Merge branch 'master' into dataserver-refactor

.github/workflows/build-and-push-docker.yml

@@ -0,0 +1,81 @@
+name: build and push docker
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+    branches:
+      - build-docker-image
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
+      -
+        name: Decide the docker image version number
+        run: |
+            if [[ -f ./docker/build-docker-image-version.txt ]]; then
+              echo "DOCKER_IMAGE_TAG=$( tail -n 1 ./docker/build-docker-image-version.txt )" >> $GITHUB_ENV
+            else
+              echo "DOCKER_IMAGE_TAG=${{ github.ref_name }}" >> $GITHUB_ENV
+            fi
+            echo ${{ env.DOCKER_IMAGE_TAG }}
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - 
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Build and push gplately amd64
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          push: true
+          platforms: linux/amd64
+          provenance: false
+          tags: |
+            gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }}
+            ghcr.io/gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }} 
+      -
+        name: Build and push gplately arm64
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          push: true
+          platforms: linux/arm64
+          provenance: false
+          tags: |
+            gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }}
+            ghcr.io/gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }}
+      -
+        name: Create cross-platform images
+        run: |
+            docker buildx imagetools create -t gplates/gplately:${{ env.DOCKER_IMAGE_TAG }} gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }} gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }}
+            docker buildx imagetools create -t ghcr.io/gplates/gplately:${{ env.DOCKER_IMAGE_TAG }} ghcr.io/gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }} ghcr.io/gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }}
+      -     
+        name: Create the latest tags
+        if: 
+        run: |
+            if [[ -f ./docker/build-docker-image-version.txt ]]; then
+              docker buildx imagetools create -t gplates/gplately:latest gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }} gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }}
+              docker buildx imagetools create -t ghcr.io/gplates/gplately:latest ghcr.io/gplates/gplately:amd64-${{ env.DOCKER_IMAGE_TAG }} ghcr.io/gplates/gplately:arm64-${{ env.DOCKER_IMAGE_TAG }} 
+            fi

.github/workflows/build_and_test.yml

@@ -24,13 +24,16 @@ jobs:
     defaults:
       run:
         shell: bash -el {0}
-
+
+    if: github.event.pull_request.draft == false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: mamba-org/setup-micromamba@v1
         with:
-          micromamba-version: "1.3.1-0"
+          micromamba-version: "1.5.8-0"
           environment-file: tests-dir/test-env.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
           init-shell: >-
             bash
             powershell

.github/workflows/deploy_documentation.yaml

@@ -1,45 +1,59 @@
-
 name: Build docs and deploy to GitHub Pages
 
-on:
+on: 
   push:
-    branches: [master]
+    branches: 
+      - master
   pull_request:
-    branches: [master]
+    branches: 
+      - master
 
 jobs:
   build-and-deploy:
-    runs-on: ubuntu-20.04
-
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    if: github.event.pull_request.draft == false
     steps:
-    - uses: actions/checkout@v2
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pdoc3
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        sudo apt-get update
-        sudo apt-get install -yq wget libboost-python-dev libboost-program-options-dev libgdal-dev libglew-dev libglu1-mesa libproj-dev libqt5core5a libqt5gui5 libqt5network5 libqt5opengl5 libqt5svg5 libqt5widgets5 libqt5xml5 libqt5xmlpatterns5 libqwt-qt5-6
-        wget https://www.earthbyte.org/webdav/ftp/earthbyte/pygplates/pygplates-py3_rev33_ubuntu-20.04-amd64.deb -O pygplates_package.deb
-        yes | sudo dpkg -i pygplates_package.deb
-    - name: Install jupyter with nbconvert
-      run: |
-        pip install jupyter
-    - name: Install gplately
-      run: |
-        pip install .
-    - name : Generate documentation with pdoc3
-      run : |
-        export PYTHONPATH=$PYTHONPATH:/usr/lib/
-        export LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$LD_PRELOAD
-        pdoc --config latex_math=True --template-dir .pdoc_template --html -o api --force gplately
-    - name: Convert jupyter notebooks to html
-      run : |
-        export PYTHONPATH=$PYTHONPATH:/usr/lib/
-        export LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$LD_PRELOAD
-        jupyter-nbconvert --to=html --output-dir=api/gplately/ Notebooks/*.ipynb
-    - name : Deploy to gh-pages
-      uses: JamesIves/github-pages-deploy-action@v4.2.2
-      with:
-        branch: gh-pages
-        folder: api/gplately/
+      - uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: "1.5.8-0"
+          environment-file: conda/doc-env.yml
+          init-shell: >-
+            bash
+          cache-environment: true
+          post-cleanup: "all"
+
+      - name: Install current gplately
+        run: |
+          pip install . --no-binary :all: --no-cache-dir --no-dependencies
+
+      - name: test pygmt
+        run: python -c "import pygmt"
+        shell: bash -el {0}
+
+      - name: test jupyter-nbconvert
+        run: jupyter-nbconvert --version
+        shell: bash -el {0}
+
+      - name: test pdoc
+        run: pdoc --version
+        shell: bash -el {0}
+
+      - name: Generate documentation with pdoc3
+        run: pdoc --config latex_math=True --template-dir .pdoc_template --html -o api --force gplately
+        shell: bash -el {0}
+
+      - name: Convert jupyter notebooks to html
+        run: jupyter-nbconvert --to=html --output-dir=api/gplately/ Notebooks/*.ipynb
+        shell: bash -el {0}
+
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4.2.2
+        with:
+          branch: gh-pages
+          folder: api/gplately/
+          target-folder: dev-doc/

.github/workflows/publish_to_pypi.yml

@@ -17,31 +17,12 @@ permissions:
 
 jobs:
   deploy:
-
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.8'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        sudo apt-get update
-        sudo apt-get install -yq wget libboost-python-dev libboost-program-options-dev libgdal-dev libglew-dev libglu1-mesa libproj-dev libqt5core5a libqt5gui5 libqt5network5 libqt5opengl5 libqt5svg5 libqt5widgets5 libqt5xml5 libqt5xmlpatterns5 libqwt-qt5-6
-        wget https://www.earthbyte.org/webdav/ftp/earthbyte/pygplates/pygplates-py3_rev33_ubuntu-20.04-amd64.deb -O pygplates_package.deb
-        yes | sudo dpkg -i pygplates_package.deb
-    - name: Build package
-      run: |
-        export PYTHONPATH=$PYTHONPATH:/usr/lib/
-        export LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$LD_PRELOAD
-        python setup.py sdist
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Publish package
+        run: |
+          chmod +x ./scripts/pypi-publish.sh
+          ./scripts/pypi-publish.sh '${{secrets.PYPI_API_TOKEN}}'

.gitignore

@@ -5,3 +5,5 @@ __pycache__
 .ipynb_checkpoints
 
 output
+
+*.log

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+  "editor.formatOnSave": true,
+  "editor.defaultFormatter": "ms-python.black-formatter",
+  "[python]": {
+    "editor.defaultFormatter": "ms-python.black-formatter"
+  },
+  "git.ignoreLimitWarning": true
+}

MANIFEST.in

@@ -0,0 +1 @@
+include gplately/logging_config.yaml