chore: added make test-notebooks command and extended test.yml to run it

.github/workflows/test.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
 
-  uv-example:
+  python:
     name: python
     runs-on: ubuntu-latest
     strategy:
@@ -31,8 +31,31 @@ jobs:
         run: uv python install ${{ matrix.python-version }}
 
       - name: Install the project
-        run: uv sync --all-extras --dev
+        run: make install-tests
 
       - name: Run tests
         run: |
           uv run pytest tests
+
+  notebooks:
+    name: notebooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.7.4"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Install the project
+        run: make install-test-notebooks
+
+      - name: Run notebooks
+        run: |
+          make test-notebooks

Makefile

@@ -3,30 +3,41 @@ SHELL = /bin/bash
 .PHONY: help
 help:
 	@echo "Commands:"
-	@echo "install  : install dependencies into virtual environment."
-	@echo "install-dev  : install all, including dev, dependencies into virtual environment for local development."
-	@echo "update   : Install new requriements into the virtual environment."
-	@echo "test     : Run pytests."
-	@echo "coverage : Run pytest with coverage report"
+	@echo "install        : Install dependencies into virtual environment."
+	@echo "install-dev    : Install all, including dev, dependencies into virtual environment for local development."
+	@echo "update         : Install new requriements into the virtual environment."
+	@echo "test           : Run pytests."
+	@echo "test-notebooks : Execute all notebooks in nbs/."
+	@echo "coverage       : Run pytest with coverage report"
 
 
-.PHONY: install
-install:
+.PHONY: install-tests
+install-tests:
 	uv sync
 
+.PHONY: install-test-notebooks
+install-test-notebooks:
+	uv sync --group nb
+
 .PHONY: install-dev
 install-dev:
-	uv sync --all-extras --dev && \
+	uv sync --all-extras && \
 	uv run pre-commit install
 
 .PHONY: update
 update:
-	uv sync --reinstall
+	uv sync --reinstall --group dev
 
 .PHONY: test
 test:
 	uv run pytest -vx tests
 
+.PHONY: test-notebooks
+test-notebooks:
+	set -e; for notebook in nbs/core/*.ipynb; do \
+		uv run jupyter execute --timeout=60 "$$notebook"; \
+	done
+
 .PHONY: coverage
 coverage:
 	uv run pytest --cov=src --cov-report html tests

README.md

@@ -6,7 +6,9 @@
 
 * `src/random_tree_models/` -> python implementation of tree algorithms
 * `tests/` -> unit tests
-* `nbs/` -> jupyter notebooks to play with the tree algorithms
+* `nbs/`
+  * `nbs/core` -> core jupyter notebooks to play with the tree algorithms
+  * `nbs/dev` -> other jupyter notebooks for other activities
 * `config/` -> requirements.txt
 
 ## setup

nbs/xgboost-profiling-histogramming-yay-or-nay.ipynb → nbs/dev/xgboost-profiling-histogramming-yay-or-nay.ipynb

@@ -112,9 +112,7 @@
     ") -> pd.DataFrame:\n",
     "    execution_stats = []\n",
     "\n",
-    "    for n_samples, n_features in itertools.product(\n",
-    "        n_samples_arr, n_features_arr\n",
-    "    ):\n",
+    "    for n_samples, n_features in itertools.product(n_samples_arr, n_features_arr):\n",
     "        X, y = sk_datasets.make_classification(\n",
     "            n_samples=n_samples,\n",
     "            n_features=n_features,\n",
@@ -125,9 +123,7 @@
     "        )\n",
     "        # sns.scatterplot(x=X[:, 0], y=X[:, 1], hue=y, alpha=0.3);\n",
     "\n",
-    "        model = xgboost.XGBoostClassifier(\n",
-    "            use_hist=use_hist, n_bins=n_bins, max_depth=4\n",
-    "        )\n",
+    "        model = xgboost.XGBoostClassifier(use_hist=use_hist, n_bins=n_bins, max_depth=4)\n",
     "\n",
     "        t0 = time.time()\n",
     "        model.fit(X, y)\n",
@@ -240,9 +236,7 @@
     ")\n",
     "ax.set(title=\"score\", ylabel=\"score [roc auc]\")\n",
     "\n",
-    "plt.suptitle(\n",
-    "    \"Time DecisionTreeClassifier.* took based on n_samples and n_features\"\n",
-    ")\n",
+    "plt.suptitle(\"Time DecisionTreeClassifier.* took based on n_samples and n_features\")\n",
     "plt.tight_layout()"
    ]
   },
@@ -315,9 +309,7 @@
     ") -> pd.DataFrame:\n",
     "    execution_stats = []\n",
     "\n",
-    "    for n_samples, n_features in itertools.product(\n",
-    "        n_samples_arr, n_features_arr\n",
-    "    ):\n",
+    "    for n_samples, n_features in itertools.product(n_samples_arr, n_features_arr):\n",
     "        X, y = sk_datasets.make_classification(\n",
     "            n_samples=n_samples,\n",
     "            n_features=n_features,\n",
@@ -328,9 +320,7 @@
     "        )\n",
     "        # sns.scatterplot(x=X[:, 0], y=X[:, 1], hue=y, alpha=0.3);\n",
     "\n",
-    "        model = xgboost.XGBoostRegressor(\n",
-    "            use_hist=use_hist, n_bins=n_bins, max_depth=4\n",
-    "        )\n",
+    "        model = xgboost.XGBoostRegressor(use_hist=use_hist, n_bins=n_bins, max_depth=4)\n",
     "\n",
     "        t0 = time.time()\n",
     "        model.fit(X, y)\n",
@@ -444,9 +434,7 @@
     ")\n",
     "ax.set(title=\"score\", ylabel=\"score [mse]\")\n",
     "\n",
-    "plt.suptitle(\n",
-    "    \"Time DecisionTreeRegressor.* took based on n_samples and n_features\"\n",
-    ")\n",
+    "plt.suptitle(\"Time DecisionTreeRegressor.* took based on n_samples and n_features\")\n",
     "plt.tight_layout()"
    ]
   },
@@ -501,11 +489,6 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": ".venv",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",

pyproject.toml

@@ -13,12 +13,14 @@ dependencies = [
     "rich>=13.3.5",
     "scikit-learn>=1.2.2",
     "seaborn>=0.12.2",
-
 ]
 
 [project.scripts]
 random-tree-models = "random_tree_models:main"
 
+[tool.uv]
+default-groups = ["test"]
+
 [tool.maturin]
 module-name = "random_tree_models._core"
 python-packages = ["random_tree_models"]
@@ -29,15 +31,19 @@ requires = ["maturin>=1.0,<2.0"]
 build-backend = "maturin"
 
 [dependency-groups]
-dev = [
+test = [
     "pytest>=7.3.1",
-    "black>=23.3.0",
+]
+nb = [
     "ipywidgets>=8.0.6",
-    "isort>=5.12.0",
     "jupyter-contrib-nbextensions>=0.7.0",
     "jupyterlab>=4.0.0",
+]
+dev = [
     "pre-commit>=3.3.2",
     "snakeviz>=2.2.0",
     "pip-audit>=2.9.0",
     "pytest-cov>=6.2.1",
+     {include-group = "nb"},
+     {include-group = "test"},
 ]