Update to JupyterLab 3 and jupyter server (#111)

* Port to JupyterLab 3

* Clean up and restore co-author

Co-authored-by: Jeremy Tuloup <[email protected]>

* Port binder to JLab3

* Deactivate coveralls

* Fix proxied server

Co-authored-by: Frederic COLLONVAL <[email protected]>

Author: jtpio

.github/workflows/build.yml

@@ -40,7 +40,9 @@ jobs:
         run: |
           conda activate test_gator
           conda install -n test_gator --file requirements_dev.txt
-          pip install .
+          python setup.py develop --skip-npm
+          # Check pip dependencies
+          python -m pip check
         shell: bash -l {0}
       - name: Test the server extension
         run: |
@@ -75,18 +77,16 @@ jobs:
           activate-environment: test_gator
           auto-update-conda: true
           channels: conda-forge
-          mamba-version: "*"
           python-version: ${{ matrix.python-version }}
           show-channel-urls: true
           use-only-tar-bz2: true
       - name: Install dependencies
         run: |
           conda activate test_gator
-          mamba install -n test_gator --file requirements_dev.txt
-          conda install -n test_gator jupyterlab=2
-          pip install .
+          conda install -n test_gator --file requirements_dev.txt
+          python setup.py develop --skip-npm
           # Check pip dependencies
-          pip check
+          python -m pip check
         shell: bash -l {0}
       - name: Test the server extension
         run: |
@@ -152,12 +152,9 @@ jobs:
         run: |
           conda activate test_gator
           conda install -n test_gator --file requirements_dev.txt
-          conda install -n test_gator jupyterlab=2
-          yarn install
-          pip install .
-
+          conda install -n test_gator jupyterlab=3
           yarn install
-          jupyter labextension link packages/common/ packages/labextension/
+          python -m pip install -e .
         shell: bash -l {0}
 
       - name: Test the extension
@@ -223,12 +220,11 @@ jobs:
         run: |
           conda activate test_gator
           mamba install -n test_gator --file requirements_dev.txt
-          conda install -n test_gator coveralls jupyterlab=2
+          conda install -n test_gator coveralls jupyterlab=3
           yarn install
-          pip install .
+          python -m pip install -e .
           # Check pip dependencies
           pip check
-          jupyter labextension link packages/common/ packages/labextension/
         shell: bash -l {0}
 
       - name: Test the extension
@@ -249,27 +245,20 @@ jobs:
           cat labextensions | grep "@mamba-org/gator-lab.*OK"
           python -m jupyterlab.browser_check
         shell: bash -l {0}
-      # - name: Integration tests
-      #   run: |
-      #     chmod -R a+rx ./e2e-tests
-      #     docker-compose -f "docker-compose.yml" run e2e ./e2e-tests/run_e2e.sh
-      # - name: Stop containers
-      #   if: always()
-      #   run: docker-compose -f "docker-compose.yml" down
 
-      - name: Install Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: 2.6
-      - name: Upload coverage
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          conda activate test_gator
-          gem install coveralls-lcov
-          pushd packages/common/
-          coveralls-lcov -v -n coverage/lcov.info > ../../common-jscoverage.json
-          popd
-          python -m pip install --upgrade coveralls
-          python -m coveralls --merge=common-jscoverage.json
-        shell: bash -l {0}
+      # - name: Install Ruby
+      #   uses: ruby/setup-ruby@v1
+      #   with:
+      #     ruby-version: 2.6
+      # - name: Upload coverage
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: |
+      #     conda activate test_gator
+      #     gem install coveralls-lcov
+      #     pushd packages/common/
+      #     coveralls-lcov -v -n coverage/lcov.info > ../../common-jscoverage.json
+      #     popd
+      #     python -m pip install --upgrade coveralls
+      #     python -m coveralls --merge=common-jscoverage.json
+      #   shell: bash -l {0}

.lintstagedrc

@@ -1,7 +1,6 @@
 {
-  "packages/**/*{.ts,.tsx,.js,.jsx,.css,.json,.md}": [
+  "**/*{.ts,.tsx,.js,.jsx,.css,.json,.md}": [
     "prettier --write",
     "git add"
   ]
 }
-

.prettierignore

@@ -1,6 +1,5 @@
 node_modules
 **/node_modules
 **/lib
-**/build
-**/static
-mamba_gator/navigator
+**/package.json
+mamba_gator

.prettierrc

@@ -1,3 +1,5 @@
 {
-  "singleQuote": true
+  "singleQuote": true,
+  "trailingComma": "none",
+  "arrowParens": "avoid"
 }

MANIFEST.in

@@ -12,6 +12,7 @@ include tsconfig.json
 include tsconfig-base.json
 include eslint-base.js
 graft packages
+graft mamba_gator/labextension
 prune packages/**/coverage
 prune packages/**/lib
 prune packages/**/build

README.md

@@ -9,15 +9,14 @@ The Mamba Navigator, a Web UI for managing conda environments
 [![Coverage Status](https://coveralls.io/repos/github/mamba-org/gator/badge.svg?branch=master)](https://coveralls.io/github/mamba-org/gator?branch=master)
 [![Swagger Validator](https://img.shields.io/swagger/valid/3.0?specUrl=https%3A%2F%2Fraw.githubusercontent.com%2Fmamba-org%2Fgator%2Fmaster%2Fmamba_gator%2Frest_api.yml)](https://petstore.swagger.io/?url=https://raw.githubusercontent.com/mamba-org/gator/master/mamba_gator/rest_api.yml)
 
-Provides Conda/Mamba environment and package management as a [standalone application](#Navigator) or as extension for [Jupyter Notebook](#Classical-Jupyter-Notebook) and [JupyterLab](#JupyterLab).
+Provides Conda/Mamba environment and package management as a [standalone application](#Navigator) or as extension for [JupyterLab](#JupyterLab).
 
 ## Install
 
 _Requirements_
 
 - conda >= 4.5 or mamba >=0.5
-- notebook >= 4.3
-- JupyterLab 2.x (for the jupyterlab extension only)
+- JupyterLab 1.x, 2.x or 3.x (for the JupyterLab extension only)
 
 > Starting from 3.4, this extension will use [mamba](https://github.com/mamba-org/mamba) instead of `conda` if it finds it.
 
@@ -31,6 +30,11 @@ To install in the JupyterLab:
 
 ```shell
 conda install -c conda-forge jupyterlab mamba_gator
+```
+
+If you use JupyterLab 1.x or 2.x, you can install the extension with the following command:
+
+```shell
 jupyter labextension install @mamba-org/gator-lab
 ```
 
@@ -61,11 +65,7 @@ Open JupyterLab: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybind
 
 ## Classical Jupyter Notebook
 
-This extension adds a _Conda_ tab to the Jupyter file browser and a _Conda Packages_ item
-to the _Kernel_ menu.  
-Clicking on either of those elements will open the standalone navigator in a new tab.
-
-![Classical Notebook integration](packages/navigator/classical_nb_integration.gif)
+The classical Jupyter Notebook is supported only for version prior to 4.1.
 
 ## Creating New Environments
 
@@ -86,12 +86,10 @@ There are three ways to create an environment:
 ## Development
 
 ```shell
-conda create -c conda-forge -y -n gator python jupyterlab=2
+conda create -c conda-forge -y -n gator python jupyterlab=3
 conda install -c conda-forge -y -n gator --file requirements_dev.txt
 conda activate gator
 pip install -e .
-jupyter nbextension install mamba_gator --py --sys-prefix --symlink
-jupyter nbextension enable mamba_gator --py --sys-prefix
 jupyter serverextension enable mamba_gator --py --sys-prefix
 
 yarn install

binder/environment.yml

@@ -2,10 +2,11 @@ channels:
   - conda-forge
 dependencies:
   - python >=3.6,<3.9
-  - jupyterlab =2
+  - jupyterlab =3
+  - jupyter-packaging >=0.7.9,<0.8.0
   - jupyter-server-proxy
   - nb_conda_kernels >=2.2.3
-  - nodejs >=11
+  - nodejs >=14
   - yarn
   - notebook >=4.3.1
   - packaging

binder/jupyter_notebook_config.py

@@ -9,9 +9,9 @@
             "--no-browser",
             '--port={port}',
             "--ip=0.0.0.0",
-            "--NotebookApp.token=''",
-            "--NotebookApp.base_url={base_url}mamba",
-            "--NotebookApp.allow_remote_access=True",
+            "--ServerApp.token=''",
+            "--ServerApp.base_url={base_url}mamba",
+            "--ServerApp.allow_remote_access=True",
         ],
         "timeout": 120,
         "absolute_url": True,

binder/postBuild

@@ -5,10 +5,9 @@ set -eux
 yarn install
 yarn run build
 python -m pip install .
+python -m pip install jupyterlab-tour
 
-# !! Be sure the version of jupyterlab-tour matches the one saved in bind/workspace.json
-jupyter labextension install jupyterlab-tour@^2.1.1 @jupyterlab/server-proxy --no-build
-jupyter labextension link packages/common/ packages/labextension --no-build
+jupyter labextension install @jupyterlab/server-proxy --no-build
 jupyter lab build --minimize=False
 
 # Import the workspace into JupyterLab

binder/workspace.json

@@ -25,7 +25,7 @@
     },
     "jupyterlab-tour:state": {
       "tutorialsDone": ["jupyterlab-tour:welcome"],
-      "version": "2.1.1"
+      "version": "3.0.0"
     },
     "conda-env:conda-env": { "data": {} }
   },