Move test files to tests/cognitive_tests/ and fix dependencies #367
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| name: NeuroFlex CI/CD | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| # Cache temporarily disabled to ensure fresh dependency installation | |
| - name: Install dependencies | |
| run: | | |
| set -ex | |
| python -m pip install --upgrade pip | |
| pip -v --version | |
| echo "Installing base dependencies..." | |
| pip install -v wheel setuptools | |
| echo "Installing core numerical packages..." | |
| pip install -v numpy==1.23.5 scipy==1.9.0 jax==0.4.13 jaxlib==0.4.13 tensorflow-cpu==2.12.0 keras==2.12.0 tensorboard==2.12.3 | |
| echo "Cloning alphafold repository..." | |
| # Clone and install alphafold with error handling | |
| if ! git clone --depth 1 https://github.com/google-deepmind/alphafold.git; then | |
| echo "Failed to clone alphafold repository" | |
| exit 1 | |
| fi | |
| echo "Installing alphafold and its dependencies..." | |
| cd alphafold | |
| if ! pip install -v -e . --no-deps; then | |
| echo "Failed to install alphafold" | |
| exit 1 | |
| fi | |
| cd .. | |
| echo "Installing alphafold dependencies..." | |
| pip install -v -r alphafold/requirements.txt | |
| echo "Installing project dependencies in batches..." | |
| # Install dependencies in smaller batches | |
| pip install -v pytest mne gymnasium | |
| pip install -v Bio ml_collections | |
| pip install -v --no-deps optax==0.1.5 | |
| # Finally, let pip resolve any remaining dependencies | |
| pip install -v -r requirements.txt | |
| - name: Create necessary directories | |
| run: | | |
| mkdir -p ${{ github.workspace }}/data | |
| mkdir -p ${{ github.workspace }}/path/to/save | |
| - name: Set ALPHAFOLD_PATH environment variable | |
| run: echo "ALPHAFOLD_PATH=${{ github.workspace }}/alphafold" >> $GITHUB_ENV | |
| - name: Run tests | |
| run: | | |
| pytest tests/ --disable-warnings | |
| env: | |
| NEUROFLEX_DATA_DIR: ${{ github.workspace }}/data | |
| NEUROFLEX_SAVE_DIR: ${{ github.workspace }}/path/to/save | |
| ALPHAFOLD_PATH: ${{ env.ALPHAFOLD_PATH }} | |
| build: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| # Cache temporarily disabled to ensure fresh dependency installation | |
| - name: Install dependencies | |
| run: | | |
| set -ex | |
| python -m pip install --upgrade pip | |
| pip -v --version | |
| echo "Installing base dependencies..." | |
| pip install -v wheel setuptools | |
| echo "Installing core numerical packages..." | |
| pip install -v numpy==1.23.5 scipy==1.9.0 jax==0.4.13 jaxlib==0.4.13 tensorflow-cpu==2.12.0 keras==2.12.0 tensorboard==2.12.3 | |
| echo "Cloning alphafold repository..." | |
| # Clone and install alphafold with error handling | |
| if ! git clone --depth 1 https://github.com/google-deepmind/alphafold.git; then | |
| echo "Failed to clone alphafold repository" | |
| exit 1 | |
| fi | |
| echo "Installing alphafold and its dependencies..." | |
| cd alphafold | |
| if ! pip install -v -e . --no-deps; then | |
| echo "Failed to install alphafold" | |
| exit 1 | |
| fi | |
| cd .. | |
| echo "Installing alphafold dependencies..." | |
| pip install -v -r alphafold/requirements.txt | |
| echo "Installing project dependencies in batches..." | |
| # Install dependencies in smaller batches | |
| pip install -v pytest mne gymnasium | |
| pip install -v Bio ml_collections | |
| pip install -v --no-deps optax==0.1.5 | |
| # Finally, let pip resolve any remaining dependencies | |
| pip install -v -r requirements.txt | |
| - name: Build package | |
| run: | | |
| pip install build | |
| python -m build | |
| - name: Check dist folder | |
| run: | | |
| ls -l dist/ | |
| publish: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install build tools | |
| run: | | |
| set -ex | |
| python -m pip install --upgrade pip | |
| pip -v --version | |
| echo "Installing base dependencies..." | |
| pip install -v wheel setuptools | |
| echo "Installing core numerical packages..." | |
| pip install -v numpy==1.23.5 scipy==1.9.0 jax==0.4.13 jaxlib==0.4.13 tensorflow-cpu==2.12.0 keras==2.12.0 tensorboard==2.12.3 | |
| echo "Cloning alphafold repository..." | |
| # Clone and install alphafold with error handling | |
| if ! git clone --depth 1 https://github.com/google-deepmind/alphafold.git; then | |
| echo "Failed to clone alphafold repository" | |
| exit 1 | |
| fi | |
| echo "Installing alphafold and its dependencies..." | |
| cd alphafold | |
| if ! pip install -v -e . --no-deps; then | |
| echo "Failed to install alphafold" | |
| exit 1 | |
| fi | |
| cd .. | |
| echo "Installing alphafold dependencies..." | |
| pip install -v -r alphafold/requirements.txt | |
| echo "Installing project dependencies in batches..." | |
| # Install dependencies in smaller batches | |
| pip install -v pytest mne gymnasium | |
| pip install -v Bio ml_collections | |
| pip install -v --no-deps optax==0.1.5 | |
| # Finally, let pip resolve any remaining dependencies | |
| pip install -v -r requirements.txt | |
| pip install -v build twine | |
| - name: Verify distribution files | |
| run: | | |
| ls -l dist/ | |
| - name: Publish to PyPI | |
| env: | |
| TWINE_USERNAME: "__token__" | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| run: | | |
| python -m twine upload dist/* --skip-existing | |
| update_workflow: | |
| needs: publish | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Update workflow | |
| run: | | |
| echo "Updating workflow in GitHub" | |
| # Add any additional steps needed to update the workflow |