bioversions 0.8.0__tar.gz → 0.8.2__tar.gz

{bioversions-0.8.0 → bioversions-0.8.2}/PKG-INFO

@@ -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 → bioversions-0.8.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bioversions"
-version = "0.8.0"
+version = "0.8.2"
 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 = "0.8.0"
+current_version = "0.8.2"
 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-0.8.0 → bioversions-0.8.2}/src/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-0.8.0 → bioversions-0.8.2}/src/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-0.8.2/src/bioversions/sources/rfam.py

@@ -0,0 +1,31 @@
+"""A getter for Rfam."""
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "RfamGetter",
+]
+
+
+class RfamGetter(Getter):
+    """A getter for Rfam."""
+
+    bioregistry_id = "rfam"
+    name = "Rfam"
+    homepage_fmt = "https://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
+    version_type = VersionType.semver_minor
+
+    def get(self) -> str:
+        """Get the latest Rfam version number."""
+        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__":
+    RfamGetter.print()

{bioversions-0.8.0 → bioversions-0.8.2}/src/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/src/bioversions/sources/rfam.py

@@ -1,24 +0,0 @@
-"""A getter for Rfam."""
-
-from bioversions.utils import Getter, VersionType, _get_ftp_version
-
-__all__ = [
-    "RfamGetter",
-]
-
-
-class RfamGetter(Getter):
-    """A getter for Rfam."""
-
-    bioregistry_id = "rfam"
-    name = "Rfam"
-    homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
-    version_type = VersionType.semver_minor
-
-    def get(self):
-        """Get the latest Rfam version number."""
-        return _get_ftp_version("ftp.ebi.ac.uk", "pub/databases/Rfam/")
-
-
-if __name__ == "__main__":
-    RfamGetter.print()