bioversions 0.6.8__tar.gz → 0.6.9__tar.gz

{bioversions-0.6.8 → bioversions-0.6.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.6.8
+Version: 0.6.9
 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-0.6.8 → bioversions-0.6.9}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-16'
-  revision: 872
+  date: '2024-12-17'
+  revision: 873
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -1382,6 +1382,8 @@ database:
     version: 23Q4
   - retrieved: '2024-06-04'
     version: 24Q2
+  - retrieved: '2024-12-17'
+    version: 24Q4
   vtype: other
 - name: DICOM Controlled Terminology
   prefix: dicom
@@ -6502,6 +6504,8 @@ database:
     version: '2024-11-29'
   - retrieved: '2024-12-10'
     version: '2024-12-06'
+  - retrieved: '2024-12-17'
+    version: '2024-12-13'
   vtype: date
 - name: Rat Strain Ontology
   prefix: rs
@@ -8173,6 +8177,8 @@ database:
     version: '2024-12-15'
   - retrieved: '2024-12-16'
     version: '2024-12-16'
+  - retrieved: '2024-12-17'
+    version: '2024-12-17'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -10900,6 +10906,8 @@ database:
     version: '2024-12-12'
   - retrieved: '2024-12-16'
     version: '2024-12-14'
+  - retrieved: '2024-12-17'
+    version: '2024-12-15'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.6.8 → bioversions-0.6.9}/docs/failures.md

@@ -3,7 +3,7 @@
 - DisGeNet - failed to resolve DisGeNet
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
-- National Cancer Institute Thesaurus - failed to resolve National Cancer Institute Thesaurus
+- Ensembl - failed to resolve Ensembl
 
 ## DisGeNet
 
@@ -144,9 +144,9 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
 
 ```
 
-## National Cancer Institute Thesaurus
+## Ensembl
 
-Using class: `NCItGetter`
+Using class: `EnsemblGetter`
 
 ```python-traceback
 Traceback (most recent call last):
@@ -196,7 +196,7 @@ Traceback (most recent call last):
     self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 369, in _raise_timeout
     raise ReadTimeoutError(
-urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='ncithesaurus.nci.nih.gov', port=443): Read timed out. (read timeout=15)
+urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='useast.ensembl.org', port=443): Read timed out. (read timeout=15)
 
 During handling of the above exception, another exception occurred:
 
@@ -228,7 +228,7 @@ Traceback (most recent call last):
   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/ncit.py", line 27, in get
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/ensembl.py", line 23, in get
     soup = get_soup(URL)
            ^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 62, in get_soup
@@ -248,7 +248,7 @@ Traceback (most recent call last):
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
     raise ReadTimeout(e, request=request)
-requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='ncithesaurus.nci.nih.gov', port=443): Read timed out. (read timeout=15)
+requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='useast.ensembl.org', port=443): Read timed out. (read timeout=15)
 
 ```
 

{bioversions-0.6.8 → bioversions-0.6.9}/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>2024-12-16T01:10:38.044862</dc:date>
+    <dc:date>2024-12-17T01:07:21.409484</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.8 → bioversions-0.6.9}/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>2024-12-16T01:10:37.944751</dc:date>
+    <dc:date>2024-12-17T01:07:21.313364</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.8 → bioversions-0.6.9}/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>2024-12-16T01:10:37.872011</dc:date>
+    <dc:date>2024-12-17T01:07:21.240918</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.8 → bioversions-0.6.9}/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 = "0.6.8"
+release = "0.6.9"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.6.8 → bioversions-0.6.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.6.8"
+version = "0.6.9"
 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 = "0.6.8"
+current_version = "0.6.9"
 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-0.6.8 → bioversions-0.6.9}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 872,
-    "date": "2024-12-16",
+    "revision": 873,
+    "date": "2024-12-17",
     "author": "runner"
   },
   "database": [
@@ -2544,6 +2544,10 @@
         {
           "retrieved": "2024-06-04",
           "version": "24Q2"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "24Q4"
         }
       ],
       "name": "DepMap",
@@ -11765,6 +11769,10 @@
         {
           "retrieved": "2024-12-10",
           "version": "2024-12-06"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "2024-12-13"
         }
       ],
       "name": "Rat Genome Database",
@@ -15014,6 +15022,10 @@
         {
           "retrieved": "2024-12-16",
           "version": "2024-12-16"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "2024-12-17"
         }
       ],
       "name": "SwissLipids",
@@ -20014,6 +20026,10 @@
         {
           "retrieved": "2024-12-16",
           "version": "2024-12-14"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "2024-12-15"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.6.8 → bioversions-0.6.9}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.8"
+VERSION = "0.6.9"
 
 
 def get_git_hash() -> str: