Add OMIM getter and update CI (#42)

Closes #41, updates to use tox-uv, and updates to test on py312

.github/workflows/tests.yml

@@ -12,15 +12,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.11", "3.8" ]
+        python-version: [ "3.12", "3.8" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: pip install tox tox-uv
       - name: Check manifest
         run: tox -e manifest
       - name: Check code quality with flake8
@@ -35,15 +35,15 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.11", "3.8" ]
+        python-version: [ "3.12", "3.8" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: pip install tox tox-uv
       - name: Test with pytest
         run:
           tox -e py

src/bioversions/sources/__init__.py

@@ -42,6 +42,7 @@
 from .npass import NPASSGetter
 from .obo import iter_obo_getters
 from .ols import extend_ols_getters
+from .omim import OMIMGetter
 from .oncotree import OncoTreeGetter
 from .pathbank import PathBankGetter
 from .pathwaycommons import PathwayCommonsGetter
@@ -127,6 +128,7 @@ def get_getters() -> List[Type[Getter]]:
         RGDGetter,
         CellosaurusGetter,
         MGIGetter,
+        OMIMGetter,
     ]
     getters.extend(iter_obo_getters())
     extend_ols_getters(getters)
@@ -143,6 +145,8 @@ def get_getter_dict() -> Mapping[str, Type[Getter]]:
             rv[norm(getter.bioregistry_id)] = getter
         rv[getter.name] = getter
         rv[norm(getter.name)] = getter
+    # TODO engineer this into the data model and backfill them
+    rv["omim.ps"] = OMIMGetter
     return rv
 
 

src/bioversions/sources/omim.py

@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for the OMIM."""
+
+
+from bioversions.utils import Getter, VersionType, get_soup
+
+__all__ = [
+    "OMIMGetter",
+]
+
+
+class OMIMGetter(Getter):
+    """A getter for OMIM."""
+
+    bioregistry_id = "omim"
+    name = "Online Mendelian Inheritance in Man"
+    date_version_fmt = "%B %d, %Y"
+    version_type = VersionType.date
+
+    def get(self) -> str:
+        """Get the latest OMIM version number."""
+        soup = get_soup("https://omim.org/")
+        for tag in soup.find_all("h5"):
+            text = tag.text.strip()
+            if text.startswith("Updated"):
+                rv = text[len("Updated") :].strip()
+                rv = rv.replace("nd", "").replace("st", "").replace("rd", "").replace("th", "")
+                return rv
+        raise ValueError
+
+
+if __name__ == "__main__":
+    OMIMGetter.print()

tox.ini

@@ -81,7 +81,7 @@ description = Run black.
 skip_install = true
 deps =
     darglint
-    flake8<5.0.0
+    flake8
     # flake8-bandit
     flake8-black
     flake8-bugbear
@@ -95,7 +95,11 @@ commands =
 description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
 
 [testenv:mypy]
-deps = mypy
+deps =
+    mypy
+    types-PyYAML
+    types-requests
+    types-tabulate
 skip_install = true
 commands = mypy --install-types --non-interactive --ignore-missing-imports src/bioversions/
 description = Run the mypy tool to check static typing on the project.
@@ -159,6 +163,7 @@ skip_install = true
 deps =
     wheel
     build
+    setuptools
 commands =
     python -m build --sdist --wheel --no-isolation