Merge pull request #5 from quadbio/notebook_and_tests

Notebook and tests

.github/workflows/build.yaml

@@ -0,0 +1,29 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -0,0 +1,67 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.12"
+          - os: ubuntu-latest
+            python: "3.12"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

analysis/[INITIALS]-[DATE]_sample_notebook.ipynb

@@ -50,23 +50,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2021-05-31T09:25:02.307098Z",
      "start_time": "2021-05-31T09:25:02.291254Z"
     }
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "The autoreload extension is already loaded. To reload it, use:\n",
-      "  %reload_ext autoreload\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%load_ext autoreload\n",
     "%autoreload 2"
@@ -81,7 +72,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2021-05-31T09:25:05.984402Z",
@@ -91,33 +82,7 @@
    },
    "outputs": [],
    "source": [
-    "# import single-cell packages\n",
-    "import scanpy as sc\n",
-    "from fancypackage.ul import DATA_DIR, FIG_DIR"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Print package versions. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Running Scanpy 1.10.3, on 2024-10-16 17:32.\n"
-     ]
-    }
-   ],
-   "source": [
-    "sc.logging.print_version_and_date()"
+    "from fancypackage.ul import DATA_DIR"
    ]
   },
   {
@@ -128,13 +93,10 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 5,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "sc.settings.figdir = str(FIG_DIR)\n",
-    "sc.settings.set_figure_params(dpi=100, dpi_save=300, frameon=False)"
+    "Define constants etc. here. "
    ]
   },
   {
@@ -167,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -189,6 +151,11 @@
     "## Main analysis"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

tests/test_basic.py

@@ -0,0 +1,12 @@
+import pytest
+
+import fancypackage
+
+
+def test_package_has_version():
+    assert fancypackage.__version__ is not None
+
+
+@pytest.mark.skip(reason="This decorator should be removed when test passes.")
+def test_example():
+    assert 1 == 0  # This test is designed to fail.