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

.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: '40-character commit hash'
         required: true
         default: ""
         type: string
+  schedule:
+    - cron: 31 2 * * *
 
 env:
   REPO_PATH:       /mnt/tlo/TLOmodel
@@ -44,8 +46,17 @@ jobs:
           else
               SHA=${{ github.sha }}
           fi
+          SHA=e7cb080ca2b100c82b3d9c7063a6c91f73e63a25
           ENV="/mnt/tlo/env-${SHA}"
+          if [[ -d "${ENV}" ]]; then
+              echo "Virtual environment directory ${ENV} already exists, leaving..."
+              # exit 1
+          fi
           WORKTREE_PATH="/mnt/tlo/${SHA}"
+          if [[ -d "${WORKTREE_PATH}" ]]; then
+              echo "Worktree directory ${WORKTREE_PATH} already exists, leaving..."
+              # exit 1
+          fi
           echo "SHA=${SHA}"
           echo "SHA=${SHA}" >> "${GITHUB_ENV}"
           echo "ENV=${ENV}"
@@ -88,6 +99,10 @@ jobs:
       - name: Generate list of tasks
         id: tasks
         run: |
+          if [[ -d "${{ output_dir }}" ]]; then
+              echo "Output directory ${{ needs.setup.outputs.output_dir }} already exists, setting RUNS_NUMBER to 0"
+              RUNS_NUMBER=0
+          fi
           RUNS="["
           for run in $(seq 0 $((${RUNS_NUMBER} - 1))); do
               RUNS="${RUNS}\"${run}\","
@@ -100,7 +115,7 @@ jobs:
   tasks:
     needs: setup
     name: Run task ${{ matrix.index }}
-    runs-on: [tlo-dev-vm-1, tasks] # Use only runners dedicated to running the tasks.
+    runs-on: [tlo-dev-vm-1] # Use only runners dedicated to running the tasks.
     timeout-minutes: 5760 # = 4 * 24 * 60 minutes = 4 days
     strategy:
       fail-fast: false
@@ -109,38 +124,38 @@ jobs:
     steps:
       - name: Run the task
         run: |
-          source "${{ 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}"
+          echo "index = ${{ matrix.index }}"
+    #       source "${{ 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() }}
+    # It depends on all the previous jobs, but it runs only if `setup` was
+    # successful
+    if: ${{ needs.setup.result == "success" }}
     timeout-minutes: 10
     needs: [setup, tasks, postprocess]
     runs-on: [tlo-dev-vm-1]
@@ -149,8 +164,8 @@ jobs:
     steps:
       - name: Cleanup worktree
         run: |
-          git -C "${REPO_PATH}" worktree remove -f "${{ needs.setup.outputs.worktree_path }}" || true
+          echo git -C "${REPO_PATH}" worktree remove -f "${{ needs.setup.outputs.worktree_path }}" || true
 
       - name: Cleanup virtual environment
         run: |
-          rm -rvf "${{ needs.setup.outputs.environment_path }}"
+          echo "${{ needs.setup.outputs.environment_path }}"