circleci: update miniforge setup#1352
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yunjunz merged 1 commit intoinsarlab:mainfrom May 29, 2025
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+ .circleci/config.yml: replace `mamba init bash` with `source conda/mamba.sh`, as suggested by its github repo readme at https://github.com/conda-forge/miniforge?tab=readme-ov-file#as-part-of-a-ci-pipeline
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Reviewer's GuideThis PR updates the CircleCI Miniforge setup to follow the official recommendations by dynamically downloading the correct OS/architecture installer and sourcing the Conda and Mamba shell scripts instead of using Sequence diagram for the updated Miniforge setup in CircleCIsequenceDiagram
participant CircleCI_Job as "CircleCI Job"
participant GitHub_Releases as "GitHub Releases"
participant Shell_Environment as "Shell Environment"
CircleCI_Job->>Shell_Environment: 1. Create/access tools directory
CircleCI_Job->>GitHub_Releases: 2. Download Miniforge (OS/Arch specific installer)
GitHub_Releases-->>CircleCI_Job: Miniforge Installer Script
CircleCI_Job->>Shell_Environment: 3. Install Miniforge from script
CircleCI_Job->>Shell_Environment: 4. Source conda.sh for initialization
CircleCI_Job->>Shell_Environment: 5. Source mamba.sh for initialization
CircleCI_Job->>Shell_Environment: 6. Update PATH in BASH_ENV for subsequent steps
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Hey @yunjunz - I've reviewed your changes and they look great!
Here's what I looked at during the review
- 🟢 General issues: all looks good
- 🟢 Security: all looks good
- 🟢 Testing: all looks good
- 🟢 Complexity: all looks good
- 🟢 Documentation: all looks good
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
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Description of proposed changes
.circleci/config.yml: replacemamba init bashwithsource conda/mamba.sh, as suggested by its GitHub repo readme at https://github.com/conda-forge/miniforge?tab=readme-ov-file#as-part-of-a-ci-pipeline, to fix the current circle CI environment setup error.Reminders
Summary by Sourcery
Improve the CircleCI miniforge setup by downloading the installer dynamically and sourcing the conda and mamba initialization scripts to resolve environment configuration errors.
Bug Fixes:
mamba init.Enhancements:
mamba init bashwithsource conda.shandsource mamba.shto configure the shell in CI.CI:
.circleci/config.ymlto install and configure Miniforge correctly in the pipeline.