Release 2.0.1 (#95)

* Canvas test failures #91
fixed workflows
fixed dockerfile for binder

* Fix unknown entity warnings (#90)

* fixed package info

* fix for #92 #93 and #94
added new workflow for releasetools

* use yarn instead of npm

* workaround for yarn caches on subprojects: from actions/setup-node#488 (comment)

---------

Co-authored-by: Manuel Martins <Manuel.Martins@ecmwf.int>
Co-authored-by: Jerry James <loganjerry@gmail.com>

.github/workflows/CI.yml

@@ -33,8 +33,7 @@ jobs:
         run: |
           sudo touch /etc/apt/sources.list.d/opensuse.list &&
           echo "deb https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/ ./" | sudo tee -a /etc/apt/sources.list.d/opensuse.list
-      - name: Download ZMQ repo key
-        run: wget https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/Release.key -O- | sudo apt-key add
+          wget https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/Release.key -O- | sudo apt-key add
       - name: Install ZMQ
         run: |
           sudo apt update && 
@@ -54,7 +53,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node-version: [19.x]
+        node-version: [ 19.x ]
 
     steps:
       - uses: actions/checkout@v3
@@ -75,13 +74,26 @@ jobs:
         uses: actions/setup-node@v3
         with:
           node-version: ${{ matrix.node-version }}
-      - run: npm install
+          registry-url: 'https://registry.npmjs.org'
+      - name: Get yarn cache directory path
+        id: yarn-cache-dir-path
+        run: echo "dir=$(yarn config get cacheFolder)" >> $GITHUB_OUTPUT
+        shell: bash
         working-directory: js
-      - run: npm run lint
+      - name: Restore yarn cache
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
+          key: yarn-cache-folder-${{ hashFiles('**/yarn.lock', '.yarnrc.yml') }}
+          restore-keys: |
+            yarn-cache-folder-
+      - run: yarn install --frozen-lockfile
+        working-directory: js
+      - run: yarn run lint
         working-directory: js
-      - run: npm run build
+      - run: yarn run build:prod
         working-directory: js
-      - run: npm run test
+      - run: yarn run test
         working-directory: js
       - uses: codecov/codecov-action@v3
 
@@ -96,8 +108,7 @@ jobs:
         run: |
           sudo touch /etc/apt/sources.list.d/opensuse.list &&
           echo "deb https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/ ./" | sudo tee -a /etc/apt/sources.list.d/opensuse.list
-      - name: Download ZMQ repo key
-        run: wget https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/Release.key -O- | sudo apt-key add
+          wget https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/Release.key -O- | sudo apt-key add
       - name: Install ZMQ
         run: |
           sudo apt update && 
@@ -108,8 +119,3 @@ jobs:
       - uses: gap-actions/build-pkg-docs@v1
         with:
           use-latex: 'true'
-      - name: Upload documentation
-        uses: actions/upload-artifact@v2
-        with:
-          name: manual
-          path: ./doc/manual.pdf

.github/workflows/NPM_PYPI.yml

@@ -0,0 +1,61 @@
+name: NPM_PYPI
+
+# Trigger the workflow on push or pull request
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  publish_js_python_packages:
+    name: Build and Publish plugins
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node-version: [ 19.x ]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+      - run: pip install jupyterlab build
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+          registry-url: 'https://registry.npmjs.org'
+      - name: Get yarn cache directory path
+        id: yarn-cache-dir-path
+        run: echo "dir=$(yarn config get cacheFolder)" >> $GITHUB_OUTPUT
+        shell: bash
+        working-directory: js
+      - name: Restore yarn cache
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
+          key: yarn-cache-folder-${{ hashFiles('**/yarn.lock', '.yarnrc.yml') }}
+          restore-keys: |
+            yarn-cache-folder-
+      - run: yarn install --frozen-lockfile
+        working-directory: js
+      - run: yarn run build:prod
+        working-directory: js
+      - name: Publish Browser extension
+        run: |
+          npm config set '//registry.npmjs.org/:_authToken' "${NPM_TOKEN}"
+          npm publish --no-workspaces
+        working-directory: js/packages/francy-extension-browser
+        env:
+          NPM_TOKEN: ${{ secrets.NPM_TOKEN }}
+      - run: python -m build --wheel --sdist
+        working-directory: js/packages/francy-extension-jupyterlab
+      - name: Publish Jupyterlab extension PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages_dir: js/packages/francy-extension-jupyterlab/dist

.github/workflows/RELEASE.yml

@@ -0,0 +1,77 @@
+name: RELEASE
+
+# Trigger the workflow on push or pull request
+on:
+  push:
+    branches:
+      - master
+
+# the `concurrency` settings ensure that not too many CI jobs run in parallel
+concurrency:
+  # group by workflow and ref; the last slightly strange component ensures that for pull
+  # requests, we limit to 1 concurrent job, but for the master branch we don't
+  group: ${{ github.workflow }}-${{ github.ref }}-${{ github.ref != 'refs/heads/master' || github.run_number }}
+  # Cancel intermediate builds, but only if it is a pull request build.
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  gap_release_tools:
+    name: Build and Publish manuals
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Configure ZMQ repos
+        run: |
+          sudo touch /etc/apt/sources.list.d/opensuse.list &&
+          echo "deb https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/ ./" | sudo tee -a /etc/apt/sources.list.d/opensuse.list
+          wget https://download.opensuse.org/repositories/network:/messaging:/zeromq:/release-stable/Debian_9.0/Release.key -O- | sudo apt-key add
+      - name: Install ZMQ
+        run: |
+          sudo apt update && 
+          sudo apt install libzmq3-dev -y
+      - uses: gap-actions/setup-gap@v2
+        with:
+          GAP_PKGS_TO_BUILD: "datastructures uuid json io crypting zeromqinterface jupyterkernel"
+          GAPBRANCH: master
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+          registry-url: 'https://registry.npmjs.org'
+      - name: Get yarn cache directory path
+        id: yarn-cache-dir-path
+        run: echo "dir=$(yarn config get cacheFolder)" >> $GITHUB_OUTPUT
+        shell: bash
+        working-directory: js
+      - name: Restore yarn cache
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
+          key: yarn-cache-folder-${{ hashFiles('**/yarn.lock', '.yarnrc.yml') }}
+          restore-keys: |
+            yarn-cache-folder-
+      - run: yarn install --frozen-lockfile
+        working-directory: js
+      - run: yarn run docs
+        working-directory: js
+      - name: GAPTools Release
+        run: |
+          # Clone Release tools
+          git clone --depth=2 -b master https://github.com/gap-system/ReleaseTools $HOME/ReleaseTools
+          # Add a new remote pointing to the GitHubPagesForGAP repository
+          git remote add gh-gap https://github.com/gap-system/GitHubPagesForGAP
+          git fetch gh-gap
+          # Create a fresh gh-pages branch from the new remote
+          git branch gh-pages gh-gap/gh-pages --no-track
+          # Create a new worktree and change into it
+          git worktree add gh-pages gh-pages
+          # Copy JavaScript documentation
+          cp -rf doc/js gh-pages/doc/
+          # Configure git
+          git config user.name "GitHub Actions Bot"
+          git config user.email "<>"
+          git config github.user "GitHub Actions Bot"
+          git config github.token "${{ secrets.GITHUB_TOKEN }}"
+          # Run Release Script
+          GAP="$HOME/gap/bin/gap.sh" $HOME/ReleaseTools/release-gap-package --push

.gitignore

@@ -89,4 +89,6 @@ gh-pages/
 
 **/build_log.json
 
-**/docs/*
+**/docs/*
+
+**/labextension/

Dockerfile

@@ -1,31 +1,29 @@
-FROM ubuntu:22.10
+FROM jupyter/minimal-notebook:latest
 
 MAINTAINER Manuel Martins <manuelmachadomartins@gmail.com>
 
+USER root
+
 ARG DEBIAN_FRONTEND="noninteractive"
 ARG WGET="wget -N --no-check-certificate --tries=5 --waitretry=5 --retry-connrefused"
 
 RUN apt update && apt -qq install -y git curl wget python3-pip inkscape pandoc texlive-xetex libgmp-dev libreadline-dev graphviz \
-    zlib1g-dev libzmq3-dev gcc g++ make autoconf && useradd -s /bin/bash -d /home/gap/ -m -G sudo gap && \
-    git clone --depth=2 -b master https://github.com/gap-system/gap.git /home/gap/master && cd /home/gap/master && \
-    ./autogen.sh && ./configure && make -j4 V=1 && ln -s /home/gap/master/bin/gap.sh /usr/local/sbin/gap && \
-    make bootstrap-pkg-minimal DOWNLOAD="$WGET" WGET="$WGET" &&  \
-    cd /home/gap/master/pkg && rm -rf /home/gap/master/pkg/francy && \
-    git clone https://github.com/gap-packages/JupyterKernel &&  \
+    zlib1g-dev libzmq3-dev gcc g++ make autoconf && \
+    git clone --depth=2 -b master https://github.com/gap-system/gap.git /opt/master && cd /opt/master && \
+    ./autogen.sh && ./configure && make -j4 V=1 && \
+    make bootstrap-pkg-full DOWNLOAD="$WGET" WGET="$WGET" &&  \
+    cd /opt/master/pkg && rm -rf /opt/master/pkg/francy && \
     git clone https://github.com/gap-packages/FrancyMonoids && \
     git clone https://github.com/gap-packages/francy && \
     git clone https://github.com/mcmartins/subgroup-lattice && \
     for pkg in 'io profilling json uuid crypting zeromqinterface jupyterkernel'; do ../bin/BuildPackages.sh --strict $pkg*; done &&  \
-    rm -rf /home/gap/master/packages-required.tar.gz && chown -R gap:gap /home/gap/master/ && \
+    rm -rf /opt/master/packages.tar.gz && chown -R jovyan: /opt/master/ && \
+    cd /opt/master/pkg/jupyterkernel && pip install . && \
+    ln -s /opt/master/pkg/francy/notebooks /home/jovyan/notebooks && \
+    ln -s /opt/master/bin/gap.sh /usr/local/sbin/gap && \
     apt purge git gcc g++ make autoconf curl wget -y
 
-USER gap
-
-ENV PATH="${PATH}:/home/gap/.local/bin"
+USER jovyan
 
 # jupyter lab extension installation
-RUN pip install jupyterlab jupyterlab-francy
-
-WORKDIR /home/gap/master/pkg/francy/notebooks
-
-CMD jupyter lab --port=8080
+RUN pip install --no-cache-dir jupyterlab jupyterlab-francy && rm -rf /home/jovyan/.jupyter/*