bioversions 0.6.7__tar.gz → 0.6.9__tar.gz

{bioversions-0.6.7 → bioversions-0.6.9}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: bioversions
-Version: 0.6.7
+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
@@ -29,6 +29,7 @@ License: MIT License
         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
+License-File: LICENSE
 Keywords: biological databases,biomedical databases,cookiecutter,databases,snekpack
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console

{bioversions-0.6.7 → bioversions-0.6.9}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-15'
-  revision: 871
+  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
@@ -8171,6 +8175,10 @@ database:
     version: '2024-12-14'
   - retrieved: '2024-12-15'
     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
@@ -10896,6 +10904,10 @@ database:
     version: '2024-12-11'
   - retrieved: '2024-12-14'
     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-0.6.7 → 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
-- Zebrafish Information Network - failed to resolve Zebrafish Information Network
+- Ensembl - failed to resolve Ensembl
 
 ## DisGeNet
 
@@ -144,9 +144,9 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
 
 ```
 
-## Zebrafish Information Network
+## Ensembl
 
-Using class: `ZfinGetter`
+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='zfin.org', 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/zfin.py", line 23, 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='zfin.org', 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-0.6.7 → 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>2024-12-15T01:12:19.389138</dc:date>
+    <dc:date>2024-12-17T01:07:21.409484</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.7 → 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>2024-12-15T01:12:19.289091</dc:date>
+    <dc:date>2024-12-17T01:07:21.313364</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.7 → 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>2024-12-15T01:12:19.212614</dc:date>
+    <dc:date>2024-12-17T01:07:21.240918</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.7 → 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 = "0.6.7"
+release = "0.6.9"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.6.7 → bioversions-0.6.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.6.7"
+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 = "0.6.7"
+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-0.6.7 → bioversions-0.6.9}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 871,
-    "date": "2024-12-15",
+    "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",
@@ -15010,6 +15018,14 @@
         {
           "retrieved": "2024-12-15",
           "version": "2024-12-15"
+        },
+        {
+          "retrieved": "2024-12-16",
+          "version": "2024-12-16"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "2024-12-17"
         }
       ],
       "name": "SwissLipids",
@@ -20006,6 +20022,14 @@
         {
           "retrieved": "2024-12-14",
           "version": "2024-12-12"
+        },
+        {
+          "retrieved": "2024-12-16",
+          "version": "2024-12-14"
+        },
+        {
+          "retrieved": "2024-12-17",
+          "version": "2024-12-15"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.6.7 → bioversions-0.6.9}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.7"
+VERSION = "0.6.9"
 
 
 def get_git_hash() -> str: