README.md

provision-with-micromamba

GitHub Action to provision a CI instance using micromamba

Inputs

environment-file

Optional The the environment.yml file for the conda environment. Default is environment.yml

environment-name

Optional Specify a custom environment name, to overwrite the name specified in the environment.yml, or in in case it was not specified in the environment.yml.

micromamba-version

Optional Specifiy a custom micromamba version. Use "latest" for bleeding edge.

extra-specs

Optional Specifiy additional specifications (packages) to install. Pretty useful when using matrix builds to pin versions of a test/run dependency.

Note: for multiple packages, use multiline syntax (see examples below)

Example usage

Note: some shells need special syntax for invocation (e.g. bash -l {0}). You can set this up in defaults.

name: test
on:
  push: null

jobs:
  test:
    runs-on: ubuntu-latest
    name: test
    steps:
      - uses: actions/checkout@v2

      - name: install mamba
        uses: mamba-org/provision-with-micromamba@main

      # linux and osx
      - name: run python
        shell: bash -l {0}
        run: |
          python -c "import numpy"

      # windows
      - name: run python
        shell: powershell
        run: |
          python -c "import numpy"
      - name: run cmd.exe
        shell: cmd /C CALL {0}
        run: >-
          micromamba info && micromamba list

Example with customization

name: test
on:
  push: null

jobs:
  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        pytest: ["6.1", "6.2"]
    name: test
    steps:
      - uses: actions/checkout@v2

      - name: install mamba
        uses: mamba-org/provision-with-micromamba@main
        with:
          environment-file: myenv.yaml
          environment-name: myenv
          extra-specs: |
            python=3.7
            pytest=${{ matrix.pytest }}

IMPORTANT

Some shells require special syntax (e.g. bash -l {0}). You can set this up with the default option:

jobs:
  myjob:
    defaults:
      run:
        shell: bash -l {0}
...

Find the reasons below (taken from setup-miniconda):

• Bash shells do not use ~/.profile or ~/.bashrc so these shells need to be explicitely declared as shell: bash -l {0} on steps that need to be properly activated (or use a default shell). This is because bash shells are executed with bash --noprofile --norc -eo pipefail {0} thus ignoring updated on bash profile files made by conda init bash. See Github Actions Documentation and thread.
• Sh shells do not use ~/.profile or ~/.bashrc so these shells need to be explicitely declared as shell: sh -l {0} on steps that need to be properly activated (or use a default shell). This is because sh shells are executed with sh -e {0} thus ignoring updated on bash profile files made by conda init bash. See Github Actions Documentation.
• Cmd shells do not run Autorun commands so these shells need to be explicitely declared as shell: cmd /C call {0} on steps that need to be properly activated (or use a default shell). This is because cmd shells are executed with %ComSpec% /D /E:ON /V:OFF /S /C "CALL "{0}"" and the /D flag disabled execution of Command Processor/Autorun Windows registry keys, which is what conda init cmd.exe sets. See Github Actions Documentation.
• For caching to work properly, you will need to set the use-only-tar-bz2 option to true.
• Some options (e.g. use-only-tar-bz2) are not available on the default conda installed on Windows VMs, be sure to use auto-update-conda or provide a version of conda compatible with the option.
• If you plan to use a environment.yaml file to set up the environment, the action will read the channelslisted in the key (if found). If you provide the channels input in the action they must not conflict with what was defined in environment.yaml, otherwise the conda solver might find conflicts and result in very long install times.
• Conda activation does not correctly work on sh. Please use bash.

Development

When developing, you need to

1. install nodejs
2. clone the repo
3. run npm install -y
4. run npm run build after making changes