revert py3.13: scipy not yet supported? #24
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| name: Run testdata set on supported python versions | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{matrix.python-version}} | |
| - name: Install poetry | |
| uses: Gr1N/setup-poetry@v9 | |
| - name: Install dependencies and package | |
| run: | | |
| poetry lock | |
| poetry show --tree | |
| poetry install | |
| - name: Run testdataset in test_data | |
| run: | | |
| poetry run edgehog --hog test_data/FastOMA_HOGs.orthoxml \ | |
| --species_tree test_data/species_tree.nwk \ | |
| --gff_directory test_data/gff3/ \ | |
| --date_edges \ | |
| --orient_edges \ | |
| --output_directory test-results | |
| - name: check produced results | |
| run: | | |
| ls test-results | |
| gunzip -c test-results/12_linearized_synteny_graph_edges.tsv.gz | head -n 10 | |
| - name: check a specific relation exists | |
| run: | | |
| gunzip -c test-results/12_linearized_synteny_graph_edges.tsv.gz | awk '/(HOG_HOG:0000285_13\tHOG_HOG:0000284_13)|(HOG_HOG:0000284_13\tHOG_HOG:0000285_13)/{count++; print $0} END {exit (count == 1 ? 0 : 1)}' |