-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
55 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,53 @@ | ||
# This workflow will install Python dependencies, run tests and lint with a variety of Python versions | ||
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | ||
|
||
# TODO: | ||
# - cache this directory $HOME/.cache/pyensembl/ | ||
# - update coveralls | ||
name: Tests | ||
on: [push, pull_request] | ||
|
||
jobs: | ||
build: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: true | ||
matrix: | ||
python-version: ["3.9", "3.10", "3.11"] | ||
|
||
steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v3 | ||
- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
cache: "pip" | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
python -m pip install flake8 pytest pytest-cov coveralls | ||
pip install -r requirements.txt | ||
pip install . | ||
- name: Lint with flake8 | ||
run: | | ||
# stop the build if there are Python syntax errors or undefined names | ||
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
- name: Run default linting script | ||
run: | | ||
./lint.sh | ||
- name: Install Ensembl data | ||
run: | | ||
echo "Before installing Ensembl releases" && df -h | ||
pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/ | ||
pyensembl install --release 81 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.81/ | ||
pyensembl install --release 95 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.95/ | ||
pyensembl install --release 95 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.95/ | ||
echo "After installing Ensembl releases" && df -h | ||
- name: Run unit tests | ||
run: | | ||
./test.sh | ||
- name: Publish coverage to Coveralls | ||
uses: coverallsapp/[email protected] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters