Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

obophenotype · Nov 4, 2024 · 7bc48d3 · 7bc48d3
2 parents 2b63cac + e280d0b
commit 7bc48d3
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diff --git a/.github/workflows/diff.yml b/.github/workflows/diff.yml
@@ -53,7 +53,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -87,7 +87,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -103,19 +103,19 @@ jobs:
           ref: ${{ steps.comment-branch.outputs.head_ref }}
       - name: Classify ontology
         if: steps.check.outputs.triggered == 'true'
-        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl
-      - name: Upload PR cl-simple.owl
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-base.owl
+      - name: Upload PR cl-base.owl
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
         with:
-          name: cl-simple-pr.owl
-          path: src/ontology/cl-simple.owl
+          name: cl-base-pr.owl
+          path: src/ontology/cl-base.owl
           retention-days: 1
   classify_main:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -129,18 +129,18 @@ jobs:
           ref: master
       - name: Classify ontology
         if: steps.check.outputs.triggered == 'true'
-        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl
-      - name: Upload master cl-simple.owl
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-base.owl
+      - name: Upload master cl-base.owl
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
         with:
-          name: cl-simple-master.owl
-          path: src/ontology/cl-simple.owl
+          name: cl-base-master.owl
+          path: src/ontology/cl-base.owl
           retention-days: 1
   diff_classification:
     needs:  [classify_branch, classify_main]
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -154,17 +154,17 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v4
         with:
-          name: cl-simple-master.owl
-          path: src/ontology/cl-simple-master.owl
+          name: cl-base-master.owl
+          path: src/ontology/cl-base-master.owl
       - name: Download PR classification
         if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v4
         with:
-          name: cl-simple-pr.owl
-          path: src/ontology/cl-simple-pr.owl
+          name: cl-base-pr.owl
+          path: src/ontology/cl-base-pr.owl
       - name: Diff classification
         if: steps.check.outputs.triggered == 'true'
-        run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-simple-master.owl/cl-simple.owl --left-catalog catalog-v001.xml --right cl-simple-pr.owl/cl-simple.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
+        run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-base-master.owl/cl-base.owl --left-catalog catalog-v001.xml --right cl-base-pr.owl/cl-base.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
       - name: Upload diff
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
@@ -191,7 +191,7 @@ jobs:
           path: classification-diff.md
       - name: Prepare reasoned comment
         if: steps.check.outputs.triggered == 'true'
-        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -simple file): </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
+        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -base file): </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
       - name: Post reasoned comment
         if: steps.check.outputs.triggered == 'true'
         env: