Merge pull request #628 from dkuegler/fix/quicktest

Fixing issues in quicktest

Author: dkuegler

.github/actions/run-tests/action.yml

@@ -41,16 +41,18 @@ runs:
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
         python -m pip install --progress-bar off .[quicktest]
         echo "::endgroup::"
-    - name: Download reference data
+    - name: Download and unpack reference data
       shell: bash
       env:
         CASE_HREF: ${{ inputs.case-href }}
         REF_DIR: ${{ inputs.reference-dir }}
       run: |
         echo "::group::Prepare processed and reference data"
         mkdir -p $REF_DIR
-        echo "REF_DIR=$REF_DIR" >> $GITHUB_ENV
-        curl -k "$CASE_HREF" | tar xf --directory "$REF_DIR"
+        curl -k "$CASE_HREF" -o "$REF_DIR/ref-download-data"
+        tar xf "$REF_DIR/ref-download-data" -C "$REF_DIR"
+        rm -f "$REF_DIR/ref-download-data"
+        echo "::endgroup::"
     - name: Recover Case data
       uses: ./.github/actions/load-processed
       with:
@@ -64,7 +66,7 @@ runs:
         REF_DIR: ${{ inputs.reference-dir }}
       shell: bash
       run: |
-        echo "::endgroup::"
         echo "::group::Run tests"
         python -m pytest test/quick_test
+        echo "::endgroup::"
 

.github/workflows/quicktest.yaml

@@ -1,8 +1,9 @@
-name: PR quicktest
+name: quicktest
 
 # File: quicktest.yaml
-# Author: Taha Abdullah
-# Created on: 2023-07-10
+# Author: David Kügler
+# Reworked on: 2024-12-01
+# Created on: 2023-07-10 by Taha Abdullah
 # Functionality: This workflow runs FastSurfer on MRI data and runs pytest to check if the results are acceptable. It
 #  also checks if the FastSurfer environment and output already exist, and if not, it creates them.
 # Usage: This workflow is triggered on a pull request to the dev and main branch. It can also be triggered manually
@@ -30,8 +31,8 @@ on:
         description: 'Which docker image should be used to run this test (build-cached => build from git)'
         default: build-cached
         type: string
-      freesurfer_build_image:
-        description: 'FreeSurfer build image to build with'
+      freesurfer-build-image:
+        description: 'FreeSurfer build image to build with (default="": deep MI/fastsurfer-build:freesurferXXX; extract version from Docker/install_fs_pruned.sh)'
         type: string
 
 permissions: read-all
@@ -60,6 +61,19 @@ jobs:
         env:
           GH_TOKEN: ${{ github.token }}
         run: |
+          echo "::group::Debug information"
+          echo "Workflow: ${{ github.workflow }}"
+          echo "Action: ${{ github.event.action }}"
+          if [[ "${{ github.event_name }}" == "pull_request" ]]
+            echo "PR: ${{ github.event.number }}"
+            echo "Event Triggered by: ${{ github.event.sender.login }}"
+          elif [[ "${{ github.event_name }}" == "workflow_dispatch" ]]
+            echo "Inputs"
+            cat <<EOF
+            ${{ toJSON(inputs) }}
+            EOF
+          fi
+          echo "::endgroup::"
           h1="Accept: application/vnd.github+json"
           h2="X-GitHub-Api-Version: 2022-11-28"
           if [[ "${{ github.event_name }}" == "pull_request" ]]
@@ -70,34 +84,31 @@ jobs:
               echo "The Workflow '${{ github.workflow }}' was triggered by 'pull_request' of type"
               echo "  '${{ github.event.action }}' but should only be triggered by 'labeled' or 'unlabeled' actions."
               echo "CONTINUE=false" > $GITHUB_OUTPUT
-              exit
             elif [[ "${{ github.event.label.name }}" == "quicktest" ]]
             then
               echo "CONTINUE=true" > $GITHUB_OUTPUT
             else
               echo "This is a different label that was attached."
               echo "CONTINUE=false" > $GITHUB_OUTPUT
-              exit
             fi
             echo "DOCKER_IMAGE=build-cached" >> $GITHUB_OUTPUT
           elif [[ "${{ github.event_name }}" == "workflow_dispatch" ]]
           then
-            if [[ "${{ inputs }}" == "{}" ]] || "${{ inputs.docker-image }}" == "" ]] ; then
+            # the inputs context is only useful/set in the workflow dispatch event case 
+            if [[ "${{ toJSON(inputs) }}" == "{}" ]] || [[ "${{ inputs.docker-image }}" == "" ]] ; then
               echo "DOCKER_IMAGE=build-cached" > $GITHUB_OUTPUT
             else
               echo "DOCKER_IMAGE=${{ inputs.docker-image }}" > $GITHUB_OUTPUT
             fi
             echo "CONTINUE=true" >> $GITHUB_OUTPUT
-            exit
-          else #  this event has no specific rules
+          else #  this event has no specific rules (invalid)
             echo "This workflow is not defined for the event ${{ github.event_name }}!"
             exit 1
           fi
           if ! gh api -H "$h1" -H "$h2" /repos/${{ github.repository }}/collaborators/${{ github.event.sender.login }}
           then
             echo "Only collaborators explicitly listed as collaborators can trigger this workflow!"
             echo "CONTINUE=false" >> $GITHUB_OUTPUT
-            exit
           fi
           # later, we might want to extract additional run options from the pr text or issue comments
           # these should just be added here 
@@ -106,10 +117,10 @@ jobs:
           # this may also need adaptations in the test script at the bottom
           echo "EXTRA_ARGS=" >> $GITHUB_OUTPUT
       - name: Checkout repository
-        if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }}
+        if: ${{ steps.parse.outputs.CONTINUE && steps.parse.outputs.DOCKER_IMAGE == 'build-cached' }}
         uses: actions/checkout@v4
       - name: Get the FreeSurfer version
-        if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }}
+        if: ${{ steps.parse.outputs.CONTINUE && steps.parse.outputs.DOCKER_IMAGE == 'build-cached' }}
         shell: bash
         id: parse-version
         run: |
@@ -120,15 +131,15 @@ jobs:
             fs_version_short="${fs_version//\./}"
             echo "FS_VERSION=$fs_version"
             echo "FS_VERSION_SHORT=$fs_version_short"
-            if [[ -n "${{ inputs.freesurfer_build_image }}" ]] ; then
-              echo "FS_BUILD_IMAGE=${{ inputs.freesurfer_build_image }}"
+            if [[ -n "${{ inputs.freesurfer-build-image }}" ]] ; then
+              echo "FS_BUILD_IMAGE=${{ inputs.freesurfer-build-image }}"
             else
               echo "FS_BUILD_IMAGE=deepmi/fastsurfer-build:freesurfer$fs_version_short"
             fi
             echo "FASTSURFER_HOME=$(pwd)"
           } > $GITHUB_OUTPUT
       - uses: Deep-MI/FastSurfer/.github/actions/build-docker@dev
-        if: ${{ steps.parse.outputs.continue && steps.parse.outputs.docker-image == 'build-cached' }}
+        if: ${{ steps.parse.outputs.CONTINUE && steps.parse.outputs.DOCKER_IMAGE == 'build-cached' }}
         # This action needs the "full" checkout (located at ${{ inputs.fastsurfer-home }})
         with:
           fastsurfer-home: ${{ steps.parse-version.outputs.FASTSURFER_HOME }}
@@ -140,6 +151,7 @@ jobs:
     needs: build-docker-latest
     runs-on: ubuntu-latest
     timeout-minutes: 180
+    if: needs.build-docker-latest.outputs.continue
     strategy:
       # the following matrix strategy will result in one run per subject as matrix is "one-dimensional".
       # Additional parameters under "include" are then added as additional (dependent) information
@@ -166,7 +178,7 @@ jobs:
           docker-image: ${{ needs.build-docker-latest.outputs.docker-image }}
           extra-args: ${{ needs.build-docker-latest.outputs.extra-args }}
   tests:
-    name: Download data and perform tests (1.0mm)
+    name: 'Download data and perform tests'
     needs: fastsurfer
     runs-on: ubuntu-latest
     timeout-minutes: 60
@@ -188,4 +200,4 @@ jobs:
           subject-id: ${{ matrix.subject-id }}
           subjects-dir: ${{ env.SUBJECTS_DIR }}
           reference-dir: ${{ env.REFERENCE_DIR }}
-          case-href: ${{ secrets[matrix.case-href] }}
+          case-href: ${{ secrets[matrix.case-key] }}