Use Pixi in macOS-intel CI by scott-huberty · Pull Request #13704 · mne-tools/mne-python

scott-huberty · 2026-02-28T00:27:54Z

I'm exploring the feasibility of using Pixi to resolve the virtual environment and run tests specifically for the MacOS Intel CI, which currently uses Mamba to create the virtual environment.

My initial strategy was to just to do pixi init --import environment.yml, so that we can leverage our already defined YAML config file to pull in all the necessary dependencies, as well as configuring prefix-dev/setup-pixi to automatically activate our virtual environment, so that we can run commands like pytest etc without having to prepend pixi run everywhere for the pixi CI...

Unfortunately the only way I could get this to work was to disable use of a login shell.. Which of course makes all the condo-like CI's fail!!

tsbinns · 2026-02-28T15:39:40Z

Hey @scott-huberty, looking at the current diff I noticed you're setting up pixi without activating the env, initing with environment.yml, then setting up again with env activation.

Found when switching to uv for the old job that the env can be activated at setup with a given Python ver and then have the required packages installed in github_actions_dependencies.sh:

mne-python/.github/workflows/tests.yml

Lines 157 to 165 in 8dd298f

    
                 - uses: astral-sh/setup-uv@v7 
        
                   with: 
        
                     version: ">=0.9" 
        
                     activate-environment: true 
        
                     cache-dependency-glob: | 
        
                       **/pylock.ci-old.toml 
        
                     python-version: ${{ matrix.python }} 
        
                   if: matrix.kind == 'old' 
        
                 - run: bash ./tools/github_actions_dependencies.sh

Wondered if a similar thing could work for pixi rather than needing 2 setups. Haven't looked through diffs for all commits, so apologies if you tried this already.

drammock · 2026-06-24T16:45:08Z

TODO @scott-huberty make it so that the matrix python version specified in tests.yml gets inserted into the pixi.toml file

- The Pixi job replaces teh MacOS pip job on main. - The MacOS pip job on main does not set MNE_TEST_ALLOW_SKIP - mne/conftest.py:1357 treats unset MNE_TEST_ALLOW_SKIP as “allow all skips"

scott-huberty

Doh... Never submitted this review, which was just 1 comment!!

drammock · 2026-07-22T19:00:48Z

after adding a "this is autogenerated" comment to the top of pixi.toml (which may need slightly altering how we write it with tomlkit, i.e., dumping a tomlkit.document() instead of a dict), I think we'll be ready to merge here. @scott-huberty and I discussed migrating some of this into mne-tools/mne-tools already, and will do that in follow-up PRs

scott-huberty · 2026-07-27T03:57:16Z

after adding a "this is autogenerated" comment to the top of pixi.toml ... I think we'll be ready to merge here.

done in e5bd471

drammock · 2026-07-29T17:29:20Z

possible problem: seems like environment is getting MNE stable release (not main/PR):

https://github.com/mne-tools/mne-python/actions/runs/30474035062/job/90651542841?pr=13704#step:18:61

probably because of this:

https://github.com/mne-tools/mne-python/actions/runs/30474035062/job/90651542841?pr=13704#step:9:372

scott-huberty · 2026-07-29T17:59:50Z

possible problem: seems like environment is getting MNE stable release (not main/PR):

https://github.com/mne-tools/mne-python/actions/runs/30474035062/job/90651542841?pr=13704#step:18:61

probably because of this:

https://github.com/mne-tools/mne-python/actions/runs/30474035062/job/90651542841?pr=13704#step:9:372

hmm The pixi.lock file has: - conda: https://conda.anaconda.org/conda-forge/noarch/mne-base-1.12.1-pyh694c41f_200.conda

EDIT: Maybe because pixi.toml requests mne-qt-browser = "*" which pulls in MNE stable.

drammock · 2026-08-05T18:27:19Z

@@ -1,5 +1,6 @@
 #!/bin/bash -ef

+# TODO: I think that DEPS is cruft. Its not set anywhere??


lingering TODO comment

drammock · 2026-08-05T18:54:50Z

    echo "MNE_LOGGING_LEVEL=warning" | tee -a $GITHUB_ENV
    echo "MNE_TEST_ALLOW_SKIP=.*(on conda|Requires (spm|brainstorm|misc) dataset|CUDA not|Flakey verbose behavior|PySide6 causes segfaults|SCIPY_ARRAY_API).*" | tee -a $GITHUB_ENV
    echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV
+# NON-DRY but just gonna get it working and then refactor.


cruft comment?

drammock · 2026-08-05T18:55:10Z


 set -eo pipefail

+


extra newline?

scott-huberty added 26 commits February 22, 2026 14:01

WIP: Add pixi CI runner

37ff4b3

FIX: syntax

9bf2882

TST: test branch

e736f17

FIX: skip cache for now

07ff86e

FIX: create pixi.toml

7fa7b7d

check

c26c307

try

1ff8624

dont install

03b2f29

try again

8b73058

activate environment

962a49e

FIX: rm cruft

05359d8

debug

460c24a

arg

5a16daa

more debug

dc25bec

tests

d1c45e2

more

14c0687

try

0376aae

hack: prepend path with executable

a207603

FIX: wrong var

4f0770f

FIX: shell

e0d0865

Found the issue (login shell). Now try to remove previous hack

7c44343

now debug failiing conda-ish CI's

fe5a459

arggh GH YAML syntax doesnt allow double quotes

c2f8a97

try using shell wrapper

de6704c

more

6e651d8

remove branch

a46fc3b

scott-huberty requested review from drammock and larsoner as code owners February 28, 2026 00:27

scott-huberty marked this pull request as draft February 28, 2026 00:28

scott-huberty and others added 5 commits July 8, 2026 21:17

[skip circle][skip azp] specify python version

814e1d1

Merge branch 'main' into pixi

5739306

update pixi toml/lock

1f9e87d

[circle skip][skip azp] need pyside6

bd5538e

Dont set MNE_TEST_ALLOW_SKIP in Pixi job

d805238

- The Pixi job replaces teh MacOS pip job on main. - The MacOS pip job on main does not set MNE_TEST_ALLOW_SKIP - mne/conftest.py:1357 treats unset MNE_TEST_ALLOW_SKIP as “allow all skips"

scott-huberty commented Jul 22, 2026

View reviewed changes

Comment thread .github/workflows/scheduled_updates.yml

scott-huberty added 2 commits July 22, 2026 11:28

merge

181f76b

regen pixi toml/lock

8bc139b

comment

e5bd471

autofix-ci Bot and others added 5 commits July 27, 2026 04:10

[autofix.ci] apply automated fixes

a62727c

ping

9cd7b0d

Merge branch 'pixi' of github.com:scott-huberty/mne-python into pixi

a7f21c7

ping

8a00162

Merge remote-tracking branch 'upstream/main' into pixi

179229b

drammock reviewed Jul 29, 2026

View reviewed changes

Comment thread tools/write-pixi-toml.py Outdated

Apply suggestion from @drammock

e4dbfc3

scott-huberty added 7 commits July 29, 2026 11:54

try...

cef741d

flag

cbc7847

fix

da2988d

fix

29565b9

try manifest path

949c14f

WIP: force mne directory

371fefa

WIP: remove step to add mne dev dep in pixi job

649ef49

drammock reviewed Aug 5, 2026

View reviewed changes

remove lock file

dc692c3

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Use Pixi in macOS-intel CI - #13704

Use Pixi in macOS-intel CI#13704
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		@@ -1,5 +1,6 @@
		#!/bin/bash -ef

		# TODO: I think that DEPS is cruft. Its not set anywhere??

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