bioversions 0.5.561__tar.gz → 0.5.562__tar.gz

{bioversions-0.5.561 → bioversions-0.5.562}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioversions
-Version: 0.5.561
+Version: 0.5.562
 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-0.5.561 → bioversions-0.5.562}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-11-27'
-  revision: 857
+  date: '2024-12-03'
+  revision: 858
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -374,6 +374,9 @@ database:
   - homepage: https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-4.4.239
     retrieved: '2024-11-02'
     version: 4.4.239
+  - homepage: https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-4.4.240
+    retrieved: '2024-12-03'
+    version: 4.4.240
   vtype: semver
 - name: Bioinformatics operations, data types, formats, identifiers and topics
   prefix: edam
@@ -853,6 +856,9 @@ database:
   - homepage: ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel237/
     retrieved: '2024-11-06'
     version: '237'
+  - homepage: ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel238/
+    retrieved: '2024-12-03'
+    version: '238'
   vtype: sequential
 - name: ChEBI Integrated Role Ontology
   prefix: chiro
@@ -984,6 +990,8 @@ database:
     version: 01-Oct-2024
   - retrieved: '2024-11-02'
     version: 01-Nov-2024
+  - retrieved: '2024-12-03'
+    version: 01-Dec-2024
   vtype: date
 - name: clinical LABoratory Ontology
   prefix: labo
@@ -1593,6 +1601,10 @@ database:
     homepage: https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-01
     retrieved: '2024-11-02'
     version: '2024-11-01'
+  - date: '2024-11-27'
+    homepage: https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-27
+    retrieved: '2024-12-03'
+    version: '2024-11-27'
   vtype: date
 - name: DisGeNet
   releases:
@@ -2096,6 +2108,8 @@ database:
     version: '2024-07-24'
   - retrieved: '2024-10-03'
     version: '2024-10-02'
+  - retrieved: '2024-12-03'
+    version: '2024-11-27'
   vtype: date
 - name: Experimental condition ontology
   prefix: xco
@@ -2985,6 +2999,9 @@ database:
   - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-10-01.json
     retrieved: '2024-10-15'
     version: '2024-10-01'
+  - 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'
   vtype: date
 - name: Histopathology Ontology
   prefix: hpath
@@ -3404,6 +3421,10 @@ database:
     homepage: ftp://ftp.ebi.ac.uk/pub/databases/interpro/102.0/
     retrieved: '2024-10-04'
     version: '102.0'
+  - date: '2024-11-28'
+    homepage: ftp://ftp.ebi.ac.uk/pub/databases/interpro/103.0/
+    retrieved: '2024-12-03'
+    version: '103.0'
   vtype: semver_minor
 - name: ITIS
   prefix: itis
@@ -3536,6 +3557,9 @@ database:
   - date: '2024-10-01'
     retrieved: '2024-09-29'
     version: '112.0'
+  - date: '2024-12-01'
+    retrieved: '2024-12-03'
+    version: '112.1'
   vtype: semver_minor
 - name: Kinetic Simulation Algorithm Ontology
   prefix: biomodels.kisao
@@ -5002,6 +5026,9 @@ database:
   - date: '2024-11-25'
     retrieved: '2024-11-27'
     version: November 25, 2024
+  - date: '2024-11-27'
+    retrieved: '2024-12-03'
+    version: November 27, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -5977,6 +6004,10 @@ database:
     homepage: https://www.pombase.org/data/releases/pombase-2024-11-01/
     retrieved: '2024-11-02'
     version: '2024-11-01'
+  - date: '2024-12-01'
+    homepage: https://www.pombase.org/data/releases/pombase-2024-12-01/
+    retrieved: '2024-12-03'
+    version: '2024-12-01'
   vtype: date
 - name: Population and Community Ontology
   prefix: pco
@@ -6203,6 +6234,9 @@ database:
   - homepage: https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/2024-11-01
     retrieved: '2024-11-01'
     version: '2024-11-01'
+  - homepage: https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/2024-12-01
+    retrieved: '2024-12-03'
+    version: '2024-12-01'
   vtype: date
 - name: Radiation Biology Ontology
   prefix: rbo
@@ -6361,6 +6395,8 @@ database:
     version: '2024-11-15'
   - retrieved: '2024-11-26'
     version: '2024-11-22'
+  - retrieved: '2024-12-03'
+    version: '2024-11-29'
   vtype: date
 - name: Rat Strain Ontology
   prefix: rs
@@ -6591,6 +6627,9 @@ database:
   - date: '2024-10-02'
     retrieved: '2024-10-03'
     version: '135'
+  - date: '2024-11-27'
+    retrieved: '2024-12-03'
+    version: '136'
   vtype: date
 - name: Rice ontology
   prefix: co_320
@@ -6710,6 +6749,9 @@ database:
   - homepage: https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_11042024.zip
     retrieved: '2024-11-05'
     version: '2024-11-04'
+  - homepage: https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_12022024.zip
+    retrieved: '2024-12-03'
+    version: '2024-12-02'
   vtype: date
 - name: Saccharomyces Genome Database
   prefix: sgd
@@ -7994,6 +8036,8 @@ database:
     version: '2024-11-26'
   - retrieved: '2024-11-27'
     version: '2024-11-27'
+  - retrieved: '2024-12-03'
+    version: '2024-12-03'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -8476,6 +8520,10 @@ database:
     homepage: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2024_05/
     retrieved: '2024-10-04'
     version: '2024_05'
+  - date: '2024-06-01'
+    homepage: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2024_06/
+    retrieved: '2024-12-03'
+    version: '2024_06'
   vtype: month
 - name: Unit Ontology
   prefix: uo
@@ -10677,6 +10725,8 @@ database:
     version: '2024-11-24'
   - retrieved: '2024-11-27'
     version: '2024-11-25'
+  - retrieved: '2024-12-03'
+    version: '2024-12-01'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

bioversions-0.5.562/docs/failures.md

@@ -0,0 +1,285 @@
+# Summary of Errors
+
+- DisGeNet - failed to resolve DisGeNet
+- Antibody Registry - failed to resolve Antibody Registry
+- DrugBank - failed to resolve DrugBank
+- MeSH - issue parsing MeSH: 
+- OncoTree - failed to resolve OncoTree
+
+## DisGeNet
+
+Using class: `DisGeNetGetter`
+
+```python-traceback
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
+    return complexjson.loads(self.text, **kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/json/__init__.py", line 346, in loads
+    return _default_decoder.decode(s)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/json/decoder.py", line 337, in decode
+    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/json/decoder.py", line 355, in raw_decode
+    raise JSONDecodeError("Expecting value", s, err.value) from None
+json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
+
+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/disgenet.py", line 24, in get
+    res_json = res.json()
+               ^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
+    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
+requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
+
+```
+
+## Antibody Registry
+
+Using class: `AntibodyRegistryGetter`
+
+```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/antibodyregistry.py", line 21, in get
+    return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+AttributeError: 'NoneType' object has no attribute 'find'
+
+```
+
+## DrugBank
+
+Using class: `DrugBankGetter`
+
+```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/drugbank.py", line 28, in get
+    res.raise_for_status()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
+    raise HTTPError(http_error_msg, response=self)
+requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
+
+```
+
+## 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
+
+```
+
+## 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-0.5.561 → bioversions-0.5.562}/docs/img/has_release_url.svg

@@ -6,11 +6,11 @@
   <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>2024-11-27T01:06:20.260233</dc:date>
+    <dc:date>2024-12-03T01:07:20.824530</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.3, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.561 → bioversions-0.5.562}/docs/img/version_date_types.svg

@@ -6,11 +6,11 @@
   <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>2024-11-27T01:06:20.204732</dc:date>
+    <dc:date>2024-12-03T01:07:20.704797</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.3, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.561 → bioversions-0.5.562}/docs/img/version_types.svg

@@ -6,11 +6,11 @@
   <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>2024-11-27T01:06:20.120163</dc:date>
+    <dc:date>2024-12-03T01:07:20.619162</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.2, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.9.3, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
    </cc:Work>

{bioversions-0.5.561 → bioversions-0.5.562}/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 = "0.5.561"
+release = "0.5.562"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.5.561 → bioversions-0.5.562}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.5.561"
+version = "0.5.562"
 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 = "0.5.561"
+current_version = "0.5.562"
 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-0.5.561 → bioversions-0.5.562}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 857,
-    "date": "2024-11-27",
+    "revision": 858,
+    "date": "2024-12-03",
     "author": "runner"
   },
   "database": [
@@ -681,6 +681,11 @@
           "retrieved": "2024-11-02",
           "version": "4.4.239",
           "homepage": "https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-4.4.239"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "4.4.240",
+          "homepage": "https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-4.4.240"
         }
       ],
       "vtype": "semver"
@@ -1573,6 +1578,11 @@
           "retrieved": "2024-11-06",
           "version": "237",
           "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel237/"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "238",
+          "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel238/"
         }
       ],
       "vtype": "sequential"
@@ -1802,6 +1812,10 @@
         {
           "retrieved": "2024-11-02",
           "version": "01-Nov-2024"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "01-Dec-2024"
         }
       ],
       "name": "CiVIC",
@@ -2884,6 +2898,12 @@
           "version": "2024-11-01",
           "homepage": "https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-01",
           "date": "2024-11-01"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-11-27",
+          "homepage": "https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-27",
+          "date": "2024-11-27"
         }
       ],
       "vtype": "date"
@@ -3823,6 +3843,10 @@
         {
           "retrieved": "2024-10-03",
           "version": "2024-10-02"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-11-27"
         }
       ],
       "vtype": "date"
@@ -5444,6 +5468,11 @@
           "retrieved": "2024-10-15",
           "version": "2024-10-01",
           "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-10-01.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_2024-11-01.json"
         }
       ],
       "name": "HGNC",
@@ -6173,6 +6202,12 @@
           "version": "102.0",
           "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/102.0/",
           "date": "2024-10-03"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "103.0",
+          "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/103.0/",
+          "date": "2024-11-28"
         }
       ],
       "vtype": "semver_minor"
@@ -6413,6 +6448,11 @@
           "retrieved": "2024-09-29",
           "version": "112.0",
           "date": "2024-10-01"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "112.1",
+          "date": "2024-12-01"
         }
       ],
       "vtype": "semver_minor"
@@ -9038,6 +9078,11 @@
           "retrieved": "2024-11-27",
           "version": "November 25, 2024",
           "date": "2024-11-25"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "November 27, 2024",
+          "date": "2024-11-27"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -10805,6 +10850,12 @@
           "version": "2024-11-01",
           "homepage": "https://www.pombase.org/data/releases/pombase-2024-11-01/",
           "date": "2024-11-01"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-12-01",
+          "homepage": "https://www.pombase.org/data/releases/pombase-2024-12-01/",
+          "date": "2024-12-01"
         }
       ],
       "name": "PomBase",
@@ -11207,6 +11258,11 @@
           "retrieved": "2024-11-01",
           "version": "2024-11-01",
           "homepage": "https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/2024-11-01"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-12-01",
+          "homepage": "https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/2024-12-01"
         }
       ],
       "name": "PubChem",
@@ -11520,6 +11576,10 @@
         {
           "retrieved": "2024-11-26",
           "version": "2024-11-22"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-11-29"
         }
       ],
       "name": "Rat Genome Database",
@@ -11948,6 +12008,11 @@
           "retrieved": "2024-10-03",
           "version": "135",
           "date": "2024-10-02"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "136",
+          "date": "2024-11-27"
         }
       ],
       "vtype": "date"
@@ -12149,6 +12214,11 @@
           "retrieved": "2024-11-05",
           "version": "2024-11-04",
           "homepage": "https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_11042024.zip"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-12-02",
+          "homepage": "https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_12022024.zip"
         }
       ],
       "name": "RxNorm",
@@ -14695,6 +14765,10 @@
         {
           "retrieved": "2024-11-27",
           "version": "2024-11-27"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-12-03"
         }
       ],
       "name": "SwissLipids",
@@ -15590,6 +15664,12 @@
           "version": "2024_05",
           "homepage": "ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2024_05/",
           "date": "2024-05-01"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024_06",
+          "homepage": "ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2024_06/",
+          "date": "2024-06-01"
         }
       ],
       "vtype": "month"
@@ -19611,6 +19691,10 @@
         {
           "retrieved": "2024-11-27",
           "version": "2024-11-25"
+        },
+        {
+          "retrieved": "2024-12-03",
+          "version": "2024-12-01"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.5.561 → bioversions-0.5.562}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.561"
+VERSION = "0.5.562"
 
 
 def get_git_hash() -> str:

bioversions-0.5.561/.idea/bioversions.iml

@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
-      <excludeFolder url="file://$MODULE_DIR$/build" />
-      <excludeFolder url="file://$MODULE_DIR$/dist" />
-      <excludeFolder url="file://$MODULE_DIR$/docs/build" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-</module>

bioversions-0.5.561/.idea/inspectionProfiles/Project_Default.xml

@@ -1,14 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <profile version="1.0">
-    <option name="myName" value="Project Default" />
-    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <option name="ignoredPackages">
-        <value>
-          <list size="1">
-            <item index="0" class="java.lang.String" itemvalue="semantic-pydantic" />
-          </list>
-        </value>
-      </option>
-    </inspection_tool>
-  </profile>
-</component>

bioversions-0.5.561/.idea/inspectionProfiles/profiles_settings.xml

@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>

bioversions-0.5.561/.idea/modules.xml

@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/bioversions.iml" filepath="$PROJECT_DIR$/.idea/bioversions.iml" />
-    </modules>
-  </component>
-</project>

bioversions-0.5.561/docs/failures.md

@@ -1,6 +0,0 @@
-# Errors
-
-- failed to resolve DisGeNet
-- failed to resolve Antibody Registry
-- failed to resolve DrugBank
-- issue parsing MeSH: