Minor curations and code updates (#1178)

* Add pattern and URI format to CRediT * Add wikidata link for Publons Researcher ID * Add Mastodon prefix * Update bioregistry.json * Use UV for tests * Update mypy
biopragmatics · Sep 3, 2024 · f2faef4 · f2faef4
1 parent dd2d282
commit f2faef4
Show file tree

Hide file tree

Showing 4 changed files with 61 additions and 16 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -21,8 +21,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install --upgrade pip setuptools wheel
-          pip install tox
+          pip install tox tox-uv
       - name: Check manifest
         run: tox -e manifest
       - name: Check code quality with flake8
@@ -36,7 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -45,8 +44,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install --upgrade pip setuptools wheel
-          pip install tox
+          pip install tox tox-uv
       - name: Check RST conformity with doc8
         run: tox -e doc8
       - name: Check docstring coverage
@@ -59,7 +57,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.11", "3.8" ]
+        python-version: [ "3.12", "3.8" ]
         pydantic: [ "pydantic1", "pydantic2" ]
     steps:
       - uses: actions/checkout@v2
@@ -69,8 +67,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install --upgrade pip setuptools wheel
-          pip install tox
+          pip install tox tox-uv
       - name: Test with pytest
         run:
           tox -e py-${{ matrix.pydantic }}

diff --git a/src/bioregistry/analysis/paper_ranking.py b/src/bioregistry/analysis/paper_ranking.py
@@ -332,8 +332,8 @@ def main(bioregistry_file, start_date, end_date):
     click.echo(f"Writing evaluation to {evaluation_path}")
     evaluation_df.to_csv(evaluation_path, sep="\t", index=False)
 
-    random_forest_clf: RandomForestClassifier = classifiers[0][1]
-    lr_clf: LogisticRegression = classifiers[1][1]
+    random_forest_clf = classifiers[0][1]
+    lr_clf = classifiers[1][1]
     importances_df = (
         pd.DataFrame(
             list(

diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
@@ -22123,14 +22123,19 @@
     "uri_format": "https://crates.io/crates/$1"
   },
   "credit": {
+    "contact": {
+      "email": "liz.allen@f1000.com",
+      "name": "Liz Allen",
+      "orcid": "0000-0002-9298-3168"
+    },
     "contributor": {
       "email": "cthoyt@gmail.com",
       "github": "cthoyt",
       "name": "Charles Tapley Hoyt",
       "orcid": "0000-0003-4423-4370"
     },
     "description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.",
-    "example": "Software",
+    "example": "software",
     "fairsharing": {
       "abbreviation": "CRediT",
       "contact": {
@@ -22183,11 +22188,12 @@
       ],
       "twitter": "contrib_roles"
     },
-    "homepage": "https://casrai.org/credit/",
+    "homepage": "https://credit.niso.org/",
     "mappings": {
       "fairsharing": "FAIRsharing.fe4816"
     },
     "name": "CASRAI Contributor Roles Taxonomy",
+    "pattern": "^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$",
     "publications": [
       {
         "doi": "10.1038/d41586-019-01715-4",
@@ -22215,7 +22221,11 @@
         "title": "How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship",
         "year": 2019
       }
-    ]
+    ],
+    "references": [
+      "https://casrai.org/credit/"
+    ],
+    "uri_format": "https://credit.niso.org/contributor-roles/$1"
   },
   "crisprdb": {
     "biocontext": {
@@ -63630,6 +63640,30 @@
       "uri_format": "https://massive.ucsd.edu/ProteoSAFe/protein_explorer.jsp?libraries=2&protein_name=$1"
     }
   },
+  "mastodon": {
+    "contributor": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "homepage": "https://mastodon.social",
+    "mappings": {
+      "wikidata": "P4033"
+    },
+    "name": "Mastodon",
+    "wikidata": {
+      "description": "address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')",
+      "example": [
+        "jz@mamot.fr",
+        "libreoffice@fosstodon.org"
+      ],
+      "name": "Mastodon address",
+      "pattern": "^[A-Za-z0-9_]+([A-Za-z0-9_\\.]+[A-Za-z0-9_]+)?@[\\d\\w\\.\\-]+[0-9a-z]+$",
+      "prefix": "P4033",
+      "uri_format": "https://fedirect.toolforge.org/?id=$1"
+    }
+  },
   "mat": {
     "aberowl": {
       "description": "Minimal set of terms for anatomy",
@@ -94174,11 +94208,24 @@
     "example": "1981638",
     "homepage": "https://publons.com/researcher",
     "mappings": {
-      "biolink": "ResearchID"
+      "biolink": "ResearchID",
+      "wikidata": "P3829"
     },
     "name": "Publons Researcher",
     "pattern": "^\\d+$",
-    "uri_format": "https://publons.com/researcher/$1"
+    "uri_format": "https://publons.com/researcher/$1",
+    "wikidata": {
+      "description": "identifier of an author or reviewer, in Publons that redirects, along with P1053, to an ID in Clarivate's Web of Science",
+      "example": [
+        "2388520",
+        "2544783",
+        "654601"
+      ],
+      "name": "Publons author ID",
+      "pattern": "^\\d+$",
+      "prefix": "P3829",
+      "uri_format": "https://publons.com/researcher/$1/"
+    }
   },
   "pubmed": {
     "biocontext": {

diff --git a/tox.ini b/tox.ini
@@ -125,8 +125,9 @@ deps =
     types-Markdown
     types-tabulate
     types-requests
+    types-python-dateutil
 skip_install = true
-commands = mypy --install-types --non-interactive --ignore-missing-imports src/bioregistry/
+commands = mypy --ignore-missing-imports src/bioregistry/
 description = Run the mypy tool to check static typing on the project.
 
 [testenv:pyroma]