Remove bp5 and improve pipelines (#8)

* Improve pipelines and skip bp5 test

.coveragerc

@@ -0,0 +1,12 @@
+# Omit numba code for now due to
+# https://github.com/numba/numba/issues/4268
+[run]
+omit = */numba/*
+parallel = true
+source = adios4dolfinx
+
+[html]
+directory= htmlcov
+
+[xml]
+output = coverage.xml

.github/workflows/build_docs.yml

@@ -2,24 +2,14 @@
 name: Deploy static content to Pages
 
 on:
-  # Runs on pushes targeting the default branch
-  push:
+  pull_request:
+    # The CI is executed on every pull request to the main branch
     branches:
-    - "**"
+      - main
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Allow one concurrent deployment
-concurrency:
-  group: "pages"
-  cancel-in-progress: true
+  workflow_call:
 
 env:
   # Directory that will be published on github pages
@@ -38,41 +28,21 @@ jobs:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v3
 
-      - name: Update pip
-        run: python3 -m pip install --upgrade pip setuptools
-
       - name: Update pip
         run: python3 -m pip install --upgrade pip setuptools
 
       - name: Install dependencies
-        run: python3 -m pip install ".[docs]"
+        run: python3 -m pip install -e ".[docs]"
 
       - name: Build docs
         run: jupyter book build -W .
 
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+      - name: Upload documentation as artifact
+        uses: actions/upload-artifact@v3
         with:
+          name: documentation
           path: ${{ env.PUBLISH_DIR }}
-
-  # Single deploy job since we're just deploying
-  deploy:
-    if: github.ref == 'refs/heads/main'
-    needs: build-docs
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      - name: Setup Pages
-        uses: actions/configure-pages@v2
+          if-no-files-found: error
 
 
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v1
+

.github/workflows/check_formatting.yml

@@ -1,23 +1,10 @@
 name: Check formatting
 
 on:
-  push:
-    # The CI is executed on every push on every branch
-    branches:
-      - main
-  pull_request:
-    # The CI is executed on every pull request to the main branch
-    branches:
-      - main
-
-  schedule:
-    # The CI is executed every day at 8am
-    - cron: "0 8 * * *"
-
+  workflow_call:
 
 jobs:
   check-code:
-
     env: 
       PYTHONPATH: /usr/local/lib/python3/dist-packages:/usr/local/lib:/usr/local/dolfinx-real/lib/python3.10/dist-packages
       DEB_PYTHON_INSTALL_LAYOUT: deb_system

.github/workflows/create_legacy_data.yml

@@ -0,0 +1,23 @@
+name: Generate legacy data
+
+on:
+  workflow_call:
+
+env:
+  data_dir: "legacy"
+
+
+jobs:
+  create-data:
+    runs-on: "ubuntu-22.04"
+    container: ghcr.io/scientificcomputing/fenics:test_2023.1.0
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Create datasets
+        run: python3 ./tests/create_legacy_data.py --output-dir=$data_dir
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ${{ env.data_dir }}
+          path: ./${{ env.data_dir }}

.github/workflows/deploy_pages.yml

@@ -0,0 +1,61 @@
+name: Github Pages
+
+on:
+  push:
+    branches: [main]
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:  
+  build-docs:
+    uses: ./.github/workflows/build_docs.yml
+
+  run-coverage:
+    uses: ./.github/workflows/test_package.yml
+
+  deploy:
+    needs: [run-coverage, build-docs]
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download docs artifact
+        # docs artifact is uploaded by build-docs job
+        uses: actions/download-artifact@v3
+        with:
+          name: documentation
+          path: "./public"
+
+      - name: Download docs artifact
+        # docs artifact is uploaded by build-docs job
+        uses: actions/download-artifact@v3
+        with:
+          name: code-coverage-report
+          path: "./public/code-coverage-report"
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: "./public"
+
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v2
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.github/workflows/test_package.yml

@@ -10,97 +10,59 @@ on:
     branches:
       - main
 
+  workflow_call:
+  workflow_dispatch:
   schedule:
     # The CI is executed every day at 8am
     - cron: "0 8 * * *"
 
-
-env:
-  data_dir: "legacy"
-
 jobs:
 
   create-datasets:
-    runs-on: "ubuntu-22.04"
-    container: ghcr.io/scientificcomputing/fenics:test_2023.1.0
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Create datasets
-        run: python3 ./tests/create_legacy_data.py --output-dir=$data_dir
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: ${{ env.data_dir }}
-          path: ./${{ env.data_dir }}
-
+    uses: ./.github/workflows/create_legacy_data.yml
 
+  check-formatting:
+    uses: ./.github/workflows/check_formatting.yml
 
   test-code:
     runs-on: "ubuntu-22.04"
-    needs: create-datasets
-    container: ghcr.io/fenics/test-env:nightly-mpich
-    # ghcr.io/fenics/dolfinx/dolfinx:nightly
+    needs: [create-datasets, check-formatting]
+    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
     env: 
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
       PYTHONPATH: /usr/local/lib/python3/dist-packages:/usr/local/lib:/usr/local/dolfinx-real/lib/python3.10/dist-packages
-      DOLFINX_BRANCH: "main"
-      BASIX_BRANCH: "main"
-      UFL_BRANCH:  "main"
-      FFCX_BRANCH: "main"
-      PETSC_ARCH: "linux-gnu-real-32"
+
     steps:
       - uses: actions/checkout@v3
 
       - name: Update pip
         run: python3 -m pip install --upgrade pip setuptools
 
-      - name: Get Basix
-        uses: actions/checkout@v3
-        with:
-          path: ./basix
-          repository: FEniCS/basix
-          ref: ${{ env.BASIX_BRANCH }}
-
-      - name: Install UFL, Basix, FFCx
-        run: |
-          cmake -G Ninja -B build-basix -DCMAKE_BUILD_TYPE="Release" -S ./basix/cpp/
-          cmake --build build-basix --parallel 3
-          cmake --install build-basix
-          BUILD_TYPE="Release" python3 -m pip install ./basix/python
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git@${{ env.UFL_BRANCH }}
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${{ env.FFCX_BRANCH }}
-
-      - name: Get DOLFINx
-        uses: actions/checkout@v3
-        with:
-          path: ./dolfinx
-          repository: FEniCS/dolfinx
-          ref: ${{ env.DOLFINX_BRANCH }}
-
-      - name: Configure C++ (DOLFINx)
-        run:
-          cmake -G Ninja -DCMAKE_BUILD_TYPE="Release" -B build-dolfinx -S ./dolfinx/cpp/
-
-      - name: Build and install C++ library (DOLFINx)
-        run: |
-          cmake --build build-dolfinx
-          cmake --install build-dolfinx
-      - name: Build Python interface (dolfinx)
-        run: BUILD_TYPE="Release" python3 -m pip -v install ./dolfinx/python/
-
       - name: Download legacy data
         uses: actions/download-artifact@v3
         with:
-          name: ${{ env.data_dir }}
-          path: ./${{ env.data_dir }}
+          name: legacy
+          path: ./legacy
 
       - name: Install package
         run: python3 -m pip install .[test]
 
       - name: Run tests
-        run: python3 -m pytest
+        run: coverage run --rcfile=.coveragerc -m mpi4py -m pytest -xvs ./tests/
 
       - name: Run tests in parallel
-        run: mpirun -n 2 python3 -m pytest
+        run: mpirun -n 2 coverage run --rcfile=.coveragerc -m mpi4py -m pytest -xvs ./tests/
+
+
+      - name: Combine coverage reports
+        run: |
+          coverage combine
+          coverage report -m
+          coverage html
+
+      - name: Upload coverage report as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: code-coverage-report
+          path: htmlcov
+          if-no-files-found: error

.gitignore

@@ -130,4 +130,11 @@ dmypy.json
 
 _build/
 
-output/
+output/
+
+*.h5
+.coverage.*
+.coverage
+*.h5
+*.xdmf
+*.bp/

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
 name = "adios4dolfinx"
-version = "0.2.1"
+version = "0.2.2"
 description = "Wrappers for reading/writing DOLFINx meshes/functions with ADIOS2"
 authors = [{name = "Jørgen S. Dokken", email = "[email protected]"}]
 license = {file = "LICENSE"}
@@ -13,6 +13,7 @@ readme = "README.md"
 [project.optional-dependencies]
 test = [
     "pytest",
+    "coverage"
 ]
 dev = [
     "pdbpp",