Update project config

.github/workflows/ndex.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@master
       - uses: actions/setup-python@v2
         with:
-          python-version: "3.13"
+          python-version: "3.14"
       - name: Install dependencies
         run: |
           pip install tox tox-uv

.github/workflows/tests.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.13", "3.10" ]
+        python-version: [ "3.14", "3.10" ]
         tox-command: [ "lint", "pyroma", "mypy" ]
     steps:
       - uses: actions/checkout@v4
@@ -48,7 +48,7 @@ jobs:
         # We only test documentation on the latest version
         # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
         # a year early, which prompted re-thinking about this.
-        python-version: [ "3.13" ]
+        python-version: [ "3.14" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"
@@ -76,7 +76,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.13", "3.10" ]
+        python-version: [ "3.14", "3.10" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"

.github/workflows/update_web.yml

@@ -14,10 +14,10 @@ jobs:
       - uses: actions/checkout@master
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
-          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+          fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
       - uses: actions/setup-python@v2
         with:
-          python-version: "3.13"
+          python-version: "3.14"
       - name: Install dependencies
         run: |
           pip install tox tox-uv

pyproject.toml

@@ -61,7 +61,7 @@ dependencies = [
     "curies>=0.13.0",
     "bioregistry>=0.13.0",
     "sssom-pydantic>=0.4.1",
-    "sssom-curator[web]>=0.3.0",
+    "sssom-curator[web]>=0.3.1",
 ]
 
 # see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups

scripts/generate_cl_mesh_mappings.py

@@ -33,12 +33,12 @@
     if has_mesh_id:
         continue
 
-    matches = gilda.ground(data["name"])
+    matches = gilda.ground(data["name"])  # type:ignore[no-untyped-call]
     if not matches:
         if data["name"].endswith(" cells"):
-            matches = gilda.ground(data["name"].replace(" cells", ""))
+            matches = gilda.ground(data["name"].replace(" cells", ""))  # type:ignore[no-untyped-call]
         elif data["name"].endswith(" cell"):
-            matches = gilda.ground(data["name"].replace(" cell", ""))
+            matches = gilda.ground(data["name"].replace(" cell", ""))  # type:ignore[no-untyped-call]
     if not matches:
         continue
 

scripts/generate_vaccine_mappings.py

@@ -2,6 +2,7 @@
 
 import click
 import pyobo
+import ssslm
 from curies.vocabulary import exact_match, lexical_matching_process
 from pyobo.sources.cpt import iter_terms
 from sssom_pydantic import MappingTool, SemanticMapping
@@ -19,10 +20,12 @@ def main() -> None:
     append_lexical_predictions("cpt", ["mesh", "vo"], mapping_tool=provenance)
 
     preds = []
-    grounder = pyobo.get_grounder(["mesh", "vo"], versions=["2023", None])
+    grounder: ssslm.Grounder = pyobo.get_grounder(["mesh", "vo"], versions=["2023", None])
     for term in iter_terms():
         texts = [term.name, *(s.name for s in term.synonyms)]
         for text in texts:
+            if not text:
+                continue
             for scored_match in grounder.get_matches(text + " vaccine"):
                 pred = SemanticMapping(
                     subject=term.reference,

scripts/generate_wikipathways_orthologs.py

@@ -16,7 +16,7 @@
 
 
 def _lexical_exact_match(name1: str, name2: str) -> bool:
-    return cast(str, normalize(name1)) == cast(str, normalize(name2))
+    return cast(str, normalize(name1)) == cast(str, normalize(name2))  # type:ignore[no-untyped-call]
 
 
 def iterate_orthologous_lexical_matches(prefix: str = "wikipathways") -> Iterable[SemanticMapping]:

tox.ini

@@ -148,10 +148,9 @@ dependency_groups =
 commands = mypy --ignore-missing-imports --strict src/ tests/ scripts/
 extras =
     web
-    pyobo
-    gilda-slim
+    predict-lexical
+    predict-embeddings
     exports
-    charts
 
 [testenv:docs-lint]
 skip_install = true