Bugfix: Nomad parsing, atom_types mapping on chemical_formula and use of chemical_symbols #77
Workflow file for this run
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| name: NOMAD dependencies compatibility | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| # Run workflow only when there are changes in pyproject.toml or dev-requirements.txt | |
| paths: | |
| - 'pyproject.toml' | |
| - 'dev-requirements.txt' | |
| jobs: | |
| validate_dependencies: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout pynxtools | |
| uses: actions/checkout@v2 | |
| - name: Checkout NOMAD from GitLab | |
| run: | | |
| git clone --depth 1 --branch develop --recurse-submodules https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git nomad | |
| git submodule update --init --recursive --depth 1 | |
| - name: Replace pynxtools dependency in NOMAD pyproject.toml | |
| working-directory: ./nomad | |
| run: | | |
| sed -i 's|pynxtools\[convert\]==[0-9]\+\(\.[0-9]\+\)\{0,2\}|pynxtools\[convert\]@git+https://github.com/FAIRmat-NFDI/pynxtools.git@${{ github.head_ref || github.ref_name }} |' pyproject.toml | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.9' | |
| - name: Install uv | |
| run: | | |
| curl -LsSf https://astral.sh/uv/install.sh | sh | |
| - name: Generate (dev-)requirements.txt from modified pyproject.toml | |
| working-directory: ./nomad | |
| run: | | |
| uv pip compile -p 3.9 --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml | |
| uv pip compile -p 3.9 --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml | |
| - name: Install NOMAD dependencies with pynxtools from current branch | |
| working-directory: ./nomad | |
| run: | | |
| uv pip install --system -r requirements.txt | |
| uv pip install --system -r requirements-dev.txt | |
| env: | |
| PYTHONPATH: "" # Ensure no pre-installed packages interfere with the test |