Tutorial propensity support

.github/workflows/tests.yml

@@ -0,0 +1,31 @@
+name: Tests
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run tests
+        run: pytest tests --tb=short

.gitignore

@@ -178,14 +178,19 @@ causarray/___*.py
 # committed documentation.
 /docs/source/tutorial/adamson/
 
-# Replogle tutorial: large data files (regenerate with prep_tutorial_data.py or
-# download from the project data repository; replogle_subset.h5ad is ~2 GB)
-docs/source/tutorial/replogle/replogle_subset.h5ad
-docs/source/tutorial/replogle/replogle_subset_norm*.h5ad
-docs/source/tutorial/replogle/replogle_normed.h5ad
-docs/source/tutorial/replogle/replogle_results.h5
-docs/source/tutorial/replogle/replogle_supt5h_go_*.csv
-docs/source/tutorial/replogle/replogle_propensity_batch12*
+# Replogle tutorial: prepared inputs under data/ and everything generated
+# under results/ are local artifacts; rebuild with the numbered scripts
+# (data/replogle_subset.h5ad is ~2 GB).
+docs/source/tutorial/replogle/data/
+docs/source/tutorial/replogle/results/**
+# the two small JIC tables are committed so the notebook runs without a refit
+!docs/source/tutorial/replogle/results/replogle-r.csv
+!docs/source/tutorial/replogle/results/replogle-r-legacy.csv
 
 # Unrelated tutorial directory (not part of causarray package docs)
 docs/source/tutorial/scp/
+
+# SCARF tutorial is currently a local analysis and is not part of the
+# committed documentation (it is absent from docs/source/index.rst).
+# Regenerate with the numbered scripts + SCARF-py.ipynb.
+/docs/source/tutorial/SCARF/