Merge pull request #134 from SCM-NV/DavidOrmrodMorley/sync-trunk-2024…

…-08-20

Manual Sync of Trunk Branches

.flake8

@@ -1,3 +1,4 @@
 [flake8]
 exclude=doc, examples
+per-file-ignores = __init__.py:F401, setup.py:F821
 select=F

.github/workflows/ci.yml

@@ -0,0 +1,137 @@
+name: CI
+
+on:
+# Run on creating or updating a PR
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+# And pushing to the trunk or fix branches
+  push:
+    branches:
+      - trunk
+      - 'fix*'
+
+# And pushing new version tags e.g. 2024.103
+    tags:
+      - '20[0-9]{2}\.[0-9]{3}'
+
+jobs:
+
+  unit-test:
+#   Run on ubuntu, mac and windows for python 3.8 (in AMS python stack) up to 3.11
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          New-Item -Path scm\plams -ItemType Directory -Force
+          
+          Get-ChildItem -Directory | Where-Object { $_.Name -ne 'scm' } | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          Get-ChildItem -File | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          echo "PYTHONPATH=$(pwd);$env:PYTHONPATH" >> $env:GITHUB_ENV
+
+      - name: Set Up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install coverage
+
+      - name: Run Unit Tests
+        working-directory: scm/plams
+        run: |
+          pwd
+          coverage run -m pytest unit_tests
+#     ToDo: Bump the fail-under threshold over time until acceptable level is reached
+      - name: Evaluate Coverage
+        working-directory: scm/plams
+        run: coverage report --omit="unit_tests/*" -i --fail-under=30
+
+
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black
+          pip install "black[jupyter]"
+          pip install flake8
+
+      - name: Run Black
+        run: |
+          black --check -t py38 -l 120 .
+
+      - name: Run Flake8
+        run: |
+          flake8 --color never --count --config .flake8 .
+          
+
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          cd doc
+          pip install -r requirements.txt
+
+#     Turn on the -W flag when building once warnings to external links have been resolved
+#     ToDo: add a warning allowlist to check the warnings logged via -w
+      - name: Build Sphinx Docs
+        working-directory: scm/plams/doc
+        run: |
+          python build_plams_doc