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Updates to GENCODE Files

add fruit fly gencode file #1

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add fruit fly gencode file

add fruit fly gencode file #1

Workflow file for this run

.github/workflows/gencode-process.yml at a8e29f0
name: Updates to GENCODE Files
on:
push:
paths:
- '**/cellxgene_schema_cli/cellxgene_schema/gencode_files/gene_info.yml'
branches-ignore:
- main
jobs:
gencode-processing:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
with:
ref: ${{ github.event.pull_request.head.ref }}
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.10"
- name: Python cache
uses: actions/cache@v4
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: gene-processing
run: |
make gene-processing -C cellxgene_schema_cli
git add ./cellxgene_schema_cli/cellxgene_schema/gencode_files/genes_*.csv.gz
git add ./cellxgene_schema_cli/cellxgene_schema/gencode_files/*_diff.txt
- name: Commit
run: |
git commit -m "AUTO: update gencode files"
git push
unit-tests:
runs-on: ubuntu-latest
needs: gencode-processing
steps:
- name: Checkout
uses: actions/checkout@v4
with:
ref: ${{ github.event.pull_request.head.ref }}
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.10"
- name: Python cache
uses: actions/cache@v4
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 -r requirements-dev.txt
- name: Unit tests
run: make unit-test
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v4