Chore: Initial code drop from physrisk

Signed-off-by: Matthew Watkins <[email protected]>

.aicoe-ci.yaml

@@ -1,8 +1,10 @@
+---
 # Setup and configuring aicoe-ci with configuration file `.aicoe-ci.yaml`
-# Example `.aicoe-ci.yaml` with a full list of config options is available here: https://github.com/AICoE/aicoe-ci/blob/master/docs/.aicoe-ci.yaml
+# Example `.aicoe-ci.yaml` with a full list of config options is available
+# here: https://github.com/AICoE/aicoe-ci/blob/master/docs/.aicoe-ci.yaml
 check:
-  # Uncomment following line to build a public image of this repo
-  # - thoth-build
+# Uncomment following line to build a public image of this repo
+# - thoth-build
 # Uncomment following lines to build a public image of this repo
 # build:
 #   build-stratergy: Source

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,14 +1,19 @@
+# Bug Reporting
+
 ---
+
 name: Bug report
 about: Create a report to help us improve
 labels: bug
+
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,7 +1,11 @@
+# Feature Requests
+
 ---
+
 name: Feature request
 about: Suggest an idea for this project
 labels: enhancement
+
 ---
 
 **Is your feature request related to a problem? Please describe.**

.github/ISSUE_TEMPLATE/major-release.md

@@ -2,7 +2,7 @@
 name: Major release
 about: Create a new major release
 title: New major release
-assignees: 'sesheta'
+assignees: "sesheta"
 labels: bot
 ---
 

.github/ISSUE_TEMPLATE/minor-release.md

@@ -2,7 +2,7 @@
 name: Minor release
 about: Create a new minor release
 title: New minor release
-assignees: 'sesheta'
+assignees: "sesheta"
 labels: bot
 ---
 

.github/ISSUE_TEMPLATE/patch-release.md

@@ -2,7 +2,7 @@
 name: Patch release
 about: Create a new patch release
 title: New patch release
-assignees: 'sesheta'
+assignees: "sesheta"
 labels: bot
 ---
 

.github/PULL_REQUEST_TEMPLATE/POLISH_TEMPLATE.md

@@ -1,13 +1,17 @@
+# Polish Notebook(s)
+
 ---
+
 name: Polish Notebook(s)
 about: Finalize notebooks prior to publishing or promoting
+
 ---
 
 ## Related Issues and Dependencies
 
 …
 
-## The following checklist items have been completed for each notebook in this PR:
+## The following checklist items have been completed for each notebook in this PR
 
 - [ ] Proofread by other team member for grammar and spelling
 - [ ] Proofread by other team member for coherence and reproducibility (does the analysis make sense as you read through the code and markdown from top to bottom?)
@@ -25,7 +29,6 @@ about: Finalize notebooks prior to publishing or promoting
 - [ ] Cell execution counts are in order (a working "run all" was performed just before PR)
 - [ ] All pre-commit checks pass
 
-
-
 ## Additional context
+
 <!-- If there is some reason that one of the above steps could not be completed, please describe what it is and why. -->

.github/PULL_REQUEST_TEMPLATE/SIMPLE_TEMPLATE.md

@@ -1,4 +1,4 @@
-## Related Issues and Dependencies
+# Related Issues and Dependencies
 
 …
 

.github/workflows/builds.yaml

@@ -0,0 +1,87 @@
+---
+name: "🧪 Test builds (matrix)"
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [opened, reopened, edited, synchronize]
+
+jobs:
+  pre-release:
+    # Don't run if pull request is NOT merged
+    # if: github.event.pull_request.merged == true
+    runs-on: "ubuntu-latest"
+    continue-on-error: true
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10"]
+    steps:
+      - name: "Populate environment variables"
+        id: setenv
+        run: |
+          echo "Action triggered by user: ${GITHUB_TRIGGERING_ACTOR}"
+          set -x
+          datetime=$(date +'%Y%m%d%H%M')
+          export datetime
+          echo "datetime=${datetime}" >> "$GITHUB_OUTPUT"
+          vernum="${{ matrix.python-version }}.${datetime}"
+          echo "vernum=${vernum}" >> "$GITHUB_OUTPUT"
+
+      - name: "Checkout repository"
+        uses: actions/checkout@v4
+
+      - name: "Set up Python ${{ matrix.python-version }}"
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: "Install dependencies"
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox tox-gh-actions
+
+      - name: "Tag for test release"
+        # Delete all local tags, then create a synthetic tag for testing
+        # Use the date/time to avoid conflicts uploading to Test PyPI
+        run: |
+          scripts/dev-versioning.sh "${{ steps.setenv.outputs.vernum }}"
+          git tag | xargs -L 1 | xargs git tag --delete
+          git tag "v${{ steps.setenv.outputs.vernum }}"
+          git checkout "tags/v${{ steps.setenv.outputs.vernum }}"
+          grep version pyproject.toml
+
+      - name: "Build with TOX (PDM backend)"
+        run: |
+          mkdir metadata
+          tox -e build
+
+      - name: "Save dependency graph"
+        uses: GuillaumeFalourd/[email protected]
+        with:
+          command_line: pdm list --graph
+          output_file_name: metadata/dependency-graph.txt
+          # yamllint disable-line rule:truthy
+          display_file_content: NO
+
+      - name: "Save file listing of build directory"
+        uses: GuillaumeFalourd/[email protected]
+        with:
+          command_line: ls -al dist/*
+          output_file_name: metadata/dist-ls.txt
+          # yamllint disable-line rule:truthy
+          display_file_content: NO
+
+      - name: Store the build metadata
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ github.ref_name }}
+          path: metadata/*
+          retention-days: 14
+
+      - name: Store the build artefacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ github.ref_name }}
+          path: dist/
+          retention-days: 14

.github/workflows/dependencies.yaml

@@ -0,0 +1,40 @@
+---
+name: "⛔️ Update dependencies"
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * MON"
+
+jobs:
+  update-dependencies:
+    name: "Update Python modules"
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: mandatory to raise the PR
+      id-token: write
+      pull-requests: write
+      repository-projects: write
+      contents: write
+
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "Setup PDM for build commands"
+        uses: pdm-project/setup-pdm@v3
+        with:
+          version: 2.10.3
+
+      - name: Update dependencies
+        uses: pdm-project/update-deps-action@main
+        with:
+          token: ${{ secrets.GH_TOKEN }}
+          commit-message: "Chore: Update dependencies and pdm.lock"
+          pr-title: "Update Python module dependencies"
+          update-strategy: eager
+          # Whether to install PDM plugins before update
+          install-plugins: "false"

.github/workflows/documentation.yaml

@@ -0,0 +1,50 @@
+---
+name: "🗒️ Build documentation"
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [closed]
+
+jobs:
+  build_and_deploy:
+    # Don't run if pull request is NOT merged
+    if: github.event.pull_request.merged == true
+    name: "Rebuild documentation"
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - name: "Checkout repository"
+        uses: actions/checkout@v4
+
+      - name: "Setup PDM for build commands"
+        uses: pdm-project/setup-pdm@v3
+
+      - name: "Set up Python ${{ matrix.python-version }}"
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: "Install dependencies"
+        run: |
+          python -m pip install --upgrade pip
+          pdm export -o requirements.txt
+          if [ -f docs/requirements.txt ]; then
+          pip install -r docs/requirements.txt; fi
+
+      - name: "Build documentation: (tox/sphinx)"
+        run: |
+          tox -e docs
+
+      - name: "Publish documentation"
+        if: success()
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html/
+          keep_files: true