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revert py3.13: scipy not yet supported? #24

revert py3.13: scipy not yet supported?

revert py3.13: scipy not yet supported? #24

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)}'