bioversions 0.5.376__py3-none-any.whl → 0.7.1__py3-none-any.whl

bioversions/templates/home.html

@@ -0,0 +1,60 @@
+{% extends "base.html" %}
+
+{% block title %}Bioversions{% endblock %}
+
+{% block content %}
+    <div class="container" style="margin-top: 50px; margin-bottom: 50px">
+        <div class="row justify-content-center">
+            <div class="card">
+                <h5 class="card-header text-center">Biological Database Latest Versions</h5>
+                <div class="card-body">
+                    <p>
+                        This web application lists the latest versions for biological databases.
+                        It refreshes once per day.
+                    </p>
+                </div>
+                <table class="table table-striped table-hover">
+                    <thead>
+                    <tr>
+                        <th>Name</th>
+                        <th>Version</th>
+                        <th>Date</th>
+                        <th class="text-center">JSON</th>
+                    </tr>
+                    </thead>
+                    <tbody>
+                    {% for row in rows %}
+                        <tr>
+                            <td>{{ row.name }}</td>
+                            <td>
+                                {% if row.homepage %}
+                                    <a href="{{ row.homepage }}">{{ row.version }} <i class="fas fa-link"></i></a>
+                                {% else %}
+                                    {{ row.version }}
+                                {% endif %}
+                            </td>
+                            <td>
+                                {% if row.date %}{{ row.date }}{% endif %}
+                            </td>
+                            <td class="text-center">
+                                <a href="{{ url_for('database', name=row.name.lower().replace(" ", "")) }}">
+                                    <i class="fas fa-download"></i>
+                                </a>
+                            </td>
+                        </tr>
+                    {% endfor %}
+                    </tbody>
+                </table>
+                <div class="card-footer">
+                    <p style="text-align: center">
+                        Developed with ❤️ by the <a href="https://indralab.github.io">INDRA Lab</a> in the
+                        <a href="https://hits.harvard.edu">Harvard Program in Therapeutic Science (HiTS)</a>.<br/>
+                        Funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).<br/>
+                        Point of contact: <a href="https://github.com/cthoyt">@cthoyt</a>.
+                        (<a href="https://github.com/biopragmatics/bioversions">Source code</a>)
+                    </p>
+                </div>
+            </div>
+        </div>
+    </div>
+{% endblock %}

bioversions/twitter_client.py

@@ -1,9 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """Utilities for interacting with Twitter."""
 
 from functools import lru_cache
-from typing import Optional
 
 import pystow
 import tweepy
@@ -11,11 +8,11 @@ import tweepy
 
 @lru_cache(maxsize=1)
 def _get_api(
-    consumer_key: Optional[str] = None,
-    consumer_secret: Optional[str] = None,
-    access_token: Optional[str] = None,
-    access_token_secret: Optional[str] = None,
-) -> Optional[tweepy.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

bioversions/utils.py

@@ -1,18 +1,16 @@
-# -*- coding: utf-8 -*-
-
 """Utilities and implementation for bioversions."""
 
 import datetime
 import enum
 import ftplib
 import os
-from typing import Any, ClassVar, List, Mapping, Optional, Union
+from collections.abc import Mapping
+from typing import Any, ClassVar
 
 import bioregistry
 import pydantic
 import pystow
 import requests
-import requests_ftp
 from bs4 import BeautifulSoup
 from cachier import cachier
 
@@ -21,8 +19,6 @@ HERE = os.path.abspath(os.path.dirname(__file__))
 DOCS = os.path.abspath(os.path.join(HERE, os.pardir, os.pardir, "docs"))
 IMG = os.path.join(DOCS, "img")
 
-requests_ftp.monkeypatch_session()
-
 
 class VersionType(enum.Enum):
     """Different types of versions."""
@@ -48,7 +44,7 @@ def norm(s: str) -> str:
 
 
 def get_soup(
-    url: str, verify: bool = True, timeout: Optional[int] = None, user_agent: Optional[str] = None
+    url: str, verify: bool = True, timeout: int | None = None, user_agent: str | None = None
 ) -> BeautifulSoup:
     """Get a beautiful soup parsed version of the given web page.
 
@@ -82,9 +78,9 @@ class MetaGetter(type):
 
     _cache = None
 
-    date_fmt: Optional[str]
-    date_version_fmt: Optional[str]
-    homepage_fmt: Optional[str]
+    date_fmt: str | None
+    date_version_fmt: str | None
+    homepage_fmt: str | None
 
     @property
     def _cache_prop(cls):
@@ -105,7 +101,7 @@ class MetaGetter(type):
             raise TypeError(f"_cache_prop was a {type(cls._cache_prop)}")
 
     @property
-    def date(cls) -> Optional[datetime.date]:
+    def date(cls) -> datetime.date | None:
         """Get the date if it's set."""
         vp = cls.version_date_parsed
         if vp is not None:
@@ -122,10 +118,12 @@ class MetaGetter(type):
         try:
             return datetime.datetime.strptime(date, cls.date_fmt).date()
         except ValueError:
-            raise ValueError(f"Issue in {cls.__name__} with date {date} and fmt {cls.date_fmt}")
+            raise ValueError(
+                f"Issue in {cls.__name__} with date {date} and fmt {cls.date_fmt}"
+            ) from None
 
     @property
-    def version_date_parsed(cls) -> Optional[datetime.date]:
+    def version_date_parsed(cls) -> datetime.date | None:
         """Get the date as a parsed class there's a format string."""
         if cls.date_version_fmt is None:
             return None
@@ -133,11 +131,12 @@ class MetaGetter(type):
             return datetime.datetime.strptime(cls.version, cls.date_version_fmt).date()
         except ValueError:
             raise ValueError(
-                f"Issue parsing {cls.__name__} version {cls.version} with fmt {cls.date_version_fmt}"
-            )
+                f"Issue parsing {cls.__name__} version {cls.version} "
+                f"with fmt {cls.date_version_fmt}"
+            ) from None
 
     @property
-    def homepage(cls) -> Optional[str]:
+    def homepage(cls) -> str | None:
         """Get the homepage's URL if a format string was specified."""
         if cls.homepage_fmt is None:
             return None
@@ -163,11 +162,11 @@ class Bioversion(pydantic.BaseModel):
     #: The version type
     vtype: VersionType
     #: The date of the current release
-    date: Optional[datetime.date]
+    date: datetime.date | None
     #: The URL for the homepage of the specific version of the database
-    homepage: Optional[str]
+    homepage: str | None
     #: The database prefix
-    bioregistry_id: Optional[str]
+    bioregistry_id: str | None
 
 
 class Getter(metaclass=MetaGetter):
@@ -179,13 +178,13 @@ class Getter(metaclass=MetaGetter):
     version_type: ClassVar[VersionType]
 
     #: The URL with `{version}` to format in the version. Specify this in the inheriting class.
-    homepage_fmt: ClassVar[Optional[str]] = None
+    homepage_fmt: ClassVar[str | None] = None
 
-    date_fmt: ClassVar[Optional[str]] = None
+    date_fmt: ClassVar[str | None] = None
 
-    date_version_fmt: ClassVar[Optional[str]] = None
+    date_version_fmt: ClassVar[str | None] = None
 
-    bioregistry_id: ClassVar[Optional[str]] = None
+    bioregistry_id: ClassVar[str | None] = None
 
     # The following are automatically calculated based on the metaclass
     version: ClassVar[str]
@@ -193,21 +192,21 @@ class Getter(metaclass=MetaGetter):
     homepage: ClassVar[str]
 
     #: Prefixes this getter works for
-    collection: ClassVar[Optional[List[str]]] = None
+    collection: ClassVar[list[str] | None] = None
 
-    def get(self) -> Union[str, Mapping[str, str], datetime.datetime]:
+    def get(self) -> str | Mapping[str, str] | datetime.datetime:
         """Get the latest of this database."""
         raise NotImplementedError
 
     @classmethod
-    def print(cls, sep: str = "\t", file=None):  # noqa:T202
+    def print(cls, sep: str = "\t", file=None):
         """Print the latest version of this database."""
         x = [cls.bioregistry_id, cls.name, cls.version]
         if cls.date:
             x.append(f"({cls.date})")
         if cls.homepage:
             x.append(cls.homepage)
-        print(*x, sep=sep, file=file)  # noqa:T201
+        print(*x, sep=sep, file=file)
 
     @classmethod
     def resolve(cls) -> Bioversion:
@@ -225,7 +224,7 @@ class Getter(metaclass=MetaGetter):
     @classmethod
     def to_dict(cls) -> Mapping[str, Any]:
         """Get a dict with the data for this database."""
-        return cls.resolve().to_dict()
+        return cls.resolve().model_dump()
 
 
 class DailyGetter(Getter):
@@ -233,7 +232,7 @@ class DailyGetter(Getter):
 
     version_type = VersionType.daily
 
-    def get(self) -> Union[str, Mapping[str, str]]:
+    def get(self) -> str | Mapping[str, str]:
         """Return a constant "daily" string."""
         return "daily"
 
@@ -246,14 +245,14 @@ class UnversionedGetter(Getter):
     #: Has this database been apparently abandoned (true) or is it still updated (false)
     abandoned: ClassVar[bool]
 
-    def get(self) -> Union[str, Mapping[str, str]]:
+    def get(self) -> str | Mapping[str, str]:
         """Return a constant unversioned string."""
         return "unversioned"
 
 
 def get_obo_version(url: str) -> str:
     """Get the data version from an OBO file."""
-    with requests.get(url, stream=True) as res:
+    with requests.get(url, stream=True, timeout=60) as res:
         for line in res.iter_lines():
             line = line.decode("utf-8")
             if line.startswith("data-version:"):

bioversions/version.py

@@ -1,22 +1,20 @@
-# -*- coding: utf-8 -*-
-
 """Version information for bioversions."""
 
 import os
-from subprocess import CalledProcessError, check_output  # noqa: S404
+from subprocess import CalledProcessError, check_output
 
 __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.376"
+VERSION = "0.7.1"
 
 
 def get_git_hash() -> str:
     """Get the bioversions git hash."""
     with open(os.devnull, "w") as devnull:
         try:
-            ret = check_output(  # noqa: S603,S607
+            ret = check_output(
                 ["git", "rev-parse", "HEAD"],
                 cwd=os.path.dirname(__file__),
                 stderr=devnull,

bioversions/wsgi.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """A web application for listing database versions."""
 
-from typing import Any, Dict
+from typing import Any
 
 import flask
 from flask_bootstrap import Bootstrap
@@ -22,7 +20,7 @@ def home():
 @app.route("/database/<name>.json")
 def database(name: str):
     """Resolve information about a given database."""
-    rv: Dict[str, Any] = dict(query=name)
+    rv: dict[str, Any] = {"query": name}
     try:
         bioversion = resolve(name)
     except KeyError: