Merge pull request #2 from equinor/pipelines

Pipelines

.devcontainer/Dockerfile

@@ -1,8 +1,8 @@
-FROM mcr.microsoft.com/devcontainers/base:bullseye
+FROM dolfinx/dolfinx:v0.7.0
 # FROM mcr.microsoft.com/devcontainers/base:jammy 
-
 ARG DEBIAN_FRONTEND=noninteractive
-ARG USER=vscode
+# RUN useradd -ms /bin/bash vscode
+# ARG USER=vscode
 
 RUN DEBIAN_FRONTEND=noninteractive \
     && apt-get update \ 
@@ -28,9 +28,11 @@ RUN DEBIAN_FRONTEND=noninteractive \
 # Python and poetry installation
 USER $USER
 ARG HOME="/home/$USER"
-ARG PYTHON_VERSION=3.11
-# ARG PYTHON_VERSION=3.10
 
+# Don't change. Dolfinx in the base image is only compiled with 3.10
+ARG PYTHON_VERSION=3.10
+
+# Use poetry pyenv
 ENV PYENV_ROOT="${HOME}/.pyenv"
 ENV PATH="${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:${HOME}/.local/bin:$PATH"
 
@@ -42,4 +44,4 @@ RUN echo "done 0" \
     && pyenv global ${PYTHON_VERSION} \
     && echo "done 3" \
     && curl -sSL https://install.python-poetry.org | python3 - \
-    && poetry config virtualenvs.in-project true
+    && poetry config virtualenvs.in-project true

.devcontainer/devcontainer.json

@@ -11,19 +11,24 @@
 	// "forwardPorts": [],
 
 	// 👇 Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "poetry install --with dev --no-interaction",
+	"postCreateCommand": "bash .devcontainer/postCreate.sh",
 
 	// 👇 Configure tool-specific properties.
 	"customizations": {
         "vscode": {
-            "extensions":["ms-python.python", "njpwerner.autodocstring"]
+            "extensions":[
+				"ms-python.python",
+				"njpwerner.autodocstring",
+				"ms-python.autopep8",
+				"ms-toolsai.jupyter",
+				"ms-python.vscode-pylance",
+				"ms-azuretools.vscode-docker"
+			]
             }
 		},
 		"features": {
-			"ghcr.io/devcontainers/features/git-lfs:1": {
-				"autoPull": true,
-				"version": "latest"
-			}
+			"ghcr.io/devcontainers/features/git-lfs:1": {},
+			"ghcr.io/devcontainers/features/docker-in-docker:2": {}
 		}
 
 	// 👇 Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.

.devcontainer/postCreate.sh

@@ -0,0 +1,2 @@
+poetry install --with dev --no-interaction
+poetry run pip install petsc4py==3.20.0 mpi4py==3.1.5 https://github.com/FEniCS/ufl/archive/refs/tags/2023.2.0.zip https://github.com/FEniCS/ffcx/archive/v0.7.0.zip https://github.com/FEniCS/basix/archive/v0.7.0.zip

.gitattributes

@@ -1,2 +1 @@
-*.gri filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text
+*.gri *.png filter=lfs diff=lfs merge=lfs -text

.github/workflows/docs.yml

@@ -5,6 +5,7 @@ name: docs
 
 on:
   workflow_dispatch:
+  workflow_call:
   push:
     branches: [ main ]
 

.github/workflows/publish.yml

@@ -0,0 +1,64 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: build
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test3d:
+    uses: equinor/warmth/.github/workflows/python-test-3d.yml@main
+    with:
+      event_type: ${{ github.event_name}}
+      action_type: ${{ github.event.action}}
+  test1d:
+    uses: equinor/warmth/.github/workflows/python-test.yml@main
+    with:
+      event_type: ${{ github.event_name}}
+      action_type: ${{ github.event.action}}
+  snyk:
+    uses: equinor/warmth/.github/workflows/snyk.yml@main
+  docs:
+    uses: equinor/warmth/.github/workflows/docs.yml@main
+
+  deploy:
+    needs: [test3d, test1d, snyk, docs]
+    environment: deploy
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+            ref: 'master'
+            fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+            python-version: '3.11'
+
+      - name: Azure key vault login
+        uses: Azure/login@v1
+        with:
+            client-id: ${{ secrets.AZURE_CLIENT_ID }}
+            tenant-id: ${{ secrets.AZURE_TENANT_ID }}
+            subscription-id: ${{ secrets.AZURE_SUBSCRIPTION_ID }}
+
+      - name: Fetch secrets
+        uses: azure/CLI@v1
+        with:
+            azcliversion: 2.42.0
+            inlineScript: |
+                echo PYPI_TOKEN=$(az keyvault secret show --vault-name PSSCloudDev --name PYPI-Token --query value -o tsv) >> $GITHUB_ENV
+        
+      - name: Install dependencies
+        run: |
+            curl -sSL https://install.python-poetry.org | python3
+            poetry install --with dev --no-interaction
+            
+      - name: Build and publish
+        run: |
+            poetry config pypi-token.pypi ${{ env.PYPI_TOKEN }}
+            poetry build
+            poetry publish

.github/workflows/python-test-3d.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests3D
+
+on:
+  workflow_call:
+    inputs:
+      event_type:
+        required: true
+        type: string
+      action_type:
+        required: true
+        type: string
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Run
+      uses: tj-actions/docker-run@v2
+      with:
+        image: dolfinx/dolfinx:v0.7.0
+        name: dolfinx
+        options: -v ${{ github.workspace }}:/warmth
+        args: |
+          cd /warmth
+          pip install .
+          pip install pytest==7.4.2 pytest-cov==4.1.0
+          pytest --cov-report=term-missing --cov=warmth/3d tests/3d | tee pytest-coverage.txt
+
+
+    - name: Comment coverage
+      if: ${{ github.event_name == 'pull_request' && github.event.action == 'opened' }}
+      uses: coroo/[email protected]
+      with:
+        pytest-coverage: pytest-coverage.txt

.github/workflows/python-test.yml

@@ -2,47 +2,72 @@
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Tests
- 
+
 on:
+  workflow_call:
+    inputs:
+      event_type:
+        required: true
+        type: string
+      action_type:
+        required: true
+        type: string
   workflow_dispatch:
   push:
-    branches: [ main, dev ]
+    branches: [main, dev]
   pull_request:
-    branches: [ main , dev ]
+    branches: [main, dev]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10','3.11']
+        python-version: ["3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        curl -sSL https://install.python-poetry.org | python3
-        poetry install --with dev --no-interaction
-
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=docs
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=docs
-
-    - name: Test with pytest
-      run: |
-        poetry run pytest --cov-report=term-missing --cov=warmth tests/ | tee pytest-coverage.txt
-
-    - name: Comment coverage
-      if: ${{ github.event_name == 'pull_request' && github.event.action == 'opened' }}
-      uses: coroo/[email protected]
-      with:
-        pytest-coverage: pytest-coverage.txt
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          curl -sSL https://install.python-poetry.org | python3
+          poetry install --with dev --no-interaction
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=docs
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=docs
+
+      - name: Test with pytest
+        run: |
+          poetry run pytest --cov-report=term-missing --ignore=tests/3d --cov=warmth tests/ | tee pytest-coverage.txt
+
+      - name: Comment coverage
+        if: ${{ github.event_name == 'pull_request' && github.event.action == 'opened' }}
+        uses: coroo/[email protected]
+        with:
+          pytest-coverage: pytest-coverage.txt
+
+      - name: check_3d_modified
+        uses: dorny/paths-filter@v2
+        id: filter3d
+        with:
+          filters: |
+            mesh3d:
+              - 'warmth/3d/**'
+    outputs:
+      filter3d: ${{ steps.filter3d.outputs.mesh3d }}
+
+  test3d:
+    needs: [build]
+    uses: equinor/warmth/.github/workflows/python-test-3d.yml@main
+    if: ${{ needs.build.outputs.filter3d }} == 'true'
+    with:
+      event_type: ${{ github.event_name}}
+      action_type: ${{ github.event.action}}

.github/workflows/snyk.yml

@@ -0,0 +1,23 @@
+name: Snyk scan
+on: 
+    push:
+        branches: [main, dev]
+    pull_request:
+        branches: [main, dev]
+    workflow_call:
+jobs:
+  security:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Run Snyk to check for vulnerabilities
+        uses: snyk/actions/python-3.10@master
+        continue-on-error: false
+        env:
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+        with:
+          args: --sarif-file-output=snyk.sarif --severity-threshold=high
+      - name: Upload result to GitHub Code Scanning
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: snyk.sarif

.gitignore

@@ -62,4 +62,8 @@ exec11/
 exec12/
 exec13/
 
-docs/_build
+docs/_build
+
+*.c
+*.o
+*.so

CONTRIBUTING.md

@@ -89,7 +89,7 @@ Standard acronyms to start the commit message with are:
 ```
     API: an (incompatible) API change (will be rare)
     PERF: performance or bench-marking
-    BLD: change related to building xtgeo
+    BLD: change related to building
     BUG: bug fix
     FIX: fixes wrt to technical issues, e.g. wrong requirements.txt
     DEP: deprecate something, or remove a deprecated object
@@ -98,7 +98,7 @@ Standard acronyms to start the commit message with are:
     CLN: code cleanup, maintenance commit (refactoring, typos, PEP, etc.)
     REV: revert an earlier commit
     TST: addition or modification of tests
-    REL: related to releasing xtgeo
+    REL: related to release
 ```
 
 ## Type hints