🔀 Merge branch 'develop' into 'security/code-scanning-alerts'

Author: shnizzedy

.circleci/main.yml

@@ -2,6 +2,9 @@
 version: 2.1
 # Singularity started failing to set up on Circle circa May 2023, so those tests are currently disabled
 
+orbs:
+  codecov: codecov/codecov@5
+
 parameters:
   branch:
     type: string
@@ -36,7 +39,8 @@ commands:
           name: "Combining and reporting coverage"
           command: |
               coverage combine
-              coverage html --ignore-errors
+              coverage xml -o coverage.xml  # Generate XML report
+      - codecov/upload
   configure-git-user:
     steps:
       - add_ssh_keys:
@@ -185,8 +189,6 @@ jobs:
       #     key: coverage-singularity-lite-{{ .Revision }}
       - set-python-version
       - combine-coverage
-      - store_artifacts:
-          path: htmlcov
   push-branch-to-docker-hub:
     parameters:
       variant:

.codecov.yml

@@ -0,0 +1,21 @@
+codecov:
+  branch: main
+
+comment:
+  layout: "diff, files"
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+  hide_project_coverage: false
+
+coverage:
+  precision: 1
+  range: "50..90"
+  round: nearest
+  status:
+    project:
+      default:   # default is the status check's name, not default settings
+        only_pulls: false
+        target: auto
+        threshold: "5"

.github/README/README.md

@@ -46,7 +46,7 @@ flowchart LR
       subgraph build_C-PAC.yml
         bCPAC[[C-PAC]]
       end
-      subgraph build_and_test.yml
+      subgraph build_and_test.yaml
         ubuntu[[Ubnutu]]-->stages[[stages]]-->build-base[[build-base]]-->build-base-standard[[build-base-standard]]
 
         Circle_tests[[Circle_tests]]
@@ -65,7 +65,7 @@ flowchart LR
         smoke-tests-participant[[smoke-tests-participant]]
       end
 
-      on_push.yml-->build_and_test.yml
+      on_push.yaml-->build_and_test.yaml
 
       delete_images.yml
     end
@@ -79,8 +79,8 @@ flowchart LR
 
     Circle_tests-->CircleCI((Run tests on Circle CI))
 
-    on_push.yml<-->get_pr_base_shas
-    on_push.yml-->update_all_preconfigs
+    on_push.yaml<-->get_pr_base_shas
+    on_push.yaml-->update_all_preconfigs
 
     cpacdockerfiles<-->C-PAC
 
@@ -94,7 +94,7 @@ flowchart LR
     bCPAC<-->local_ghcr
     stages<-->local_ghcr
 
-    push>git push]-->on_push.yml
+    push>git push]-->on_push.yaml
 
     smoke-tests-participant-->smoke_test_human
     smoke-tests-participant-->smoke_test_nhp

.github/workflows/build_and_test.yml renamed to .github/workflows/build_and_test.yaml

@@ -52,6 +52,10 @@ on:
         description: 'third phase of staging images to rebuild (base images)'
         type: string
         required: true
+      test_mode:
+        description: 'lite or full?'
+        type: string
+        default: None
 
 jobs:
   Ubuntu:
@@ -192,7 +196,7 @@ jobs:
         run: |
             sed -i -e 's/^/\.github\/Dockerfiles\//' .github/stage_requirements/${{ matrix.variant }}.txt
             echo 'dev/docker_data/required_afni_pkgs.txt' >> .github/stage_requirements/${{ matrix.variant }}.txt
-            echo '.github/workflows/build_and_test.yml' >> .github/stage_requirements/${{ matrix.variant }}.txt
+            echo '.github/workflows/build_and_test.yaml' >> .github/stage_requirements/${{ matrix.variant }}.txt
             echo '.github/stage_requirements/${{ matrix.variant }}.txt' >> .github/stage_requirements/${{ matrix.variant }}.txt
       - name: Set tag & see if it exists
         continue-on-error: true
@@ -264,7 +268,7 @@ jobs:
         run: |
             sed -i -e 's/^/\.github\/Dockerfiles\//' .github/stage_requirements/standard.txt
             echo 'dev/docker_data/required_afni_pkgs.txt' >> .github/stage_requirements/standard.txt
-            echo '.github/workflows/build_and_test.yml' >> .github/stage_requirements/standard.txt
+            echo '.github/workflows/build_and_test.yaml' >> .github/stage_requirements/standard.txt
             echo '.github/stage_requirements/standard.txt' >> .github/stage_requirements/standard.txt
       - name: Set tag & see if it exists
         continue-on-error: true
@@ -333,19 +337,21 @@ jobs:
     if: github.ref_name == 'develop' || github.ref_name == 'main'
     uses: ./.github/workflows/smoke_test_participant.yml
 
-  regtest-lite:
-    name: Run lite regression test
+  check_test_mode:
+    name: check_test_mode
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo ${{ inputs.test_mode }}
+
+  regtest:
+    name: Run regression and integration test
     needs:
       - C-PAC
     secrets: inherit
-    if: contains(github.event.head_commit.message, '[run reg-suite]')
-    uses: ./.github/workflows/regression_test_lite.yml
-
-  regtest-full:
-    name: Run full regression test
-    needs:
-      - smoke-tests-participant
-    uses: ./.github/workflows/regression_test_full.yml
+    if: inputs.test_mode == 'lite'
+    uses: ./.github/workflows/regtest.yaml
+    with:
+      test_mode: ${{ inputs.test_mode }}
 
   Circle_tests:
     name: Run tests on CircleCI

.github/workflows/on_push.yml renamed to .github/workflows/on_push.yaml

@@ -107,10 +107,36 @@ jobs:
           echo "phase_three=${phase_three}" >> $GITHUB_OUTPUT
           echo "rebuild_phase_three=${rebuild_phase_three}" >> $GITHUB_OUTPUT
 
+  check_pr:
+    runs-on: ubuntu-latest
+    outputs:
+      test_mode: ${{ steps.check_pr.outputs.test_mode }}
+    steps:
+      - name: Check out C-PAC
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+      - name: Check if commit is in a PR to develop
+        id: check_pr
+        run: |
+          TEST_MODE=none
+          if echo "${{ github.event.head_commit.message }}" | grep -q '\[run reg-suite lite\]'
+          then
+            TEST_MODE=lite
+          elif gh pr list --base develop --json number,state,draft | jq 'any(.[]; .state == "OPEN" or .draft == true)'; then
+            TEST_MODE=lite
+          elif gh pr list --base main --json number,state,draft | jq 'any(.[]; .state == "OPEN" or .draft == true)'; then
+            TEST_MODE=full
+          fi
+          echo "test_mode=${TEST_MODE}"
+          echo "test_mode=${TEST_MODE}" >> $GITHUB_OUTPUT
+
   build-stages:
     name: Build multistage image stages
-    needs: check-updated-preconfigs
-    uses: ./.github/workflows/build_and_test.yml
+    needs:
+      - check_pr
+      - check-updated-preconfigs
+    uses: ./.github/workflows/build_and_test.yaml
     secrets: inherit
     with:
       phase_one: ${{ needs.check-updated-preconfigs.outputs.phase_one }}
@@ -119,3 +145,4 @@ jobs:
       rebuild_phase_two: ${{ needs.check-updated-preconfigs.outputs.rebuild_phase_two }}
       phase_three: ${{ needs.check-updated-preconfigs.outputs.phase_three }}
       rebuild_phase_three: ${{ needs.check-updated-preconfigs.outputs.rebuild_phase_three }}
+      test_mode: ${{ needs.check_pr.outputs.test_mode }}