Merge pull request #118 from helicalAI/include-release-build

Include release build

.github/workflows/main.yml

@@ -4,7 +4,6 @@ on:
   pull_request:
     branches:
       - main
-      - release
 
 jobs:
   tests:

.github/workflows/release.yml

@@ -0,0 +1,144 @@
+name: Release
+
+on:
+  pull_request:
+    branches:
+      - release
+
+permissions:
+  contents: write
+
+jobs:
+  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 .
+            
+      # 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: |
+          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/
+
+      # Does not seem to work but would be nice to have
+      # - name: Pytest coverage comment
+      #   uses: MishaKav/pytest-coverage-comment@main
+      #   with:
+      #     pytest-coverage-path: ./pytest-coverage.txt
+      #     junitxml-path: ./pytest.xml
+
+
+      - name: Execute Geneformer v1
+        run: |
+          python examples/run_models/run_geneformer.py ++model_name="gf-12L-30M-i2048"
+
+      - name: Execute Geneformer v2
+        run: |
+          python examples/run_models/run_geneformer.py ++model_name="gf-12L-95M-i4096"
+
+      - name: Execute scGPT
+        run: |
+          python examples/run_models/run_scgpt.py
+
+      - name: Execute UCE
+        run: |
+          python examples/run_models/run_uce.py
+
+      - name: Execute Hyena
+        run: |
+          python examples/run_models/run_hyena_dna.py
+
+      - name: Execute benchmarking
+        run: |
+          pip install scanorama
+          python examples/run_benchmark.py
+
+  notebooks:
+    needs: 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
+            
+      - 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: Install dependencies
+        run: |
+          pip install build
+
+      - name: Extract version
+        id: get_version
+        run: |
+          # Extract version from setup.py (or adjust for your version file)
+          VERSION=$(python setup.py --version)
+          echo "::set-output name=version::$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 "[email protected]"
+          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 }}
+

setup.py

@@ -1,10 +1,7 @@
 from setuptools import setup, find_packages
-# from helical.version import __version__
 
 setup(
     name='helical',
-    # version=__version__,
-
     url='https://github.com/helicalAI/helical-package.git',
     author='Benoit Putzeys, Maxime Allard',
     author_email='[email protected], [email protected]',