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Prevent conda defaults channel usage in CI/CD workflows#11

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copilot/prevent-defaults-channel-usage
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Prevent conda defaults channel usage in CI/CD workflows#11
Copilot wants to merge 3 commits intomainfrom
copilot/prevent-defaults-channel-usage

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Copilot AI commented Dec 17, 2025

CI/CD workflows that create conda environments were not explicitly preventing use of the defaults channel, which could be implicitly included even when other channels are specified.

Changes

  • Explicit defaults removal: Added remove-defaults: true to setup-miniconda configuration
  • Channel specification: Centralized channel list (conda-forge,bioconda) in environment variable
  • Planemo channel enforcement: Added --conda_channels and --conda_ensure_channels flags to planemo test command
  • Verification step: Added pre-test check that fails the build if defaults channel is present in conda config
  • Security hardening: Added add-anaconda-token: false to prevent inadvertent defaults access
env:
  CONDA_CHANNELS: conda-forge,bioconda

steps:
  - uses: conda-incubator/setup-miniconda@v3
    with:
      channels: ${{ env.CONDA_CHANNELS }}
      remove-defaults: true
      add-anaconda-token: false

Only planemo-test.yml was affected. Other workflows don't use conda.

Original prompt

None of the CI/CD actions that create a conda environment can use the defaults channel. Make sure this never happens. This is done by specifying both the channels that we do want (i.e. conda-forge and bioconda) and by indicating that this is an override (--override-channels), otherwise the defaults channel is implicitly used.


✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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rvosa commented Dec 17, 2025

@copilot pipelines are failing: defaults is still present

…tainability

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
Copilot AI changed the title [WIP] Prevent usage of defaults channel in conda environment Prevent conda defaults channel usage in CI/CD workflows Dec 17, 2025
Copilot AI requested a review from rvosa December 17, 2025 16:17
@rvosa rvosa closed this Dec 17, 2025
@rvosa rvosa deleted the copilot/prevent-defaults-channel-usage branch December 17, 2025 16:38
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2 participants