Merge branch 'master' into import-biomappings-sssom-cli

.github/workflows/auto-pr-ontobot.yml

@@ -47,7 +47,7 @@ jobs:
         id: gh-script-issue
         uses: actions/github-script@v6
         with:
-          # github-token: ${{ secrets.GH_TOKEN }}
+          github-token: ${{ secrets.ONTOBOT_TOKEN }}
           script: |
             const issue_number = context.issue.number
             const repo = context.repo.owner+"/"+context.repo.repo
@@ -57,7 +57,7 @@ jobs:
         id: gh-script-repo
         uses: actions/github-script@v6
         with:
-          # github-token: ${{ secrets.GH_TOKEN }}
+          github-token: ${{ secrets.ONTOBOT_TOKEN }}
           script: |
             const repo = context.repo.owner+"/"+context.repo.repo
             return repo
@@ -78,7 +78,7 @@ jobs:
           ochange process-issue ${{ env.resource }} \
           -r ${{ steps.gh-script-repo.outputs.result }} \
           -n ${{ steps.gh-script-issue.outputs.result }} \
-          -g ${{ secrets.GH_TOKEN }} \
+          -g ${{ secrets.ONTOBOT_TOKEN }} \
           -p UBERON
 
       - name: Create Pull Request
@@ -93,4 +93,4 @@ jobs:
           committer: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com>
           base: ${{ github.head_ref }}
           branch: ${{ env.branch-name }}
-          # token: ${{ secrets.GH_TOKEN }}
+          token: ${{ secrets.ONTOBOT_TOKEN }}

.github/workflows/diff.yml

@@ -20,7 +20,7 @@ jobs:
           trigger: '#gogoeditdiff'
         env:
           GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-      - uses: docker-practice/actions-setup-docker@master
+      - uses: better0fdead/actions-setup-docker@better0fdead/increase-timeout
         if: steps.check.outputs.triggered == 'true'
       - run: |
           set -x
@@ -30,7 +30,7 @@ jobs:
         run: docker pull obolibrary/odklite
         if: steps.check.outputs.triggered == 'true'
       # Checks-out current branch
-      - uses: xt0rted/pull-request-comment-branch@v1
+      - uses: xt0rted/pull-request-comment-branch@v2.0.0
         id: comment-branch
       - uses: actions/checkout@v3
         if: steps.check.outputs.triggered == 'true'
@@ -92,12 +92,11 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
       - name: Post reasoned comment
         if: steps.check.outputs.triggered == 'true'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../comment.md"
           identifier: "REASONED"
+          github_token: ${{secrets.GITHUB_TOKEN}}
       - uses: actions/checkout@v3
         if: steps.check.outputs.triggered == 'true'
       - name: Download edit diff
@@ -110,12 +109,11 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
       - name: Post comment
         if: steps.check.outputs.triggered == 'true'
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        uses: NejcZdovc/[email protected]
+        uses: NejcZdovc/[email protected]
         with:
           file: "../../edit-comment.md"
           identifier: "UNREASONED"
+          github_token: ${{secrets.GITHUB_TOKEN}}
 
 
 

.github/workflows/qc.yml

@@ -1,4 +1,4 @@
-# This is a basic workflow to help you get started with Actions
+# Basic ODK workflow
 
 name: CI
 
@@ -7,8 +7,12 @@ on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
     branches: [ master ]
+    paths:
+      - 'src/**'
   pull_request:
     branches: [ master ]
+    paths:
+      - 'src/**'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -19,12 +23,11 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4.3
-
+    container: obolibrary/odkfull:v1.5
     # 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
         id: check
@@ -53,7 +56,7 @@ jobs:
           github_token: ${{secrets.GITHUB_TOKEN}}
           file: "../../comment.md"
           identifier: "TAXON_CONSTRAINTS_REASONING"
-
+  
       - name: Last rows of QC report
         if: steps.check.outcome == 'failure'
         run: |

docs/odk-workflows/RepoManagement.md

@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/uberon-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/uberon-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```

docs/odk-workflows/RepositoryFileStructure.md

@@ -18,14 +18,15 @@ These are the current imports in UBERON
 | ------ | --- | ---- |
 | pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None |
 | cl | http://purl.obolibrary.org/obo/cl.owl | None |
-| go | http://purl.obolibrary.org/obo/go.owl | None |
+| go | http://purl.obolibrary.org/obo/go/go-base.owl | None |
 | envo | http://purl.obolibrary.org/obo/envo.owl | None |
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | bspo | http://purl.obolibrary.org/obo/bspo.owl | None |
 | chebi | https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
+| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | None |
 | nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
 | orcidio | https://w3id.org/orcidio/orcidio.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
@@ -41,6 +42,7 @@ These are the components in UBERON
 
 | Filename | URL |
 | -------- | --- |
+| disjoint_union_over.owl | None |
 | mappings.owl | None |
 | in-subset.owl | None |
 | hra_subset.owl | None |