add notebook tests

cbouy · Dec 22, 2023 · ea4a6cd · ea4a6cd
1 parent 8bff942
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -22,17 +22,18 @@ jobs:
 
     - name: Get prerelease version tags
       if: env.IS_PRERELEASE == 'true'
+      id: prerelease-check
       run: |
         py_dirty_tag=$(awk '/__version__ = "[[:digit:]+]\.[[:digit:]+]\.[[:digit:]+]\-.+"/ {print $3}' ./mols2grid/_version.py)
         py_is_pre=$(test -z "$py_dirty_tag" && echo "false" || echo "true")
         js_version_string=$(grep '"version":' ./package.json)
         js_dirty_tag=$(echo "$js_version_string" | cut -d- -f2)
         js_is_pre=$(test "$js_version_string" == "$js_dirty_tag" && echo "false" || echo "true")
-        echo "py_is_pre=$py_is_pre" >> $GITHUB_ENV
-        echo "js_is_pre=$js_is_pre" >> $GITHUB_ENV
+        echo "py=$py_is_pre" >> $GITHUB_OUTPUT
+        echo "js=$js_is_pre" >> $GITHUB_OUTPUT
 
     - name: Fail if prerelease is not correctly versioned
-      if: (env.IS_PRERELEASE == 'true') && !( env.py_is_pre && env.js_is_pre )
+      if: (env.IS_PRERELEASE == 'true') && !( steps.prerelease-check.outputs.py && steps.prerelease-check.outputs.js )
       uses: actions/github-script@v3
       with:
         script: |

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,32 +19,20 @@ concurrency:
 jobs:
   tests:
     name: ${{ matrix.label }}
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         include:
-          - label: CI-old
-            os: ubuntu-latest
+          - label: rdkit-2021
             python-version: 3.8
-            extra_dependencies: "rdkit==2020.03.1 boost-cpp=1.72.0=h359cf19_6"
-          - label: CI-edge
-            os: ubuntu-latest
+            extra_dependencies: "rdkit==2021.03.1"
+          - label: rdkit-latest
             python-version: "3.10"
             extra_dependencies: "rdkit"
-          - label: CI-py3.9-rdkit2022
-            os: ubuntu-latest
-            python-version: 3.9
-            extra_dependencies: "rdkit==2022.03.1"
 
     steps:
       - uses: actions/checkout@v3
 
-      - name: Install node
-        uses: actions/setup-node@v3
-        with:
-          node-version: 18
-          cache: "yarn"
-
       - name: Install Firefox
         uses: browser-actions/setup-firefox@latest
 
@@ -64,14 +52,26 @@ jobs:
         with:
           path: ~/conda_pkgs_dir
           key:
-            conda-${{ hashFiles('environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
+            conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
 
       - name: Cache pip
         uses: actions/cache@v3
         with:
           path: ~/.cache/pip
-          key: pip-${{ hashFiles('setup.cfg') }}
+          key: pip-${{ hashFiles('pyproject.toml') }}
           restore-keys: pip-
+
+      - name: Get yarn cache directory path
+        id: yarn-cache-dir-path
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
+
+      - name: Cache yarn
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
+          key: yarn-${{ hashFiles('yarn.lock') }}
+          restore-keys: |
+            yarn-
 
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -93,13 +93,15 @@ jobs:
 
       - name: Install remaining conda dependencies
         run: |
-          mamba install ${{ matrix.extra_dependencies }}
+          mamba install 'jupyterlab>=3,<5' ipywidgets=8 ${{ matrix.extra_dependencies }}
           mamba list
 
-      - name: Install package through pip
+      - name: Build and install package
         run: |
           pip install .[tests,build]
+          jupyter labextension develop . --overwrite
           pip list
+          jupyter labextension list
       
       - name: Run tests
         run: |
@@ -143,3 +145,106 @@ jobs:
         run: |
           pip install dist/mols2grid-*.whl
           python test_install.py
+
+  notebook-tests:
+    name: ${{ matrix.label }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - label: JLab-3-Widgets-7
+            extra_dependencies: "jupyterlab>=3.2 ipywidgets=7"
+          - label: JLab-4-Widgets-8
+            extra_dependencies: "jupyterlab=4 ipywidgets=8"
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Cache conda
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
+
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-${{ hashFiles('pyproject.toml') }}
+          restore-keys: pip-
+
+      - name: Get yarn cache directory path
+        id: yarn-ui-cache-dir-path
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
+
+      - name: Cache yarn
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.yarn-ui-cache-dir-path.outputs.dir }}
+          key: yarn-ui-${{ hashFiles('tests/notebooks/yarn.lock') }}
+          restore-keys: |
+            yarn-ui-
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: "3.10"
+          environment-file: tests/environment.yml
+          use-only-tar-bz2: true
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+
+      - name: Install remaining conda dependencies
+        run: |
+          mamba install rdkit jupyter-packaging~=0.10 ${{ matrix.extra_dependencies }}
+          mamba list
+
+      - name: Build the extension
+        run: |
+          pip install -e .[build]
+          jupyter labextension develop . --overwrite
+          jupyter labextension list
+
+      - name: Install Test Dependencies
+        run: |
+          npm install
+          npx playwright install chromium
+        working-directory: tests/notebooks
+
+      - name: Execute integration tests
+        working-directory: tests/notebooks
+        run: |
+          npx playwright test
+
+      - name: Upload Playwright Test assets
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: notebooks-test-assets
+          path: |
+            tests/notebooks/test-results
+
+      - name: Upload Playwright Test report
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: notebooks-test-report
+          path: |
+            tests/notebooks/playwright-report
+
+      - name: Update snapshots
+        if: failure()
+        working-directory: tests/notebooks
+        run: |
+          jlpm test:update
+
+      - name: Upload updated snapshots
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: notebook-updated-snapshots
+          path: tests/notebooks/tests
diff --git a/.gitignore b/.gitignore
@@ -127,10 +127,7 @@ dist
 .vscode-test
 
 # yarn v2
-.yarn/cache
-.yarn/unplugged
-.yarn/build-state.yml
-.yarn/install-state.gz
+**/.yarn/
 .pnp.*
 
 ### Node Patch ###
@@ -369,10 +366,16 @@ $RECYCLE.BIN/
 # -------------
 **/coverage/
 
+# UI-tests
+# --------
+tests/notebooks/test-results
+tests/notebooks/playwright-report
+
 # ======
 # Custom
 # ======
 
+.yarnrc.yml
 mols2grid/nbextension/index.*
 mols2grid/labextension
 .vscode/

diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
@@ -1,15 +1,22 @@
+# Dev guide
+
 This is a short guide to setup a dev environment for mols2grid.
 
+## Installation
+
 1. Install conda or mamba
-2. Create a new environment. Python 3.7+ (prefer 3.8):
+2. Create a new environment. Python 3.8+ (prefer 3.10):
    ```
    conda env create --name mols2grid --file docs/environment.yml
    ```
-3. Install all the package dependencies in editable mode:
+3. Install the package in editable mode:
    ```
    pip install -e .[dev]
+   jupyter labextension develop . --overwrite
    ```
 
+## Tests
+
 To run tests locally:
 - Install Firefox (needed for UI testing)
 - Test your installation:
@@ -19,15 +26,34 @@ To run tests locally:
 - You can select/skip the UI testing by specifying the `webdriver` mark in the pytest
   command: `-m webdriver` to select UI tests only, or `-m "not webdriver"` to skip them.
 
+### Notebook test
+
+The CI pipeline contains an additional test that runs a simple notebook (see [](tests/notebooks/))
+to make sure that there are no issues with the widget and the different versions of JupyterLab and
+IPywidgets. This test requires the version of the package to **NOT** be a prerelease and thus the
+versions in [](package.json) and [](mols2grid/_version.py) should strictly follow the `X.Y.Z` scheme
+(i.e. no `X.Y.Z-a1`).
+
+If this pipeline fails, the CI will automatically produce an artifact named
+`notebook-updated-snapshots` containing the captures that were produced while running the test.
+Review these snapshots and if they seem correct, commit them to the
+[](tests/notebooks/tests/mols2grid.test.ts-snapshots) directory.
+
+## Formatting
+
 We use `black` and `isort` for formatting so either install the corresponding extension
 from your IDE or install the package with `pip install black isort`. The configuration
 is done inside the `pyproject.toml` file.
 
+## Pull requests
+
 Making a pull request will automatically run the tests and documentation build for you.
 Don't forget to update the `CHANGELOG.md` file with your changes.
 
+## Release
+
 For versioning, you'll have to update both `package.json` and `mols2grid/_version.py`
-files.
+files (but this should be done by a maintainer directly).
 
 The build and deployment process is run automatically when making a release on
 GitHub.

diff --git a/docs/contents.md b/docs/contents.md
@@ -17,21 +17,35 @@
 
 # 🐍 Installation
 ---
-
-mols2grid was developped for Python 3.7+ and requires rdkit (>=2020.03.1), pandas and jinja2 as dependencies.  
-The easiest way to install it is from conda:
+
+The easiest way to install `mols2grid` is from conda:
 ```shell
 conda install -c conda-forge mols2grid
 ```
 
 Alternatively, you can also use pip:
 ```shell
-pip install rdkit mols2grid
+pip install 'mols2grid[rdkit]'
+```
+
+## Troubleshooting
+
+If you see a JavaScript error message such as:
+```text
+Failed to load model class 'MolGridModel' from module 'mols2grid'
+Error: Module mols2grid, version XXX is not registered, however, YYY is
+```
+
+Or if you notice that the selections, callbacks and interactive filtering aren't working as intended, you may have to manually activate the extension:
+
+```shell
+jupyter labextension enable mols2grid
 ```
 
-If you notice that the selections, callbacks and interactive filtering aren't working as intended, you may have to manually activate the extension:
-- for Jupyter Lab: `jupyter labextension install mols2grid`
-- for Jupyter Notebook: `jupyter nbextension install mols2grid`
+You should also make sure that you have installed compatible versions of `ipywidgets` and the
+`jupyterlab`/`notebook` stack. The following specs are currently supported:
+- `ipywidgets=7`, `jupyterlab=3`, `notebook=6`
+- `ipywidgets=8`, `jupyterlab=4`, `notebook=7`
 
 **Compatibility**
 

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -3,15 +3,12 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - ipykernel==6.26.0
-  - ipywidgets==7.8.0
-  - notebook<7.0.0
+  - ipywidgets=8
+  - notebook=7
   - mistune<3.0.0
-  - jedi==0.19.1
-  - jinja2==3.1.2
   - nbsphinx==0.8.8
-  - nodejs==18.18.2
-  - pandas==2.1.4
+  - nodejs==18.12.1
+  - pandas=2.1
   - rdkit==2023.09.3
   - recommonmark==0.7.1
   - sphinx==4.5.0

diff --git a/mols2grid/_version.py b/mols2grid/_version.py
@@ -1 +1 @@
-__version__ = "2.0.1-a2"
+__version__ = "2.0.1"
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "mols2grid",
-  "version": "2.0.1a2",
+  "version": "2.0.1",
   "description": "Custom widget for the Python mols2grid package",
   "keywords": [
     "jupyter",
@@ -54,7 +54,7 @@
   "devDependencies": {
     "@babel/core": "^7.5.0",
     "@babel/preset-env": "^7.5.0",
-    "@jupyterlab/builder": "^3.0.0",
+    "@jupyterlab/builder": "^4.0.0",
     "@lumino/application": "^1.6.0",
     "@lumino/widgets": "^1.6.0",
     "@types/jest": "^26.0.0",