Merge branch 'main' into add_paper_rankings_to_exports

.github/workflows/paper_ranking.yml

@@ -24,8 +24,9 @@ jobs:
 
     - name: Install dependencies
       run: |
+        # TODO update to using uv
         python -m pip install --upgrade pip
-        pip install -r src/bioregistry/analysis/paper_ranking_requirements.txt
+        pip install .[paper-ranking]
 
     - name: Set Date Variables
       id: set-date-variables
@@ -43,6 +44,7 @@ jobs:
       id: run-ranking-script
       run: |
         echo "PYTHONPATH=$PYTHONPATH"  # Verify PYTHONPATH
+        # TODO update to using python -m
         python src/bioregistry/analysis/paper_ranking.py --start-date ${{ env.START_DATE }} --end-date ${{ env.END_DATE }}
 
     - name: Configure Git

.github/workflows/tests.yml

@@ -66,14 +66,9 @@ jobs:
       matrix:
         os: [ ubuntu-latest, windows-latest ]
         python-version: [ "3.12", "3.9" ]
-        pydantic: [ "pydantic1", "pydantic2" ]
         exclude:
           - os: windows-latest
             python-version: 3.9
-          - python-version: 3.9
-            pydantic: "pydantic1"
-          - os: windows-latest
-            pydantic: "pydantic1"
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"
@@ -83,7 +78,7 @@ jobs:
           cache-dependency-glob: "pyproject.toml"
       - name: Test with pytest and generate coverage file
         run:
-          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e py-${{ matrix.pydantic }}
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e py
       - name: Upload coverage report to codecov
         uses: codecov/codecov-action@v4
         if: success()

docs/_data/curation.yml

@@ -231,6 +231,9 @@ formatter:
 - homepage: https://openlhs.github.io/HOSO/
   name: Healthcare Organizations and Services Ontology
   prefix: hoso
+- homepage: https://icd.who.int/en
+  name: ICD 11 Codes
+  prefix: icd11.code
 - homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry
   name: Internet Engineering Task Force Language Tag
   prefix: ietf.language
@@ -303,9 +306,6 @@ formatter:
 - homepage: https://ftp.ncbi.nlm.nih.gov/pubmed/xmlprovidernames.txt
   name: NLM Publisher Codes
   prefix: nlm.publisher
-- homepage: http://bidd.group/NPASS/
-  name: Natural Product Activity and Species Source Database
-  prefix: npass
 - homepage: https://mail.nbfgr.res.in/nrfc/index.php
   name: National Repository of Fish Cell Lines
   prefix: nrfc
@@ -3304,9 +3304,6 @@ wikidata:
 - homepage: https://www.gbif.org/species
   name: Global Biodiversity Information Facility
   prefix: gbif
-- homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
-  name: Genetic Code
-  prefix: gc
 - homepage: https://www.ebi.ac.uk
   name: GWAS Catalog
   prefix: gcst
@@ -3810,8 +3807,11 @@ wikidata:
     System
   prefix: icd10pcs
 - homepage: https://icd.who.int/
-  name: International Classification of Diseases, 11th Revision
+  name: International Classification of Diseases, 11th Revision (Foundation Component)
   prefix: icd11
+- homepage: https://icd.who.int/en
+  name: ICD 11 Codes
+  prefix: icd11.code
 - homepage: https://caninecommons.cancer.gov/#/
   name: Integrated Canine Data Commons
   prefix: icdc
@@ -4775,6 +4775,9 @@ wikidata:
 - homepage: https://www.ncbi.nlm.nih.gov/
   name: Assembly
   prefix: ncbi.assembly
+- homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
+  name: Genetic Code
+  prefix: ncbi.gc
 - homepage: https://www.ncbi.nlm.nih.gov/genome
   name: NCBI Genome
   prefix: ncbi.genome
@@ -6356,6 +6359,9 @@ wikidata:
 - homepage: https://ifaa.unifr.ch/
   name: Terminologia Histologica
   prefix: th
+- homepage: https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages
+  name: Theiler Stage
+  prefix: theiler
 - homepage: https://www.thermofisher.com
   name: Thermo Fisher Scientific
   prefix: thermofisher