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Custom dataloader registry support #12

Custom dataloader registry support

Custom dataloader registry support #12

name: test (custom dataloaders)
on:
push:
branches: [main, "[0-9]+.[0-9]+.x"]
pull_request:
branches: [main, "[0-9]+.[0-9]+.x"]
types: [labeled, synchronize, opened]
schedule:
- cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
workflow_dispatch:
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
# if PR has label "custom_dataloader" or "all tests" or if scheduled or manually triggered
if: >-
(
contains(github.event.pull_request.labels.*.name, 'custom_dataloader') ||
contains(github.event.pull_request.labels.*.name, 'all tests') ||
contains(github.event_name, 'schedule') ||
contains(github.event_name, 'workflow_dispatch')
)
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -e {0} # -e to fail on error
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
python: ["3.11"]
name: integration
env:
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
cache: "pip"
cache-dependency-path: "**/pyproject.toml"
- name: Install dependencies
run: |
python -m pip install --upgrade pip wheel uv
python -m uv pip install --system "scvi-tools[tests] @ ."
python -m pip install tiledbsoma
python -m pip install s3fs
- name: Install Specific Branch of Repository
env:
GH_TOKEN: ${{ secrets.GH_TOKEN }}
run: |
git config --global url."https://${GH_TOKEN}:[email protected]/".insteadOf "https://github.com/"
git clone --single-branch --branch ebezzi/census-scvi-datamodule https://github.com/ori-kron-wis/cellxgene-census.git
- name: Run specific custom dataloader pytest
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
COLUMNS: 120
run: |
coverage run -m pytest -v --color=yes --custom-dataloader-tests
coverage report
- uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}