bioversions 0.5.562__tar.gz → 0.5.563__tar.gz

{bioversions-0.5.562 → bioversions-0.5.563}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioversions
-Version: 0.5.562
+Version: 0.5.563
 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-0.5.562 → bioversions-0.5.563}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-03'
-  revision: 858
+  date: '2024-12-04'
+  revision: 859
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -5029,6 +5029,9 @@ database:
   - date: '2024-11-27'
     retrieved: '2024-12-03'
     version: November 27, 2024
+  - date: '2024-12-02'
+    retrieved: '2024-12-04'
+    version: December 2, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -8038,6 +8041,8 @@ database:
     version: '2024-11-27'
   - retrieved: '2024-12-03'
     version: '2024-12-03'
+  - retrieved: '2024-12-04'
+    version: '2024-12-04'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -10727,6 +10732,8 @@ database:
     version: '2024-11-25'
   - retrieved: '2024-12-03'
     version: '2024-12-01'
+  - retrieved: '2024-12-04'
+    version: '2024-12-02'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.5.562 → bioversions-0.5.563}/docs/failures.md

@@ -4,7 +4,6 @@
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
 - MeSH - issue parsing MeSH: 
-- OncoTree - failed to resolve OncoTree
 
 ## DisGeNet
 
@@ -184,102 +183,3 @@ ValueError
 
 ```
 
-## OncoTree
-
-Using class: `OncoTreeGetter`
-
-```python-traceback
-Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
-    response = conn.getresponse()
-               ^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 507, in getresponse
-    httplib_response = super().getresponse()
-                       ^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 1428, in getresponse
-    response.begin()
-  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 331, in begin
-    version, status, reason = self._read_status()
-                              ^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 292, in _read_status
-    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
-               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/socket.py", line 720, in readinto
-    return self._sock.recv_into(b)
-           ^^^^^^^^^^^^^^^^^^^^^^^
-TimeoutError: timed out
-
-The above exception was the direct cause of the following exception:
-
-Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
-    resp = conn.urlopen(
-           ^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 843, in urlopen
-    retries = retries.increment(
-              ^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
-    raise reraise(type(error), error, _stacktrace)
-          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
-    raise value
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
-    response = self._make_request(
-               ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 538, in _make_request
-    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: HTTPConnectionPool(host='oncotree.mskcc.org', port=80): Read timed out. (read timeout=5)
-
-During handling of the above exception, another exception occurred:
-
-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/oncotree.py", line 23, in get
-    res = requests.get(
-          ^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
-    return request("get", url, params=params, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
-    return session.request(method=method, url=url, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
-    resp = self.send(prep, **send_kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
-    r = adapter.send(request, **kwargs)
-        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  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: HTTPConnectionPool(host='oncotree.mskcc.org', port=80): Read timed out. (read timeout=5)
-
-```
-

{bioversions-0.5.562 → bioversions-0.5.563}/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>2024-12-03T01:07:20.824530</dc:date>
+    <dc:date>2024-12-04T01:07:33.175950</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.562 → bioversions-0.5.563}/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>2024-12-03T01:07:20.704797</dc:date>
+    <dc:date>2024-12-04T01:07:33.068547</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.562 → bioversions-0.5.563}/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>2024-12-03T01:07:20.619162</dc:date>
+    <dc:date>2024-12-04T01:07:32.986430</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.562 → bioversions-0.5.563}/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 = "0.5.562"
+release = "0.5.563"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.5.562 → bioversions-0.5.563}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.5.562"
+version = "0.5.563"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -223,7 +223,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.5.562"
+current_version = "0.5.563"
 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-0.5.562 → bioversions-0.5.563}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 858,
-    "date": "2024-12-03",
+    "revision": 859,
+    "date": "2024-12-04",
     "author": "runner"
   },
   "database": [
@@ -9083,6 +9083,11 @@
           "retrieved": "2024-12-03",
           "version": "November 27, 2024",
           "date": "2024-11-27"
+        },
+        {
+          "retrieved": "2024-12-04",
+          "version": "December 2, 2024",
+          "date": "2024-12-02"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -14769,6 +14774,10 @@
         {
           "retrieved": "2024-12-03",
           "version": "2024-12-03"
+        },
+        {
+          "retrieved": "2024-12-04",
+          "version": "2024-12-04"
         }
       ],
       "name": "SwissLipids",
@@ -19695,6 +19704,10 @@
         {
           "retrieved": "2024-12-03",
           "version": "2024-12-01"
+        },
+        {
+          "retrieved": "2024-12-04",
+          "version": "2024-12-02"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.5.562 → bioversions-0.5.563}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.562"
+VERSION = "0.5.563"
 
 
 def get_git_hash() -> str: