Merge branch 'master' into issue-764

.github/workflows/diff.yml

@@ -1,55 +1,92 @@
 name: 'Create ROBOT diffs on Pull requests'
 
-on:
-  # Triggers the workflow on pull request events for the master branch
-  pull_request:
-    branches: [ master ]
+on: 
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
+  issue_comment:
+        types: [created]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   edit_file:
+    if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
     container: obolibrary/odklite:v1.3.0
     steps:
-      - uses: actions/checkout@v2
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: xt0rted/pull-request-comment-branch@v1
+        id: comment-branch
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
+        with:
+          ref: ${{ steps.comment-branch.outputs.head_ref }}
+          path: branch
       # Checks-out main branch under "main" directory
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
         with:
           ref: master
           path: master
       - name: Diff classification
-        run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/cl-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right src/ontology/cl-edit.owl --right-catalog src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
+        if: steps.check.outputs.triggered == 'true'
+        run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/cl-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right branch/src/ontology/cl-edit.owl --right-catalog branch/src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
       - name: Upload diff
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v2
         with:
           name: edit-diff.md
           path: edit-diff.md
   classify_branch:
+    if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
     container: obolibrary/odklite:v1.3.0
     steps:
-      - uses: actions/checkout@v2
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: xt0rted/pull-request-comment-branch@v1
+        id: comment-branch
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
+        with:
+          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
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v2
         with:
           name: cl-simple-pr.owl
           path: src/ontology/cl-simple.owl
           retention-days: 1
   classify_main:
+    if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
     container: obolibrary/odklite:v1.3.0
     steps:
-      - uses: actions/checkout@v2
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
         with:
           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
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v2
         with:
           name: cl-simple-master.owl
@@ -62,20 +99,31 @@ jobs:
     runs-on: ubuntu-latest
     container: obolibrary/odklite:v1.3.0
     steps:
-      - uses: actions/checkout@v2
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
       - name: Download master classification
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v2
         with:
           name: cl-simple-master.owl
           path: src/ontology/cl-simple-master.owl
       - name: Download PR classification
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v2
         with:
           name: cl-simple-pr.owl
           path: src/ontology/cl-simple-pr.owl
       - name: Diff classification
+        if: steps.check.outputs.triggered == 'true'
         run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-simple-master.owl/cl-simple.owl --left-catalog catalog-v001.xml --right cl-simple-pr.owl/cl-simple.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
       - name: Upload diff
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v2
         with:
           name: classification-diff.md
@@ -84,30 +132,44 @@ jobs:
     needs: [diff_classification, edit_file]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: khan/[email protected]
+        id: check
+        with:
+          trigger: '#gogoeditdiff'
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
       - name: Download reasoned diff
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v2
         with:
           name: classification-diff.md
           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"
       - name: Post reasoned comment
+        if: steps.check.outputs.triggered == 'true'
         env:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
         uses: NejcZdovc/[email protected]
         with:
           file: "../../comment.md"
           identifier: "REASONED"
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        if: steps.check.outputs.triggered == 'true'
       - name: Download edit diff
+        if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v2
         with:
           name: edit-diff.md
           path: edit-diff.md
       - name: Prepare edit file comment
+        if: steps.check.outputs.triggered == 'true'
         run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" >edit-comment.md; cat edit-diff.md/edit-diff.md >>edit-comment.md"
       - name: Post comment
+        if: steps.check.outputs.triggered == 'true'
         env:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
         uses: NejcZdovc/[email protected]

.github/workflows/docs.yml

@@ -5,6 +5,9 @@ name: Docs
 on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
+  push:
+    branches:
+      - master
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

.github/workflows/qc.yml

@@ -24,7 +24,7 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         env:

README.md

@@ -20,12 +20,14 @@ To browse the ontology, we recommend using OLS:
 https://www.ebi.ac.uk/ols/ontologies/cl
 
 For more details on CL see:
-- https://cell-ontology.github.io/
-- [OBO Foundry](http://obofoundry.org/ontology/cl.html)
+- [CL Website](https://cell-ontology.github.io/)
+- [CL on the OBO Foundry](http://obofoundry.org/ontology/cl.html)
 
-Documentation for the Cell Ontology is also available at https://obophenotype.github.io/cell-ontology/.
 
-Editors: see the README in [src/ontology](src/ontology)
+Editors documentation: 
+* [CL Editor doc](https://obophenotype.github.io/cell-ontology/)
+* [Generic ODK workflows](src/ontology/README-editors.md)
+* [OBO Academy oBook](https://oboacademy.github.io/obook/getting-started/) - General ontology editor and developer documentation and tutorials.
 
 Training materials from the 2020 CL Training Workshop are available at https://github.com/obophenotype/cell-ontology-training.
 
@@ -40,6 +42,10 @@ Fourth Monday of month, 10am PT/1pm ET (CL & Uberon)
 
 Diehl,A.D., Meehan,T.F., Bradford,Y.M., Brush,M.H., Dahdul,W.M., Dougall,D.S., He,Y., Osumi-Sutherland,D., Ruttenberg,A., Sarntivijai,S., et al. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semantics, 7, 44.
 
+## GitHub Actions Triggers
+
+To trigger an automated human readable diff, add the following tag to a comment in your pull request: #gogoeditdiff
+
 ## Applications
 
 CL is used in a number of applications including: