Merge pull request #81 from monarch-initiative/pato_and_repo

General fixes and update for current build; PATO placeholders

.github/workflows/docs.yml

@@ -1,31 +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@v3
-        with:
-          fetch-depth: 0
-
-      - name: Install dependencies
-        run: |
-          pip install mkdocs
-          pip install mkdocs-material
-          pip install mkdocs-mermaid2-plugin
 
       - 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
-        run: |
-          mkdocs gh-deploy --config-file $CONFIG_FILE
+

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                e6c8433a2061b8c344c045ae57324b457c3c5c0b221faaaec4373a8c55c52c2b
+CONFIG_HASH=                f62edbb77b824d9d98a8a8d1bf6f269d7845bea52b68c8563b61f981b9734253
 
 
 # ----------------------------------------
@@ -365,7 +365,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 
 $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
-		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>"  \
+		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \