Replacement date-aware tree-build pipeline

.github/workflows/dvc.yml

@@ -26,6 +26,7 @@ jobs:
         run: |
           python3 -m pip install --upgrade pip
           python3 -m pip install '.[dev]'
+          python3 -m pip install -r requirements.txt
       - name: Checkout merge ref
         if: github.event_name == 'pull_request_target'
         uses: actions/checkout@v7
@@ -44,6 +45,6 @@ jobs:
           [ -n "${{ secrets.DVC_READONLY_SECRET_ACCESS_KEY }}" ] || { echo "DVC_READONLY_SECRET_ACCESS_KEY secret is not set"; exit 1; }
           dvc remote modify onezoom-r2 access_key_id ${{ secrets.DVC_READONLY_ACCESS_KEY_ID }}
           dvc remote modify onezoom-r2 secret_access_key ${{ secrets.DVC_READONLY_SECRET_ACCESS_KEY }}
-          dvc freeze make_js_treefiles
+          dvc freeze versioned_outputs
           dvc repro --allow-missing --dry | tee /dev/stderr | grep -q "Data and pipelines are up to date."
           if dvc data status --not-in-remote | grep -q "Not in remote"; then exit 1; fi

.github/workflows/tests.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install '.[dev]'
+          python3 -m pip install -r requirements.txt
       - name: Test with pytest
         run: |
           python3 -m pytest tests --conf-file tests/appconfig.ini

README.markdown

@@ -13,7 +13,7 @@ The first step to using this repo is to create a Python virtual environment and
     source .venv/bin/activate
 
     # Install it
-    pip install -e '.[dev]'
+    pip install -r requirements.txt
 
     # Set up git hooks including linting and DVC
     pre-commit install --hook-type pre-push --hook-type post-checkout --hook-type pre-commit

data/.gitignore

@@ -1,2 +1,7 @@
 /js_output
 /output_files
+/node_ages.json
+/dated_tree/
+/taxon_map.csv
+/out
+/out_versioned