Remove conda default channel #765

jan-janssen · 2025-07-28T07:19:13Z

Summary by CodeRabbit

Chores
- Streamlined conda environment setup in deployment and pipeline workflows by updating Miniconda configuration and simplifying channel management. No changes affecting user-facing features.

coderabbitai · 2025-07-28T07:19:19Z

Walkthrough

The GitHub Actions workflow files were updated to use version v3.2.0 of the conda-incubator/setup-miniconda action instead of v3. The manual creation of a .condarc file was removed, and conda channel configuration is now passed directly as action parameters. No source code or exported entities were changed.

Changes

Cohort / File(s)	Change Summary
Deploy Workflow Update `.github/workflows/deploy.yml`	Updated to use `setup-miniconda@v3.2.0`, removed manual `.condarc` creation, passed conda channel parameters directly including `channels: conda-forge` and `conda-remove-defaults: "true"`.
Pipeline Workflow Update `.github/workflows/pipeline.yml`	Updated all jobs to use `setup-miniconda@v3.2.0`, removed `.condarc` creation, set channels and defaults via parameters consistently across jobs.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~7 minutes

Possibly related PRs

Remove conda default channel #396: Both PRs address conda channel configuration in GitHub Actions workflows, but this PR removes manual .condarc creation while the related PR introduces it; both modify the same workflow steps.

Poem

🐇
In workflows where conda once did dwell,
The .condarc is gone—farewell!
Now channels are set with a line or two,
And actions upgraded, shiny and new.
With v3.2.0, the pipelines hop,
A rabbit’s delight—no need to stop!

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.github/workflows/deploy.yml (1 hunks)
.github/workflows/pipeline.yml (13 hunks)

✅ Files skipped from review due to trivial changes (1)

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GitHub Check: notebooks_integration
GitHub Check: benchmark (ubuntu-latest, 3.13, .ci_support/environment-mpich.yml)
GitHub Check: benchmark (ubuntu-latest, 3.13, .ci_support/environment-openmpi.yml)

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codecov · 2025-07-28T07:22:32Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.47%. Comparing base (4adfb3d) to head (93ba29c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #765   +/-   ##
=======================================
  Coverage   97.47%   97.47%           
=======================================
  Files          32       32           
  Lines        1423     1423           
=======================================
  Hits         1387     1387           
  Misses         36       36

☔ View full report in Codecov by Sentry.
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coderabbitai

Actionable comments posted: 0

♻️ Duplicate comments (12)

.github/workflows/pipeline.yml (12)

85-91: Duplicate of the comment above – same action tag and boolean quoting issues.

117-123: Duplicate of the comment above – same action tag and boolean quoting issues.

150-156: Duplicate of the comment above – same action tag and boolean quoting issues.

175-181: Duplicate of the comment above – same action tag and boolean quoting issues.

203-209: Duplicate of the comment above – same action tag and boolean quoting issues.

234-240: Duplicate of the comment above – same action tag and boolean quoting issues.

280-286: Duplicate of the comment above – same action tag and boolean quoting issues.

318-324: Duplicate of the comment above – same action tag and boolean quoting issues.

353-359: Duplicate of the comment above – same action tag and boolean quoting issues.

374-379: Duplicate of the comment above – same action tag and boolean quoting issues.

393-399: Duplicate of the comment above – same action tag and boolean quoting issues.

431-437: Duplicate of the comment above – same action tag and boolean quoting issues.

🧹 Nitpick comments (2)

.github/workflows/deploy.yml (1)
22-27: Pin the action to a commit SHA and pass the boolean natively

Security ‒ conda-incubator/setup-miniconda@v3.2.0 is still a mutable tag. Follow GitHub recommendations and pin to the full commit SHA to guard against supply-chain attacks.

Typing ‒ conda-remove-defaults is a boolean input; quoting it ("true") turns it into a YAML string. Although the action coerces strings, passing the native boolean avoids surprises:
-    - uses: conda-incubator/setup-miniconda@v3.2.0
+    - uses: conda-incubator/setup-miniconda@<commit-sha>

-        conda-remove-defaults: "true"
+        conda-remove-defaults: true
Validate that .ci_support/environment-openmpi.yml resolves without the defaults channel; otherwise add explicit conda-forge labels or pin versions.
.github/workflows/pipeline.yml (1)

65-71: Same security & boolean-typing concerns apply here

Repeat the hard-pin + boolean advice for every setup-miniconda@v3.2.0 invocation in this workflow to keep the pipeline homogeneous and secure.

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📒 Files selected for processing (2)

.github/workflows/deploy.yml (1 hunks)
.github/workflows/pipeline.yml (13 hunks)

jan-janssen · 2025-07-28T07:38:24Z

@liamhuber Even with the new option to remove the default environment, I get the following results:

  /home/runner/miniconda3/condabin/conda config --show-sources --json
  {
    "/home/runner/.condarc": {
      "channels": [
        "conda-forge",
        "defaults"
      ],
      "notify_outdated_conda": false
    },
    "/home/runner/miniconda3/.condarc": {
      "channels": [
        "conda-forge"
      ]
    },
    "cmd_line": {
      "json": true
    }
  }

While with my previous version I explicitly overwrite the configuration in the home folder:

 /home/runner/miniconda3/condabin/conda config --show-sources
  ==> /home/runner/miniconda3/.condarc <==
  channels:
    - conda-forge
  
  ==> /home/runner/.condarc <==
  auto_update_conda: False
  auto_activate_base: True
  changeps1: False
  pkgs_dirs:
    - /home/runner/conda_pkgs_dir
  channels:
    - conda-forge
  always_yes: True
  solver: libmamba

While I agree that using the built-in option requires slightly fewer lines, the appearance of the defaults channel in the configuration file still makes me feel a bit uneasy. So I prefer to stay with the previous version.

liamhuber · 2025-07-28T14:44:25Z

It must just be that here we fail to pass some flag to setup-miniconda. I'm copy-pasting the report from two runs so we can easily look at both

setup-miniconda input log from the centralized actions

Run conda-incubator/setup-miniconda@v3
  with:
    python-version: 3.12
    miniforge-variant: Miniforge3
    miniforge-version: latest
    channels: conda-forge
    conda-remove-defaults: true
    channel-priority: strict
    activate-environment: ./cached-miniforge/my-env
    environment-file: ./environment.yml
    auto-activate-base: true
    auto-update-conda: false
    remove-profiles: true
    conda-solver: libmamba
    clean-patched-environment-file: true
    run-post: true

Here:

Run conda-incubator/setup-miniconda@v3.2.0
  with:
    python-version: 3.13
    miniforge-version: latest
    miniforge-variant: Miniforge3
    channels: conda-forge
    conda-remove-defaults: true
    environment-file: .ci_support/environment-mini.yml
    activate-environment: test
    auto-activate-base: true
    auto-update-conda: false
    remove-profiles: true
    conda-solver: libmamba
    clean-patched-environment-file: true
    run-post: true

liamhuber · 2025-07-28T14:45:35Z

@jan-janssen, yeah, the only difference I see is the channel-priority: strict, which you already speculated on in the meeting. Let's hope adding that resolves things!

jan-janssen · 2025-07-28T16:17:59Z

Now I see why I was confused:

 /home/runner/miniconda3/condabin/conda config --show-sources --json
  {
    "/home/runner/.condarc": {
      "channels": [
        "conda-forge",
        "defaults"
      ],
      "notify_outdated_conda": false
    },
    "/home/runner/miniconda3/.condarc": {
      "channels": [
        "conda-forge"
      ]
    },
    "cmd_line": {
      "json": true
    }
  }
  /home/runner/miniconda3/condabin/conda config --remove channels defaults --file /home/runner/.condarc
  Adding pkgs_dir '/home/runner/conda_pkgs_dir'
  /home/runner/miniconda3/condabin/conda config --add pkgs_dirs /home/runner/conda_pkgs_dir
  auto_activate: true
  /home/runner/miniconda3/condabin/conda config --set auto_activate true
  Warning: 
  CondaKeyError: 'auto_activate': unknown parameter
  
  
  
  CondaKeyError: 'auto_activate': unknown parameter
  
  /home/runner/miniconda3/condabin/conda config --set auto_activate_base true
  auto_update_conda: false
  /home/runner/miniconda3/condabin/conda config --set auto_update_conda false
  channel_priority: strict
  /home/runner/miniconda3/condabin/conda config --set channel_priority strict
  solver: libmamba
  /home/runner/miniconda3/condabin/conda config --set solver libmamba
  always_yes: true
  /home/runner/miniconda3/condabin/conda config --set always_yes true
  changeps1: false
  /home/runner/miniconda3/condabin/conda config --set changeps1 false
  /home/runner/miniconda3/condabin/conda config --show-sources
  ==> /home/runner/miniconda3/.condarc <==
  channels:
    - conda-forge
  
  ==> /home/runner/.condarc <==
  auto_update_conda: False
  auto_activate_base: True
  notify_outdated_conda: False
  changeps1: False
  pkgs_dirs:
    - /home/runner/conda_pkgs_dir
  channel_priority: strict
  channels:
    - conda-forge
  always_yes: True
  solver: libmamba

The command /home/runner/miniconda3/condabin/conda config --show-sources is called twice once before the channel is removed and once afterwards. So I basically just looked at the wrong place.

Remove conda default channel

d582eea

coderabbitai bot reviewed Jul 28, 2025

View reviewed changes

jan-janssen linked an issue Jul 28, 2025 that may be closed by this pull request

[Feature] Remove manual .condarc creation in continuous integration #731

Closed

jan-janssen marked this pull request as draft July 28, 2025 07:47

jan-janssen force-pushed the remove_conda_channel branch from 7f5ccd8 to 2ff2346 Compare July 28, 2025 14:50

jan-janssen force-pushed the remove_conda_channel branch from 2ff2346 to d582eea Compare July 28, 2025 16:36

downgrade to v3

93ba29c

jan-janssen marked this pull request as ready for review July 28, 2025 17:39

jan-janssen merged commit d0639b2 into main Jul 28, 2025
31 checks passed

jan-janssen deleted the remove_conda_channel branch July 28, 2025 17:54

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