bioversions 0.5.559__py3-none-any.whl → 0.5.561__py3-none-any.whl

bioversions/__init__.py

@@ -3,7 +3,7 @@
 from .sources import get_rows, get_version, resolve
 
 __all__ = [
+    "get_rows",
     "get_version",
     "resolve",
-    "get_rows",
 ]

bioversions/resources/__init__.py

@@ -7,17 +7,18 @@ from pathlib import Path
 import yaml
 
 __all__ = [
-    "VERSIONS_PATH",
     "EXPORT_PATH",
+    "VERSIONS_PATH",
     "load_versions",
-    "write_versions",
     "write_export",
+    "write_versions",
 ]
 
 HERE = Path(__file__).parent.resolve()
 VERSIONS_PATH = HERE.joinpath(HERE, "versions.json")
 
 ROOT = HERE.parent.parent.parent.resolve()
+PYPROJECT_TOML_PATH = ROOT.joinpath("pyproject.toml")
 DOCS = ROOT.joinpath("docs")
 EXPORTS_DIRECTORY = DOCS.joinpath("_data")
 EXPORT_PATH = EXPORTS_DIRECTORY.joinpath("versions.yml")
@@ -26,6 +27,11 @@ FAILURES_PATH = DOCS.joinpath("failures.md")
 
 def load_versions():
     """Load Bioversions data."""
+    if not VERSIONS_PATH.is_file():
+        raise RuntimeError(
+            f"bioversions was not packaged/built/installed properly -"
+            f"{VERSIONS_PATH.name} was not found inside the distribution"
+        )
     with open(VERSIONS_PATH) as file:
         return json.load(file)
 
@@ -35,13 +41,20 @@ def _date_converter(o):
         return o.strftime("%Y-%m-%d")
 
 
-def write_versions(versions, indent: int = 2, **kwargs):
+def write_versions(versions, indent: int = 2, **kwargs) -> None:
     """Write Bioversions data."""
+    _ensure_editable()
     with open(VERSIONS_PATH, "w") as file:
         json.dump(versions, file, indent=indent, default=_date_converter, **kwargs)
 
 
-def write_export(versions):
+def write_export(versions) -> None:
     """Write Bioversions data to the export directory."""
+    _ensure_editable()
     with open(EXPORT_PATH, "w") as file:
         yaml.safe_dump(versions, file)
+
+
+def _ensure_editable() -> None:
+    if not PYPROJECT_TOML_PATH.is_file():
+        raise RuntimeError("can not make export when bioversions is not installed in editable mode")

bioversions/resources/update.py

@@ -15,7 +15,7 @@ from bioversions.resources import (
     write_export,
     write_versions,
 )
-from bioversions.sources import _iter_versions
+from bioversions.sources import FailureTuple, _iter_versions
 from bioversions.version import get_git_hash
 
 __all__ = [
@@ -48,10 +48,10 @@ def _update(force: bool):  # noqa:C901
     today = datetime.now().strftime("%Y-%m-%d")
 
     changes = False
-    errors = []
-    for bv, error in _iter_versions(use_tqdm=True):
-        if error is not None or bv is None:
-            errors.append(error)
+    failure_tuples = []
+    for bv in _iter_versions(use_tqdm=True):
+        if isinstance(bv, FailureTuple):
+            failure_tuples.append(bv)
             continue
 
         if bv.name in versions:
@@ -97,7 +97,16 @@ def _update(force: bool):  # noqa:C901
         write_export(rv)
         write_versions(rv)
 
-    FAILURES_PATH.write_text("# Errors\n\n" + "\n".join(f"- {error}" for error in errors))
+    if failure_tuples:
+        click.secho(f"Writing failure summary to {FAILURES_PATH}")
+        text = "# Summary of Errors\n\n"
+        for t in failure_tuples:
+            text += f"- {t.name} - {t.message}\n"
+        text += "\n"
+        for t in failure_tuples:
+            text += f"## {t.name}\n\nUsing class: `{t.clstype}`\n\n"
+            text += f"```python-traceback\n{t.trace}\n```\n\n"
+        FAILURES_PATH.write_text(text)
 
 
 def _log_update(bv) -> None:

bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 856,
-    "date": "2024-11-26",
+    "revision": 857,
+    "date": "2024-11-27",
     "author": "runner"
   },
   "database": [
@@ -9033,6 +9033,11 @@
           "retrieved": "2024-11-24",
           "version": "November 22, 2024",
           "date": "2024-11-22"
+        },
+        {
+          "retrieved": "2024-11-27",
+          "version": "November 25, 2024",
+          "date": "2024-11-25"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -14686,6 +14691,10 @@
         {
           "retrieved": "2024-11-26",
           "version": "2024-11-26"
+        },
+        {
+          "retrieved": "2024-11-27",
+          "version": "2024-11-27"
         }
       ],
       "name": "SwissLipids",
@@ -19598,6 +19607,10 @@
         {
           "retrieved": "2024-11-26",
           "version": "2024-11-24"
+        },
+        {
+          "retrieved": "2024-11-27",
+          "version": "2024-11-25"
         }
       ],
       "name": "Zebrafish Information Network",

bioversions/sources/__init__.py

@@ -4,8 +4,10 @@ from __future__ import annotations
 
 import ftplib
 import logging
+import traceback
 from collections.abc import Iterable, Mapping
 from functools import lru_cache
+from typing import NamedTuple
 
 from tqdm import tqdm
 
@@ -70,9 +72,9 @@ from .zfin import ZfinGetter
 from ..utils import Bioversion, Getter, norm, refresh_daily
 
 __all__ = [
-    "resolve",
     "get_rows",
     "get_version",
+    "resolve",
 ]
 
 logger = logging.getLogger(__name__)
@@ -189,14 +191,23 @@ def get_rows(use_tqdm: bool | None = False) -> list[Bioversion]:
     """Get the rows, refreshing once per day."""
     return [
         bioversion
-        for bioversion, error in _iter_versions(use_tqdm=use_tqdm)
-        if error is None and bioversion is not None
+        for bioversion in _iter_versions(use_tqdm=use_tqdm)
+        if isinstance(bioversion, Bioversion)
     ]
 
 
+class FailureTuple(NamedTuple):
+    """Holds information about failures."""
+
+    name: str
+    clstype: str
+    message: str
+    trace: str
+
+
 def _iter_versions(
     use_tqdm: bool | None = False,
-) -> Iterable[tuple[Bioversion, None] | tuple[None, str]]:
+) -> Iterable[Bioversion | FailureTuple]:
     it = tqdm(get_getters(), disable=not use_tqdm)
 
     for cls in it:
@@ -206,10 +217,10 @@ def _iter_versions(
         except (OSError, AttributeError, ftplib.error_perm):
             msg = f"failed to resolve {cls.name}"
             tqdm.write(msg)
-            yield None, msg
+            yield FailureTuple(cls.name, cls.__name__, msg, traceback.format_exc())
         except ValueError as e:
             msg = f"issue parsing {cls.name}: {e}"
             tqdm.write(msg)
-            yield None, msg
+            yield FailureTuple(cls.name, cls.__name__, msg, traceback.format_exc())
         else:
-            yield yv, None
+            yield yv

bioversions/sources/expasy.py

@@ -10,7 +10,7 @@ __all__ = [
     "ExPASyGetter",
 ]
 
-URL = "ftp://ftp.expasy.org/databases/enzyme/enzuser.txt"
+URL = "https://ftp.expasy.org/databases/enzyme/enzuser.txt"
 
 
 class ExPASyGetter(Getter):

bioversions/sources/obo.py

@@ -5,11 +5,11 @@ from collections.abc import Iterable
 from bioversions.utils import Getter, OBOFoundryGetter, VersionType
 
 __all__ = [
-    "iter_obo_getters",
     "ChebiGetter",
-    "GoGetter",
     "DoidGetter",
+    "GoGetter",
     "PrGetter",
+    "iter_obo_getters",
 ]
 
 

bioversions/utils.py

@@ -11,7 +11,6 @@ import bioregistry
 import pydantic
 import pystow
 import requests
-import requests_ftp
 from bs4 import BeautifulSoup
 from cachier import cachier
 
@@ -20,8 +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."""

bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.559"
+VERSION = "0.5.561"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.559.dist-info → bioversions-0.5.561.dist-info}/METADATA

@@ -1,7 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: bioversions
-Version: 0.5.559
+Version: 0.5.561
 Summary: Get the current version for biological databases
+Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
+Project-URL: Homepage, https://github.com/biopragmatics/bioversions
+Project-URL: Repository, https://github.com/biopragmatics/bioversions.git
+Project-URL: Documentation, https://bioversions.readthedocs.io
 Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 License: MIT License
@@ -25,63 +29,59 @@ License: MIT License
         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
-        
-Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
-Project-URL: Homepage, https://github.com/biopragmatics/bioversions
-Project-URL: Repository, https://github.com/biopragmatics/bioversions.git
-Project-URL: Documentation, https://bioversions.readthedocs.io
-Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
+Keywords: biological databases,biomedical databases,cookiecutter,databases,snekpack
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
+Classifier: Framework :: Pytest
+Classifier: Framework :: Sphinx
+Classifier: Framework :: tox
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
-Classifier: Framework :: Pytest
-Classifier: Framework :: tox
-Classifier: Framework :: Sphinx
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Typing :: Typed
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: requests
-Requires-Dist: requests-ftp
 Requires-Dist: beautifulsoup4
+Requires-Dist: bioregistry[align]>=0.10.0
 Requires-Dist: cachier>=2.2.1
-Requires-Dist: pystow>=0.1.0
 Requires-Dist: click
 Requires-Dist: click-default-group
 Requires-Dist: dataclasses-json
-Requires-Dist: tabulate
+Requires-Dist: lxml
 Requires-Dist: more-click
+Requires-Dist: psycopg2-binary
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pystow>=0.1.0
 Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: tabulate
 Requires-Dist: tqdm
-Requires-Dist: bioregistry[align]>=0.10.0
-Requires-Dist: lxml
-Requires-Dist: pydantic>=2.0
-Requires-Dist: psycopg2-binary
 Provides-Extra: charts
-Requires-Dist: matplotlib; extra == "charts"
-Requires-Dist: seaborn; extra == "charts"
+Requires-Dist: matplotlib; extra == 'charts'
+Requires-Dist: seaborn; extra == 'charts'
 Provides-Extra: docs
-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: sphinx-automodapi; extra == 'docs'
+Requires-Dist: sphinx-click; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme>=3.0; extra == 'docs'
+Requires-Dist: sphinx>=8; extra == 'docs'
 Provides-Extra: slack
-Requires-Dist: slack-sdk; extra == "slack"
+Requires-Dist: slack-sdk; extra == 'slack'
 Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: coverage; extra == "tests"
+Requires-Dist: coverage; extra == 'tests'
+Requires-Dist: pytest; extra == 'tests'
 Provides-Extra: twitter
-Requires-Dist: tweepy; extra == "twitter"
+Requires-Dist: tweepy; extra == 'twitter'
 Provides-Extra: web
-Requires-Dist: flask; extra == "web"
-Requires-Dist: bootstrap-flask; extra == "web"
+Requires-Dist: bootstrap-flask; extra == 'web'
+Requires-Dist: flask; extra == 'web'
+Description-Content-Type: text/markdown
 
 <p align="center">
   <img src="https://github.com/biopragmatics/bioversions/raw/main/docs/source/logo.png" height="150">

{bioversions-0.5.559.dist-info → bioversions-0.5.561.dist-info}/RECORD

@@ -1,17 +1,17 @@
-bioversions/__init__.py,sha256=JXXSH1eWkPWqXXqs7vqtyNkBWHKqCrANmLVOs3df8s0,194
+bioversions/__init__.py,sha256=fwSqW_i6TOuEMYijL28J37ILIwDwZyhNNaH7BEHqujg,194
 bioversions/__main__.py,sha256=TnmQZvX7vgBdyZruaMQUaz2FcuxSiRuCrQ9OHy3pYic,108
 bioversions/charts.py,sha256=3_BcyAAxUp4bBq9UwAEdJBo4MngxnQxvqQs-atRHYzI,2419
 bioversions/cli.py,sha256=k5sPKa-ff8iuuiB7ldRvHPWcZZ0V3szDSMq9zwdIa84,1563
 bioversions/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioversions/slack_client.py,sha256=p9HmnyRCVuQvje0RbdDK9QuRlSw__WwFCJ8Be9cIkzM,1209
 bioversions/twitter_client.py,sha256=9d5Am0FSs7_EgGdjkxqpo98vPir9rjIXIxhZMmLgK5Q,1285
-bioversions/utils.py,sha256=rrtu9K2QTqbg_EaSnl83xe3XSssrZeVmsCl4APvI3Qo,10398
-bioversions/version.py,sha256=FjDpiqZTRrWED7T-MkO4rRJibocGc7IPjRQmYj5Cxt4,587
+bioversions/utils.py,sha256=x5d4p12VMlD5F8-y_J6JE5sct7BCV1d-zO-y5bSamSM,10342
+bioversions/version.py,sha256=Q_aK7ZD4dIa2_ZaP3nze3oVJcrS8vQdZo_Kzb6aOoAU,587
 bioversions/wsgi.py,sha256=-F7pUZipcQgj1T_f-9QCZBVdQ9sZBH93x3hxh9h7klU,794
-bioversions/resources/__init__.py,sha256=q6p1gt5COyyIhsifGMBQxiHvQZH5q-SsPAHUQnFUivk,1147
-bioversions/resources/update.py,sha256=5BFypXcJ0rXrQgTyFplB-FqOkzTHUXAYNFtu76dzgOA,3261
-bioversions/resources/versions.json,sha256=6VfR9GfJ_yHs9lfFZ_A82HrqoiyX1y9aTxS4ZlLZq5I,477322
-bioversions/sources/__init__.py,sha256=ezGCq9b3yp_YS4nfYJmoC1w23sBn2nhRmGS-5Uli5cI,5983
+bioversions/resources/__init__.py,sha256=Nxw6w6_gRC4B_JwvbAAKpNR2rIpkNRZ5UkBIMdNqldY,1659
+bioversions/resources/update.py,sha256=btT_tdp0NKBRdshf4VuOe-vHWq0QQtcWWFcXS8QUfLU,3626
+bioversions/resources/versions.json,sha256=z4LobxLg8z-ltiARxDt08VuLIwNBtjCeCC8WUgg53o8,477637
+bioversions/sources/__init__.py,sha256=pXONlDoxWIVRTSdCN3RDr3aMY38QGPOt0EwPAMCaIF8,6248
 bioversions/sources/antibodyregistry.py,sha256=6GF_9v8A_8Y4o6_nsZ9cAOP5vK3ZbPQ5qeL99UefR80,680
 bioversions/sources/bigg.py,sha256=iVrxyvKiEIUXs6FM2AiLDYa-yYDNGMONmiIv_R6KBg4,661
 bioversions/sources/biogrid.py,sha256=FcQA8AIN7TwWdwRQb_r5hUZwh9Ztl13GeGXKXv1Kcag,734
@@ -28,7 +28,7 @@ bioversions/sources/disgenet.py,sha256=PALIRkPBkT2csrN-Fnn-AZzCc9Z2M2hekE-_FrqE-
 bioversions/sources/drugbank.py,sha256=WZwhVFK16CGeLDFCPCxtHHyGeEgwlpbINLm1868fPxY,994
 bioversions/sources/drugcentral.py,sha256=wH2xL-CWpeVP2042CnWm1X-w3YJv2m5FigTw1ht1cLg,1116
 bioversions/sources/ensembl.py,sha256=mUd5_LsI6oSU4a8DJLSam9lkndf6Zfun0VaxZIye2tI,737
-bioversions/sources/expasy.py,sha256=3cRqQS_LiDzwF-hE26abD_FWEVMHa6v3UiTvK-ETRs0,769
+bioversions/sources/expasy.py,sha256=5C9m9Okygaq2D7zuuTnkOD4V24QU4C89ldztfLtiqnI,771
 bioversions/sources/flybase.py,sha256=L1qs0OF0OhjdknwV6DfvnnlxP37Z09hjuk-pz1Un2GM,754
 bioversions/sources/gtdb.py,sha256=lbtmSh4uhy6-Ve_slwO-Y7_wHRVySuof1I_rR-FQ05k,1001
 bioversions/sources/guidetopharmacology.py,sha256=WAasA6ZlyqJiqP70VrrCEpi2-JW7UMrUunAuE6pTk_g,1377
@@ -48,7 +48,7 @@ bioversions/sources/moalmanac.py,sha256=DMotSYD4sGOTZaJgn_iPeUfEdhjlgmzoKKLYS-L6
 bioversions/sources/msigdb.py,sha256=honGI0qErm5wsZsr0hwWXiw32D3n5xxH5gX3xUEh3po,778
 bioversions/sources/ncit.py,sha256=6rwzQSCHEIeZ1wt2ymCyfevM64479ngrpBEHxfLc2oc,1015
 bioversions/sources/npass.py,sha256=tRaQJJXQQ5fgVLUaUQRrEUMvN963BGdY1zN__KgE1hY,714
-bioversions/sources/obo.py,sha256=_C5SSmVX_BCAeTpc45isQdUtnRlEZ-V3kuhngj_GtGk,1713
+bioversions/sources/obo.py,sha256=cnt0cLpM8wtCG14e6-dYu63qxX6YAd9PzrE5SKJ_8Lc,1713
 bioversions/sources/ols.py,sha256=Zet7BQwluY8f00RvDcyu7EVg4IscnrhxNG4UJhwsL8Y,2697
 bioversions/sources/omim.py,sha256=F87kmMIAxeeXCqrILQNz5250v4p4YsBkA6l02SagHis,880
 bioversions/sources/oncotree.py,sha256=abA58H43gA_TtiOBawBZUzPK7elAPYqWIP7lFd6KqO4,1032
@@ -73,9 +73,8 @@ bioversions/sources/wikipathways.py,sha256=STw8Bivc3IZLYIx-KwpxHLUmRTqNfHm0wQywD
 bioversions/sources/zfin.py,sha256=3Ooz3lDx8J42OAoyU8eJI-fRnMRiYyUMcj4fDE5DVLQ,683
 bioversions/templates/base.html,sha256=AKB6aT39U9VtOM2zvW_Um5IgYO9Ky-CLpByxy5XXO5M,713
 bioversions/templates/home.html,sha256=z98FSslCRP2K39xbHpSPgk19j7Z21PSbRGAtaXI0Md0,2756
-bioversions-0.5.559.dist-info/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-bioversions-0.5.559.dist-info/METADATA,sha256=t_jDkzfhp26CtebftLMSjgv1agYMJV8I9iwALgcJZjU,19665
-bioversions-0.5.559.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-bioversions-0.5.559.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.5.559.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
-bioversions-0.5.559.dist-info/RECORD,,
+bioversions-0.5.561.dist-info/METADATA,sha256=rjXiJDrGumeJ0XNv-KaOvEQET2gewODoBd5eAb7gfu4,19725
+bioversions-0.5.561.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+bioversions-0.5.561.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
+bioversions-0.5.561.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+bioversions-0.5.561.dist-info/RECORD,,

{bioversions-0.5.559.dist-info → bioversions-0.5.561.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: hatchling 1.26.3
 Root-Is-Purelib: true
 Tag: py3-none-any
-

bioversions-0.5.559.dist-info/top_level.txt

@@ -1 +0,0 @@
-bioversions