copilot-setup-steps.yml

# This file was generated based on the recommendations from https://docs.github.com/en/enterprise-cloud@latest/copilot/customizing-copilot/customizing-the-development-environment-for-copilot-coding-agent#preinstalling-tools-or-dependencies-in-copilots-environment

name: "Copilot Setup Steps"

# Automatically run the setup steps when they are changed to allow for easy validation, and
# allow manual testing through the repository's "Actions" tab
on:
  workflow_dispatch:
  push:
    paths:
      - .github/workflows/copilot-setup-steps.yml
  pull_request:
    paths:
      - .github/workflows/copilot-setup-steps.yml

env:
  EXAMPLES_FOLDER: examples

jobs:
  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
  copilot-setup-steps:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout code with submodule
        uses: actions/checkout@v4
        with:
          submodules: recursive
          fetch-depth: 0

      - name: Setup conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          activate-environment: biobuddy
          python-version: 3.11.11

      - name: Install dependencies
        run: | 
          pip install . && pip uninstall -y biobuddy
          pip install scipy==1.15.2 numpy==1.25.2 lxml ezc3d

      - name: Install test dependencies
        run: |
          pip install pytest pytest-cov codecov black
          conda install -c opensim-org opensim=4.5.1
          conda install -c conda-forge biorbd=1.11.2 deepdiff

      - name: Set environment variables for Copilot
        run: |
          echo "CONDA_PREFIX=$CONDA_PREFIX" >> $GITHUB_ENV
          echo "PYTHONPATH=$CONDA_PREFIX/lib/python3.11/site-packages:$PYTHONPATH" >> $GITHUB_ENV
          echo "PATH=$CONDA_PREFIX/bin:$PATH" >> $GITHUB_ENV

      - name: Verify environment setup
        run: |
          echo "Python location: $(which python)"
          echo "Conda prefix: $CONDA_PREFIX"
          echo "Python path: $PYTHONPATH"
          python -c "import sys; print('Python sys.path:'); [print(f'  {p}') for p in sys.path]"