bioversions 0.8.0__py3-none-any.whl → 0.8.2__py3-none-any.whl

bioversions/resources/update.py

@@ -107,6 +107,8 @@ def _update(force: bool):  # noqa:C901
             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.rstrip() + "\n")
+    else:
+        FAILURES_PATH.write_text("# No Errors :)\n")
 
 
 def _log_update(bv) -> None:

bioversions/resources/versions.json

@@ -1,8 +1,8 @@
 {
   "annotations": {
-    "revision": 990,
-    "date": "2025-05-06",
-    "author": "runner"
+    "revision": 992,
+    "date": "2025-05-07",
+    "author": "cthoyt"
   },
   "database": [
     {
@@ -528,6 +528,16 @@
           "retrieved": "2025-05-06",
           "version": "2025-05-05",
           "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-06",
+          "homepage": "https://antibodyregistry.org/"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-07",
+          "homepage": "https://antibodyregistry.org/"
         }
       ],
       "name": "Antibody Registry",
@@ -4136,6 +4146,12 @@
           "version": "113",
           "homepage": "https://www.ensembl.org",
           "date": "2024-10-01"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "114",
+          "homepage": "https://www.ensembl.org",
+          "date": "2025-05-01"
         }
       ],
       "name": "Ensembl",
@@ -5345,6 +5361,11 @@
           "retrieved": "2025-02-25",
           "version": "2025_01",
           "homepage": "http://ftp.flybase.net/releases/FB2025_01/"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025_02",
+          "homepage": "https://s3ftp.flybase.org/releases/FB2025_02/"
         }
       ],
       "name": "FlyBase",
@@ -5852,6 +5873,12 @@
           "version": "220",
           "homepage": "https://gtdb.ecogenomic.org/",
           "date": "2024-04-24"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "226",
+          "homepage": "https://gtdb.ecogenomic.org/",
+          "date": "2025-04-16"
         }
       ],
       "name": "Genome Taxonomy Database",
@@ -6296,6 +6323,11 @@
           "retrieved": "2025-04-03",
           "version": "2025-04-01",
           "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-04-01.json"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-06",
+          "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-05-06.json"
         }
       ],
       "name": "HGNC",
@@ -10547,6 +10579,14 @@
         {
           "retrieved": "2025-05-04",
           "version": "2025-05-02"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-05"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-06"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -17096,6 +17136,10 @@
         {
           "retrieved": "2025-05-06",
           "version": "2025-05-06"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-07"
         }
       ],
       "name": "SwissLipids",
@@ -22644,6 +22688,14 @@
         {
           "retrieved": "2025-05-06",
           "version": "2025-05-04"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-05"
+        },
+        {
+          "retrieved": "2025-05-07",
+          "version": "2025-05-06"
         }
       ],
       "name": "Zebrafish Information Network",

bioversions/sources/rfam.py

@@ -1,6 +1,8 @@
 """A getter for Rfam."""
 
-from bioversions.utils import Getter, VersionType, _get_ftp_version
+import requests
+
+from bioversions.utils import Getter, VersionType
 
 __all__ = [
     "RfamGetter",
@@ -12,12 +14,17 @@ class RfamGetter(Getter):
 
     bioregistry_id = "rfam"
     name = "Rfam"
-    homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
+    homepage_fmt = "https://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
     version_type = VersionType.semver_minor
 
-    def get(self):
+    def get(self) -> str:
         """Get the latest Rfam version number."""
-        return _get_ftp_version("ftp.ebi.ac.uk", "pub/databases/Rfam/")
+        res = requests.get("https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/README", timeout=15)
+        for line in res.iter_lines():
+            line = line.decode("utf8").strip()
+            if line.startswith("Release "):
+                return line[len("Release ") :]
+        raise ValueError
 
 
 if __name__ == "__main__":

bioversions/version.py

@@ -8,7 +8,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.8.0"
+VERSION = "0.8.2"
 
 
 def get_git_hash() -> str:

{bioversions-0.8.0.dist-info → bioversions-0.8.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.8.0
+Version: 0.8.2
 Summary: Get the current version for biological databases
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
 Author: Charles Tapley Hoyt

{bioversions-0.8.0.dist-info → bioversions-0.8.2.dist-info}/RECORD

@@ -1,8 +1,8 @@
 bioversions/.DS_Store,sha256=ae189687e1d36349b4c5c5dd6a5ecd9a79635474d4ba76e63cb2ae00487c00a9,6148
-bioversions/version.py,sha256=d08d0aa1a4f853521269d1e11e2d7ee4dff8c21ce25eeb4b47928a9855e10bed,605
+bioversions/version.py,sha256=2b1b42c67011aa866e54e447db5177beb365d310067d85b407f772c80df85fbe,605
 bioversions/charts.py,sha256=be29a2fde227a4bd02611112f1cbe58a00e261e435fc8f00e82104a15dadbdfe,2457
-bioversions/resources/update.py,sha256=339d2963c35d6b5e03e6fb97894bd90ea39cc94376aaee9ab8d0ccf23b1ff0c5,3530
-bioversions/resources/versions.json,sha256=ea28e4edb4e7cb548d635c79149a51483cc3a0fbf22887abc630db18fa41cbd3,554814
+bioversions/resources/update.py,sha256=847565839bacfe2d0fea36202e428cb98e33476b6f13398f950f10386583c473,3593
+bioversions/resources/versions.json,sha256=8c2fed52ff39a94541f34e510d7d64f8a7a6355fe3a00f40d1c7ac52b1f0ffdf,556303
 bioversions/resources/__init__.py,sha256=371c3ac3afe0442e01fc9c2f6c000aa4d476ac8a6435167952404831d36a95d6,1659
 bioversions/__init__.py,sha256=0fc58200e829534318812aa56075dc5a716d8b9343f60f1580c27cc3e91eea62,354
 bioversions/slack_client.py,sha256=bda7d71401bc03f7dc19fec98d7d5abad5083285cb5c97b5b575b1f9459a1285,1293
@@ -56,7 +56,7 @@ bioversions/sources/pr.py,sha256=6c440e95057d35b7d0273d9c26bc2e0dec45cfe22f541e4
 bioversions/sources/unversioned.py,sha256=c2f328c3bca5b9bbd0ede38ce93bd5a8d1cd079757902865f6c83c3ed05794f4,53
 bioversions/sources/bigg.py,sha256=895af1caf2a2108517b3a14cd8088b0d86bec980cd18c38d9a222ffd1e8a060e,661
 bioversions/sources/obo.py,sha256=727b7470ba4cf30b421b5e1eebe758bbadeac57e9801df4fceb13948a27ff0b7,1713
-bioversions/sources/rfam.py,sha256=3c8de33a8920baac6789fd07160da00752f524ed25ad045b3b48a24716eda5a8,540
+bioversions/sources/rfam.py,sha256=c6c0695b8975324ce12a11351c36258b241644d611cb23ee4d70e7c2cc2aa082,775
 bioversions/sources/chembl.py,sha256=35cfa0149a5eac1c8efe2577b43aa47e359874558ef48ce227022d7bd0b60932,1513
 bioversions/sources/pfam.py,sha256=a2509a19315b2524a4974101d2215794c639b2ede25832449819524f4c3efff8,975
 bioversions/sources/interpro.py,sha256=1fa75923bd60517a3b2f661e7c24e2243e2ab90440bf2621e670c36e1da2baf1,1238
@@ -75,8 +75,8 @@ bioversions/templates/home.html,sha256=cfdf054ac94244fd8adfdc5b1e948f824d7d8fb67
 bioversions/templates/base.html,sha256=00a07a693dfd53d56d38cdb3bd6fd49b922060ef4acbe08ba41cb1cb95d73b93,713
 bioversions/__main__.py,sha256=0e97cd1eac70162293fb809292e2cba2464218394244001f3f9e0c74b8f71351,128
 bioversions/wsgi.py,sha256=b611913189165699cd67480f3d17308344ac935e31c693017aabea89bd0ba8ab,825
-bioversions-0.8.0.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-bioversions-0.8.0.dist-info/WHEEL,sha256=1c77bbda0b527f376a68ced20cbc1aac3efc7bc4d7c10cc4323a905ef79ae8db,78
-bioversions-0.8.0.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
-bioversions-0.8.0.dist-info/METADATA,sha256=723173d74c837a0ea045ff3732817196371cecc2ca52ea9847c7bbb04b58a452,18672
-bioversions-0.8.0.dist-info/RECORD,,
+bioversions-0.8.2.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+bioversions-0.8.2.dist-info/WHEEL,sha256=1c77bbda0b527f376a68ced20cbc1aac3efc7bc4d7c10cc4323a905ef79ae8db,78
+bioversions-0.8.2.dist-info/entry_points.txt,sha256=4cdd92beb5155987fe3fa990cbaa0268658f0e30d27ed349fada88c48b97484e,54
+bioversions-0.8.2.dist-info/METADATA,sha256=e1482b48640b744c314c677fce78127f3c13f0edf7d566e8618e475b1b53df40,18672
+bioversions-0.8.2.dist-info/RECORD,,