add more tests

.github/actions/build-docs/action.yml

@@ -10,33 +10,38 @@ runs:
   using: "composite"
   steps:
   - name: Install dependency
+    shell: bash
     run: |
       sudo apt-get install -y pandoc jq
       pip install --user sphinx==7.* pydata-sphinx-theme==0.15.* pandoc nbsphinx \
         Pygments==2.16.* sphinx-autodoc-typehints myst-parser \
         markupsafe==2.1.* sphinx-plotly-directive
 
   - name: Build doc
+    shell: bash
     run: sphinx-build ${GITHUB_WORKSPACE}/docs _build/html
 
   - name: Get SnapATAC2 version
     id: get_version
+    shell: bash
     run: |
       VERSION_NUMBER=$(python -c "import snapatac2;print('.'.join(snapatac2.__version__.split('.')[:2]))")
       echo $VERSION_NUMBER
       echo "VERSION=$VERSION_NUMBER" >> $GITHUB_ENV
       IS_DEV=$(python -c "import snapatac2;print('dev' in snapatac2.__version__)")
-      echo $IS_DEV
-      BRANCH_NAME=${{ github.event.workflow_run.head_branch }}
-      if [[ $IS_DEV == "True" && $BRANCH_NAME == "main" ]]; then
-        echo "DEPLOY_DEV=true" >> $GITHUB_ENV
-      elif [[ $BRANCH_NAME =~ ^v[0-9]+ || $BRANCH_NAME == "main" ]]; then
-        echo "DEPLOY_VERSION=true" >> $GITHUB_ENV
+      if [[ $IS_DEV == "True" ]]; then
+        echo "DEPLOYMENT=dev" >> $GITHUB_ENV
+      else
+        echo "DEPLOYMENT=stable" >> $GITHUB_ENV
       fi
+      echo "============================== Info ================================"
+      echo "DEPLOYMENT=${{ env.DEPLOYMENT }}"
+      echo "VERSION=${{ env.VERSION }}"
+      echo "===================================================================="
 
   - name: Deploy 🚀
     uses: JamesIves/github-pages-deploy-action@v4
-    if: ${{ env.DEPLOY_DEV == 'true' }}
+    if: ${{ env.DEPLOYMENT == 'dev' }}
     with:
       single-commit: true
       branch: gh-pages
@@ -46,7 +51,7 @@ runs:
 
   - name: Deploy (version) 🚀
     uses: JamesIves/github-pages-deploy-action@v4
-    if: ${{ env.DEPLOY_VERSION == 'true' }}
+    if: ${{ env.DEPLOYMENT == 'stable' }}
     with:
       single-commit: true
       branch: gh-pages
@@ -55,6 +60,7 @@ runs:
       target-folder: /version/${{ env.VERSION }}/
 
   - name: Fetch JSON and Get Preferred Version
+    shell: bash
     run: |
       #JSON=$(cat ${GITHUB_WORKSPACE}/docs/_static/versions.json)
       JSON=$(curl -s "https://raw.githubusercontent.com/kaizhang/SnapATAC2/main/docs/_static/versions.json")

.github/workflows/test_python.yml

@@ -21,23 +21,16 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --user --upgrade pip
-        pip install --user coverage pytest hypothesis==6.72.4 wheel
+        pip install --user pytest hypothesis==6.72.4 wheel
 
-    - name: Build wheel files
+    - name: Build Python package
       run: |
         cd ${GITHUB_WORKSPACE}/snapatac2-python
-        mkdir ${GITHUB_WORKSPACE}/wheel_files
-        pip wheel . --wheel-dir ${GITHUB_WORKSPACE}/wheel_files
-
-    - name: Test Python package
-      run: |
-        pip install --user ${GITHUB_WORKSPACE}/wheel_files/*.whl
-        coverage run -m pytest ${GITHUB_WORKSPACE}/snapatac2-python/tests
+        pip install --user .
+        pytest tests
 
     - uses: ./.github/actions/build-docs
-
-    - name: Upload Coverage to Codecov
-      uses: codecov/codecov-action@v3
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
 
   build-wheel:
     needs: build-and-test

snapatac2-python/tests/test_tools.py

@@ -140,3 +140,23 @@ def test_import(datadir):
         outputs = snap.ex.export_fragments(data, groupby="group", out_dir=str(datadir), suffix='.bed.gz')
 
         assert read_bed(list(outputs.values())[0]) == read_bed(fl)
+
+def test_tile_matrix(datadir):
+    def total_count(adata, bin_size):
+        return snap.pp.add_tile_matrix(
+            adata,
+            bin_size=bin_size,
+            inplace=False,
+            counting_strategy='insertion',
+            ).X.sum()
+
+    data = snap.pp.import_data(
+        snap.datasets.pbmc500(downsample=True),
+        chrom_sizes=snap.genome.hg38,
+        min_num_fragments=0,
+        sorted_by_barcode=False,
+    )
+
+    counts = [total_count(data, i) for i in [500, 1000, 5000, 10000]]
+    for i in range(1, len(counts)):
+        assert counts[i] == counts[i - 1], f"Bin size {i} failed"