Merge branch 'main' of https://github.com/petercarbsmith/ca-biositing

Author: avi9664

.codespellrc

@@ -0,0 +1,2 @@
+[codespell]
+ignore-words-list = fallow

.github/workflows/cd.yml

@@ -27,7 +27,7 @@ jobs:
       matrix:
         package: [datamodels, pipeline, webservice]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Check datamodels build

.github/workflows/ci.yml

@@ -28,12 +28,12 @@ jobs:
         runs-on: [ubuntu-latest, macos-14]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Set up pixi
-        uses: prefix-dev/setup-pixi@v0.9.2
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
           pixi-version: v0.59.0
           environments: ${{ matrix.python-version }}
@@ -54,6 +54,6 @@ jobs:
           pixi run pytest src/ca_biositing/webservice --cov=ca_biositing.webservice --cov-report=xml --cov-append --cov-report=term-missing
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.5.1
+        uses: codecov/codecov-action@v5.5.2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/copilot-setup-steps.yml

@@ -26,10 +26,10 @@ jobs:
     # If you do not check out your code, Copilot will do this for you.
     steps:
       - name: Checkout code
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up pixi
-        uses: prefix-dev/setup-pixi@v0.9.2
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
           pixi-version: v0.56.0
           cache: false # No caching

.github/workflows/gh-pages.yml

@@ -0,0 +1,63 @@
+name: Deploy Resource Info to GitHub Pages
+
+on:
+  workflow_dispatch:
+  pull_request:
+    paths: &asset-paths
+      - "resources/assets/resource_info.csv"
+      - "resources/assets/resource_info_header_mapping.json"
+      - "resources/assets/index.html"
+      - "scripts/validate_headers.py"
+      - "scripts/csv_to_json.py"
+      - ".github/workflows/gh-pages.yml"
+  push:
+    branches:
+      - main
+    paths: *asset-paths
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  validate:
+    name: Validate resource info assets
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Validate header mapping is in sync with CSV
+        run: python scripts/validate_headers.py
+
+  build-and-deploy:
+    name: Build and deploy to GitHub Pages
+    needs: validate
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Convert CSV to JSON
+        run: python scripts/csv_to_json.py
+
+      - name: Build site
+        run: |
+          mkdir -p _site
+          cp resources/assets/resource_info.json _site/
+          cp resources/assets/resource_info_header_mapping.json _site/
+          cp resources/assets/index.html _site/
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v4
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -33,9 +33,30 @@ venv/
 # Local Data
 data/interim/
 data/processed/
+data/landiq/*.shp
+data/landiq/*.shx
+data/landiq/*.dbf
+data/landiq/*.prj
+data/landiq/*.cpg
+data/landiq/*.xml
+*.csv
+!src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/landiq/*.csv
+!resources/assets/*.csv
 
 # Credentials
 credentials.json
 
 # macOS
 .DS_Store
+
+# Jupyter Notebooks
+.ipynb_checkpoints/
+
+# Tools
+pgschema
+
+# Pulumi
+.pulumi/
+
+# Agents Braindump
+.agents/

.pre-commit-config.yaml

@@ -11,6 +11,7 @@ repos:
       - id: check-merge-conflict
       - id: check-symlinks
       - id: check-yaml
+        exclude: ^mkdocs\.yml$
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
@@ -27,7 +28,7 @@ repos:
     rev: "v2.4.1"
     hooks:
       - id: codespell
-        exclude: (\.ipynb$|pixi\.lock)
+        exclude: (\.ipynb$|pixi\.lock|temp_external_datasets/)
 
   - repo: local
     hooks:
@@ -38,7 +39,7 @@ repos:
         exclude: .pre-commit-config.yaml
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.34.1"
+    rev: "0.36.2"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

.vscode/settings.json

@@ -1,4 +1,14 @@
 {
+  // For the Python language server / IntelliSense in VS Code.
+  // These are NOT runtime PYTHONPATH entries — they help the language server
+  // resolve imports across the PEP 420 namespace packages.
+  "python.analysis.extraPaths": [
+    "${workspaceFolder}/src/ca_biositing/pipeline",
+    "${workspaceFolder}/src/ca_biositing/datamodels",
+    "${workspaceFolder}/src/ca_biositing/webservice"
+  ],
   "python.defaultInterpreterPath": "${workspaceFolder}/.pixi/envs/default/bin/python",
-  "python-envs.defaultEnvManager": "ms-python.python:system"
+  "python-envs.defaultEnvManager": "ms-python.python:system",
+  // Ensure the Jupyter extension starts notebooks with the workspace as root.
+  "jupyter.notebookFileRoot": "${workspaceFolder}"
 }