bioversions 0.8.71__py3-none-any.whl → 0.8.73__py3-none-any.whl

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/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/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/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/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/version.py

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

{bioversions-0.8.71.dist-info → bioversions-0.8.73.dist-info}/METADATA

@@ -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.dist-info → bioversions-0.8.73.dist-info}/RECORD

@@ -5,9 +5,9 @@ bioversions/cli.py,sha256=75eaa237668bef45ef6f16b5c5a20036aef228995b872dda224a54
 bioversions/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
 bioversions/resources/__init__.py,sha256=371c3ac3afe0442e01fc9c2f6c000aa4d476ac8a6435167952404831d36a95d6,1659
 bioversions/resources/update.py,sha256=847565839bacfe2d0fea36202e428cb98e33476b6f13398f950f10386583c473,3593
-bioversions/resources/versions.json,sha256=d910a99d7dbf202c416a31992d52a023d6ef972394e06b516074d5510950fa2a,594520
+bioversions/resources/versions.json,sha256=aa51da8b13d1924509a5ba0b8305a8d26c90c12cea48cc0bd988386b3be4d918,595554
 bioversions/slack_client.py,sha256=bda7d71401bc03f7dc19fec98d7d5abad5083285cb5c97b5b575b1f9459a1285,1293
-bioversions/sources/__init__.py,sha256=cc622715bc9bb41063a03c2b3ca34e7cc140ced8fbae8484526fe29e82d94d55,7677
+bioversions/sources/__init__.py,sha256=a77413228a424c676de0420c55a8837c4aebb8d51e78addc9eac36b14a43b344,8906
 bioversions/sources/antibodyregistry.py,sha256=5c29963e1d7bd40780582ce9539d6120bd593d0cda6f3b763b08af876a2bef8f,713
 bioversions/sources/bigg.py,sha256=895af1caf2a2108517b3a14cd8088b0d86bec980cd18c38d9a222ffd1e8a060e,661
 bioversions/sources/biogrid.py,sha256=df37707dbc42423111e9be6a98c7b866312430d042712d392170a8f2cf8b2daf,742
@@ -16,7 +16,7 @@ bioversions/sources/chebi.py,sha256=53b5cdbb8810bb790027764284d97efa01ee12f7c259
 bioversions/sources/chembl.py,sha256=35cfa0149a5eac1c8efe2577b43aa47e359874558ef48ce227022d7bd0b60932,1513
 bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
 bioversions/sources/civic.py,sha256=321967e8b7c7a7aecf896b49e6ad4520d0b00a114103a71f71a49c775291f11e,1086
-bioversions/sources/complexportal.py,sha256=1adea98029a1aef5e13d7038812734ed37bfa2c9e8f6038cb3c8216b4eff1d19,671
+bioversions/sources/complexportal.py,sha256=9ce9ac2b433c471d69d16d902e36af7665132d58993cb20ed7c47ee746d6870a,673
 bioversions/sources/daily.py,sha256=501fcf689d9b11035b08255c208c5bca0bb631f79e9a8fee3d268f85d07b4033,256
 bioversions/sources/depmap.py,sha256=00b9fb914b27902ef2023f5c2d899a4235829b6b20d3045643e4fbe8deea4168,641
 bioversions/sources/dgi.py,sha256=8b613bedea979b8bbadfcbe4b2fd539e4d29deccf329d936c83a72626d8808bc,940
@@ -33,7 +33,7 @@ bioversions/sources/homologene.py,sha256=4da5b4037dcf2d2e3cd38ceb45664a0e6a3fcf0
 bioversions/sources/icd10.py,sha256=ef9ec91178149d2e9b8dc6ef63bfd74211ada63768046dfc75c02b53828f0ac4,929
 bioversions/sources/icd11.py,sha256=00b75086f6ecd8e81444665944cd6139725fcee36b0d817b54506b0cc91bc580,996
 bioversions/sources/icf.py,sha256=2cf0e779aec4a03845ad091e5ab4fea91aaa10bbd91b5ede9f771c828a8d3771,946
-bioversions/sources/intact.py,sha256=06e67eda7e8eededc74f63eb1c73db0648665dae78323d7d92625c76ff4f7c05,596
+bioversions/sources/intact.py,sha256=c408ebadc99e69bdb789d4b91c5bbb56cbbc621ff5e36e63a967e83ed4736ba5,598
 bioversions/sources/interpro.py,sha256=1fa75923bd60517a3b2f661e7c24e2243e2ab90440bf2621e670c36e1da2baf1,1238
 bioversions/sources/itis.py,sha256=99a480060d52ac6e06404be347080c28af56e984e80cc4763f0a98266212a1df,582
 bioversions/sources/kegg.py,sha256=24574e015a28f77f77451a3b48dbb54b740ff36e7e310bbdf434ee4f63adb094,1014
@@ -72,11 +72,11 @@ bioversions/sources/wikipathways.py,sha256=493c3c062bdcdc864b608c7e2b0a711cb5264
 bioversions/sources/zfin.py,sha256=dcea33de50f1f09e36380a3253c78923e7d19cc46263250c723e1f0c4e4354b4,683
 bioversions/templates/base.html,sha256=00a07a693dfd53d56d38cdb3bd6fd49b922060ef4acbe08ba41cb1cb95d73b93,713
 bioversions/templates/home.html,sha256=cfdf054ac94244fd8adfdc5b1e948f824d7d8fb676d4f49b44602d69723431dd,2756
-bioversions/utils.py,sha256=f83a7ac31bc688117b31c5297d4d9bce8ffd5b63ecc32e6c531bf075952d5e25,10715
-bioversions/version.py,sha256=6f621f70d93c557c44dc93975f18d786f9692387e5b6963941b8d1083462c91b,606
+bioversions/utils.py,sha256=118c35036bc7409b06b1ec3831407f710bf122d95726128b3767cb7532d677f3,10751
+bioversions/version.py,sha256=36165b0e1cc977562f09d23b888faa52224e3a9dd6c66fa217db97fd99aa689b,606
 bioversions/wsgi.py,sha256=b611913189165699cd67480f3d17308344ac935e31c693017aabea89bd0ba8ab,825
-bioversions-0.8.71.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-bioversions-0.8.71.dist-info/WHEEL,sha256=cc8ae5806c5874a696cde0fcf78fdf73db4982e7c824f3ceab35e2b65182fa1a,79
-bioversions-0.8.71.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
-bioversions-0.8.71.dist-info/METADATA,sha256=e8e4cdeddaa825a4dbb54a2da7d940e2063b4fe2a0755928912d3396c198d754,18673
-bioversions-0.8.71.dist-info/RECORD,,
+bioversions-0.8.73.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+bioversions-0.8.73.dist-info/WHEEL,sha256=cc8ae5806c5874a696cde0fcf78fdf73db4982e7c824f3ceab35e2b65182fa1a,79
+bioversions-0.8.73.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
+bioversions-0.8.73.dist-info/METADATA,sha256=ca48dd3e22adc7ce3ee075f655ec8c012e861c1c4585b6122161217afa86c6d3,18673
+bioversions-0.8.73.dist-info/RECORD,,