Issue 897: Reduce EpiAutoGP to a script

.github/workflows/pipeline-run-check.yaml

@@ -60,7 +60,7 @@ jobs:
 
       - name: Install Julia dependencies
         run: |
-          julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+          julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
 
       - name: Download test data
         uses: actions/download-artifact@v8
@@ -103,7 +103,7 @@ jobs:
 
       - name: Install Julia dependencies
         run: |
-          julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+          julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
 
       - name: Download test data
         uses: actions/download-artifact@v8
@@ -146,7 +146,7 @@ jobs:
 
       - name: Install Julia dependencies
         run: |
-          julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+          julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
 
       - name: Download test data
         uses: actions/download-artifact@v8
@@ -189,7 +189,7 @@ jobs:
 
       - name: Install Julia dependencies
         run: |
-          julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+          julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
 
       - name: Download test data
         uses: actions/download-artifact@v8

.github/workflows/test.yaml

@@ -30,6 +30,7 @@ jobs:
         run: |
           uv run pytest \
             --ignore=pipelines/tests/test_epiautogp_parquet_interop.py \
+            --ignore=pipelines/tests/test_epiautogp_parquet.py \
             --cov=pipelines --cov-report=term --cov-report=xml:pipelines-coverage.xml .
 
       - name: Upload results to Codecov
@@ -88,7 +89,7 @@ jobs:
           path: ${{ runner.temp }}/package
 
   epiautogp-test:
-    name: Run EpiAutoGP tests and collect coverage
+    name: Run EpiAutoGP runner output tests
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -99,36 +100,19 @@ jobs:
         with:
           version: "1.11"
 
-      - name: Run tests
-        uses: julia-actions/julia-runtest@v1
-        with:
-          project: EpiAutoGP
-          coverage: true
-
-      - name: Process coverage
-        uses: julia-actions/julia-processcoverage@v1
-        with:
-          directories: EpiAutoGP/src
-
-      - name: Upload results to Codecov
-        uses: codecov/codecov-action@v6
-        with:
-          env_vars: OS,PYTHON
-          fail_ci_if_error: true
-          flags: epiautogp
-          files: lcov.info
-          token: ${{ secrets.CODECOV_TOKEN }}
-          verbose: true
+      - name: Install Julia dependencies
+        run: |
+          julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
 
       - name: Set up R with hewr
         uses: ./.github/actions/setup-hewr
 
       - name: Set up Pyrenew-HEW via UV
         uses: ./.github/actions/setup-pyrenew-hew
 
-      - name: Instantiate EpiAutoGP Julia project
+      - name: Run direct EpiAutoGP parquet test
         run: |
-          julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+          uv run pytest pipelines/tests/test_epiautogp_parquet.py -q
 
       - name: Run EpiAutoGP parquet interop test
         run: |

.gitignore

@@ -358,6 +358,7 @@ target/
 # https://github.com/github/gitignore/blob/main/Julia.gitignore
 # Manifest files generated by the package manager
 Manifest.toml
+!pipelines/epiautogp/Manifest.toml
 
 # Files generated by invoking Julia with --code-coverage
 *.jl.cov

.pre-commit-config.yaml

@@ -37,7 +37,7 @@ repos:
     hooks:
       - id: detect-secrets
         args: ["--baseline", ".secrets.baseline"]
-        exclude: package.lock.json
+        exclude: ^(package\.lock\.json|pipelines/epiautogp/Manifest\.toml)$
   # R
   - repo: https://github.com/posit-dev/air-pre-commit
     rev: 0.9.0
@@ -59,3 +59,4 @@ repos:
     hooks:
       - id: typos
         args: ["--force-exclude"]
+        exclude: ^pipelines/epiautogp/Manifest\.toml$

Containerfile

@@ -25,15 +25,25 @@ ENV UV_PYTHON_CACHE_DIR=/root/.cache/uv/python
 # R package - hewr
 COPY ./hewr /cfa-stf-routine-forecasting/hewr
 
-# Julia package - EpiAutoGP
-COPY ./EpiAutoGP /cfa-stf-routine-forecasting/EpiAutoGP
+# Julia environment for direct NowcastAutoGP runner
+# Copy only Julia environment metadata first so dependency installation is cached
+# independently of changes to pipeline source files. The full pipelines tree is
+# copied later.
+COPY ./pipelines/epiautogp/Project.toml \
+     ./pipelines/epiautogp/Manifest.toml \
+     /cfa-stf-routine-forecasting/pipelines/epiautogp/
 
 # Set working directory
 WORKDIR /cfa-stf-routine-forecasting
 
-# Cache Julia packages and artifacts
-RUN --mount=type=cache,target=/root/.julia \
-    julia --project=EpiAutoGP -e 'using Pkg; Pkg.instantiate()'
+# Instantiate Julia dependencies into the image so the runtime container can run
+# the EpiAutoGP subprocess without downloading packages. This is a script
+# environment under pipelines/epiautogp, so we commit its Manifest.toml for a
+# reproducible EpiAutoGP dependency set.
+RUN julia --project=pipelines/epiautogp -e 'using Pkg; Pkg.instantiate()'
+
+
+
 
 # Install hewr
 RUN Rscript -e "install.packages('pak')"