Adding testing to the CI.

.github/workflows/ci.yml

@@ -16,16 +16,28 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
-      - run: |
+      # Run Ruff
+      - name: Run Ruff
+        run: |
           pip install uv
           uv pip install --system ruff
           ruff check
+      # Run Codespell
+      - name: Run Codespell
+        run: |
+          pip install codespell
+          codespell codespell src/**/*.py
 
   Test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os:
+          - ubuntu-latest
+          - macos-latest # arm64 (Apple Silicon)
+          - macos-13 # latest Intel release
+          - windows-latest
 
     steps:
       - uses: actions/checkout@v4
@@ -37,9 +49,70 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - run: |
-          pipx install hatch
-          hatch run test
-
+          pip install pytest-notebook
+          pip install pre-commit
+          pre-commit run --all
+          pre-commit install
+      # pipx install hatch
+      # hatch run test --cover --nb-test-files
+      - name: Install IPyNiiVue & Deps
+        run: pip install -e .
+      - name: Test import
+        run: |
+          python -c "import ipyniivue"
+      - name: Test IPyNiiVue
+        run: |
+          pip install pytest-cov
+          pip install --upgrade pip ipython ipykernel
+          ipython kernel install --name "python3" --user
+          mkdir -p ./reports
+          pytest --cov --cov-report=json:./reports/coverage.json --cov-report=xml:./reports/coverage.xml
+      - name: Upload ipyniivue test coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage_ipyniivue-${{ matrix.os }}-py${{ matrix.python-version }}
+          path: ./reports/coverage.json
+      - name: Generate Markdown summary of code coverage
+        uses: irongut/[email protected]
+        with:
+          filename: ./reports/coverage.xml
+          format: markdown
+          output: both
+          thresholds: "10 10"
+      - name: Add test results to job summary
+        run: |
+          cat ./code-coverage-results.md >> $GITHUB_STEP_SUMMARY
+      - name: Test example notebooks
+        run: |
+          pip install nbmake
+          rm -rf ./reports
+          mkdir -p ./reports
+          pytest --nbmake examples/*ipynb --cov --cov-report=json:./reports/coverage.json --cov-report=xml:./reports/coverage.xml
+      - name: Upload ipyniivue example notbooks coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage_ipyniivue_notebooks-${{ matrix.os }}-py${{ matrix.python-version }}
+          path: ./reports/coverage.json
+      - name: Generate Markdown summary of code coverage
+        uses: irongut/[email protected]
+        with:
+          filename: ./reports/coverage.xml
+          format: markdown
+          output: both
+          thresholds: "10 10"
+      - name: Add test results to job summary
+        run: |
+          cat ./code-coverage-results.md >> $GITHUB_STEP_SUMMARY
+      #     coverage run -m pytest  --nb-test-files
+      # nbt-test-files check for changes in the output of the notebook.
+      # This does not work for our purpose since we wipe the output
+      # before committing changes to facilitate integration with git.
+      # - name: Upload coverage to codecov (Only do this for the ubuntu-latest job)
+      #   if: matrix.os == 'ubuntu-latest'
+      #   uses: codecov/codecov-action@v5
+      #   with:
+      #     token: ${{secrets.CODECOV_TOKEN}}
+      #
   LintJavaScript:
     name: JavaScript / Lint
     runs-on: macos-14

examples/additive_voxels.ipynb

@@ -92,8 +92,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

examples/basic_multiplanar.ipynb

@@ -78,13 +78,6 @@
     "nv.is_colorbar = True\n",
     "nv.view_mode_hot_key = \"KeyN\""
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -102,8 +95,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/drawing.ipynb

@@ -109,14 +109,6 @@
     "for widget in widgetArray:\n",
     "    display(widget[\"widget\"])"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "32e9b296-bae2-47c4-9912-e99e5cb6a85e",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -134,8 +126,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/example_sideview.ipynb

@@ -1,5 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "52de1125",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# This is not part of IPyNiiVue dependencies so it has to be installed independently\n",
+    "!pip install ipylab"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -81,14 +92,6 @@
     "nv.volumes[0].opacity = 0.5\n",
     "nv.volumes[1].colormap = \"green\""
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c7b34b44-2940-4f0e-99b5-2e16ad3d23f3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -106,8 +109,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

examples/mesh_and_volume.ipynb

@@ -63,14 +63,6 @@
     "\n",
     "nv"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "851a559d-59e8-40bc-b1f0-9380f9844855",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -88,8 +80,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/mesh_layers.ipynb

@@ -89,8 +89,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "pygments_lexer": "ipython3"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

examples/prototypes/meshes_(GIfTI, FreeSurfer, MZ3, OBJ, STL, legacy VTK).ipynb

@@ -53,13 +53,6 @@
     "\n",
     "# nv1.setMeshShader(nv1.meshes[0].id, \"Outline\"); does not seem to exist yet."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -77,8 +70,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/prototypes/torso_regions.ipynb

@@ -83,14 +83,6 @@
     "}\n",
     "nv.setDrawColormap(cmap);"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "94a1c95a-308b-4259-ac29-7512c48239b2",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -108,8 +100,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/prototypes/trajectory.ipynb

@@ -61,13 +61,6 @@
     "\n",
     "nv"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -85,8 +78,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

examples/widgets.ipynb

@@ -71,7 +71,7 @@
     "        value=3,\n",
     "        description=\"Slice Type:\",\n",
     "    ),\n",
-    "    \"object\": nv,\n",
+    "    \"obj\": nv,\n",
     "    \"attribute\": \"slice_type\",\n",
     "}\n",
     "widgetArray.append(widget_slice_type)\n",
@@ -85,7 +85,7 @@
     "        description=\"Scan Opacity:\",\n",
     "        orientation=\"horizontal\",\n",
     "    ),\n",
-    "    \"object\": nv.volumes[0],\n",
+    "    \"obj\": nv.volumes[0],\n",
     "    \"attribute\": \"opacity\",\n",
     "}\n",
     "widgetArray.append(widget_scan_opacity)\n",
@@ -99,7 +99,7 @@
     "        description=\"Hippocampus Opacity:\",\n",
     "        orientation=\"horizontal\",\n",
     "    ),\n",
-    "    \"object\": nv.volumes[1],\n",
+    "    \"obj\": nv.volumes[1],\n",
     "    \"attribute\": \"opacity\",\n",
     "}\n",
     "widgetArray.append(widget_hippo_opacity)\n",
@@ -110,7 +110,7 @@
     "        value=\"Gray\",\n",
     "        description=\"Scan Colormap:\",\n",
     "    ),\n",
-    "    \"object\": nv.volumes[0],\n",
+    "    \"obj\": nv.volumes[0],\n",
     "    \"attribute\": \"colormap\",\n",
     "}\n",
     "widgetArray.append(widget_scan_colormap)\n",
@@ -121,7 +121,7 @@
     "        value=\"Red\",\n",
     "        description=\"Hippocampus Colormap:\",\n",
     "    ),\n",
-    "    \"object\": nv.volumes[1],\n",
+    "    \"obj\": nv.volumes[1],\n",
     "    \"attribute\": \"colormap\",\n",
     "}\n",
     "widgetArray.append(widget_hippo_colormap)\n",
@@ -150,14 +150,6 @@
     "for widget in widgetArray:\n",
     "    display(widget[\"widget\"])"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4c94695d-b936-472e-a4f1-7dc216833388",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -175,8 +167,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,