bioversions 0.6.11__tar.gz → 0.6.13__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {bioversions-0.6.11 → bioversions-0.6.13}/PKG-INFO +1 -1
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/_data/versions.yml +23 -2
- bioversions-0.6.13/docs/failures.md +145 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/img/has_release_url.svg +1 -1
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/img/version_date_types.svg +1 -1
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/img/version_types.svg +1 -1
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/conf.py +1 -1
- {bioversions-0.6.11 → bioversions-0.6.13}/pyproject.toml +2 -2
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/resources/versions.json +39 -2
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/version.py +1 -1
- bioversions-0.6.11/docs/failures.md +0 -274
- {bioversions-0.6.11 → bioversions-0.6.13}/.cruft.json +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/CODE_OF_CONDUCT.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/CONTRIBUTING.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/codecov.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/workflows/cruft.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/workflows/tests.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.github/workflows/update.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.gitignore +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/.readthedocs.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/LICENSE +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/MANIFEST.in +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/README.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/_config.yml +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/_includes/footer.html +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/_includes/head.html +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/download.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/index.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/cli.rst +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/index.rst +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/installation.rst +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/logo.png +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/source/usage.rst +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/docs/summary.md +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/__init__.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/__main__.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/charts.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/cli.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/py.typed +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/resources/__init__.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/resources/update.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/slack_client.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/__init__.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/antibodyregistry.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/bigg.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/biogrid.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/cellosaurus.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/chebi.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/chembl.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/chemidplus.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/civic.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/complexportal.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/daily.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/depmap.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/dgi.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/disgenet.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/drugbank.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/drugcentral.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/ensembl.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/expasy.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/flybase.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/gtdb.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/guidetopharmacology.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/hgnc.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/homologene.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/icd10.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/icd11.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/icf.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/intact.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/interpro.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/itis.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/kegg.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/mesh.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/mgi.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/mirbase.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/moalmanac.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/msigdb.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/ncit.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/npass.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/obo.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/ols.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/omim.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/oncotree.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pathbank.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pathwaycommons.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pfam.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pombase.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pr.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/pubchem.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/reactome.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/rfam.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/rgd.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/rhea.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/rxnorm.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/sgd.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/slm.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/stringdb.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/umls.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/uniprot.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/unversioned.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/wikipathways.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/sources/zfin.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/templates/base.html +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/templates/home.html +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/twitter_client.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/utils.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/src/bioversions/wsgi.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/tests/test_bioversions.py +0 -0
- {bioversions-0.6.11 → bioversions-0.6.13}/tox.ini +0 -0
@@ -1,6 +1,6 @@
|
|
1
1
|
Metadata-Version: 2.4
|
2
2
|
Name: bioversions
|
3
|
-
Version: 0.6.
|
3
|
+
Version: 0.6.13
|
4
4
|
Summary: Get the current version for biological databases
|
5
5
|
Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
|
6
6
|
Project-URL: Homepage, https://github.com/biopragmatics/bioversions
|
@@ -1,7 +1,7 @@
|
|
1
1
|
annotations:
|
2
2
|
author: runner
|
3
|
-
date: '2024-12-
|
4
|
-
revision:
|
3
|
+
date: '2024-12-21'
|
4
|
+
revision: 877
|
5
5
|
database:
|
6
6
|
- name: A nomenclatural ontology for biological names
|
7
7
|
prefix: nomen
|
@@ -739,6 +739,9 @@ database:
|
|
739
739
|
- date: '2024-09-10'
|
740
740
|
retrieved: '2024-09-11'
|
741
741
|
version: '50.0'
|
742
|
+
- date: '2024-12-19'
|
743
|
+
retrieved: '2024-12-20'
|
744
|
+
version: '51.0'
|
742
745
|
vtype: sequential
|
743
746
|
- name: Cellular Microscopy Phenotype Ontology
|
744
747
|
prefix: cmpo
|
@@ -1619,6 +1622,10 @@ database:
|
|
1619
1622
|
homepage: https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-27
|
1620
1623
|
retrieved: '2024-12-03'
|
1621
1624
|
version: '2024-11-27'
|
1625
|
+
- date: '2024-12-18'
|
1626
|
+
homepage: https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-12-18
|
1627
|
+
retrieved: '2024-12-20'
|
1628
|
+
version: '2024-12-18'
|
1622
1629
|
vtype: date
|
1623
1630
|
- name: DisGeNet
|
1624
1631
|
releases:
|
@@ -5131,6 +5138,12 @@ database:
|
|
5131
5138
|
- date: '2024-12-17'
|
5132
5139
|
retrieved: '2024-12-19'
|
5133
5140
|
version: December 17, 2024
|
5141
|
+
- date: '2024-12-18'
|
5142
|
+
retrieved: '2024-12-20'
|
5143
|
+
version: December 18, 2024
|
5144
|
+
- date: '2024-12-19'
|
5145
|
+
retrieved: '2024-12-21'
|
5146
|
+
version: December 19, 2024
|
5134
5147
|
vtype: date
|
5135
5148
|
- name: 'OntoAvida: ontology for Avida digital evolution platform'
|
5136
5149
|
prefix: ontoavida
|
@@ -8189,6 +8202,10 @@ database:
|
|
8189
8202
|
version: '2024-12-18'
|
8190
8203
|
- retrieved: '2024-12-19'
|
8191
8204
|
version: '2024-12-19'
|
8205
|
+
- retrieved: '2024-12-20'
|
8206
|
+
version: '2024-12-20'
|
8207
|
+
- retrieved: '2024-12-21'
|
8208
|
+
version: '2024-12-21'
|
8192
8209
|
vtype: date
|
8193
8210
|
- name: SWO (The Software Ontology)
|
8194
8211
|
prefix: swo
|
@@ -10922,6 +10939,10 @@ database:
|
|
10922
10939
|
version: '2024-12-16'
|
10923
10940
|
- retrieved: '2024-12-19'
|
10924
10941
|
version: '2024-12-17'
|
10942
|
+
- retrieved: '2024-12-20'
|
10943
|
+
version: '2024-12-18'
|
10944
|
+
- retrieved: '2024-12-21'
|
10945
|
+
version: '2024-12-19'
|
10925
10946
|
vtype: date
|
10926
10947
|
- name: Zebrafish Phenotype Ontology
|
10927
10948
|
prefix: zp
|
@@ -0,0 +1,145 @@
|
|
1
|
+
# Summary of Errors
|
2
|
+
|
3
|
+
- DisGeNet - failed to resolve DisGeNet
|
4
|
+
- Antibody Registry - failed to resolve Antibody Registry
|
5
|
+
- DrugBank - failed to resolve DrugBank
|
6
|
+
|
7
|
+
## DisGeNet
|
8
|
+
|
9
|
+
Using class: `DisGeNetGetter`
|
10
|
+
|
11
|
+
```python-traceback
|
12
|
+
Traceback (most recent call last):
|
13
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
|
14
|
+
return complexjson.loads(self.text, **kwargs)
|
15
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
16
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
|
17
|
+
return _default_decoder.decode(s)
|
18
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
19
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
|
20
|
+
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
|
21
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
22
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
|
23
|
+
raise JSONDecodeError("Expecting value", s, err.value) from None
|
24
|
+
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
25
|
+
|
26
|
+
During handling of the above exception, another exception occurred:
|
27
|
+
|
28
|
+
Traceback (most recent call last):
|
29
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
30
|
+
yv = resolve(cls.name)
|
31
|
+
^^^^^^^^^^^^^^^^^
|
32
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
33
|
+
return _resolve_helper_cached(name)
|
34
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
35
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
36
|
+
return _calc_entry(core, key, func, args, kwds)
|
37
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
38
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
39
|
+
func_res = func(*args, **kwds)
|
40
|
+
^^^^^^^^^^^^^^^^^^^
|
41
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
42
|
+
return _resolve_helper(name)
|
43
|
+
^^^^^^^^^^^^^^^^^^^^^
|
44
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
45
|
+
return getter.resolve()
|
46
|
+
^^^^^^^^^^^^^^^^
|
47
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
48
|
+
version=cls.version,
|
49
|
+
^^^^^^^^^^^
|
50
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
51
|
+
if isinstance(cls._cache_prop, str):
|
52
|
+
^^^^^^^^^^^^^^^
|
53
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
54
|
+
cls._cache = cls().get()
|
55
|
+
^^^^^^^^^^^
|
56
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
|
57
|
+
res_json = res.json()
|
58
|
+
^^^^^^^^^^
|
59
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
|
60
|
+
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
|
61
|
+
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
62
|
+
|
63
|
+
```
|
64
|
+
|
65
|
+
## Antibody Registry
|
66
|
+
|
67
|
+
Using class: `AntibodyRegistryGetter`
|
68
|
+
|
69
|
+
```python-traceback
|
70
|
+
Traceback (most recent call last):
|
71
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
72
|
+
yv = resolve(cls.name)
|
73
|
+
^^^^^^^^^^^^^^^^^
|
74
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
75
|
+
return _resolve_helper_cached(name)
|
76
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
77
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
78
|
+
return _calc_entry(core, key, func, args, kwds)
|
79
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
80
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
81
|
+
func_res = func(*args, **kwds)
|
82
|
+
^^^^^^^^^^^^^^^^^^^
|
83
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
84
|
+
return _resolve_helper(name)
|
85
|
+
^^^^^^^^^^^^^^^^^^^^^
|
86
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
87
|
+
return getter.resolve()
|
88
|
+
^^^^^^^^^^^^^^^^
|
89
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
90
|
+
version=cls.version,
|
91
|
+
^^^^^^^^^^^
|
92
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
93
|
+
if isinstance(cls._cache_prop, str):
|
94
|
+
^^^^^^^^^^^^^^^
|
95
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
96
|
+
cls._cache = cls().get()
|
97
|
+
^^^^^^^^^^^
|
98
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/antibodyregistry.py", line 21, in get
|
99
|
+
return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
|
100
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
101
|
+
AttributeError: 'NoneType' object has no attribute 'find'
|
102
|
+
|
103
|
+
```
|
104
|
+
|
105
|
+
## DrugBank
|
106
|
+
|
107
|
+
Using class: `DrugBankGetter`
|
108
|
+
|
109
|
+
```python-traceback
|
110
|
+
Traceback (most recent call last):
|
111
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
112
|
+
yv = resolve(cls.name)
|
113
|
+
^^^^^^^^^^^^^^^^^
|
114
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
115
|
+
return _resolve_helper_cached(name)
|
116
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
117
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
118
|
+
return _calc_entry(core, key, func, args, kwds)
|
119
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
120
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
121
|
+
func_res = func(*args, **kwds)
|
122
|
+
^^^^^^^^^^^^^^^^^^^
|
123
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
124
|
+
return _resolve_helper(name)
|
125
|
+
^^^^^^^^^^^^^^^^^^^^^
|
126
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
127
|
+
return getter.resolve()
|
128
|
+
^^^^^^^^^^^^^^^^
|
129
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
130
|
+
version=cls.version,
|
131
|
+
^^^^^^^^^^^
|
132
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
133
|
+
if isinstance(cls._cache_prop, str):
|
134
|
+
^^^^^^^^^^^^^^^
|
135
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
136
|
+
cls._cache = cls().get()
|
137
|
+
^^^^^^^^^^^
|
138
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
|
139
|
+
res.raise_for_status()
|
140
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
|
141
|
+
raise HTTPError(http_error_msg, response=self)
|
142
|
+
requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
|
143
|
+
|
144
|
+
```
|
145
|
+
|
@@ -6,7 +6,7 @@
|
|
6
6
|
<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#">
|
7
7
|
<cc:Work>
|
8
8
|
<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
|
-
<dc:date>2024-12-
|
9
|
+
<dc:date>2024-12-21T01:00:53.003670</dc:date>
|
10
10
|
<dc:format>image/svg+xml</dc:format>
|
11
11
|
<dc:creator>
|
12
12
|
<cc:Agent>
|
@@ -6,7 +6,7 @@
|
|
6
6
|
<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#">
|
7
7
|
<cc:Work>
|
8
8
|
<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
|
-
<dc:date>2024-12-
|
9
|
+
<dc:date>2024-12-21T01:00:52.908275</dc:date>
|
10
10
|
<dc:format>image/svg+xml</dc:format>
|
11
11
|
<dc:creator>
|
12
12
|
<cc:Agent>
|
@@ -6,7 +6,7 @@
|
|
6
6
|
<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#">
|
7
7
|
<cc:Work>
|
8
8
|
<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
|
-
<dc:date>2024-12-
|
9
|
+
<dc:date>2024-12-21T01:00:52.837547</dc:date>
|
10
10
|
<dc:format>image/svg+xml</dc:format>
|
11
11
|
<dc:creator>
|
12
12
|
<cc:Agent>
|
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
|
|
4
4
|
|
5
5
|
[project]
|
6
6
|
name = "bioversions"
|
7
|
-
version = "0.6.
|
7
|
+
version = "0.6.13"
|
8
8
|
description = "Get the current version for biological databases"
|
9
9
|
readme = "README.md"
|
10
10
|
authors = [
|
@@ -222,7 +222,7 @@ known-first-party = [
|
|
222
222
|
docstring-code-format = true
|
223
223
|
|
224
224
|
[tool.bumpversion]
|
225
|
-
current_version = "0.6.
|
225
|
+
current_version = "0.6.13"
|
226
226
|
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-]+)*))?"
|
227
227
|
serialize = [
|
228
228
|
"{major}.{minor}.{patch}-{release}+{build}",
|
@@ -1,7 +1,7 @@
|
|
1
1
|
{
|
2
2
|
"annotations": {
|
3
|
-
"revision":
|
4
|
-
"date": "2024-12-
|
3
|
+
"revision": 877,
|
4
|
+
"date": "2024-12-21",
|
5
5
|
"author": "runner"
|
6
6
|
},
|
7
7
|
"database": [
|
@@ -1378,6 +1378,11 @@
|
|
1378
1378
|
"retrieved": "2024-09-11",
|
1379
1379
|
"version": "50.0",
|
1380
1380
|
"date": "2024-09-10"
|
1381
|
+
},
|
1382
|
+
{
|
1383
|
+
"retrieved": "2024-12-20",
|
1384
|
+
"version": "51.0",
|
1385
|
+
"date": "2024-12-19"
|
1381
1386
|
}
|
1382
1387
|
],
|
1383
1388
|
"name": "Cellosaurus",
|
@@ -2928,6 +2933,12 @@
|
|
2928
2933
|
"version": "2024-11-27",
|
2929
2934
|
"homepage": "https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-11-27",
|
2930
2935
|
"date": "2024-11-27"
|
2936
|
+
},
|
2937
|
+
{
|
2938
|
+
"retrieved": "2024-12-20",
|
2939
|
+
"version": "2024-12-18",
|
2940
|
+
"homepage": "https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology/releases/2024-12-18",
|
2941
|
+
"date": "2024-12-18"
|
2931
2942
|
}
|
2932
2943
|
],
|
2933
2944
|
"vtype": "date"
|
@@ -9261,6 +9272,16 @@
|
|
9261
9272
|
"retrieved": "2024-12-19",
|
9262
9273
|
"version": "December 17, 2024",
|
9263
9274
|
"date": "2024-12-17"
|
9275
|
+
},
|
9276
|
+
{
|
9277
|
+
"retrieved": "2024-12-20",
|
9278
|
+
"version": "December 18, 2024",
|
9279
|
+
"date": "2024-12-18"
|
9280
|
+
},
|
9281
|
+
{
|
9282
|
+
"retrieved": "2024-12-21",
|
9283
|
+
"version": "December 19, 2024",
|
9284
|
+
"date": "2024-12-19"
|
9264
9285
|
}
|
9265
9286
|
],
|
9266
9287
|
"name": "Online Mendelian Inheritance in Man",
|
@@ -15044,6 +15065,14 @@
|
|
15044
15065
|
{
|
15045
15066
|
"retrieved": "2024-12-19",
|
15046
15067
|
"version": "2024-12-19"
|
15068
|
+
},
|
15069
|
+
{
|
15070
|
+
"retrieved": "2024-12-20",
|
15071
|
+
"version": "2024-12-20"
|
15072
|
+
},
|
15073
|
+
{
|
15074
|
+
"retrieved": "2024-12-21",
|
15075
|
+
"version": "2024-12-21"
|
15047
15076
|
}
|
15048
15077
|
],
|
15049
15078
|
"name": "SwissLipids",
|
@@ -20056,6 +20085,14 @@
|
|
20056
20085
|
{
|
20057
20086
|
"retrieved": "2024-12-19",
|
20058
20087
|
"version": "2024-12-17"
|
20088
|
+
},
|
20089
|
+
{
|
20090
|
+
"retrieved": "2024-12-20",
|
20091
|
+
"version": "2024-12-18"
|
20092
|
+
},
|
20093
|
+
{
|
20094
|
+
"retrieved": "2024-12-21",
|
20095
|
+
"version": "2024-12-19"
|
20059
20096
|
}
|
20060
20097
|
],
|
20061
20098
|
"name": "Zebrafish Information Network",
|
@@ -1,274 +0,0 @@
|
|
1
|
-
# Summary of Errors
|
2
|
-
|
3
|
-
- DisGeNet - failed to resolve DisGeNet
|
4
|
-
- Antibody Registry - failed to resolve Antibody Registry
|
5
|
-
- DrugBank - failed to resolve DrugBank
|
6
|
-
- InterPro - failed to resolve InterPro
|
7
|
-
|
8
|
-
## DisGeNet
|
9
|
-
|
10
|
-
Using class: `DisGeNetGetter`
|
11
|
-
|
12
|
-
```python-traceback
|
13
|
-
Traceback (most recent call last):
|
14
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
|
15
|
-
return complexjson.loads(self.text, **kwargs)
|
16
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
17
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
|
18
|
-
return _default_decoder.decode(s)
|
19
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
20
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
|
21
|
-
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
|
22
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
23
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
|
24
|
-
raise JSONDecodeError("Expecting value", s, err.value) from None
|
25
|
-
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
26
|
-
|
27
|
-
During handling of the above exception, another exception occurred:
|
28
|
-
|
29
|
-
Traceback (most recent call last):
|
30
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
31
|
-
yv = resolve(cls.name)
|
32
|
-
^^^^^^^^^^^^^^^^^
|
33
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
34
|
-
return _resolve_helper_cached(name)
|
35
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
36
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
37
|
-
return _calc_entry(core, key, func, args, kwds)
|
38
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
39
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
40
|
-
func_res = func(*args, **kwds)
|
41
|
-
^^^^^^^^^^^^^^^^^^^
|
42
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
43
|
-
return _resolve_helper(name)
|
44
|
-
^^^^^^^^^^^^^^^^^^^^^
|
45
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
46
|
-
return getter.resolve()
|
47
|
-
^^^^^^^^^^^^^^^^
|
48
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
49
|
-
version=cls.version,
|
50
|
-
^^^^^^^^^^^
|
51
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
52
|
-
if isinstance(cls._cache_prop, str):
|
53
|
-
^^^^^^^^^^^^^^^
|
54
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
55
|
-
cls._cache = cls().get()
|
56
|
-
^^^^^^^^^^^
|
57
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
|
58
|
-
res_json = res.json()
|
59
|
-
^^^^^^^^^^
|
60
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
|
61
|
-
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
|
62
|
-
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
63
|
-
|
64
|
-
```
|
65
|
-
|
66
|
-
## Antibody Registry
|
67
|
-
|
68
|
-
Using class: `AntibodyRegistryGetter`
|
69
|
-
|
70
|
-
```python-traceback
|
71
|
-
Traceback (most recent call last):
|
72
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
73
|
-
yv = resolve(cls.name)
|
74
|
-
^^^^^^^^^^^^^^^^^
|
75
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
76
|
-
return _resolve_helper_cached(name)
|
77
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
78
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
79
|
-
return _calc_entry(core, key, func, args, kwds)
|
80
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
81
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
82
|
-
func_res = func(*args, **kwds)
|
83
|
-
^^^^^^^^^^^^^^^^^^^
|
84
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
85
|
-
return _resolve_helper(name)
|
86
|
-
^^^^^^^^^^^^^^^^^^^^^
|
87
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
88
|
-
return getter.resolve()
|
89
|
-
^^^^^^^^^^^^^^^^
|
90
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
91
|
-
version=cls.version,
|
92
|
-
^^^^^^^^^^^
|
93
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
94
|
-
if isinstance(cls._cache_prop, str):
|
95
|
-
^^^^^^^^^^^^^^^
|
96
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
97
|
-
cls._cache = cls().get()
|
98
|
-
^^^^^^^^^^^
|
99
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/antibodyregistry.py", line 21, in get
|
100
|
-
return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
|
101
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
102
|
-
AttributeError: 'NoneType' object has no attribute 'find'
|
103
|
-
|
104
|
-
```
|
105
|
-
|
106
|
-
## DrugBank
|
107
|
-
|
108
|
-
Using class: `DrugBankGetter`
|
109
|
-
|
110
|
-
```python-traceback
|
111
|
-
Traceback (most recent call last):
|
112
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
113
|
-
yv = resolve(cls.name)
|
114
|
-
^^^^^^^^^^^^^^^^^
|
115
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
116
|
-
return _resolve_helper_cached(name)
|
117
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
118
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
119
|
-
return _calc_entry(core, key, func, args, kwds)
|
120
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
121
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
122
|
-
func_res = func(*args, **kwds)
|
123
|
-
^^^^^^^^^^^^^^^^^^^
|
124
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
125
|
-
return _resolve_helper(name)
|
126
|
-
^^^^^^^^^^^^^^^^^^^^^
|
127
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
128
|
-
return getter.resolve()
|
129
|
-
^^^^^^^^^^^^^^^^
|
130
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
131
|
-
version=cls.version,
|
132
|
-
^^^^^^^^^^^
|
133
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
134
|
-
if isinstance(cls._cache_prop, str):
|
135
|
-
^^^^^^^^^^^^^^^
|
136
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
137
|
-
cls._cache = cls().get()
|
138
|
-
^^^^^^^^^^^
|
139
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
|
140
|
-
res.raise_for_status()
|
141
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
|
142
|
-
raise HTTPError(http_error_msg, response=self)
|
143
|
-
requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
|
144
|
-
|
145
|
-
```
|
146
|
-
|
147
|
-
## InterPro
|
148
|
-
|
149
|
-
Using class: `InterProGetter`
|
150
|
-
|
151
|
-
```python-traceback
|
152
|
-
Traceback (most recent call last):
|
153
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
|
154
|
-
response = self._make_request(
|
155
|
-
^^^^^^^^^^^^^^^^^^^
|
156
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 490, in _make_request
|
157
|
-
raise new_e
|
158
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
|
159
|
-
self._validate_conn(conn)
|
160
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1095, in _validate_conn
|
161
|
-
conn.connect()
|
162
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 730, in connect
|
163
|
-
sock_and_verified = _ssl_wrap_socket_and_match_hostname(
|
164
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
165
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname
|
166
|
-
ssl_sock = ssl_wrap_socket(
|
167
|
-
^^^^^^^^^^^^^^^^
|
168
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket
|
169
|
-
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
|
170
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
171
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl
|
172
|
-
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
|
173
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
174
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
|
175
|
-
return self.sslsocket_class._create(
|
176
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
177
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
|
178
|
-
self.do_handshake()
|
179
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
|
180
|
-
self._sslobj.do_handshake()
|
181
|
-
ConnectionResetError: [Errno 104] Connection reset by peer
|
182
|
-
|
183
|
-
During handling of the above exception, another exception occurred:
|
184
|
-
|
185
|
-
Traceback (most recent call last):
|
186
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
|
187
|
-
resp = conn.urlopen(
|
188
|
-
^^^^^^^^^^^^^
|
189
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 843, in urlopen
|
190
|
-
retries = retries.increment(
|
191
|
-
^^^^^^^^^^^^^^^^^^
|
192
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
|
193
|
-
raise reraise(type(error), error, _stacktrace)
|
194
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
195
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 38, in reraise
|
196
|
-
raise value.with_traceback(tb)
|
197
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
|
198
|
-
response = self._make_request(
|
199
|
-
^^^^^^^^^^^^^^^^^^^
|
200
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 490, in _make_request
|
201
|
-
raise new_e
|
202
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
|
203
|
-
self._validate_conn(conn)
|
204
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1095, in _validate_conn
|
205
|
-
conn.connect()
|
206
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 730, in connect
|
207
|
-
sock_and_verified = _ssl_wrap_socket_and_match_hostname(
|
208
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
209
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname
|
210
|
-
ssl_sock = ssl_wrap_socket(
|
211
|
-
^^^^^^^^^^^^^^^^
|
212
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket
|
213
|
-
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
|
214
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
215
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl
|
216
|
-
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
|
217
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
218
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
|
219
|
-
return self.sslsocket_class._create(
|
220
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
221
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
|
222
|
-
self.do_handshake()
|
223
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
|
224
|
-
self._sslobj.do_handshake()
|
225
|
-
urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
|
226
|
-
|
227
|
-
During handling of the above exception, another exception occurred:
|
228
|
-
|
229
|
-
Traceback (most recent call last):
|
230
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
231
|
-
yv = resolve(cls.name)
|
232
|
-
^^^^^^^^^^^^^^^^^
|
233
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
234
|
-
return _resolve_helper_cached(name)
|
235
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
236
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
237
|
-
return _calc_entry(core, key, func, args, kwds)
|
238
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
239
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
240
|
-
func_res = func(*args, **kwds)
|
241
|
-
^^^^^^^^^^^^^^^^^^^
|
242
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
243
|
-
return _resolve_helper(name)
|
244
|
-
^^^^^^^^^^^^^^^^^^^^^
|
245
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
246
|
-
return getter.resolve()
|
247
|
-
^^^^^^^^^^^^^^^^
|
248
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
249
|
-
version=cls.version,
|
250
|
-
^^^^^^^^^^^
|
251
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
252
|
-
if isinstance(cls._cache_prop, str):
|
253
|
-
^^^^^^^^^^^^^^^
|
254
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
255
|
-
cls._cache = cls().get()
|
256
|
-
^^^^^^^^^^^
|
257
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/interpro.py", line 28, in get
|
258
|
-
res = session.get(
|
259
|
-
^^^^^^^^^^^^
|
260
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 602, in get
|
261
|
-
return self.request("GET", url, **kwargs)
|
262
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
263
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
|
264
|
-
resp = self.send(prep, **send_kwargs)
|
265
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
266
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
|
267
|
-
r = adapter.send(request, **kwargs)
|
268
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
269
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 682, in send
|
270
|
-
raise ConnectionError(err, request=request)
|
271
|
-
requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
|
272
|
-
|
273
|
-
```
|
274
|
-
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|