bioversions 0.8.71__tar.gz → 0.8.73__tar.gz

{bioversions-0.8.71 → bioversions-0.8.73}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.8.71
+Version: 0.8.73
 Summary: Get the current version for biological databases
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
 Author: Charles Tapley Hoyt

{bioversions-0.8.71 → bioversions-0.8.73}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bioversions"
-version = "0.8.71"
+version = "0.8.73"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -260,7 +260,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.8.71"
+current_version = "0.8.73"
 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-0.8.71 → bioversions-0.8.73}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 1061,
-    "date": "2025-07-15",
+    "revision": 1063,
+    "date": "2025-07-17",
     "author": "runner"
   },
   "database": [
@@ -809,6 +809,16 @@
           "retrieved": "2025-07-15",
           "version": "2025-07-14",
           "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-07-16",
+          "version": "2025-07-15",
+          "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-07-17",
+          "version": "2025-07-16",
+          "homepage": "https://antibodyregistry.org/"
         }
       ],
       "name": "Antibody Registry",
@@ -5780,6 +5790,11 @@
           "retrieved": "2025-05-07",
           "version": "2025_02",
           "homepage": "https://s3ftp.flybase.org/releases/FB2025_02/"
+        },
+        {
+          "retrieved": "2025-07-17",
+          "version": "2025_03",
+          "homepage": "https://s3ftp.flybase.org/releases/FB2025_03/"
         }
       ],
       "name": "FlyBase",
@@ -9637,6 +9652,11 @@
           "retrieved": "2025-07-03",
           "version": "25.06e",
           "date": "2025-06-30"
+        },
+        {
+          "retrieved": "2025-07-16",
+          "version": "25.07b",
+          "date": "2025-07-14"
         }
       ],
       "name": "National Cancer Institute Thesaurus",
@@ -11364,6 +11384,14 @@
         {
           "retrieved": "2025-07-13",
           "version": "2025-07-11"
+        },
+        {
+          "retrieved": "2025-07-16",
+          "version": "2025-07-14"
+        },
+        {
+          "retrieved": "2025-07-17",
+          "version": "2025-07-15"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -18363,6 +18391,14 @@
         {
           "retrieved": "2025-07-15",
           "version": "2025-07-15"
+        },
+        {
+          "retrieved": "2025-07-16",
+          "version": "2025-07-16"
+        },
+        {
+          "retrieved": "2025-07-17",
+          "version": "2025-07-17"
         }
       ],
       "name": "SwissLipids",
@@ -24234,6 +24270,10 @@
         {
           "retrieved": "2025-07-15",
           "version": "2025-07-13"
+        },
+        {
+          "retrieved": "2025-07-17",
+          "version": "2025-07-15"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.8.71 → bioversions-0.8.73}/src/bioversions/sources/__init__.py

@@ -75,7 +75,66 @@ from .zfin import ZfinGetter
 from ..utils import Getter, VersionResult, norm, refresh_daily
 
 __all__ = [
+    "AntibodyRegistryGetter",
+    "BiGGGetter",
+    "BioGRIDGetter",
+    "CellosaurusGetter",
+    "ChEBIGetter",
+    "ChEMBLGetter",
+    "ChemIDplusGetter",
+    "CiVICGetter",
+    "ComplexPortalGetter",
+    "DGIGetter",
+    "DepMapGetter",
+    "DisGeNetGetter",
+    "DrugBankGetter",
+    "DrugCentralGetter",
+    "EnsemblGetter",
+    "ExPASyGetter",
+    "FlybaseGetter",
+    "GTDBGetter",
+    "GuideToPharmacologyGetter",
+    "HGNCGetter",
+    "HomoloGeneGetter",
+    "ICD10Getter",
+    "ICD11Getter",
+    "ICFGetter",
+    "ITISGetter",
+    "IntActGetter",
+    "InterProGetter",
+    "KEGGGetter",
+    "MGIGetter",
+    "MOAlmanacGetter",
+    "MSigDBGetter",
+    "MeshGetter",
+    "MirbaseGetter",
+    "NCBIGeneGetter",
+    "NCItGetter",
+    "NPASSGetter",
+    "OMIMGetter",
+    "OncoTreeGetter",
+    "PRGetter",
+    "PathBankGetter",
+    "PathwayCommonsGetter",
+    "PfamGetter",
+    "PombaseGetter",
+    "PubChemGetter",
+    "RGDGetter",
+    "ReactomeGetter",
+    "RfamGetter",
+    "RheaGetter",
+    "RxNormGetter",
+    "SILVAGetter",
+    "SPDXGetter",
+    "SgdGetter",
+    "SignorGetter",
+    "StringDBGetter",
+    "SwissLipidGetter",
+    "UMLSGetter",
+    "UniProtGetter",
     "VersionFailure",
+    "WikiPathwaysGetter",
+    "ZfinGetter",
     "clear_cache",
     "get_rows",
     "get_version",
@@ -257,8 +316,8 @@ def iter_versions(
             it.set_postfix(name=cls.name)
             try:
                 yv = resolve(cls.name)
-            except (OSError, AttributeError, ftplib.error_perm):
-                msg = f"[{cls.bioregistry_id or cls.name}] failed to resolve"
+            except (OSError, AttributeError, ftplib.error_perm) as e:
+                msg = f"[{cls.bioregistry_id or cls.name}] failed to resolve: {e}"
                 tqdm.write(msg)
                 yield VersionFailure(cls.name, cls.__name__, msg, traceback.format_exc())
             except (ValueError, KeyError) as e:

{bioversions-0.8.71 → bioversions-0.8.73}/src/bioversions/sources/complexportal.py

@@ -12,7 +12,7 @@ class ComplexPortalGetter(Getter):
 
     bioregistry_id = "complexportal"
     name = "Complex Portal"
-    homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/{version}/"
+    homepage_fmt = "https://ftp.ebi.ac.uk/pub/databases/intact/complex/{version}/"
     date_version_fmt = "%Y-%m-%d"
     version_type = VersionType.date
 

{bioversions-0.8.71 → bioversions-0.8.73}/src/bioversions/sources/intact.py

@@ -12,7 +12,7 @@ class IntActGetter(Getter):
 
     bioregistry_id = "intact"
     name = "IntAct"
-    homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/intact/{version}/"
+    homepage_fmt = "https://ftp.ebi.ac.uk/pub/databases/intact/{version}/"
     date_version_fmt = "%Y-%m-%d"
     version_type = VersionType.date
 

{bioversions-0.8.71 → bioversions-0.8.73}/src/bioversions/utils.py

@@ -317,11 +317,13 @@ def _get_ftp_version(host: str, directory: str) -> str:
 
 
 def _get_ftp_date_version(host: str, directory: str) -> str:
-    with ftplib.FTP(host) as ftp:
-        ftp.login()
-        ftp.cwd(directory)
-        names = sorted([name for name in ftp.nlst() if _is_iso_8601(name)])
-    return names[-1]
+    url = f"https://{host}/{directory}"
+    soup = get_soup(url)
+    return max(
+        text
+        for anchor in soup.find_all("a")
+        if anchor.text and _is_iso_8601(text := anchor.text.rstrip("/"))
+    )
 
 
 def _is_iso_8601(s: str) -> bool:

{bioversions-0.8.71 → bioversions-0.8.73}/src/bioversions/version.py

@@ -8,7 +8,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.8.71"
+VERSION = "0.8.73"
 
 
 def get_git_hash() -> str: