Replace chebi slim URL, update ODK 1.6

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+# Basic ODK workflow
+name: Docs
+
+# Controls when the action will run. 
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yaml
+

.github/workflows/qc.yml

@@ -4,11 +4,11 @@ name: CI
 
 # Controls when the action will run. 
 on:
-  # Triggers the workflow on push or pull request events but only for the master branch
+  # Triggers the workflow on push or pull request events but only for the main branch
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.3.0
+    container: obolibrary/odkfull:v1.6
 
     # 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@v4
 
       - name: Run ontology QC checks
         env:
-          DEFAULT_BRANCH: master
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 

.gitignore

@@ -1,8 +1,75 @@
+# ODK-managed rules, do not modify
+# If you need to add your own ignore rules, you may do so below
+# the "End ODK-managed rules" marker at the end of this file.
+.DS_Store
+semantic.cache
+bin/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+*-relation-graph.tsv.gz
+.template.db
+
+.github/token.txt
+
+/caro.owl
+/caro.obo
+/caro.json
+/caro.db
+/caro-base.*
+/caro-basic.*
+/caro-full.*
+/caro-simple.*
+/caro-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/caro.owl
+src/ontology/caro.obo
+src/ontology/caro.json
+src/ontology/caro.db
+src/ontology/caro-base.*
+src/ontology/caro-basic.*
+src/ontology/caro-full.*
+src/ontology/caro-simple.*
+src/ontology/caro-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-caro-edit.owl
+src/ontology/caro-edit.properties
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
+
+# End of ODK-managed rules
 *.norm
 *.old
 *.qlf
-*.tmp.obo
-*.tmp.owl
 *.tmp.ttl
 .\#*
 .idea
@@ -11,14 +78,12 @@
 .sparqlprog_history
 .token
 .vscode
-/caro-base.*
 /caro-with-equivalents.*
 /caro.*
 /subsets/caro-minimal.*
 LOG
 \#*\#
 _site/
-bin/
 env/
 imports/*.json
 src/.DS_Store
@@ -40,33 +105,25 @@ src/ontology/caro-lastbuild.obo
 src/ontology/caro-ncit.owl
 src/ontology/caro-qc.*
 src/ontology/caro-with-equivalents.*
-src/ontology/caro.json
-src/ontology/caro.obo
-src/ontology/caro.owl
 src/ontology/caroRelease_2020-09-01.txt
 src/ontology/caro_current_release.owl
 src/ontology/compare/
 src/ontology/debug.owl
 src/ontology/disjoint_sibs.owl
-src/ontology/dosdp-tools.log
-src/ontology/ed_definitions_merged.owl
 src/ontology/edit-merged.owl
 src/ontology/filtered.obo
 src/ontology/filtered.owl
 src/ontology/imports/*.json
 src/ontology/imports/*_newterms.txt
-src/ontology/imports/*_terms_combined.txt
 src/ontology/imports/equivalencies.obo
 src/ontology/imports/equivalencies.owl
 src/ontology/imports/omo_terms.txt
 src/ontology/imports/seed.txt
 src/ontology/merged.owl
-src/ontology/patterns 
 src/ontology/reasoned-plus-equivalents.owl
 src/ontology/reasoned.owl
 src/ontology/reports
 src/ontology/roundtrip.obo
-src/ontology/seed.txt
 src/ontology/skos.ttl
 src/ontology/sources/*
 src/ontology/sources/*.json
@@ -80,19 +137,14 @@ src/ontology/subsets/caro-minimal.obo
 src/ontology/subsets/caro-minimal.owl
 src/ontology/subsets/caro-minimal.owl.tmp.owl
 src/ontology/subsets/caro-minimal.owl.tmp2.owl
-src/ontology/target/
 src/ontology/tbn.obo
 src/ontology/tbn.owl
 src/ontology/test_nomerge
 src/ontology/tmp
 src/ontology/tmp/
-src/ontology/tmp/*
-src/ontology/mirror/*
-src/patterns/all_pattern_terms.txt
 src/patterns/data/default/*.ofn
 src/patterns/data/default/*.txt
-src/patterns/pattern_owl_seed.txt
 target/
 unmapped-*
 venv
-weights-*
+weights-*