bioversions 0.7.39__py3-none-any.whl → 0.7.41__py3-none-any.whl

bioversions/__main__.py

@@ -1,4 +1,4 @@
-"""Command line interface for bioversions."""
+"""Entrypoint module, in case you use `python -m bioversions`."""
 
 from .cli import main
 

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/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/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/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 940,
-    "date": "2025-03-05",
+    "revision": 942,
+    "date": "2025-03-20",
     "author": "runner"
   },
   "database": [
@@ -334,6 +334,11 @@
           "retrieved": "2025-03-05",
           "version": "2025-03-05",
           "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-19",
+          "homepage": "https://antibodyregistry.org/"
         }
       ],
       "name": "Antibody Registry",
@@ -2190,6 +2195,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2.238"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2.239"
         }
       ],
       "vtype": "date"
@@ -4095,7 +4104,7 @@
     },
     {
       "name": "ExPASy",
-      "prefix": "eccode",
+      "prefix": "ec",
       "releases": [
         {
           "retrieved": "2021-01-02",
@@ -4342,6 +4351,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "4.195"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "4.196"
         }
       ],
       "vtype": "date"
@@ -4853,6 +4866,10 @@
         {
           "retrieved": "2025-01-28",
           "version": "2025-01-14"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-28"
         }
       ],
       "vtype": "date"
@@ -4988,7 +5005,7 @@
       ],
       "name": "FlyBase",
       "prefix": "flybase",
-      "vtype": "date"
+      "vtype": "month"
     },
     {
       "releases": [
@@ -5909,6 +5926,11 @@
           "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 +6021,10 @@
         {
           "retrieved": "2024-09-01",
           "version": "2024-08-19"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-24"
         }
       ],
       "vtype": "semver"
@@ -7231,6 +7257,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "4.1.190"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "4.1.191"
         }
       ],
       "name": "Mass spectrometry ontology",
@@ -7928,6 +7958,12 @@
           "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 +8565,11 @@
           "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",
@@ -9895,6 +9936,14 @@
         {
           "retrieved": "2025-03-05",
           "version": "2025-03-03"
+        },
+        {
+          "retrieved": "2025-03-06",
+          "version": "2025-03-04"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-18"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -10749,6 +10798,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2.0.58"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2.0.59"
         }
       ],
       "name": "Ontology of units of Measure",
@@ -12533,6 +12586,10 @@
         {
           "retrieved": "2025-03-04",
           "version": "2025-02-28"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-14"
         }
       ],
       "name": "Rat Genome Database",
@@ -12638,6 +12695,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "6.242"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "6.243"
         }
       ],
       "vtype": "date"
@@ -16101,6 +16162,14 @@
         {
           "retrieved": "2025-03-05",
           "version": "2025-03-05"
+        },
+        {
+          "retrieved": "2025-03-06",
+          "version": "2025-03-06"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-20"
         }
       ],
       "name": "SwissLipids",
@@ -16596,6 +16665,10 @@
         {
           "retrieved": "2025-02-27",
           "version": "2025-02-22"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-23"
         }
       ],
       "name": "The Statistical Methods Ontology",
@@ -17189,6 +17262,10 @@
         {
           "retrieved": "2025-01-05",
           "version": "2024-12-29"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-02-26"
         }
       ],
       "vtype": "semver"
@@ -17724,6 +17801,12 @@
           "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"
@@ -21419,6 +21502,14 @@
         {
           "retrieved": "2025-03-05",
           "version": "2025-03-03"
+        },
+        {
+          "retrieved": "2025-03-06",
+          "version": "2025-03-04"
+        },
+        {
+          "retrieved": "2025-03-20",
+          "version": "2025-03-19"
         }
       ],
       "name": "Zebrafish Information Network",

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/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/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/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
 

bioversions/sources/flybase.py

@@ -1,31 +1,37 @@
 """A getter for FlyBase."""
 
-import ftplib
+import re
 
-from bioversions.utils import Getter, VersionType
+from bioversions.utils import Getter, VersionType, get_soup
 
 __all__ = [
     "FlybaseGetter",
 ]
 
+URL = "http://flybase-ftp.s3-website-us-east-1.amazonaws.com/releases/index.html"
+PATTERN = re.compile(r"FB\d{4}_\d{2}")
+
 
 class FlybaseGetter(Getter):
     """A getter for FlyBase."""
 
     bioregistry_id = "flybase"
     name = "FlyBase"
-    homepage_fmt = "http://ftp.flybase.net/releases/FB{version}/"
-    version_type = VersionType.date
+    homepage_fmt = "http://flybase-ftp.s3-website-us-east-1.amazonaws.com/releases/FB{version}/"
+    version_type = VersionType.month
 
     def get(self):
         """Get the latest flybase version number."""
-        with ftplib.FTP("ftp.flybase.net") as ftp:
-            ftp.login()
-            ftp.cwd("releases")
-            for name in sorted(ftp.nlst(), reverse=True):
-                if name.startswith("FB2"):
-                    return name[len("FB") :]
-        raise ValueError
+        soup = get_soup(URL)
+
+        releases = []
+        # We check links to find ones that look like releases
+        for anchor_tag in soup.find_all("a", href=True):
+            match = PATTERN.search(anchor_tag.text)
+            if match:
+                releases.append(match.group().removeprefix("FB"))
+        latest_version = max(releases)
+        return latest_version
 
 
 if __name__ == "__main__":

bioversions/sources/guidetopharmacology.py

@@ -26,7 +26,9 @@ class GuideToPharmacologyGetter(Getter):
     def get(self) -> dict[str, str]:
         """Get the latest Guide to Pharmacology version number."""
         soup = get_soup(URL)
-        text = soup.findAll("div", {"class": "contentboxfullhelp"})[4].div.ul.li.a.text
+        divs = list(soup.find_all("div", {"class": "contentboxfullhelp"}))
+        # the type ignore is because mypy doesn't understand the attribute-based dispatch
+        text = divs[4].div.ul.li.a.text  # type:ignore[attr-defined]
         search = RE.search(text)
         if not search:
             raise ValueError(

bioversions/sources/kegg.py

@@ -5,7 +5,7 @@ from typing import ClassVar
 
 import bioregistry
 
-from bioversions.utils import Getter, VersionType, get_soup
+from bioversions.utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "KEGGGetter",
@@ -25,9 +25,12 @@ class KEGGGetter(Getter):
     def get(self) -> Mapping[str, str]:
         """Get the latest KEGG version number."""
         soup = get_soup(URL)
-        header = soup.find("h4")
-        sibling = header.next_sibling.strip()
-        version, date = (part.strip() for part in sibling.split(",", 1))
+        header = find(soup, "h4")
+        sibling = header.next_sibling
+        if not sibling:
+            raise ValueError
+        sibling_text = sibling.text.strip()
+        version, date = (part.strip() for part in sibling_text.split(",", 1))
         version = version[len("Release ") :]
         return {"version": version, "date": date}
 

bioversions/sources/moalmanac.py

@@ -1,6 +1,6 @@
 """A getter for the Molecular Oncology Almanac."""
 
-from ..utils import Getter, VersionType, get_soup
+from ..utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "MOAlmanacGetter",
@@ -18,8 +18,9 @@ class MOAlmanacGetter(Getter):
     def get(self) -> str:
         """Get the latest MOAlmanac version number."""
         soup = get_soup("https://moalmanac.org/")
-        sub_footer = soup.find("div", {"class": "text-right"})
-        version = sub_footer.find("a").text.strip("v").strip(".")
+        sub_footer = find(soup, "div", {"class": "text-right"})
+        anchor = find(sub_footer, "a")
+        version = anchor.text.strip("v").strip(".")
         return version
 
 

bioversions/sources/ncit.py

@@ -1,17 +1,14 @@
 """A getter for the NCI Thesaurus."""
 
-import re
+import requests
 
-from ..utils import Getter, VersionType, get_soup
+from ..utils import Getter, VersionType
 
 __all__ = [
     "NCItGetter",
 ]
 
-URL = "https://ncithesaurus.nci.nih.gov/ncitbrowser/"
-PATTERN = re.compile(
-    r"Version:([0-9]{2}\.[0-9]{2}[a-z]) " r"\(Release date:([0-9]{4}-[0-9]{2}-[0-9]{2})"
-)
+URL = "https://evsexplore.semantics.cancer.gov/evsexplore/api/v1/metadata/terminologies"
 
 
 class NCItGetter(Getter):
@@ -19,19 +16,16 @@ class NCItGetter(Getter):
 
     bioregistry_id = "ncit"
     name = "National Cancer Institute Thesaurus"
-    date_fmt = "%Y-%m-%d"
+    date_fmt = "%B %d, %Y"
     version_type = VersionType.other
 
     def get(self) -> dict[str, str]:
         """Get the latest NCIt version number."""
-        soup = get_soup(URL)
-        version_str = soup.find("span", {"class": "vocabularynamelong_ncit"}).contents[0]
-        match = re.search(PATTERN, version_str)
-        if match is None:
-            raise ValueError(f"could not parse version from {URL}")
+        records = requests.get(URL, timeout=5).json()
+        ncit_record = next(record for record in records if record["terminology"] == "ncit")
         return {
-            "version": match.group(1),
-            "date": match.group(2),
+            "version": ncit_record["version"],
+            "date": ncit_record["date"],
         }
 
 

bioversions/sources/npass.py

@@ -1,6 +1,6 @@
 """A getter for NPASS."""
 
-from bioversions.utils import Getter, VersionType, get_soup
+from bioversions.utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "NPASSGetter",
@@ -19,7 +19,9 @@ class NPASSGetter(Getter):
     def get(self) -> str:
         """Get the latest NPASS version number."""
         soup = get_soup(URL)
-        for li in soup.find(name="footer").find(name="ul").findAll(name="li"):
+        footer = find(soup, name="footer")
+        ul = find(footer, name="ul")
+        for li in ul.find_all(name="li"):
             if li.text.startswith("Version:"):
                 return li.text[len("Version: ") :]
         raise ValueError(f"could not parse NPASS version from {URL}")

bioversions/sources/pathbank.py

@@ -1,6 +1,6 @@
 """A getter for PathBank."""
 
-from bioversions.utils import Getter, VersionType, get_soup
+from bioversions.utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "PathBankGetter",
@@ -19,13 +19,11 @@ class PathBankGetter(Getter):
     def get(self) -> str:
         """Get the latest PathBank version number."""
         soup = get_soup(URL)
-        version = (
-            soup.find(id="main")
-            .find(name="footer")
-            .find(**{"class": "wishart-clear"})
-            .find(name="strong")
-        )
-        return version.text
+        main = find(soup, id="main")
+        footer = find(main, name="footer")
+        clear = find(footer, **{"class": "wishart-clear"})
+        strong = find(clear, name="strong")
+        return strong.text
 
 
 if __name__ == "__main__":

bioversions/sources/pathwaycommons.py

@@ -1,6 +1,6 @@
 """A getter for Pathway Commons."""
 
-from bioversions.utils import Getter, VersionType, get_soup
+from bioversions.utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "PathwayCommonsGetter",
@@ -18,10 +18,10 @@ class PathwayCommonsGetter(Getter):
     def get(self) -> str:
         """Get the latest Pathway Commons version number."""
         soup = get_soup(URL)
-        boost = soup.find(**{"class": "boost"})
-        boost = boost.text[len("Version ") :]
-        boost = boost.split(":")[0]
-        return boost
+        boost = find(soup, {"class": "boost"})
+        boost_text = boost.text[len("Version ") :]
+        boost_text = boost_text.split(":")[0]
+        return boost_text
 
 
 if __name__ == "__main__":

bioversions/sources/rxnorm.py

@@ -2,7 +2,7 @@
 
 from datetime import datetime
 
-from ..utils import Getter, VersionType, get_soup
+from ..utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "RxNormGetter",
@@ -22,7 +22,8 @@ class RxNormGetter(Getter):
     def get(self) -> datetime:
         """Get the latest RxNorm version number."""
         soup = get_soup(URL)
-        raw_version = soup.find("th", {"class": "current"}).contents[2].strip()
+        tag = find(soup, "th", {"class": "current"})
+        raw_version = tag.contents[2].text.strip()
         raw_fmt = "%B %d, %Y"
         return datetime.strptime(raw_version, raw_fmt)
 

bioversions/sources/umls.py

@@ -1,8 +1,6 @@
 """A getter for UMLS."""
 
-from datetime import datetime
-
-from bioversions.utils import Getter, VersionType, get_soup
+from bioversions.utils import Getter, VersionType, find, get_soup
 
 __all__ = [
     "UMLSGetter",
@@ -18,15 +16,13 @@ class UMLSGetter(Getter):
     name = "UMLS"
     version_type = VersionType.other
 
-    def get(self) -> datetime:
+    def get(self) -> str:
         """Get the latest UMLS version number."""
         soup = get_soup(URL)
-        version_tag = (
-            soup.find("main")
-            .find("div", {"class": "grid-row grid-gap-1"})
-            .find("div", {"class": "tablet:grid-col-12"})
-            .find("h2")
-        )
+        main_tag = find(soup, "main")
+        t1 = find(main_tag, "div", {"class": "grid-row grid-gap-1"})  # type:ignore
+        t2 = find(t1, "div", {"class": "tablet:grid-col-12"})
+        version_tag = find(t2, "h2")
         version = version_tag.text.split()[0]
         return version
 

bioversions/utils.py

@@ -11,7 +11,7 @@ import bioregistry
 import pydantic
 import pystow
 import requests
-from bs4 import BeautifulSoup
+from bs4 import BeautifulSoup, Tag
 from cachier import cachier
 
 BIOVERSIONS_HOME = pystow.join("bioversions")
@@ -64,6 +64,14 @@ def get_soup(
     return soup
 
 
+def find(element: Tag, *args: Any, **kwargs: Any) -> Tag:
+    """Find a sub-element."""
+    tag = element.find(*args, **kwargs)
+    if not isinstance(tag, Tag):
+        raise ValueError(f"could not find an element matching {args=} and {kwargs=}")
+    return tag
+
+
 #: A decorator for functions whose return values
 #: should be cached and refreshed once per day
 refresh_daily = cachier(

bioversions/version.py

@@ -5,9 +5,10 @@ from subprocess import CalledProcessError, check_output
 
 __all__ = [
     "VERSION",
+    "get_git_hash",
 ]
 
-VERSION = "0.7.39"
+VERSION = "0.7.41"
 
 
 def get_git_hash() -> str:

bioversions/wsgi.py

@@ -12,13 +12,13 @@ Bootstrap(app)
 
 
 @app.route("/")
-def home():
+def home() -> str:
     """Show the home page with a list of latest database versions."""
     return flask.render_template("home.html", rows=get_rows())
 
 
 @app.route("/database/<name>.json")
-def database(name: str):
+def database(name: str) -> flask.Response:
     """Resolve information about a given database."""
     rv: dict[str, Any] = {"query": name}
     try:
@@ -27,7 +27,7 @@ def database(name: str):
         rv["success"] = False
     else:
         rv["success"] = True
-        rv["result"] = bioversion.dict()
+        rv["result"] = bioversion.model_dump()
     return flask.jsonify(rv)
 
 

{bioversions-0.7.39.dist-info → bioversions-0.7.41.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.7.39
+Version: 0.7.41
 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-0.7.39.dist-info → bioversions-0.7.41.dist-info}/RECORD

@@ -1,7 +1,6 @@
-bioversions/charts.py,sha256=dff05cc80031529e1b06af54c0011d241a383278319d0c6fa90b3e6ad4476332,2419
-bioversions/twitter_client.py,sha256=f5de409b4152b3bfc4806763931aa9a3df2f3e2afdae32172318593262e02b94,1285
-bioversions/__main__.py,sha256=4e799066f5fbbe005dc99aee68c4146b3d8572ec52891b82ad0f4e1f2de96227,108
-bioversions/version.py,sha256=ee8defb1849b04389c2bca31520d81b0a6e904fced49c6e4d9b4609e90e98f91,586
+bioversions/charts.py,sha256=be29a2fde227a4bd02611112f1cbe58a00e261e435fc8f00e82104a15dadbdfe,2457
+bioversions/__main__.py,sha256=0e97cd1eac70162293fb809292e2cba2464218394244001f3f9e0c74b8f71351,128
+bioversions/version.py,sha256=806e526120fac60479632e127dadb4fe18b9544c5bd9738a55464a9e3a86a69d,606
 bioversions/sources/interpro.py,sha256=1fa75923bd60517a3b2f661e7c24e2243e2ab90440bf2621e670c36e1da2baf1,1238
 bioversions/sources/uniprot.py,sha256=c3e16b68fc8a65e12d9a3b3288fedbd9a8e0e7b47f0a69f0fb032fb072c68a1b,924
 bioversions/sources/itis.py,sha256=99a480060d52ac6e06404be347080c28af56e984e80cc4763f0a98266212a1df,582
@@ -12,26 +11,26 @@ bioversions/sources/intact.py,sha256=06e67eda7e8eededc74f63eb1c73db0648665dae783
 bioversions/sources/disgenet.py,sha256=3c02c84643c1913d9cb2b37e1679fe019cc273d67633685e904fbf16ba84f8bc,739
 bioversions/sources/slm.py,sha256=84fe81b16cf8cb3cdc817f4ed56482364bb46a9d3af1f01c3726273b26d106d6,766
 bioversions/sources/dgi.py,sha256=8b613bedea979b8bbadfcbe4b2fd539e4d29deccf329d936c83a72626d8808bc,940
-bioversions/sources/kegg.py,sha256=89f784cc7b97ad22436b59b5616c35dd4e82ef1f2335d4001a99a8620d3a00ca,913
+bioversions/sources/kegg.py,sha256=24574e015a28f77f77451a3b48dbb54b740ff36e7e310bbdf434ee4f63adb094,1014
 bioversions/sources/bigg.py,sha256=895af1caf2a2108517b3a14cd8088b0d86bec980cd18c38d9a222ffd1e8a060e,661
 bioversions/sources/pubchem.py,sha256=57e6f33479eef0935322abde994efe3292f91c7c6bb1889c5724c99ebd7d72f9,526
 bioversions/sources/ensembl.py,sha256=994779fcbb08ea8494e1af0324b49a9bd9649dd7fa65fba7d156b1648c9edad2,737
 bioversions/sources/silva.py,sha256=e677f3502f516b48977191274ad08d593e4c683442281043a819dde028157274,984
 bioversions/sources/icd10.py,sha256=f3ace5f72c5e532cb758a8104b9e48fb56cafa47a01f9f6c6458b06062856805,703
-bioversions/sources/expasy.py,sha256=e42f66f4e93281aab60fbceeb939e4383e15db8414e02f3d95dced7cbb62aa72,771
+bioversions/sources/expasy.py,sha256=625d33571c58d40584ac5ad572da0999e6bec4db7327c0860b9f017836034f9e,767
 bioversions/sources/homologene.py,sha256=4da5b4037dcf2d2e3cd38ceb45664a0e6a3fcf01332bd6f15ffcc089a526779c,622
 bioversions/sources/msigdb.py,sha256=8689c6234a84ae6e70b19b2bd21c165e2c37d83de7e71c47e605f7c54121de9a,778
 bioversions/sources/signor.py,sha256=f0a0bd043c1344027e31fe8fc4e5922f44e86044ca16370e6d66368161f05c83,969
-bioversions/sources/ncit.py,sha256=eabc33412087108799d70b76ca60b27debcceb8e3bf6782ba41107c5f2dcda87,1015
+bioversions/sources/ncit.py,sha256=887238481b9cd61f525019541624d03f455f4e0c4465d4ba40fbcf704aac231b,832
 bioversions/sources/gtdb.py,sha256=95bb664a1e2e872ebe55efec9703be63bff01d15724aea1fd48feb47e150d399,1001
-bioversions/sources/pathwaycommons.py,sha256=f7c9ef2ed143a9c1ec755c6dd8bbbc5797682df4ae3ae621c2980fa80ec16619,661
+bioversions/sources/pathwaycommons.py,sha256=34b6bc0f44d87fa4a4abf7ee4adf8a350117b5623786feeff187987c9bc947f6,686
 bioversions/sources/depmap.py,sha256=00b9fb914b27902ef2023f5c2d899a4235829b6b20d3045643e4fbe8deea4168,641
 bioversions/sources/antibodyregistry.py,sha256=5c29963e1d7bd40780582ce9539d6120bd593d0cda6f3b763b08af876a2bef8f,713
 bioversions/sources/reactome.py,sha256=12ae2e1cc763c323eaab9d90ec4f6cbdcea1cd9645b40e6d32d93c76333006f7,596
 bioversions/sources/oncotree.py,sha256=69b039f07e37800fd3b623816b00595333caede9403d8a9620fee515de8aa8ee,1032
 bioversions/sources/rfam.py,sha256=3c8de33a8920baac6789fd07160da00752f524ed25ad045b3b48a24716eda5a8,540
 bioversions/sources/civic.py,sha256=321967e8b7c7a7aecf896b49e6ad4520d0b00a114103a71f71a49c775291f11e,1086
-bioversions/sources/flybase.py,sha256=2f5aacd0e1743a18dd927c15e837ef9e79713f7ed9d3d863ba4fa9cf5527d863,754
+bioversions/sources/flybase.py,sha256=cf898bc12970d7840d14d8a6c0022d6712dbeea09ba0269f95af0e51d8fa3de1,1016
 bioversions/sources/daily.py,sha256=501fcf689d9b11035b08255c208c5bca0bb631f79e9a8fee3d268f85d07b4033,256
 bioversions/sources/sgd.py,sha256=3e05c0bf0aa5c78f10b869e75473a5d2e034323b84ec89748e2055e1f69835d0,1084
 bioversions/sources/pombase.py,sha256=e65348dc0aaed5f9c35049c5d117ee7103abf8714f620afbfa5e084eded1c986,766
@@ -45,38 +44,38 @@ bioversions/sources/omim.py,sha256=7aad8a3615748f5171db47098a1cdbec36b1e8596e0e8
 bioversions/sources/stringdb.py,sha256=9afd81dd24d02469cce66e246cb6f696e4a501ba3e7e8dc7aff0f022563a37b2,787
 bioversions/sources/chembl.py,sha256=35cfa0149a5eac1c8efe2577b43aa47e359874558ef48ce227022d7bd0b60932,1513
 bioversions/sources/rhea.py,sha256=ddcb28b84fa2a76520ecc123703e785ff3d4bccb93638af442d3883f54fbd57e,806
-bioversions/sources/guidetopharmacology.py,sha256=5806ac03a665caa262a8fef456bac21298b6f895bb50cad4ba702e13aa5393f8,1377
-bioversions/sources/rxnorm.py,sha256=ba8a68262850132282d79c6ab5293f4997c496672ca614b26da8e22ee6856253,1010
+bioversions/sources/guidetopharmacology.py,sha256=7864d5d2b74f25d3baa4a91f9a24caec4777a19c442e0055112d2f790998b0e0,1523
+bioversions/sources/rxnorm.py,sha256=abb4a225e16e57c6f59102558c41504711ba81cdb5e07bf557c70ceab552c541,1040
 bioversions/sources/rgd.py,sha256=64f6cfd7bff88004699b00832560ef033f14f2977e70684ebef546b431a04d23,766
-bioversions/sources/__init__.py,sha256=bc68aa57c4ca0680e547dbd7992b7a4fe0f888131ba7cf91bf18499a227a2df4,6367
+bioversions/sources/__init__.py,sha256=d475777684fbb0fd5b2bbfba5344dfce5bc6e2ef27742d2fe00200229cdf6f92,7156
 bioversions/sources/icf.py,sha256=0580247e61d6b50b0c08d5331a97d188a5671dda4333298628bc327af313c08a,720
-bioversions/sources/npass.py,sha256=b516902495d04397e054b51a51046b11432f37deb7046758d7337ffca804d616,714
-bioversions/sources/biogrid.py,sha256=15c400f0020ded3c167704506ffaf985467087d66d975dc67865ca5efd4a71a8,734
+bioversions/sources/npass.py,sha256=09355592fd1fee53e99165316c6b6053931927589a58e255b3db2aefde02c103,763
+bioversions/sources/biogrid.py,sha256=df37707dbc42423111e9be6a98c7b866312430d042712d392170a8f2cf8b2daf,742
 bioversions/sources/mgi.py,sha256=4d7f95d3171616692db2c8d195d8d86f9f751c2b6885e63df70d054c7d9c2199,841
-bioversions/sources/pathbank.py,sha256=620621044418e05d3d720ed2e01704107e260fa97a2c38ee0d1bf507f7bce62f,693
-bioversions/sources/moalmanac.py,sha256=0cca2d4980f8b0639365a2609ff88f7947c47618e5826ce828a2d84be2fa4eba,749
+bioversions/sources/pathbank.py,sha256=ad5a8a277ab673881cb6a520fe78bd7d29b6273d2882475ec07fb2b0f762003b,704
+bioversions/sources/moalmanac.py,sha256=2f314cc81d89e0e604514217ed5346508dab890603eb6a20f4fb9d3c97144801,781
 bioversions/sources/cellosaurus.py,sha256=d17ae067aade4a433c0f350b26d681dda881603d1057734750b67ef19950ee01,975
 bioversions/sources/drugbank.py,sha256=599c215452b5e8219e2c31423c2c6d1c7c867848309696c834b9b5f3af1f3f16,994
 bioversions/sources/mirbase.py,sha256=ab70baf82cbebc42f22424029e9838a6f7a846b9587ea81be37d779871b90a9e,996
 bioversions/sources/mesh.py,sha256=5ea8cf53950980e1d5736f1cffa37b46225dd45f51a1418f5c69a621a368a6f3,971
 bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
-bioversions/sources/umls.py,sha256=ff9cfd631a1d39804a29a901db6da32e68e6e1c526e04e30a1be82359ea155aa,817
+bioversions/sources/umls.py,sha256=276513c45b33d31f5eaa1395ef176b9ed5ae8013c4ecd4332b4f627880115146,803
 bioversions/sources/obo.py,sha256=727b7470ba4cf30b421b5e1eebe758bbadeac57e9801df4fceb13948a27ff0b7,1713
 bioversions/sources/ols.py,sha256=35e49f5841e26161ebb063e2bba5f58754031b98128ac132532ef528346f69ac,2929
 bioversions/sources/zfin.py,sha256=dcea33de50f1f09e36380a3253c78923e7d19cc46263250c723e1f0c4e4354b4,683
-bioversions/slack_client.py,sha256=a7d1e69f244256e42f8ded116dd0caf50b91952c3ffd6c05089f017bd7089333,1209
+bioversions/slack_client.py,sha256=bda7d71401bc03f7dc19fec98d7d5abad5083285cb5c97b5b575b1f9459a1285,1293
 bioversions/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
 bioversions/resources/__init__.py,sha256=371c3ac3afe0442e01fc9c2f6c000aa4d476ac8a6435167952404831d36a95d6,1659
-bioversions/resources/update.py,sha256=6c819d96095f445905cad830239ffc7f67a4bdbcae5b6cb1b62c6c97704beeca,3642
-bioversions/resources/versions.json,sha256=fde3ba2adaa6cdafdebfb6755ef0b6019260c85aed54295706179169152e14b5,523524
-bioversions/utils.py,sha256=d96017bd9986329496f7c5b9bf7072d466517c6981c3aff36f7658c4954e206d,10437
-bioversions/wsgi.py,sha256=f85ee95198a9710823d53fdffbd40264155d43db19047f77c7787187d87b9255,794
+bioversions/resources/update.py,sha256=610e47d0ca8a475740237911e32c146b186b31f3b1ca22501bf099cca07de9d3,3521
+bioversions/resources/versions.json,sha256=c632a408a7576d81e5c0ca0d0f0f9e5aaba0090e2dbfdd4ad9041c6f64c88fea,525881
+bioversions/utils.py,sha256=65760e94607996df0ef32e6d946b03b1b2a2faa8ff9bee37d1822fe9136bf4fa,10706
+bioversions/wsgi.py,sha256=b611913189165699cd67480f3d17308344ac935e31c693017aabea89bd0ba8ab,825
 bioversions/__init__.py,sha256=7f04aa5bf8ba4ceb843188a32f6f09dfb20b2300f067284d35a1fb0441eaba38,194
-bioversions/cli.py,sha256=939b0f29af9f7fc8aeba207b95d46f1cf59c659d15deccc348cabdcf07486bce,1563
+bioversions/cli.py,sha256=75eaa237668bef45ef6f16b5c5a20036aef228995b872dda224a54dcb30ad2d5,1639
 bioversions/templates/base.html,sha256=00a07a693dfd53d56d38cdb3bd6fd49b922060ef4acbe08ba41cb1cb95d73b93,713
 bioversions/templates/home.html,sha256=cfdf054ac94244fd8adfdc5b1e948f824d7d8fb676d4f49b44602d69723431dd,2756
-bioversions-0.7.39.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-bioversions-0.7.39.dist-info/WHEEL,sha256=92b1076a87444a608e101305744f03ef99e792a629ea2ddd7828b8200771ef04,78
-bioversions-0.7.39.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
-bioversions-0.7.39.dist-info/METADATA,sha256=c54115874cf1d13bcb67c05e3306a372ed97b34fc2256530158a6ed9adbd61bc,19271
-bioversions-0.7.39.dist-info/RECORD,,
+bioversions-0.7.41.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+bioversions-0.7.41.dist-info/WHEEL,sha256=36cac5c30d0d6b59913f9667f03e5fb51bd59748669ecd8f9b7e1c30b881950f,78
+bioversions-0.7.41.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
+bioversions-0.7.41.dist-info/METADATA,sha256=d3cf8d4858cbd48c299b4d1f41ae6382906da226c865afb463e6b4ef7e897a8d,18673
+bioversions-0.7.41.dist-info/RECORD,,

{bioversions-0.7.39.dist-info → bioversions-0.7.41.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.6.4
+Generator: uv 0.6.8
 Root-Is-Purelib: true
 Tag: py3-none-any

bioversions/twitter_client.py

@@ -1,45 +0,0 @@
-"""Utilities for interacting with Twitter."""
-
-from functools import lru_cache
-
-import pystow
-import tweepy
-
-
-@lru_cache(maxsize=1)
-def _get_api(
-    consumer_key: str | None = None,
-    consumer_secret: str | None = None,
-    access_token: str | None = None,
-    access_token_secret: str | None = None,
-) -> tweepy.API | None:
-    consumer_key = pystow.get_config("bioversions", "consumer_key", passthrough=consumer_key)
-    consumer_secret = pystow.get_config(
-        "bioversions", "consumer_secret", passthrough=consumer_secret
-    )
-    access_token = pystow.get_config("bioversions", "access_token", passthrough=access_token)
-    access_token_secret = pystow.get_config(
-        "bioversions", "access_token_secret", passthrough=access_token_secret
-    )
-
-    if consumer_key and consumer_secret and access_token and access_token_secret:
-        auth = tweepy.OAuthHandler(consumer_key, consumer_secret)
-        auth.set_access_token(access_token, access_token_secret)
-
-        # Create API object
-        api = tweepy.API(auth)
-        return api
-
-    return None
-
-
-def post(text: str):
-    """Post the message to Twitter."""
-    api = _get_api()
-    if api is None:
-        return None
-    return api.update_status(text)
-
-
-if __name__ == "__main__":
-    post("Twitter test!")