bioversions 0.6.0__tar.gz → 0.6.1__tar.gz

{bioversions-0.6.0 → bioversions-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioversions
-Version: 0.6.0
+Version: 0.6.1
 Summary: Get the current version for biological databases
 Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
 Project-URL: Homepage, https://github.com/biopragmatics/bioversions

{bioversions-0.6.0 → bioversions-0.6.1}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-08'
-  revision: 864
+  date: '2024-12-09'
+  revision: 865
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -3012,6 +3012,9 @@ database:
   - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json
     retrieved: '2024-12-03'
     version: '2024-11-01'
+  - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json
+    retrieved: '2024-12-09'
+    version: '2024-12-03'
   vtype: date
 - name: Histopathology Ontology
   prefix: hpath
@@ -3871,6 +3874,9 @@ database:
   - homepage: ftp://nlmpubs.nlm.nih.gov/online/mesh/2024
     retrieved: '2023-12-01'
     version: '2024'
+  - homepage: ftp://nlmpubs.nlm.nih.gov/online/mesh/2025
+    retrieved: '2024-12-09'
+    version: '2025'
   vtype: year
 - name: Metabolomics Standards Initiative Ontology
   prefix: msio
@@ -8085,6 +8091,8 @@ database:
     version: '2024-12-07'
   - retrieved: '2024-12-08'
     version: '2024-12-08'
+  - retrieved: '2024-12-09'
+    version: '2024-12-09'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo

{bioversions-0.6.0 → bioversions-0.6.1}/docs/failures.md

@@ -3,7 +3,6 @@
 - DisGeNet - failed to resolve DisGeNet
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
-- MeSH - issue parsing MeSH: 
 
 ## DisGeNet
 
@@ -144,42 +143,3 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
 
 ```
 
-## MeSH
-
-Using class: `MeshGetter`
-
-```python-traceback
-Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
-    yv = resolve(cls.name)
-         ^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
-    return _resolve_helper_cached(name)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
-    return _calc_entry(core, key, func, args, kwds)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
-    func_res = func(*args, **kwds)
-               ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
-    return _resolve_helper(name)
-           ^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
-    return getter.resolve()
-           ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
-    version=cls.version,
-            ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
-    if isinstance(cls._cache_prop, str):
-                  ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
-    cls._cache = cls().get()
-                 ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/mesh.py", line 28, in get
-    raise ValueError
-ValueError
-
-```
-

{bioversions-0.6.0 → bioversions-0.6.1}/docs/img/has_release_url.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-08T20:49:19.605329</dc:date>
+    <dc:date>2024-12-09T01:08:53.382904</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.0 → bioversions-0.6.1}/docs/img/version_date_types.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-08T20:49:19.553264</dc:date>
+    <dc:date>2024-12-09T01:08:53.331110</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.0 → bioversions-0.6.1}/docs/img/version_types.svg

@@ -6,7 +6,7 @@
   <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-08T20:49:19.417755</dc:date>
+    <dc:date>2024-12-09T01:08:53.199753</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.0 → bioversions-0.6.1}/docs/source/conf.py

@@ -26,7 +26,7 @@ copyright = f"{date.today().year}, Charles Tapley Hoyt"
 author = "Charles Tapley Hoyt"
 
 # The full version, including alpha/beta/rc tags.
-release = "0.6.0"
+release = "0.6.1"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.6.0 → bioversions-0.6.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.6.0"
+version = "0.6.1"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -222,7 +222,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.6.0"
+current_version = "0.6.1"
 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-0.6.0 → bioversions-0.6.1}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 864,
-    "date": "2024-12-08",
+    "revision": 865,
+    "date": "2024-12-09",
     "author": "runner"
   },
   "database": [
@@ -5491,6 +5491,11 @@
           "retrieved": "2024-12-03",
           "version": "2024-11-01",
           "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2024-12-03",
+          "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json"
         }
       ],
       "name": "HGNC",
@@ -7047,6 +7052,11 @@
           "retrieved": "2023-12-01",
           "version": "2024",
           "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2024"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2025",
+          "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2025"
         }
       ],
       "name": "MeSH",
@@ -14854,6 +14864,10 @@
         {
           "retrieved": "2024-12-08",
           "version": "2024-12-08"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2024-12-09"
         }
       ],
       "name": "SwissLipids",

bioversions-0.6.1/src/bioversions/sources/hgnc.py

@@ -0,0 +1,42 @@
+"""A getter for HGNC."""
+
+import logging
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "HGNCGetter",
+]
+
+logger = logging.getLogger(__name__)
+
+PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
+URL = "https://storage.googleapis.com/storage/v1/b/public-download-files/o?prefix=hgnc/archive/archive/monthly"
+PREFIX = "hgnc/archive/archive/monthly/json/hgnc_complete_set_"
+SUFFIX = ".json"
+
+
+class HGNCGetter(Getter):
+    """A getter for HGNC."""
+
+    bioregistry_id = "hgnc"
+    name = "HGNC"
+    homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
+
+    version_type = VersionType.date
+
+    def get(self) -> str:
+        """Get the latest monthly HGNC version number."""
+        res = requests.get(URL, timeout=5)
+        items = res.json()["items"]
+        return max(
+            item["name"].removeprefix(PREFIX).removesuffix(SUFFIX)
+            for item in items
+            if (name := item["name"]).startswith(PREFIX) and name.endswith(SUFFIX)
+        )
+
+
+if __name__ == "__main__":
+    HGNCGetter.print()

{bioversions-0.6.0 → bioversions-0.6.1}/src/bioversions/sources/mesh.py

@@ -8,6 +8,10 @@ __all__ = [
     "MeshGetter",
 ]
 
+#: In 2024 and before, these were .gz, but after
+#: became .xml files
+SUFFIXES = [".xml", ".xml.gz", ".gz"]
+
 
 class MeshGetter(Getter):
     """A getter for MeSH."""
@@ -22,9 +26,12 @@ class MeshGetter(Getter):
         with ftplib.FTP("nlmpubs.nlm.nih.gov") as ftp:
             ftp.login()
             ftp.cwd("/online/mesh/MESH_FILES/xmlmesh/")
-            for name, _ in ftp.mlsd():
-                if name.startswith("desc") and name.endswith(".gz"):
-                    return name[len("desc") : -len(".gz")]
+            names = [name for name, _ in ftp.mlsd()]
+
+        for name in names:
+            for suffix in SUFFIXES:
+                if name.startswith("desc") and name.endswith(suffix):
+                    return name[len("desc") : -len(suffix)]
         raise ValueError
 
 

{bioversions-0.6.0 → bioversions-0.6.1}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.0"
+VERSION = "0.6.1"
 
 
 def get_git_hash() -> str:

bioversions-0.6.0/src/bioversions/sources/hgnc.py

@@ -1,47 +0,0 @@
-"""A getter for HGNC."""
-
-import datetime
-import logging
-
-import requests
-
-from bioversions.utils import Getter, VersionType
-
-__all__ = [
-    "HGNCGetter",
-]
-
-logger = logging.getLogger(__name__)
-
-PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
-PREFIX = "hgnc_complete_set_"
-SUFFIX = ".json"
-
-
-class HGNCGetter(Getter):
-    """A getter for HGNC."""
-
-    bioregistry_id = "hgnc"
-    name = "HGNC"
-    homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
-
-    version_type = VersionType.date
-
-    def get(self) -> str:
-        """Get the latest HGNC version number."""
-        today = datetime.date.today()
-        this_year = int(today.strftime("%Y"))
-        this_month = int(today.strftime("%m"))
-        maybe = today.strftime("%Y-%m-01")
-        res = requests.head(self.homepage_fmt.format(version=maybe), timeout=15)
-        if res.status_code == 200:
-            return maybe
-        if this_month == 1:
-            maybe_last_month = f"{this_year - 1}-12-01"
-        else:
-            maybe_last_month = f"{this_year}-{this_month - 1}-01"
-        return maybe_last_month
-
-
-if __name__ == "__main__":
-    HGNCGetter.print()