Merge pull request #96 from martinRenou/jlab4_lumino2_widgets8

JupyterLab 4 Lumino 2 and ipywidgets 8 update
twosigma · Nov 29, 2023 · 1d20c43 · 1d20c43
2 parents 1224973 + 89957e6
commit 1d20c43
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Showing 36 changed files with 16,662 additions and 9,283 deletions.
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -59,14 +59,12 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-conda-
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          activate-environment: beakerx_tabledisplay
+          environment-name: beakerx_tabledisplay
           environment-file: configuration.yml
-          auto-activate-base: false
           channels: conda-forge
-          miniconda-version: "latest"
 
       - name: Get yarn cache directory path
         id: yarn-cache-dir-path
@@ -89,23 +87,22 @@ jobs:
       - name: Install dependencies
         run: |
           set -eux
-          conda install jupyterlab=3 jupyter-packaging
 
           pip install beakerx_tabledisplay
           beakerx_tabledisplay install
 
       - name: Install browser
         working-directory: ui-tests
         run: |
-          yarn install
+          jlpm install
           # Install only Chromium browser
-          yarn playwright install chromium
+          jlpm playwright install chromium
 
       - name: Execute benchmark tests on reference
         continue-on-error: true
         working-directory: ui-tests
         run: |
-          yarn run test -u
+          jlpm run test -u
 
       # Second run the benchmark on the new reference
       - name: Checkout latest version
@@ -127,15 +124,15 @@ jobs:
       - name: Install browser
         working-directory: ui-tests
         run: |
-          yarn install
+          jlpm install
           # Install only Chromium browser
-          yarn playwright install chromium
+          jlpm playwright install chromium
 
       - name: Execute benchmark tests on PR
         continue-on-error: true
         working-directory: ui-tests
         run: |
-          yarn run test
+          jlpm run test
 
       - name: Generate the report
         env:

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -18,32 +18,15 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v2
 
-    - name: Cache Conda
-      uses: actions/cache@v1
+    - name: Install Conda environment with Micromamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        path: ~/.conda
-        key: ${{ runner.os }}-mconda-${{ hashFiles('**/configuration.yml') }}
-        restore-keys: |
-          ${{ runner.os }}-conda-
-
-    - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: beakerx_tabledisplay
+        environment-name: beakerx_tabledisplay
         environment-file: configuration.yml
-        auto-activate-base: false
         channels: conda-forge
-        miniconda-version: "latest"
-
-    - name: Verify conda version
-      shell: bash
-      run: conda --version
-
-    - name: Install build dependencies
-      run: conda install jupyterlab=3 jupyter-packaging
 
     - name: Build BeakerX tabledisplay
-      run: (cd beakerx_tabledisplay; pip install -e .)
+      run: (cd beakerx_tabledisplay; pip install .)
 
     - name: Check installation files (nbextension and lab3 extension)
       run: |
@@ -53,11 +36,6 @@ jobs:
         test -d $CONDA_PREFIX/share/jupyter/labextensions/@beakerx/beakerx-tabledisplay
         test -f $CONDA_PREFIX/share/jupyter/labextensions/@beakerx/beakerx-tabledisplay/package.json
 
-    - name: Check nbextension and labextension (Lab3)
-      run: |
-        jupyter nbextension list 2>&1 | grep -ie "beakerx_tabledisplay/extension.*enabled" -
-        jupyter labextension list 2>&1 | grep -ie "@beakerx/beakerx-tabledisplay.*enabled.*ok" -
-
     - name: Build wheel
       run: |
         cd beakerx_tabledisplay
@@ -99,37 +77,28 @@ jobs:
         name: dist ${{ github.run_number }}
         path: ./dist
 
-    - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Install Conda environment with Micromamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        activate-environment: beakerx_tabledisplay
+        environment-name: beakerx_tabledisplay
         environment-file: configuration.yml
-        auto-activate-base: false
         channels: conda-forge
-        miniconda-version: "latest"
-
-    - name: Install jupyterlab2
-      run: conda install jupyterlab=2
 
     - name: Install the wheel
       run: |
         cd dist
         pip install -vv beakerx_tabledisplay*.whl
 
-    - name: Manually install labextension for lab2
-      run: jupyter labextension install @jupyter-widgets/jupyterlab-manager beakerx_tabledisplay/js
-
-    - name: Check installation files (nbextension and lab3 extension)
+    - name: Check installation files (nbextension and lab extension)
       run: |
         test -d $CONDA_PREFIX/share/jupyter/nbextensions/beakerx_tabledisplay
         test -f $CONDA_PREFIX/share/jupyter/nbextensions/beakerx_tabledisplay/extension.js
         test -f $CONDA_PREFIX/share/jupyter/nbextensions/beakerx_tabledisplay/index.js
         test -d $CONDA_PREFIX/share/jupyter/labextensions/@beakerx/beakerx-tabledisplay
         test -f $CONDA_PREFIX/share/jupyter/labextensions/@beakerx/beakerx-tabledisplay/package.json
 
-    - name: Check nbextension and labextension (Lab2)
+    - name: Check nbextension and labextension
       run: |
-        jupyter nbextension list 2>&1 | grep -ie "beakerx_tabledisplay/extension.*enabled" -
         jupyter labextension list 2>&1 | grep -ie "@beakerx/beakerx-tabledisplay.*enabled.*ok" -
 
     - name: Run e2e tests (table v1)

diff --git a/beakerx_tabledisplay/MANIFEST.in b/beakerx_tabledisplay/MANIFEST.in
@@ -20,4 +20,3 @@ global-exclude *.pyc
 global-exclude *.pyo
 global-exclude .git
 global-exclude .ipynb_checkpoints
-
diff --git a/beakerx_tabledisplay/beakerx_tabledisplay/__init__.py b/beakerx_tabledisplay/beakerx_tabledisplay/__init__.py
@@ -14,7 +14,6 @@
 
 from ._version import version_info, __version__
 from .commands import beakerx_parse
-from .handlers import load_jupyter_server_extension
 from .tabledisplay import *
 from .tableitems import *
 from .object import beakerx_tabledisplay

diff --git a/beakerx_tabledisplay/beakerx_tabledisplay/commands.py b/beakerx_tabledisplay/beakerx_tabledisplay/commands.py
@@ -16,7 +16,6 @@
 import sys
 
 import beakerx_tabledisplay
-from notebook import notebookapp as app
 
 from .install import install, uninstall
 
@@ -39,16 +38,11 @@ def uninstall_subparser(subparser):
     return subparser
 
 
-def run_jupyter(jupyter_commands):
-    app.launch_new_instance(jupyter_commands)
-
-
 def init_parser():
     parser = argparse.ArgumentParser()
     parser.add_argument('-v', '--version',
                         action='version',
                         version=beakerx_tabledisplay.__version__)
-    parser.set_defaults(func=run_jupyter)
 
     subparsers = parser.add_subparsers()
     install_subparser(subparsers)
@@ -59,9 +53,7 @@ def init_parser():
 def beakerx_parse():
     parser = init_parser()
     args, jupyter_commands = parser.parse_known_args()
-    if args.func == run_jupyter:
-        args.func(jupyter_commands)
-    elif not jupyter_commands:
+    if not jupyter_commands:
         args.func(args)
     else:
         parser.parse_args(jupyter_commands)
diff --git a/beakerx_tabledisplay/beakerx_tabledisplay/handlers.py b/beakerx_tabledisplay/beakerx_tabledisplay/handlers.py
diff --git a/beakerx_tabledisplay/js/.yarnrc.yml b/beakerx_tabledisplay/js/.yarnrc.yml
@@ -0,0 +1,2 @@
+nodeLinker: node-modules
+enableImmutableInstalls: false
diff --git a/beakerx_tabledisplay/js/package.json b/beakerx_tabledisplay/js/package.json
@@ -20,14 +20,14 @@
     "url": "https://github.com/twosigma/beakerx_tabledisplay.git"
   },
   "scripts": {
-    "build": "yarn run clean && yarn run build:css && yarn run build:js && webpack",
-    "build:labextension": "yarn run build && jupyter labextension build .",
-    "build:labextension:dev": "yarn run build && jupyter labextension build --development True .",
+    "build": "jlpm run clean && jlpm run build:css && jlpm run build:js && webpack && jlpm run build:labextension",
+    "build:labextension": "jupyter labextension build .",
+    "build:labextension:dev": "jupyter labextension build --development True .",
     "build:css": "sass sass/table_display.scss css/table_display.css",
     "build:js": "tsc",
     "watch:js": "tsc --watch",
     "watch:webpack": "webpack --watch --progress",
-    "prepublish": "yarn run build",
+    "prepublish": "jlpm run build",
     "test": "karma start --single-run",
     "clean": "rimraf lib css dist ../beakerx_tabledisplay/labextension",
     "lint": "eslint src/ --ext .ts",
@@ -36,8 +36,8 @@
     "prettier:fix": "prettier --check src/**/*.{ts,js} --write"
   },
   "devDependencies": {
-    "@jupyterlab/builder": "^3.2.5",
-    "@jupyter-widgets/controls": "^3.0.0",
+    "@jupyter-widgets/controls": "^5",
+    "@jupyterlab/builder": "^4",
     "@types/chai": "^4.2.11",
     "@types/expect.js": "^0.3.29",
     "@types/mocha": "^7.0.2",
@@ -63,30 +63,31 @@
     "karma-webpack": "^4.0.2",
     "mocha": "^7.1.2",
     "prettier": "^2.0.5",
+    "rimraf": "^5.0.1",
     "sass": "^1.26.5",
     "sass-loader": "^8.0.2",
     "sinon": "^9.0.2",
     "sinon-chai": "^3.5.0",
     "style-loader": "^1.2.1",
     "to-string-loader": "^1.1.6",
     "ts-loader": "^7.0.4",
-    "typescript": "^3.8.3",
+    "typescript": "^5",
     "url-loader": "^4.1.0",
     "webpack": "^5",
     "webpack-cli": "^4"
   },
   "dependencies": {
-    "@jupyterlab/application": "^3.2.5",
-    "@jupyter-widgets/base": "^4.0.0",
-    "@lumino/algorithm": "^1.3.3",
-    "@lumino/commands": "^1.11.3",
-    "@lumino/coreutils": "^1.5.3",
-    "@lumino/datagrid": "^0.18.0",
+    "@jupyter-widgets/base": "^4 || ^5 || ^6",
+    "@jupyterlab/application": "^4",
+    "@lumino/algorithm": "^2",
+    "@lumino/commands": "^2",
+    "@lumino/coreutils": "^2",
+    "@lumino/datagrid": "^2",
     "@lumino/datastore": "^0.11.0",
-    "@lumino/disposable": "^1.4.3",
-    "@lumino/messaging": "^1.4.3",
-    "@lumino/signaling": "^1.4.3",
-    "@lumino/widgets": "^1.14.0",
+    "@lumino/disposable": "^2",
+    "@lumino/messaging": "^2",
+    "@lumino/signaling": "^2",
+    "@lumino/widgets": "^2",
     "d3-scale": "2",
     "file-loader": "^6.0.0",
     "katex": "^0.11.1",

diff --git a/beakerx_tabledisplay/js/src/dataGrid/BeakerXDataGrid.ts b/beakerx_tabledisplay/js/src/dataGrid/BeakerXDataGrid.ts
@@ -51,9 +51,7 @@ declare global {
 }
 
 export class BeakerXDataGrid extends DataGrid {
-  id: string;
   store: BeakerXDataStore;
-  dataModel: BeakerXDataGridModel;
   highlighterManager: HighlighterManager;
   columnManager: ColumnManager;
   columnPosition: ColumnPosition;
@@ -115,6 +113,14 @@ export class BeakerXDataGrid extends DataGrid {
     this.columnManager.createColumnMenus();
   }
 
+  get dataModel(): BeakerXDataGridModel {
+    return super.dataModel as BeakerXDataGridModel;
+  }
+
+  set dataModel(value: BeakerXDataGridModel) {
+    super.dataModel = value;
+  }
+
   scrollTo(x: number, y: number): void {
     super.scrollTo(x, y);
     if (this.tableDisplayView.canLoadMore() && this.maxScrollY <= y) {

diff --git a/beakerx_tabledisplay/js/src/dataGrid/highlighter/HighlighterManager.ts b/beakerx_tabledisplay/js/src/dataGrid/highlighter/HighlighterManager.ts
@@ -14,7 +14,7 @@
  *  limitations under the License.
  */
 
-import { each, filter, iter, toArray } from '@lumino/algorithm';
+import { each, filter, toArray } from '@lumino/algorithm';
 import { CellRenderer } from '@lumino/datagrid';
 import { Theme } from '../../utils/Theme';
 import { BeakerXDataGrid } from '../BeakerXDataGrid';
@@ -95,7 +95,7 @@ export class HighlighterManager {
 
   getColumnHighlighters(column, highlighterType?: HIGHLIGHTER_TYPE): Highlighter[] {
     return toArray(
-      filter(iter(this.highlighters), (highlighter: Highlighter) => {
+      filter(this.highlighters, (highlighter: Highlighter) => {
         return highlighterType
           ? highlighter.column === column && highlighter.state.type === highlighterType
           : highlighter.column === column;
@@ -174,7 +174,7 @@ export class HighlighterManager {
     let background = Theme.DEFAULT_COLOR;
     const column = this.dataGrid.getColumn(config);
 
-    each(iter(this.highlighters), (highlighter) => {
+    each(this.highlighters, (highlighter: Highlighter) => {
       if (highlighter.column === column || highlighter.state.style === HIGHLIGHTER_STYLE.FULL_ROW) {
         background = highlighter.getBackgroundColor(config);
       }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -20,4 +20,3 @@ global-exclude *.pyc
		global-exclude *.pyo
		global-exclude .git
		global-exclude .ipynb_checkpoints
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		nodeLinker: node-modules
		enableImmutableInstalls: false