Merge pull request #8 from underworldcode/development

The usual siphon of Development into Main

Author: lmoresi

.github/.devcontainer/DOCKERFILE_GHCS

@@ -7,11 +7,6 @@ RUN conda install -n base -c conda-forge mamba
 COPY .devcontainer/uw_environment.yml  /tmp/conda-tmp/
 RUN  mamba env update -n base --file /tmp/conda-tmp/uw_environment.yml 
 
-RUN export PETSC_DIR=/opt/conda \
-    && pip install petsc4py 
-
-RUN pip install gmsh
-
 # Add other dependencies that can't be installed correctly.
 
 ##

.github/.devcontainer/devcontainer.json

@@ -20,4 +20,4 @@
     "postCreateCommand": "conda init && cd /workspaces/underworld3 && export PETSC_DIR=/opt/conda && python3 setup.py build_ext && sudo -E /opt/conda/bin/pip install ."
     // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
     // "remoteUser": "root"
-}
+}

.github/.devcontainer/uw_environment.yml

@@ -0,0 +1 @@
+../../environment.yml

.github/.devcontainer/uw_environment.yml

@@ -16,38 +16,43 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: ./.github/workflows/envs/build_uw_docs.yml
+          environment-file: ./environment.yml
           cache-downloads: true
-          cache-env: true
+          cache-environment: true
+
+          # # gmsh is such a pig to install properly
+          # - name: Add gmsh package
+          #   shell: bash -l {0}
+          #   run: |
+          #     pip install gmsh
+
 
       # the following may be needed if conda-forge is out of date
       # - name: Add compatible petsc4py
       #   shell: bash -l {0}
       #   run: |
       #     export PETSC_DIR="/home/runner/micromamba-root/envs/uw3_docs"
       #     pip3 install petsc4py==3.18 --upgrade
-
       - name: Build UW3
         shell: bash -l {0}
         run: |
-          export PETSC_DIR="/home/runner/micromamba-root/envs/uw3_docs"
+          export PETSC_DIR="/home/runner/micromamba/envs/uw3_test/lib"
           VERSION=`python3 setup.py --version`
           echo "UW - version " ${VERSION}
-
-          python3 setup.py develop
-          pip3 install -e .
+          ./compile.sh
 
       - name: Build docs with pdoc
         shell: bash -l {0}
         run: |
           VERSION=`python3 setup.py --version`
           echo "VERSION=$(echo $VERSION)" >> $GITHUB_ENV
           # mkdir -p docs
+          pip install pdoc3
           ./build_api_docs.sh
 
       # There is an action to build the jupyter book to a different directory

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-name: Build and test UW3
+name: test_uw3
 
 # We should trigger this from an upload event. Note that pdoc requires us to import the
 # built code, so this is a building test as well as documentation deployment
@@ -15,58 +15,29 @@ on:
   workflow_dispatch:
 
 jobs:
-  deploy:
-    runs-on: ubuntu-20.04
+  test:
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: ./.github/workflows/envs/build_uw_test.yml
+          environment-file: ./environment.yml
           cache-downloads: true
           cache-environment: true
 
-      # the following may be needed if conda-forge is out of date
-      # - name: Add compatible petsc4py
-      #   shell: bash -l {0}
-      #   run: |
-      #    export PETSC_DIR="/home/runner/micromamba-root/envs/uw3_test"
-      #    pip3 install petsc4py==3.18 --upgrade
-
-      # gmsh is such a pig to install properly
-      - name: Add gmsh package
-        shell: bash -l {0}
-        run: |
-          pip install gmsh
-
       - name: Build UW3
         shell: bash -l {0}
         run: |
           export PETSC_DIR="/home/runner/micromamba/envs/uw3_test/lib"
           VERSION=`python3 setup.py --version`
           echo "UW - version " ${VERSION}
 
-          python3 setup.py develop
-          pip3 install -e .
+          ## TODO. Use compile.sh once it is in development
+          pip install -e . --no-build-isolation
 
-      # Test - split into short, low memory tests 0???_*
-      #        and longer, solver-based tests 1???_*
-
-      - name: Run pytest
+      - name: Run tests 
         shell: bash -l {0}
         run: |
-          pytest tests/test_00??*py
-          pytest tests/test_0[1-9]??*py
-
-          # Poisson solver tests
-          pytest tests/test_100[0-9]*py
-
-          # Stokes solver tests
-          pytest tests/test_1010*py
-          pytest tests/test_1011*py
-          pytest tests/test_1050*py
-
-          # Advection/Diffusion solvers
-          pytest tests/test_1100*py
-          pytest tests/test_1110*py
+          ./test.sh

.github/workflows/build_deploy_pdoc.yml

@@ -1,32 +1,33 @@
-name: Docker Image CI
+name: Image Build and Push
 
 on:
-  push:
-    branches: ["development"]
+  push: 
+    branches:
+      - development
+
 jobs:
-  build:
+  push-to-dockerhub:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Exact branch name
         run: echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_PWORD }}
+          username: ${{ secrets.XXX_USERNAME }}
+          password: ${{ secrets.XXX_PWORD }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4.1.1
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true
           file: ./Dockerfile
           platforms: linux/amd64
           # see https://github.com/docker/build-push-action/issues/276 for syntax help
-          tags: julesg/underworld3:${{ env.BRANCH }}
-          #-$(date +%s)
+          tags: underworldcode/underworld3:${{ env.BRANCH }} #-$(date +%s)

.github/workflows/build_uw3_and_test.yml

@@ -22,7 +22,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: docs/joss-paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled