bioversions 0.7.2__py3-none-any.whl → 0.7.3__py3-none-any.whl

bioversions/resources/update.py

@@ -106,7 +106,7 @@ def _update(force: bool):  # noqa:C901
         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)
+        FAILURES_PATH.write_text(text.rstrip() + "\n")
 
 
 def _log_update(bv) -> None:

bioversions/resources/versions.json

@@ -1,8 +1,8 @@
 {
   "annotations": {
-    "revision": 902,
-    "date": "2025-01-15",
-    "author": "runner"
+    "revision": 904,
+    "date": "2025-01-28",
+    "author": "cthoyt"
   },
   "database": [
     {
@@ -204,6 +204,11 @@
           "retrieved": "2025-01-15",
           "version": "2025-01-14",
           "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-27",
+          "homepage": "https://antibodyregistry.org/"
         }
       ],
       "name": "Antibody Registry",
@@ -2022,6 +2027,10 @@
         {
           "retrieved": "2025-01-12",
           "version": "2.233"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2.234"
         }
       ],
       "vtype": "date"
@@ -4109,6 +4118,10 @@
         {
           "retrieved": "2025-01-12",
           "version": "4.191"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "4.192"
         }
       ],
       "vtype": "date"
@@ -4608,6 +4621,10 @@
         {
           "retrieved": "2025-01-05",
           "version": "2024-12-31"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-14"
         }
       ],
       "vtype": "date"
@@ -6510,6 +6527,10 @@
         {
           "retrieved": "2025-01-14",
           "version": "2024-12-16"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-24"
         }
       ],
       "name": "ITIS",
@@ -7057,6 +7078,10 @@
         {
           "retrieved": "2024-12-15",
           "version": "2.145"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2.146"
         }
       ],
       "vtype": "date"
@@ -9441,6 +9466,10 @@
         {
           "retrieved": "2025-01-15",
           "version": "2025-01-13"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-24"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -11998,6 +12027,10 @@
         {
           "retrieved": "2025-01-14",
           "version": "2025-01-10"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-24"
         }
       ],
       "name": "Rat Genome Database",
@@ -12095,6 +12128,10 @@
         {
           "retrieved": "2024-12-15",
           "version": "6.238"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "6.239"
         }
       ],
       "vtype": "date"
@@ -12826,6 +12863,19 @@
       "name": "SIGNOR",
       "vtype": "date"
     },
+    {
+      "releases": [
+        {
+          "retrieved": "2025-01-28",
+          "version": "138.2",
+          "homepage": "https://www.arb-silva.de/",
+          "date": "2024-03-14"
+        }
+      ],
+      "name": "SILVA ribosomal RNA database",
+      "prefix": "silva.taxon",
+      "vtype": "sequential"
+    },
     {
       "releases": [
         {
@@ -15382,6 +15432,10 @@
         {
           "retrieved": "2025-01-15",
           "version": "2025-01-15"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-28"
         }
       ],
       "name": "SwissLipids",
@@ -16125,6 +16179,10 @@
         {
           "retrieved": "2024-11-10",
           "version": "2024-11-02"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-11"
         }
       ],
       "name": "Unified Phenotype Ontology",
@@ -20516,6 +20574,10 @@
         {
           "retrieved": "2025-01-15",
           "version": "2025-01-13"
+        },
+        {
+          "retrieved": "2025-01-28",
+          "version": "2025-01-27"
         }
       ],
       "name": "Zebrafish Information Network",

bioversions/sources/__init__.py

@@ -64,6 +64,7 @@ from .rhea import RheaGetter
 from .rxnorm import RxNormGetter
 from .sgd import SgdGetter
 from .signor import SignorGetter
+from .silva import SILVAGetter
 from .slm import SwissLipidGetter
 from .stringdb import StringDBGetter
 from .umls import UMLSGetter
@@ -142,6 +143,7 @@ def get_getters() -> list[type[Getter]]:
         ICD11Getter,
         CiVICGetter,
         GTDBGetter,
+        SILVAGetter,
         SignorGetter,
     ]
     getters.extend(iter_obo_getters())
@@ -220,7 +222,7 @@ def _iter_versions(
             msg = f"failed to resolve {cls.name}"
             tqdm.write(msg)
             yield FailureTuple(cls.name, cls.__name__, msg, traceback.format_exc())
-        except ValueError as e:
+        except (ValueError, KeyError) as e:
             msg = f"issue parsing {cls.name}: {e}"
             tqdm.write(msg)
             yield FailureTuple(cls.name, cls.__name__, msg, traceback.format_exc())

bioversions/sources/kegg.py

@@ -20,7 +20,7 @@ class KEGGGetter(Getter):
     name = "KEGG"
     date_fmt = "%B %d, %Y"
     version_type = VersionType.semver_minor
-    collection: ClassVar[list[str]] = ["kegg", *bioregistry.get_has_parts("kegg")]
+    collection: ClassVar[list[str]] = ["kegg", *(bioregistry.get_has_parts("kegg") or [])]
 
     def get(self) -> Mapping[str, str]:
         """Get the latest KEGG version number."""

bioversions/sources/ols.py

@@ -1,7 +1,8 @@
 """Get versions from the OLS."""
 
 import logging
-from collections.abc import Iterable, Mapping
+from collections.abc import Iterable
+from typing import cast
 
 import bioregistry
 from bioregistry.external.ols import get_ols_processing
@@ -16,9 +17,13 @@ ols_processing = get_ols_processing()
 
 def _get_version_type(bioregistry_id: str) -> VersionType | None:
     ols_id = bioregistry.get_ols_prefix(bioregistry_id)
+    if ols_id is None:
+        raise ValueError(f"Missing OLS prefix for bioregistry:{bioregistry_id}")
     ols_config = ols_processing.get(ols_id)
     if ols_config is None:
-        raise
+        raise ValueError(
+            f"Missing OLS configuration for bioregistry:{bioregistry_id} / ols:{ols_id}"
+        )
 
     ols_version_type = ols_config.version_type
     ols_version_date_format = ols_config.version_date_format
@@ -61,12 +66,12 @@ def make_ols_getter(bioregistry_id: str) -> type[Getter] | None:
         """A getter for OLS data from the Bioregistry."""
 
         bioregistry_id = _brid
-        name = _name
+        name = cast(str, _name)
         version_type = _version_type  # type:ignore
 
-        def get(self) -> str | Mapping[str, str]:
+        def get(self) -> str:
             """Get the version from the Bioregistry."""
-            return version
+            return cast(str, version)
 
     return OlsGetter
 

bioversions/sources/silva.py

@@ -0,0 +1,41 @@
+"""A getter for SILVA."""
+
+from datetime import datetime
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "SILVAGetter",
+]
+
+URL = "https://www.arb-silva.de/fileadmin/silva_databases/current/VERSION.txt"
+HEADER_FMT = "%a, %d %b %Y %H:%M:%S %Z"
+
+
+class SILVAGetter(Getter):
+    """A getter for the SILVA."""
+
+    bioregistry_id = "silva.taxon"
+    name = "SILVA ribosomal RNA database"
+    version_type = VersionType.sequential
+    homepage_fmt = "https://www.arb-silva.de/"
+
+    def get(self):
+        """Get the latest SILVA version number from VERSION.txt."""
+        res = requests.get(URL, timeout=15)
+
+        # Get version from the content
+        rv = {"version": res.text.strip()}
+
+        # Get date from the Last-Modified header
+        date_str = res.headers.get("Last-Modified")
+        if date_str:
+            rv["date"] = datetime.strptime(date_str, HEADER_FMT)
+
+        return rv
+
+
+if __name__ == "__main__":
+    SILVAGetter.print()

bioversions/utils.py

@@ -271,6 +271,8 @@ class OBOFoundryGetter(Getter):
     @property
     def key(self) -> str:
         """Get the OBO Foundry key."""
+        if self.bioregistry_id is None:
+            raise ValueError("missing bioregistry ID")
         rv = bioregistry.get_obofoundry_prefix(self.bioregistry_id)
         if rv is None:
             raise ValueError

bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.7.2"
+VERSION = "0.7.3"
 
 
 def get_git_hash() -> str:

{bioversions-0.7.2.dist-info → bioversions-0.7.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.7.2
+Version: 0.7.3
 Summary: Get the current version for biological databases
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
 Author: Charles Tapley Hoyt
@@ -33,7 +33,7 @@ Requires-Dist: tabulate
 Requires-Dist: more-click
 Requires-Dist: pyyaml
 Requires-Dist: tqdm
-Requires-Dist: bioregistry[align]>=0.10.0
+Requires-Dist: bioregistry[align]>=0.11.35
 Requires-Dist: lxml
 Requires-Dist: pydantic>=2.0
 Requires-Dist: psycopg2-binary
@@ -127,7 +127,7 @@ While https://biopragmatics.github.io/bioversions provides a daily updated
 static listing of the database, you can run a dynamic version with an API from
 your shell with:
 
-```bash
+```console
 $ bioversions web
 ```
 
@@ -151,25 +151,40 @@ assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'
 You can use `bioversions get` to incorporate the latest versions in your shell
 scripts or REPL usage like in:
 
-```bash
+```console
 $ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
 ```
 
 ## 🚀 Installation
 
 The most recent release can be installed from
-[PyPI](https://pypi.org/project/bioversions/) with:
+[PyPI](https://pypi.org/project/bioversions/) with uv:
+
+```console
+$ uv pip install bioversions
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install bioversions
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-python3 -m pip install bioversions
+$ uv --preview pip install git+https://github.com/biopragmatics/bioversions.git
 ```
 
-The most recent code and data can be installed directly from GitHub with:
+or with pip:
 
 ```console
-python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
+$ UV_PREVIEW=1 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
@@ -235,22 +250,24 @@ $ cd bioversions
 $ uv --preview pip install -e .
 ```
 
-Alternatively, install using legacy pip with `UV_PREVIEW` mode enabled until the
-uv build backend becomes a stable feature:
+Alternatively, install using pip:
 
 ```console
 $ UV_PREVIEW=1 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
 guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Update with the following:
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
 
 ```console
-python3 -m pip install cruft
-cruft update
+$ cruft update
 ```
 
 More info on Cruft's update command is available
@@ -259,11 +276,11 @@ More info on Cruft's update command is available
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
-`python3 -m pip install tox tox-uv`, the unit tests in the `tests/` folder can
-be run reproducibly with:
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
+unit tests in the `tests/` folder can be run reproducibly with:
 
 ```console
-tox -e py
+$ tox -e py
 ```
 
 Additionally, these tests are automatically re-run with each commit in a
@@ -274,10 +291,10 @@ Additionally, these tests are automatically re-run with each commit in a
 The documentation can be built locally using the following:
 
 ```console
-git clone git+https://github.com/biopragmatics/bioversions.git
-cd bioversions
-tox -e docs
-open docs/build/html/index.html
+$ git clone git+https://github.com/biopragmatics/bioversions.git
+$ cd bioversions
+$ tox -e docs
+$ open docs/build/html/index.html
 ```
 
 The documentation automatically installs the package as well as the `docs` extra
@@ -357,10 +374,11 @@ Note that this deprecates previous workflows using `.pypirc`.
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
-`python3 -m pip install tox tox-uv`, run the following from the console:
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run
+the following from the console:
 
 ```console
-tox -e finish
+$ tox -e finish
 ```
 
 This script does the following:

{bioversions-0.7.2.dist-info → bioversions-0.7.3.dist-info}/RECORD

@@ -1,81 +1,83 @@
-bioversions/resources/update.py,sha256=6ed4ffb5da7434a05176c85fe15b8e7bebc75aad1042d7165857174bc4147cb5,3626
+bioversions/twitter_client.py,sha256=f5de409b4152b3bfc4806763931aa9a3df2f3e2afdae32172318593262e02b94,1285
+bioversions/.DS_Store,sha256=ae189687e1d36349b4c5c5dd6a5ecd9a79635474d4ba76e63cb2ae00487c00a9,6148
+bioversions/version.py,sha256=d777c535bb20992e18738384d097b4813a784f2964c2a6e83b567655f7554a4d,585
+bioversions/charts.py,sha256=dff05cc80031529e1b06af54c0011d241a383278319d0c6fa90b3e6ad4476332,2419
+bioversions/resources/update.py,sha256=6c819d96095f445905cad830239ffc7f67a4bdbcae5b6cb1b62c6c97704beeca,3642
+bioversions/resources/versions.json,sha256=830da40d2bc3f0654bbb041276f93be1a6df062130778740514285e8f1b7e4e0,502086
 bioversions/resources/__init__.py,sha256=371c3ac3afe0442e01fc9c2f6c000aa4d476ac8a6435167952404831d36a95d6,1659
-bioversions/resources/versions.json,sha256=d452d188d5eb49c93973c4daeb3293d5b3d51e44fd782564afd5d70d9ce28d01,500631
-bioversions/wsgi.py,sha256=f85ee95198a9710823d53fdffbd40264155d43db19047f77c7787187d87b9255,794
+bioversions/__init__.py,sha256=7f04aa5bf8ba4ceb843188a32f6f09dfb20b2300f067284d35a1fb0441eaba38,194
+bioversions/slack_client.py,sha256=a7d1e69f244256e42f8ded116dd0caf50b91952c3ffd6c05089f017bd7089333,1209
+bioversions/cli.py,sha256=939b0f29af9f7fc8aeba207b95d46f1cf59c659d15deccc348cabdcf07486bce,1563
+bioversions/utils.py,sha256=d96017bd9986329496f7c5b9bf7072d466517c6981c3aff36f7658c4954e206d,10437
 bioversions/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
-bioversions/sources/mesh.py,sha256=5ea8cf53950980e1d5736f1cffa37b46225dd45f51a1418f5c69a621a368a6f3,971
-bioversions/sources/rfam.py,sha256=3c8de33a8920baac6789fd07160da00752f524ed25ad045b3b48a24716eda5a8,540
-bioversions/sources/bigg.py,sha256=895af1caf2a2108517b3a14cd8088b0d86bec980cd18c38d9a222ffd1e8a060e,661
-bioversions/sources/itis.py,sha256=99a480060d52ac6e06404be347080c28af56e984e80cc4763f0a98266212a1df,582
-bioversions/sources/chembl.py,sha256=35cfa0149a5eac1c8efe2577b43aa47e359874558ef48ce227022d7bd0b60932,1513
-bioversions/sources/daily.py,sha256=501fcf689d9b11035b08255c208c5bca0bb631f79e9a8fee3d268f85d07b4033,256
-bioversions/sources/stringdb.py,sha256=9afd81dd24d02469cce66e246cb6f696e4a501ba3e7e8dc7aff0f022563a37b2,787
+bioversions/sources/disgenet.py,sha256=3c02c84643c1913d9cb2b37e1679fe019cc273d67633685e904fbf16ba84f8bc,739
+bioversions/sources/oncotree.py,sha256=69b039f07e37800fd3b623816b00595333caede9403d8a9620fee515de8aa8ee,1032
+bioversions/sources/signor.py,sha256=f0a0bd043c1344027e31fe8fc4e5922f44e86044ca16370e6d66368161f05c83,969
+bioversions/sources/uniprot.py,sha256=c3e16b68fc8a65e12d9a3b3288fedbd9a8e0e7b47f0a69f0fb032fb072c68a1b,924
+bioversions/sources/expasy.py,sha256=e42f66f4e93281aab60fbceeb939e4383e15db8414e02f3d95dced7cbb62aa72,771
+bioversions/sources/biogrid.py,sha256=15c400f0020ded3c167704506ffaf985467087d66d975dc67865ca5efd4a71a8,734
+bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
+bioversions/sources/kegg.py,sha256=89f784cc7b97ad22436b59b5616c35dd4e82ef1f2335d4001a99a8620d3a00ca,913
 bioversions/sources/slm.py,sha256=84fe81b16cf8cb3cdc817f4ed56482364bb46a9d3af1f01c3726273b26d106d6,766
-bioversions/sources/pathbank.py,sha256=620621044418e05d3d720ed2e01704107e260fa97a2c38ee0d1bf507f7bce62f,693
+bioversions/sources/homologene.py,sha256=4da5b4037dcf2d2e3cd38ceb45664a0e6a3fcf01332bd6f15ffcc089a526779c,622
 bioversions/sources/dgi.py,sha256=8b613bedea979b8bbadfcbe4b2fd539e4d29deccf329d936c83a72626d8808bc,940
-bioversions/sources/kegg.py,sha256=748eee42969987ae6b64e76eb6a71734e9319f71c6c03373697c948718937515,905
-bioversions/sources/mirbase.py,sha256=ab70baf82cbebc42f22424029e9838a6f7a846b9587ea81be37d779871b90a9e,996
-bioversions/sources/ncit.py,sha256=eabc33412087108799d70b76ca60b27debcceb8e3bf6782ba41107c5f2dcda87,1015
-bioversions/sources/pfam.py,sha256=a2509a19315b2524a4974101d2215794c639b2ede25832449819524f4c3efff8,975
-bioversions/sources/ols.py,sha256=65eb7b050c25b98f1fd3446f0dccaeec4560e08b1c9eb871346e14261c2c2fc6,2697
-bioversions/sources/wikipathways.py,sha256=493c3c062bdcdc864b608c7e2b0a711cb526453a8d7c79b4c10cb00e68bed30b,798
-bioversions/sources/intact.py,sha256=06e67eda7e8eededc74f63eb1c73db0648665dae78323d7d92625c76ff4f7c05,596
-bioversions/sources/icf.py,sha256=0580247e61d6b50b0c08d5331a97d188a5671dda4333298628bc327af313c08a,720
 bioversions/sources/moalmanac.py,sha256=0cca2d4980f8b0639365a2609ff88f7947c47618e5826ce828a2d84be2fa4eba,749
-bioversions/sources/expasy.py,sha256=e42f66f4e93281aab60fbceeb939e4383e15db8414e02f3d95dced7cbb62aa72,771
-bioversions/sources/interpro.py,sha256=1fa75923bd60517a3b2f661e7c24e2243e2ab90440bf2621e670c36e1da2baf1,1238
-bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
-bioversions/sources/cellosaurus.py,sha256=d17ae067aade4a433c0f350b26d681dda881603d1057734750b67ef19950ee01,975
-bioversions/sources/gtdb.py,sha256=95bb664a1e2e872ebe55efec9703be63bff01d15724aea1fd48feb47e150d399,1001
-bioversions/sources/oncotree.py,sha256=69b039f07e37800fd3b623816b00595333caede9403d8a9620fee515de8aa8ee,1032
-bioversions/sources/rxnorm.py,sha256=ba8a68262850132282d79c6ab5293f4997c496672ca614b26da8e22ee6856253,1010
-bioversions/sources/__init__.py,sha256=0b99d733a9b78ad746a5b8f970d9874c2b13fe81fc60e22412e2f9fc243a166d,6303
-bioversions/sources/mgi.py,sha256=4d7f95d3171616692db2c8d195d8d86f9f751c2b6885e63df70d054c7d9c2199,841
-bioversions/sources/civic.py,sha256=3eee261f77648892b6a61c3aeeddfff2bf94e63dee9fc91fcbb22a2f44c05dea,1132
-bioversions/sources/depmap.py,sha256=00b9fb914b27902ef2023f5c2d899a4235829b6b20d3045643e4fbe8deea4168,641
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