[CI] Run calibration jobs on schedule instead of pushes to master

UCL · Nov 28, 2023 · eca8220 · eca8220
1 parent e7cb080
commit eca8220
Showing 1 changed file with 94 additions and 91 deletions.
diff --git a/.github/workflows/calibration.yaml b/.github/workflows/calibration.yaml
@@ -2,14 +2,16 @@ name: Calibration
 
 on:
   push:
-    branches: "master"
+    branches: "mg/nightly-calibration"
   workflow_dispatch:
     inputs:
       commit:
-        description: 'Commit'
+        description: 'Commit hash (40 characters)'
         required: true
         default: ""
         type: string
+  schedule:
+    - cron: 31 2 * * *
 
 env:
   REPO_PATH:       /mnt/tlo/TLOmodel
@@ -44,6 +46,7 @@ jobs:
           else
               SHA=${{ github.sha }}
           fi
+          SHA=e7cb080ca2b100c82b3d9c7063a6c91f73e63a25
           ENV="/mnt/tlo/env-${SHA}"
           WORKTREE_PATH="/mnt/tlo/${SHA}"
           echo "SHA=${SHA}"
@@ -55,102 +58,102 @@ jobs:
           echo "WORKTREE_PATH=${WORKTREE_PATH}" >> "${GITHUB_ENV}"
           echo "worktree_path=${WORKTREE_PATH}" >> "${GITHUB_OUTPUT}"
 
-      - name: Clone remote TLO repository and fetch desired commit
-        run: |
-          # If the repository doesn't exist on disk, clone it.
-          if [[ ! -d "${REPO_PATH}" ]]; then
-              git clone --depth=1 --branch="${{ github.ref_name }}" "https://github.com/${{ github.repository }}.git" "${REPO_PATH}"
-          fi
-          # In any case, fetch the requested commit.
-          git -C "${REPO_PATH}" fetch --depth=1 origin "${SHA}"
+      # - name: Clone remote TLO repository and fetch desired commit
+      #   run: |
+      #     # If the repository doesn't exist on disk, clone it.
+      #     if [[ ! -d "${REPO_PATH}" ]]; then
+      #         git clone --depth=1 --branch="${{ github.ref_name }}" "https://github.com/${{ github.repository }}.git" "${REPO_PATH}"
+      #     fi
+      #     # In any case, fetch the requested commit.
+      #     git -C "${REPO_PATH}" fetch --depth=1 origin "${SHA}"
 
-      - name: Create worktree
-        run: |
-          git -C "${REPO_PATH}" worktree add "${WORKTREE_PATH}" ${SHA}
+      # - name: Create worktree
+      #   run: |
+      #     git -C "${REPO_PATH}" worktree add "${WORKTREE_PATH}" ${SHA}
 
-      - name: Create virtual environment
-        run: |
-          python${PYTHON_VER} -m venv "${ENV}"
-          source "${ENV}/bin/activate"
-          pip install -r requirements/dev.txt
-          pip install -e .
-        working-directory: "${{ env.WORKTREE_PATH }}"
+      # - name: Create virtual environment
+      #   run: |
+      #     python${PYTHON_VER} -m venv "${ENV}"
+      #     source "${ENV}/bin/activate"
+      #     pip install -r requirements/dev.txt
+      #     pip install -e .
+      #   working-directory: "${{ env.WORKTREE_PATH }}"
 
-      - name: Generate output directory
-        id: out-dir
-        run: |
-          commit_dir=$(git show -s --date=format:'%Y-%m-%d_%H%M%S' --format=%cd_%h "${SHA}")
-          output_dir="${OUTPUT_ROOT}/${commit_dir}"
-          echo "output_dir=${output_dir}"
-          echo "output_dir=${output_dir}" >> "${GITHUB_OUTPUT}"
-        working-directory: "${{ env.WORKTREE_PATH }}"
+      # - name: Generate output directory
+      #   id: out-dir
+      #   run: |
+      #     commit_dir=$(git show -s --date=format:'%Y-%m-%d_%H%M%S' --format=%cd_%h "${SHA}")
+      #     output_dir="${OUTPUT_ROOT}/${commit_dir}"
+      #     echo "output_dir=${output_dir}"
+      #     echo "output_dir=${output_dir}" >> "${GITHUB_OUTPUT}"
+      #   working-directory: "${{ env.WORKTREE_PATH }}"
 
-      - name: Generate list of tasks
-        id: tasks
-        run: |
-          RUNS="["
-          for run in $(seq 0 $((${RUNS_NUMBER} - 1))); do
-              RUNS="${RUNS}\"${run}\","
-          done
-          RUNS="${RUNS}]"
-          echo "tasks=${RUNS}"
-          echo "tasks=${RUNS}" >> "${GITHUB_OUTPUT}"
+      # - name: Generate list of tasks
+      #   id: tasks
+      #   run: |
+      #     RUNS="["
+      #     for run in $(seq 0 $((${RUNS_NUMBER} - 1))); do
+      #         RUNS="${RUNS}\"${run}\","
+      #     done
+      #     RUNS="${RUNS}]"
+      #     echo "tasks=${RUNS}"
+      #     echo "tasks=${RUNS}" >> "${GITHUB_OUTPUT}"
 
-  # Run the tasks.
-  tasks:
-    needs: setup
-    name: Run task ${{ matrix.index }}
-    runs-on: [tlo-dev-vm-1, tasks] # Use only runners dedicated to running the tasks.
-    timeout-minutes: 5760 # = 4 * 24 * 60 minutes = 4 days
-    strategy:
-      fail-fast: false
-      matrix:
-        index: ${{ fromJSON(needs.setup.outputs.tasks) }}
-    steps:
-      - name: Run the task
-        run: |
-          source "${{ needs.setup.outputs.environment_path }}/bin/activate"
-          draw=0
-          task_output_dir="${{ needs.setup.outputs.output_dir }}/${RUN_NAME}/${draw}/${{ matrix.index }}"
-          mkdir -p "${task_output_dir}"
+  # # Run the tasks.
+  # tasks:
+  #   needs: setup
+  #   name: Run task ${{ matrix.index }}
+  #   runs-on: [tlo-dev-vm-1, tasks] # Use only runners dedicated to running the tasks.
+  #   timeout-minutes: 5760 # = 4 * 24 * 60 minutes = 4 days
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       index: ${{ fromJSON(needs.setup.outputs.tasks) }}
+  #   steps:
+  #     - name: Run the task
+  #       run: |
+  #         source "${{ needs.setup.outputs.environment_path }}/bin/activate"
+  #         draw=0
+  #         task_output_dir="${{ needs.setup.outputs.output_dir }}/${RUN_NAME}/${draw}/${{ matrix.index }}"
+  #         mkdir -p "${task_output_dir}"
 
-          tlo scenario-run --output-dir "${task_output_dir}" --draw "${draw}" ${{ matrix.index }} "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/scenarios/long_run_all_diseases.py"
-        working-directory: "${{ needs.setup.outputs.worktree_path }}"
+  #         tlo scenario-run --output-dir "${task_output_dir}" --draw "${draw}" ${{ matrix.index }} "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/scenarios/long_run_all_diseases.py"
+  #       working-directory: "${{ needs.setup.outputs.worktree_path }}"
 
-  # Do the postprocessing
-  postprocess:
-    name: Post processing
-    needs: [setup, tasks]
-    runs-on: [tlo-dev-vm-1, postprocess] # Use only the runners dedicated to postprocessing
-    strategy:
-      fail-fast: false
-    steps:
-      - name: Run post-processing
-        run: |
-          source "${{ needs.setup.outputs.environment_path }}/bin/activate"
-          task_output_dir="${{ needs.setup.outputs.output_dir }}/${PROCESS_NAME}"
-          mkdir -p "${task_output_dir}"
+  # # Do the postprocessing
+  # postprocess:
+  #   name: Post processing
+  #   needs: [setup, tasks]
+  #   runs-on: [tlo-dev-vm-1, postprocess] # Use only the runners dedicated to postprocessing
+  #   strategy:
+  #     fail-fast: false
+  #   steps:
+  #     - name: Run post-processing
+  #       run: |
+  #         source "${{ needs.setup.outputs.environment_path }}/bin/activate"
+  #         task_output_dir="${{ needs.setup.outputs.output_dir }}/${PROCESS_NAME}"
+  #         mkdir -p "${task_output_dir}"
 
-          python3 "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/analysis_scripts/process.py" "${task_output_dir}" "${RUN_NAME}" "${{ needs.setup.outputs.worktree_path }}/resources"
-        working-directory: "${{ needs.setup.outputs.worktree_path }}"
+  #         python3 "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/analysis_scripts/process.py" "${task_output_dir}" "${RUN_NAME}" "${{ needs.setup.outputs.worktree_path }}/resources"
+  #       working-directory: "${{ needs.setup.outputs.worktree_path }}"
 
-  # Cleanup stage, to remove temporary directories and such
-  cleanup:
-    name: Cleanup job
-    # It depends on all the previous jobs, but it always runs, regardless of
-    # their success (or maybe check that only `setup` was
-    # successful?)
-    if: ${{ always() }}
-    timeout-minutes: 10
-    needs: [setup, tasks, postprocess]
-    runs-on: [tlo-dev-vm-1]
-    strategy:
-      fail-fast: false
-    steps:
-      - name: Cleanup worktree
-        run: |
-          git -C "${REPO_PATH}" worktree remove -f "${{ needs.setup.outputs.worktree_path }}" || true
+  # # Cleanup stage, to remove temporary directories and such
+  # cleanup:
+  #   name: Cleanup job
+  #   # It depends on all the previous jobs, but it always runs, regardless of
+  #   # their success (or maybe check that only `setup` was
+  #   # successful?)
+  #   if: ${{ always() }}
+  #   timeout-minutes: 10
+  #   needs: [setup, tasks, postprocess]
+  #   runs-on: [tlo-dev-vm-1]
+  #   strategy:
+  #     fail-fast: false
+  #   steps:
+  #     - name: Cleanup worktree
+  #       run: |
+  #         git -C "${REPO_PATH}" worktree remove -f "${{ needs.setup.outputs.worktree_path }}" || true
 
-      - name: Cleanup virtual environment
-        run: |
-          rm -rvf "${{ needs.setup.outputs.environment_path }}"
+  #     - name: Cleanup virtual environment
+  #       run: |
+  #         rm -rvf "${{ needs.setup.outputs.environment_path }}"