bioversions 0.7.40__tar.gz → 0.7.42__tar.gz

{bioversions-0.7.40 → bioversions-0.7.42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.7.40
+Version: 0.7.42
 Summary: Get the current version for biological databases
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
 Author: Charles Tapley Hoyt
@@ -39,13 +39,7 @@ Requires-Dist: pydantic>=2.0
 Requires-Dist: psycopg2-binary
 Requires-Dist: matplotlib ; extra == 'charts'
 Requires-Dist: seaborn ; extra == 'charts'
-Requires-Dist: sphinx>=8 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme>=3.0 ; extra == 'docs'
-Requires-Dist: sphinx-click ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
 Requires-Dist: slack-sdk ; extra == 'slack'
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: coverage[toml] ; extra == 'tests'
 Requires-Dist: tweepy ; extra == 'twitter'
 Requires-Dist: flask ; extra == 'web'
 Requires-Dist: bootstrap-flask ; extra == 'web'
@@ -58,9 +52,7 @@ Project-URL: Funding, https://github.com/sponsors/cthoyt
 Project-URL: Homepage, https://github.com/biopragmatics/bioversions
 Project-URL: Repository, https://github.com/biopragmatics/bioversions.git
 Provides-Extra: charts
-Provides-Extra: docs
 Provides-Extra: slack
-Provides-Extra: tests
 Provides-Extra: twitter
 Provides-Extra: web
 Description-Content-Type: text/markdown
@@ -173,18 +165,15 @@ $ python3 -m pip install bioversions
 The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-$ uv --preview pip install git+https://github.com/biopragmatics/bioversions.git
+$ uv pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
 or with pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+$ python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are
@@ -247,18 +236,15 @@ To install in development mode, use the following:
 ```console
 $ git clone git+https://github.com/biopragmatics/bioversions.git
 $ cd bioversions
-$ uv --preview pip install -e .
+$ uv pip install -e .
 ```
 
 Alternatively, install using pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install -e .
+$ python3 -m pip install -e .
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ### Updating Package Boilerplate
 
 This project uses `cruft` to keep boilerplate (i.e., configuration, contribution

{bioversions-0.7.40 → bioversions-0.7.42}/README.md

@@ -106,18 +106,15 @@ $ python3 -m pip install bioversions
 The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-$ uv --preview pip install git+https://github.com/biopragmatics/bioversions.git
+$ uv pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
 or with pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+$ python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are
@@ -180,18 +177,15 @@ To install in development mode, use the following:
 ```console
 $ git clone git+https://github.com/biopragmatics/bioversions.git
 $ cd bioversions
-$ uv --preview pip install -e .
+$ uv pip install -e .
 ```
 
 Alternatively, install using pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install -e .
+$ python3 -m pip install -e .
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ### Updating Package Boilerplate
 
 This project uses `cruft` to keep boilerplate (i.e., configuration, contribution

{bioversions-0.7.40 → bioversions-0.7.42}/pyproject.toml

@@ -1,12 +1,10 @@
 [build-system]
-requires = ["uv>=0.5.13,<0.6.0"]
-# The uv backend entered preview mode in https://github.com/astral-sh/uv/pull/8886/files
-# with the 0.5.0 release. See also https://github.com/astral-sh/uv/issues/3957 for tracking.
-build-backend = "uv"
+requires = ["uv_build>=0.6.6,<0.7"]
+build-backend = "uv_build"
 
 [project]
 name = "bioversions"
-version = "0.7.40"
+version = "0.7.42"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -69,7 +67,8 @@ dependencies = [
     "psycopg2-binary",
 ]
 
-[project.optional-dependencies]
+# see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups
+[dependency-groups]
 tests = [
     "pytest",
     "coverage[toml]",
@@ -77,9 +76,53 @@ tests = [
 docs = [
     "sphinx>=8",
     "sphinx-rtd-theme>=3.0",
-    "sphinx-click", 
+    "sphinx-click",
     "sphinx_automodapi",
 ]
+lint = [
+    "ruff",
+]
+typing = [
+    { include-group = "tests" },
+    "mypy",
+    "pydantic",
+    "types-PyYAML",
+    "types-python-dateutil",
+    "types-requests",
+    "types-tabulate",
+]
+docs-lint = [
+    { include-group = "docs" },
+    "doc8",
+]
+format-docs = [
+    { include-group = "docs" },
+    "docstrfmt",
+]
+doctests = [
+    "xdoctest",
+    "pygments",
+]
+pyroma = [
+    "pyroma",
+    "pygments",
+]
+# follow https://github.com/astral-sh/uv/issues/6298 for switching to a uv-based version bump workflow
+bump = [
+    "bump-my-version",
+]
+build = [
+    "uv",
+    "uv-build",
+]
+release = [
+    { include-group = "build" },
+    "uv",
+    "keyring",
+]
+
+# see https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#dependencies-optional-dependencies
+[project.optional-dependencies]
 slack = [
     "slack_sdk",
 ]
@@ -138,6 +181,9 @@ source = [
 omit = [
     "tests/*",
     "docs/*",
+    "src/bioversions/version.py",
+    "src/bioversions/__main__.py",
+    "src/bioversions/cli.py",
 ]
 
 [tool.coverage.paths]
@@ -214,7 +260,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.7.40"
+current_version = "0.7.42"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

bioversions-0.7.42/src/bioversions/__main__.py

@@ -0,0 +1,6 @@
+"""Entrypoint module, in case you use `python -m bioversions`."""
+
+from .cli import main
+
+if __name__ == "__main__":
+    main()

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/charts.py

@@ -13,13 +13,13 @@ from bioversions.utils import IMG, VersionType
 sns.set(style="whitegrid")
 
 
-def version_types_pie_chart():
+def version_types_pie_chart() -> None:
     """Make a pie chart with types of versions."""
-    counts = Counter(
+    counter = Counter(
         "Missing" if getter.version_type is None else getter.version_type.value
         for getter in get_getters()
     )
-    labels, counts = zip(*counts.most_common(), strict=False)
+    labels, counts = zip(*counter.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,
@@ -34,14 +34,14 @@ def version_types_pie_chart():
     plt.close(fig)
 
 
-def verioning_date_formats_pie_chart():
+def verioning_date_formats_pie_chart() -> None:
     """Make a pie chart with types of date/month versions."""
-    counts = Counter(
+    counter = Counter(
         getter.date_version_fmt
         for getter in get_getters()
         if getter.version_type in {VersionType.date, VersionType.month}
     )
-    labels, counts = zip(*counts.most_common(), strict=False)
+    labels, counts = zip(*counter.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,
@@ -56,14 +56,14 @@ def verioning_date_formats_pie_chart():
     plt.close(fig)
 
 
-def has_release_url():
+def has_release_url() -> None:
     """Make a pie chart for how many have a release URL."""
-    counts = Counter(
+    counter = Counter(
         "Has Stable Version URL" if getter.homepage_fmt is not None else "No Stable Version URL"
         for getter in get_getters()
         if getter.version_type != VersionType.unversioned
     )
-    labels, counts = zip(*counts.most_common(), strict=False)
+    labels, counts = zip(*counter.most_common(), strict=False)
     fig, ax = plt.subplots()
     ax.pie(
         counts,
@@ -79,7 +79,7 @@ def has_release_url():
 
 
 @click.command()
-def charts():
+def charts() -> None:
     """Generate charts for bioversions."""
     version_types_pie_chart()
     verioning_date_formats_pie_chart()

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/cli.py

@@ -1,4 +1,4 @@
-"""Command line interface for bioversions."""
+"""Command line interface for :mod:`bioversions`."""
 
 import click
 from click_default_group import DefaultGroup
@@ -10,7 +10,7 @@ from bioversions.resources.update import update
 
 @click.group(cls=DefaultGroup, default="web", default_if_no_args=True)
 @click.version_option()
-def main():
+def main() -> None:
     """The bioversions CLI."""  # noqa:D401
 
 
@@ -25,19 +25,19 @@ web = make_web_command(
 )
 
 
-@main.command()
+@main.command()  # type:ignore
 @click.argument("key")
-@verbose_option
-def get(key: str):
+@verbose_option  # type:ignore
+def get(key: str) -> None:
     """Print the version."""
     from . import get_version
 
     click.echo(get_version(key))
 
 
-@main.command()
+@main.command()  # type:ignore
 @click.option("--terse", "-t", is_flag=True)
-def ls(terse: bool):
+def ls(terse: bool) -> None:
     """List versions."""
     from . import get_rows
 

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/resources/update.py

@@ -29,7 +29,7 @@ def _get_clean_dict(d):
 
 @click.command()
 @click.option("--force", is_flag=True)
-def update(force: bool):
+def update(force: bool) -> None:
     """Update the data file."""
     with logging_redirect_tqdm():
         _update(force=force)
@@ -123,13 +123,6 @@ def _log_update(bv) -> None:
     else:
         slack_client.post(text)
 
-    try:
-        from .. import twitter_client
-    except ImportError:
-        pass
-    else:
-        twitter_client.post(text)
-
 
 if __name__ == "__main__":
     update()

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 941,
-    "date": "2025-03-06",
+    "revision": 943,
+    "date": "2025-03-21",
     "author": "runner"
   },
   "database": [
@@ -334,6 +334,16 @@
           "retrieved": "2025-03-05",
           "version": "2025-03-05",
           "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-19",
+          "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-03-21",
+          "version": "2025-03-20",
+          "homepage": "https://antibodyregistry.org/"
         }
       ],
       "name": "Antibody Registry",
@@ -2190,6 +2200,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2.238"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2.239"
         }
       ],
       "vtype": "date"
@@ -4095,7 +4109,7 @@
     },
     {
       "name": "ExPASy",
-      "prefix": "eccode",
+      "prefix": "ec",
       "releases": [
         {
           "retrieved": "2021-01-02",
@@ -4342,6 +4356,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "4.195"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "4.196"
         }
       ],
       "vtype": "date"
@@ -4853,6 +4871,10 @@
         {
           "retrieved": "2025-01-28",
           "version": "2025-01-14"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-28"
         }
       ],
       "vtype": "date"
@@ -4988,7 +5010,7 @@
       ],
       "name": "FlyBase",
       "prefix": "flybase",
-      "vtype": "date"
+      "vtype": "month"
     },
     {
       "releases": [
@@ -5909,6 +5931,11 @@
           "retrieved": "2025-02-12",
           "version": "2025-02-04",
           "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-02-04.json"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-04",
+          "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-03-04.json"
         }
       ],
       "name": "HGNC",
@@ -5999,6 +6026,10 @@
         {
           "retrieved": "2024-09-01",
           "version": "2024-08-19"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-24"
         }
       ],
       "vtype": "semver"
@@ -7231,6 +7262,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "4.1.190"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "4.1.191"
         }
       ],
       "name": "Mass spectrometry ontology",
@@ -7928,6 +7963,12 @@
           "version": "2025-02-07",
           "homepage": "https://github.com/vanallenlab/moalmanac-db/releases/tag/v.2025-02-07",
           "date": "2025-02-07"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-06",
+          "homepage": "https://github.com/vanallenlab/moalmanac-db/releases/tag/v.2025-03-06",
+          "date": "2025-03-06"
         }
       ],
       "name": "Molecular Oncology Almanac",
@@ -8529,6 +8570,11 @@
           "retrieved": "2024-12-12",
           "version": "24.11d",
           "date": "2024-11-25"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "25.03c",
+          "date": "2025-03-17"
         }
       ],
       "name": "National Cancer Institute Thesaurus",
@@ -9899,6 +9945,14 @@
         {
           "retrieved": "2025-03-06",
           "version": "2025-03-04"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-18"
+        },
+        {
+          "retrieved": "2025-03-21",
+          "version": "2025-03-19"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -10753,6 +10807,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2.0.58"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2.0.59"
         }
       ],
       "name": "Ontology of units of Measure",
@@ -12537,6 +12595,10 @@
         {
           "retrieved": "2025-03-04",
           "version": "2025-02-28"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-14"
         }
       ],
       "name": "Rat Genome Database",
@@ -12642,6 +12704,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "6.242"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "6.243"
         }
       ],
       "vtype": "date"
@@ -16109,6 +16175,14 @@
         {
           "retrieved": "2025-03-06",
           "version": "2025-03-06"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-20"
+        },
+        {
+          "retrieved": "2025-03-21",
+          "version": "2025-03-21"
         }
       ],
       "name": "SwissLipids",
@@ -16604,6 +16678,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2025-02-22"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-23"
         }
       ],
       "name": "The Statistical Methods Ontology",
@@ -17197,6 +17275,10 @@
         {
           "retrieved": "2025-01-05",
           "version": "2024-12-29"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-26"
         }
       ],
       "vtype": "semver"
@@ -17732,6 +17814,12 @@
           "version": "20250210",
           "homepage": "http://data.wikipathways.org/20250210/",
           "date": "2025-02-10"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "20250310",
+          "homepage": "http://data.wikipathways.org/20250310/",
+          "date": "2025-03-10"
         }
       ],
       "vtype": "date"
@@ -21431,6 +21519,10 @@
         {
           "retrieved": "2025-03-06",
           "version": "2025-03-04"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-19"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/slack_client.py

@@ -6,6 +6,7 @@ from functools import lru_cache
 import pystow
 from slack_sdk import WebClient
 from slack_sdk.errors import SlackApiError
+from slack_sdk.web import SlackResponse
 
 __all__ = [
     "post",
@@ -22,7 +23,7 @@ def _get_client(token: str | None = None) -> WebClient | None:
     return WebClient(token=token)
 
 
-def post(text: str, channel: str = "random", token: str | None = None):
+def post(text: str, channel: str = "random", token: str | None = None) -> SlackResponse | None:
     """Post the message to a given Slack channel."""
     client = _get_client(token)
     if client is None:
@@ -40,6 +41,7 @@ def post(text: str, channel: str = "random", token: str | None = None):
         if not e.response["ok"]:
             raise ValueError('Response is not "ok"') from e
         logger.warning(f"Got an error: {e.response['error']}")
+        return None
     else:
         return response
 

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/sources/__init__.py

@@ -7,7 +7,7 @@ import logging
 import traceback
 from collections.abc import Iterable, Mapping
 from functools import lru_cache
-from typing import NamedTuple
+from typing import Literal, NamedTuple, overload
 
 from tqdm import tqdm
 
@@ -186,9 +186,35 @@ def _resolve_helper(name: str) -> Bioversion:
     return getter.resolve()
 
 
-def get_version(name: str) -> str:
-    """Resolve a database name to its version string."""
-    return resolve(name).version
+# docstr-coverage:excused `overload`
+@overload
+def get_version(name: str, *, strict: Literal[True] = True) -> str: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_version(name: str, *, strict: Literal[False] = False) -> str | None: ...
+
+
+def get_version(name: str, *, strict: bool = True) -> str | None:
+    """Resolve a database name to its version string.
+
+    :param name:
+        The name of the resource to get the version from. Often, this is a Bioregistry
+        prefix, but sometimes can be an ad-hoc key for a database.
+    :param strict:
+        Re-raises errors in version resolution by default. Set explicitly to
+        ``false`` to return None on errors.
+    :return: The version of the resource as a string
+    """
+    try:
+        rv = resolve(name).version
+    except Exception:
+        if strict:
+            raise
+        return None
+    else:
+        return rv
 
 
 def get_rows(use_tqdm: bool | None = False) -> list[Bioversion]:

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/sources/biogrid.py

@@ -1,6 +1,6 @@
 """A getter for BioGRID."""
 
-from ..utils import Getter, VersionType, get_soup
+from ..utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "BioGRIDGetter",
@@ -20,8 +20,8 @@ class BioGRIDGetter(Getter):
     def get(self) -> str:
         """Get the latest BioGRID version number."""
         soup = get_soup(URL)
-        manifest = soup.find(id="manifestDesc")
-        header = manifest.find("h2")
+        manifest = find(soup, id="manifestDesc")
+        header = find(manifest, "h2")
         return header.text[len("BioGRID Release ") :]
 
 

{bioversions-0.7.40 → bioversions-0.7.42}/src/bioversions/sources/expasy.py

@@ -16,7 +16,7 @@ URL = "https://ftp.expasy.org/databases/enzyme/enzuser.txt"
 class ExPASyGetter(Getter):
     """A getter for ExPASy."""
 
-    bioregistry_id = "eccode"
+    bioregistry_id = "ec"
     name = "ExPASy"
     version_type = VersionType.date