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Docs + Schema Fixes #182

Docs + Schema Fixes

Docs + Schema Fixes #182

Workflow file for this run

# Built from:
# https://docs.github.com/en/actions/guides/building-and-testing-python
---
name: Build and test htan2-data-model
on: [pull_request]
jobs:
test:
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
steps:
- name: Check out repository
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Poetry
run: |
python -m pip install --user poetry
export PATH="$HOME/.local/bin:$PATH"
poetry --version
- name: Install dependencies
run: |
export PATH="$HOME/.local/bin:$PATH"
poetry install --no-interaction --no-root
- name: Install project
run: |
export PATH="$HOME/.local/bin:$PATH"
poetry install --no-interaction
- name: Run test suite
run: |
export PATH="$HOME/.local/bin:$PATH"
make test
- name: Generate Synapse-compatible JSON schemas
run: |
export PATH="$HOME/.local/bin:$PATH"
for module in Clinical WES Biospecimen Sequencing Imaging scRNA-seq DigitalPathology MultiplexMicroscopy SpatialOmics; do
if [ -f modules/$module/Makefile ] && grep -q "^gen-synapse-schema:" modules/$module/Makefile; then
echo "Generating Synapse schema for $module module..."
make -C modules/$module gen-synapse-schema
else
echo "Skipping $module module (no gen-synapse-schema target)"
fi
done