Merge pull request #40 from ArcInstitute/setup-ci

Setup ci

Author: noamteyssier

.github/workflows/ci.yml

@@ -0,0 +1,93 @@
+name: "CI"
+
+on: [push, pull_request]
+
+jobs:
+  all_jobs:
+    runs-on: ubuntu-latest
+    needs: [formatting, type-checking, pytest]
+    steps:
+      - name: Complete
+        run: echo "Complete"
+
+  install-job:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+  formatting:
+    runs-on: ubuntu-latest
+
+    needs: [install-job]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: run formatting
+        run: |
+          uv run ruff format --check
+
+  type-checking:
+    runs-on: ubuntu-latest
+
+    needs: [install-job]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: run type checking
+        run: |
+          uv run ty check
+
+  pytest:
+    runs-on: ubuntu-latest
+
+    needs: [install-job]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: run pytest
+        run: |
+          uv run pytest -v

.github/workflows/release.yml

@@ -0,0 +1,32 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write # Required for trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install build dependencies
+        run: uv sync --all-extras
+
+      - name: Build the project
+        run: uv build
+
+      - name: Publish to PyPI
+        run: uv publish

pyproject.toml

@@ -36,4 +36,5 @@ dev = [
     "marimo>=0.16.5",
     "pytest>=8.4.2",
     "ruff>=0.12.9",
+    "ty>=0.0.16",
 ]

src/pycyto/__main__.py

@@ -56,7 +56,9 @@ def convert(
     adata = convert_mtx_to_anndata(
         mtx_path, feature_path, barcode_path, dtype="int32" if integer else "float32"
     )
-    adata.write(output, compression="gzip" if compress else None)
+    adata.write(  # type: ignore[misc]
+        filename=output, compression="gzip" if compress else None
+    )
 
 
 @app.command()

src/pycyto/aggregate.py

@@ -32,11 +32,11 @@ def _write_h5ad(
     sample: str,
     compress: bool = False,
     mode: str = "gex",
-):
+) -> None:
     adata.obs_names_make_unique()  # always make unique
-    output_path = os.path.join(sample_outdir, f"{sample}_{mode}.h5ad")
-    adata.write_h5ad(
-        output_path,
+    output_path: str = os.path.join(sample_outdir, f"{sample}_{mode}.h5ad")
+    adata.write_h5ad(  # type: ignore[misc]
+        filename=output_path,
         compression="gzip" if compress else None,
     )
     logger.debug(

src/pycyto/convert.py

@@ -57,13 +57,13 @@ def convert_mtx_to_anndata(
         feature_path, sep="\t", header=None, index_col=0
     ).index.astype(str)
     features.name = "feature"
-    adata.obs_names = features  # type: ignore
+    adata.obs_names = features
 
     barcodes = pd.read_csv(
         barcode_path, sep="\t", header=None, index_col=0
     ).index.astype(str)
     barcodes.name = "barcode"
-    adata.var_names = barcodes  # type: ignore
+    adata.var_names = barcodes
 
     # convert to cell x gene
     adata = adata.T