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Increase anndata version to 0.11. #33

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Increase anndata version to 0.11.

Increase anndata version to 0.11. #33

Workflow file for this run

.github/workflows/release.yml at f300c52
name: Release
on:
pull_request:
branches:
- release
permissions:
contents: write
jobs:
fresh-install:
runs-on: ubuntu-20.04
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: setup python
uses: actions/setup-python@v5
with:
python-version: 3.11.8
# Do not install mamba-ssm as it is not supported for machines without GPUs
- name: Install dependencies
run: |
pip install .
tests:
runs-on: self-hosted
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: setup python
uses: actions/setup-python@v5
with:
python-version: 3.11.8
- name: Install dependencies
run: |
pip install -r requirements-dev.txt
pip install .[mamba-ssm]
# First download before tests as they make use of the downloaded files
- name: Download all files
run: |
python ci/download_all.py
- name: Execute unittests
run: |
CUDA_VISIBLE_DEVICES=-1 pytest --cov-report=html:html_cov --cov-branch --cov-report term --cov=helical ci/
- name: Upload coverage report
uses: actions/upload-artifact@v4
with:
name: coverage-report
path: html_cov/
integration-tests:
needs: tests
runs-on: self-hosted
env:
CUDA_VISIBLE_DEVICES: 0
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: setup python
uses: actions/setup-python@v5
with:
python-version: 3.11.8
# because jobs may not be run in the same order, we need to install the dependencies again
- name: Install helical
run: |
pip install .[mamba-ssm]
# Required to get the data
- name: Download all files
run: |
python ci/download_all.py
- name: Execute Geneformer v1
run: |
python examples/run_models/run_geneformer.py ++model_name="gf-12L-30M-i2048" ++device="cuda"
- name: Fine-tune Geneformer v1
run: |
python examples/fine_tune_models/fine_tune_geneformer.py ++model_name="gf-12L-30M-i2048" ++device="cuda"
- name: Execute Geneformer v2
run: |
python examples/run_models/run_geneformer.py ++model_name="gf-12L-95M-i4096" ++device="cuda"
- name: Fine-tune Geneformer v2
run: |
python examples/fine_tune_models/fine_tune_geneformer.py ++model_name="gf-12L-30M-i2048" ++device="cuda"
- name: Execute scGPT
run: |
python examples/run_models/run_scgpt.py ++device="cuda"
- name: Fine-tune scGPT
run: |
python examples/fine_tune_models/fine_tune_scgpt.py ++device="cuda"
- name: Execute UCE
run: |
python examples/run_models/run_uce.py ++device="cuda"
- name: Fine-tune UCE
run: |
python examples/fine_tune_models/fine_tune_UCE.py ++device="cuda"
- name: Execute Hyena
run: |
python examples/run_models/run_hyena_dna.py ++device="cuda"
- name: Fine-tune Hyena
run: |
python examples/fine_tune_models/fine_tune_hyena_dna.py ++device="cuda"
- name: Execute Helix-mRNA
run: |
python examples/run_models/run_helix_mrna.py ++device="cuda"
- name: Fine-tune Helix-mRNA
run: |
python examples/fine_tune_models/fine_tune_helix_mrna.py ++device="cuda"
- name: Execute Mamba2-mRNA
run: |
python examples/run_models/run_mamba2_mrna.py ++device="cuda"
- name: Fine-tune Mamba2-mRNA
run: |
python examples/fine_tune_models/fine_tune_mamba2_mrna.py ++device="cuda"
- name: Execute Caduceus
run: |
python examples/run_models/run_caduceus.py
- name: Fine-tune Caduceus
run: |
python examples/fine_tune_models/fine_tune_caduceus.py
notebooks:
needs: tests
runs-on: self-hosted
env:
CUDA_VISIBLE_DEVICES: 0
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: setup python
uses: actions/setup-python@v5
with:
python-version: 3.11.8
# because jobs may not be run in the same order, we need to install the dependencies again
- name: Install helical
run: |
pip install .[mamba-ssm]
- name: Reduce datasets to speedup checks
run: |
sed -i 's/train\[:65%\]/train\[:5%\]/g' ./examples/notebooks/Cell-Type-Annotation.ipynb
sed -i 's/train\[70%:\]/train\[5%:7%\]/g' ./examples/notebooks/Cell-Type-Annotation.ipynb
sed -i 's/get_anndata_from_hf_dataset(ds\[\\"train\\"\])/get_anndata_from_hf_dataset(ds\[\\"train\\"\])[:100]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
sed -i 's/get_anndata_from_hf_dataset(ds\[\\"test\\"\])/get_anndata_from_hf_dataset(ds\[\\"test\\"\])[:10]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
sed -i 's/list(np.array(train_dataset.obs\[\\"LVL1\\"].tolist()))/list(np.array(train_dataset.obs\[\\"LVL1\\"].tolist()))[:100]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
sed -i 's/list(np.array(test_dataset.obs\[\\"LVL1\\"].tolist()))/list(np.array(test_dataset.obs\[\\"LVL1\\"].tolist()))[:10]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
- name: Run Notebooks
run: |
pytest --durations=0 --nbmake ./examples/notebooks/*.ipynb
release:
needs: notebooks
runs-on: self-hosted
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: setup python
uses: actions/setup-python@v5
with:
python-version: 3.11.8
- name: Install dependencies
run: |
pip install build
- name: Extract version
id: get_version
run: |
# Extract version from pyproject.toml (or adjust for your version file)
VERSION=$(grep "version =" pyproject.toml | cut -d '"' -f 2)
echo "::set-output name=version::$VERSION"
- name: Check if tag exists
id: check_tag
run: |
if git rev-parse "v${{ steps.get_version.outputs.version }}" >/dev/null 2>&1; then
echo "Tag v${{ steps.get_version.outputs.version }} already exists."
exit 1
fi
- name: Create Git tag
if: steps.check_tag.outcome == 'success'
run: |
git config user.name "github-actions"
git config user.email "github-actions@github.com"
git tag "v${{ steps.get_version.outputs.version }}"
git push origin "v${{ steps.get_version.outputs.version }}"
- name: Build package
run: python -m build
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }}