

zacharyburnett force-pushed the install_conda_packages_directly branch from e374ea0 to 44ac21e Compare May 5, 2026 13:49

zacharyburnett mentioned this pull request May 8, 2026

remove conda parameter after deprecation period #361

Closed

zacharyburnett force-pushed the install_conda_packages_directly branch 4 times, most recently from 9c26605 to a90895a Compare June 3, 2026 18:17

zacharyburnett mentioned this pull request Jun 3, 2026

test OpenAstronomy workflow change spacetelescope/wfc3tools#119

Draft

zacharyburnett force-pushed the install_conda_packages_directly branch 3 times, most recently from f811cdf to 33c1c36 Compare June 3, 2026 18:39

zacharyburnett marked this pull request as draft June 3, 2026 18:49

zacharyburnett force-pushed the install_conda_packages_directly branch 4 times, most recently from b9211da to 76f3014 Compare June 3, 2026 19:05

zacharyburnett marked this pull request as ready for review June 3, 2026 19:09

zacharyburnett requested a review from Cadair June 3, 2026 19:09

Cadair reviewed Jun 3, 2026

View reviewed changes

zacharyburnett force-pushed the install_conda_packages_directly branch from f659f25 to 7747782 Compare June 3, 2026 19:53

Cadair added this to the 3.0 milestone Jun 8, 2026

zacharyburnett and others added 8 commits June 8, 2026 11:34

install conda_packages: directly with micromamba

2fba03b

fix called wrong context

77e4bb4

[pre-commit.ci] auto fixes from pre-commit.com hooks

aa5562d

for more information, see https://pre-commit.ci

add conda_channels input

197e587

[pre-commit.ci] auto fixes from pre-commit.com hooks

cf56417

for more information, see https://pre-commit.ci

remove conda test toxenvs

d556863

actually insert conda packages and channels into matrix

93e1d21

unpin uv

d252a22

Cadair force-pushed the install_conda_packages_directly branch from 7747782 to d252a22 Compare June 8, 2026 10:39

whoops

56967b4

Cadair force-pushed the install_conda_packages_directly branch 8 times, most recently from 679fd0f to a8d11d4 Compare June 8, 2026 14:31

Make a test of system package clib

3f3a3d0

Cadair force-pushed the install_conda_packages_directly branch from a8d11d4 to 3f3a3d0 Compare June 8, 2026 14:33

use underscore instead of hyphen in matrix to align with workflow input

9529d60

Conversation

zacharyburnett commented May 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

pllim commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

zacharyburnett commented Jun 3, 2026

Uh oh!

Cadair commented Jun 3, 2026

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Cadair commented Jun 3, 2026

Uh oh!

codecov-commenter commented Jun 3, 2026

Codecov Report

Uh oh!

Cadair commented Jun 8, 2026

Uh oh!

zacharyburnett commented Jun 9, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

zacharyburnett commented May 5, 2026 •

edited

Loading