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Updates to Ontology Files

Update cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml #65

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Update cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml

Update cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml #65

Workflow file for this run

.github/workflows/ontology_process.yml at 1c6b35d
name: Updates to Ontology Files
on:
push:
paths:
- '**/cellxgene_schema_cli/cellxgene_schema/ontology_files/gene_info.yml'
- '**/cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml'
branches-ignore:
- main
jobs:
ontology-processing:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
with:
ref: ${{ github.event.pull_request.head.ref }}
- name: ontology changes
uses: dorny/paths-filter@v2
id: filter
with:
filters: |
owl_info:
- 'cellxgene_schema_cli/cellxgene_schema/ontology_files/owl_info.yml'
gene_info:
- 'cellxgene_schema_cli/cellxgene_schema/ontology_files/gene_info.yml'
- name: Set up Python 3.8
uses: actions/setup-python@v1
with:
python-version: 3.8
- name: Python cache
uses: actions/cache@v1
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: install requirements
run: |
pip install -r cellxgene_schema_cli/requirements.txt
- name: setup git
run: |
git config user.name github-actions
git config user.email [email protected]
- name: owl-processing
if: ${{ steps.filter.outputs.owl_info == 'true' }}
run: |
make download-ontologies -C cellxgene_schema_cli
git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/all_ontology.json.gz
- name: gene-processing
if: ${{ steps.filter.outputs.gene_info == 'true' }}
run: |
make gene-processing -C cellxgene_schema_cli
git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/genes_*.csv.gz
git add ./cellxgene_schema_cli/cellxgene_schema/ontology_files/*_diff.txt
- name: Commit
if: ${{ steps.filter.outputs.gene_info == 'true' || steps.filter.outputs.owl_info == 'true' }}
run: |
git commit -m "AUTO: update ontologies"
git push
unit-tests:
runs-on: ubuntu-latest
needs: ontology-processing
steps:
- name: Checkout
uses: actions/checkout@v3
with:
ref: ${{ github.event.pull_request.head.ref }}
- name: Set up Python 3.8
uses: actions/setup-python@v1
with:
python-version: 3.8
- name: Python cache
uses: actions/cache@v1
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install dependencies
run: |
pip install -r cellxgene_schema_cli/requirements.txt
pip install pytest
- name: Unit tests
run: make unit-test
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2