Update to 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

@@ -4,7 +4,7 @@ name: CI
 
 # Controls when the action will run. 
 on:
-  # Triggers the workflow on push or pull request events but only for the main branch
+  # Triggers the workflow on push or pull request events but only for the master branch
   push:
     branches: [ master ]
   pull_request:
@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4.3
+    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=true
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 

.gitignore

@@ -1,31 +1,76 @@
+# 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
+
+/ecto.owl
+/ecto.obo
+/ecto.json
+/ecto.db
+/ecto-base.*
+/ecto-basic.*
+/ecto-full.*
+/ecto-simple.*
+/ecto-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
 src/ontology/mirror
 src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
 src/ontology/ecto.owl
 src/ontology/ecto.obo
 src/ontology/ecto.json
+src/ontology/ecto.db
 src/ontology/ecto-base.*
 src/ontology/ecto-basic.*
 src/ontology/ecto-full.*
 src/ontology/ecto-simple.*
 src/ontology/ecto-simple-non-classified.*
-semantic.cache
-bin/
+
 src/ontology/seed.txt
-src/ontology/target/
 src/ontology/dosdp-tools.log
-src/patterns/imports/seed_sorted.txt
 src/ontology/ed_definitions_merged.owl
-src/ontology/patterns 
-*.tmp.obo
-*.tmp.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-ecto-edit.owl
+src/ontology/ecto-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/ontology/Dockerfile
 src/patterns/all_pattern_terms.txt
+
+# End of ODK-managed rules
+src/patterns/imports/seed_sorted.txt
+src/ontology/Dockerfile
 src/ontology/reports
 src/ontology/tmp
-src/ontology/imports/*_terms_combined.txt
 src/mapping/exposure-*.obo
 src/mapping/tmp*
 snomed.obo