bioversions 0.6.32__tar.gz → 0.6.34__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.
Files changed (108) hide show
  1. {bioversions-0.6.32 → bioversions-0.6.34}/PKG-INFO +1 -1
  2. {bioversions-0.6.32 → bioversions-0.6.34}/docs/_data/versions.yml +18 -2
  3. {bioversions-0.6.32 → bioversions-0.6.34}/docs/failures.md +37 -154
  4. {bioversions-0.6.32 → bioversions-0.6.34}/docs/img/has_release_url.svg +1 -1
  5. {bioversions-0.6.32 → bioversions-0.6.34}/docs/img/version_date_types.svg +1 -1
  6. {bioversions-0.6.32 → bioversions-0.6.34}/docs/img/version_types.svg +1 -1
  7. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/conf.py +1 -1
  8. {bioversions-0.6.32 → bioversions-0.6.34}/pyproject.toml +2 -2
  9. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/resources/versions.json +30 -2
  10. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/version.py +1 -1
  11. {bioversions-0.6.32 → bioversions-0.6.34}/.cruft.json +0 -0
  12. {bioversions-0.6.32 → bioversions-0.6.34}/.github/CODE_OF_CONDUCT.md +0 -0
  13. {bioversions-0.6.32 → bioversions-0.6.34}/.github/CONTRIBUTING.md +0 -0
  14. {bioversions-0.6.32 → bioversions-0.6.34}/.github/codecov.yml +0 -0
  15. {bioversions-0.6.32 → bioversions-0.6.34}/.github/workflows/cruft.yml +0 -0
  16. {bioversions-0.6.32 → bioversions-0.6.34}/.github/workflows/tests.yml +0 -0
  17. {bioversions-0.6.32 → bioversions-0.6.34}/.github/workflows/update.yml +0 -0
  18. {bioversions-0.6.32 → bioversions-0.6.34}/.gitignore +0 -0
  19. {bioversions-0.6.32 → bioversions-0.6.34}/.readthedocs.yml +0 -0
  20. {bioversions-0.6.32 → bioversions-0.6.34}/LICENSE +0 -0
  21. {bioversions-0.6.32 → bioversions-0.6.34}/MANIFEST.in +0 -0
  22. {bioversions-0.6.32 → bioversions-0.6.34}/README.md +0 -0
  23. {bioversions-0.6.32 → bioversions-0.6.34}/docs/_config.yml +0 -0
  24. {bioversions-0.6.32 → bioversions-0.6.34}/docs/_includes/footer.html +0 -0
  25. {bioversions-0.6.32 → bioversions-0.6.34}/docs/_includes/head.html +0 -0
  26. {bioversions-0.6.32 → bioversions-0.6.34}/docs/download.md +0 -0
  27. {bioversions-0.6.32 → bioversions-0.6.34}/docs/index.md +0 -0
  28. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/cli.rst +0 -0
  29. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/index.rst +0 -0
  30. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/installation.rst +0 -0
  31. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/logo.png +0 -0
  32. {bioversions-0.6.32 → bioversions-0.6.34}/docs/source/usage.rst +0 -0
  33. {bioversions-0.6.32 → bioversions-0.6.34}/docs/summary.md +0 -0
  34. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/__init__.py +0 -0
  35. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/__main__.py +0 -0
  36. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/charts.py +0 -0
  37. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/cli.py +0 -0
  38. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/py.typed +0 -0
  39. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/resources/__init__.py +0 -0
  40. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/resources/update.py +0 -0
  41. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/slack_client.py +0 -0
  42. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/__init__.py +0 -0
  43. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/antibodyregistry.py +0 -0
  44. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/bigg.py +0 -0
  45. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/biogrid.py +0 -0
  46. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/cellosaurus.py +0 -0
  47. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/chebi.py +0 -0
  48. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/chembl.py +0 -0
  49. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/chemidplus.py +0 -0
  50. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/civic.py +0 -0
  51. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/complexportal.py +0 -0
  52. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/daily.py +0 -0
  53. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/depmap.py +0 -0
  54. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/dgi.py +0 -0
  55. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/disgenet.py +0 -0
  56. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/drugbank.py +0 -0
  57. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/drugcentral.py +0 -0
  58. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/ensembl.py +0 -0
  59. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/expasy.py +0 -0
  60. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/flybase.py +0 -0
  61. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/gtdb.py +0 -0
  62. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/guidetopharmacology.py +0 -0
  63. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/hgnc.py +0 -0
  64. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/homologene.py +0 -0
  65. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/icd10.py +0 -0
  66. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/icd11.py +0 -0
  67. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/icf.py +0 -0
  68. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/intact.py +0 -0
  69. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/interpro.py +0 -0
  70. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/itis.py +0 -0
  71. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/kegg.py +0 -0
  72. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/mesh.py +0 -0
  73. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/mgi.py +0 -0
  74. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/mirbase.py +0 -0
  75. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/moalmanac.py +0 -0
  76. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/msigdb.py +0 -0
  77. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/ncit.py +0 -0
  78. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/npass.py +0 -0
  79. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/obo.py +0 -0
  80. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/ols.py +0 -0
  81. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/omim.py +0 -0
  82. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/oncotree.py +0 -0
  83. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pathbank.py +0 -0
  84. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pathwaycommons.py +0 -0
  85. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pfam.py +0 -0
  86. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pombase.py +0 -0
  87. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pr.py +0 -0
  88. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/pubchem.py +0 -0
  89. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/reactome.py +0 -0
  90. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/rfam.py +0 -0
  91. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/rgd.py +0 -0
  92. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/rhea.py +0 -0
  93. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/rxnorm.py +0 -0
  94. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/sgd.py +0 -0
  95. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/slm.py +0 -0
  96. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/stringdb.py +0 -0
  97. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/umls.py +0 -0
  98. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/uniprot.py +0 -0
  99. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/unversioned.py +0 -0
  100. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/wikipathways.py +0 -0
  101. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/sources/zfin.py +0 -0
  102. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/templates/base.html +0 -0
  103. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/templates/home.html +0 -0
  104. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/twitter_client.py +0 -0
  105. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/utils.py +0 -0
  106. {bioversions-0.6.32 → bioversions-0.6.34}/src/bioversions/wsgi.py +0 -0
  107. {bioversions-0.6.32 → bioversions-0.6.34}/tests/test_bioversions.py +0 -0
  108. {bioversions-0.6.32 → bioversions-0.6.34}/tox.ini +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bioversions
3
- Version: 0.6.32
3
+ Version: 0.6.34
4
4
  Summary: Get the current version for biological databases
5
5
  Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
6
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  Project-URL: Homepage, https://github.com/biopragmatics/bioversions
@@ -1,7 +1,7 @@
1
1
  annotations:
2
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  author: runner
3
- date: '2025-01-09'
4
- revision: 896
3
+ date: '2025-01-11'
4
+ revision: 898
5
5
  database:
6
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  - name: A nomenclatural ontology for biological names
7
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  prefix: nomen
@@ -5190,6 +5190,12 @@ database:
5190
5190
  - date: '2025-01-07'
5191
5191
  retrieved: '2025-01-09'
5192
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  version: January 7, 2025
5193
+ - date: '2025-01-08'
5194
+ retrieved: '2025-01-10'
5195
+ version: January 8, 2025
5196
+ - date: '2025-01-09'
5197
+ retrieved: '2025-01-11'
5198
+ version: January 9, 2025
5193
5199
  vtype: date
5194
5200
  - name: 'OntoAvida: ontology for Avida digital evolution platform'
5195
5201
  prefix: ontoavida
@@ -8306,6 +8312,10 @@ database:
8306
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  version: '2025-01-08'
8307
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  - retrieved: '2025-01-09'
8308
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  version: '2025-01-09'
8315
+ - retrieved: '2025-01-10'
8316
+ version: '2025-01-10'
8317
+ - retrieved: '2025-01-11'
8318
+ version: '2025-01-11'
8309
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  vtype: date
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  - name: SWO (The Software Ontology)
8311
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  prefix: swo
@@ -9173,6 +9183,10 @@ database:
9173
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  homepage: http://data.wikipathways.org/20241210/
9174
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  retrieved: '2024-12-11'
9175
9185
  version: '20241210'
9186
+ - date: '2025-01-10'
9187
+ homepage: http://data.wikipathways.org/20250110/
9188
+ retrieved: '2025-01-11'
9189
+ version: '20250110'
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  vtype: date
9177
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  - name: Woody Plant Ontology ontology
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  prefix: co_357
@@ -11083,6 +11097,8 @@ database:
11083
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  version: '2025-01-06'
11084
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  - retrieved: '2025-01-09'
11085
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  version: '2025-01-07'
11100
+ - retrieved: '2025-01-10'
11101
+ version: '2025-01-08'
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  vtype: date
11087
11103
  - name: Zebrafish Phenotype Ontology
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  prefix: zp
@@ -3,8 +3,7 @@
3
3
  - DisGeNet - failed to resolve DisGeNet
4
4
  - Antibody Registry - failed to resolve Antibody Registry
5
5
  - DrugBank - failed to resolve DrugBank
6
- - Protein Ontology - failed to resolve Protein Ontology
7
- - Protein Ontology - failed to resolve Protein Ontology
6
+ - Zebrafish Information Network - failed to resolve Zebrafish Information Network
8
7
 
9
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  ## DisGeNet
10
9
 
@@ -145,36 +144,36 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
145
144
 
146
145
  ```
147
146
 
148
- ## Protein Ontology
147
+ ## Zebrafish Information Network
149
148
 
150
- Using class: `PRGetter`
149
+ Using class: `ZfinGetter`
151
150
 
152
151
  ```python-traceback
153
152
  Traceback (most recent call last):
154
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 464, in _make_request
155
- self._validate_conn(conn)
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- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1093, in _validate_conn
157
- conn.connect()
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- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 741, in connect
159
- sock_and_verified = _ssl_wrap_socket_and_match_hostname(
160
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 920, in _ssl_wrap_socket_and_match_hostname
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- ssl_sock = ssl_wrap_socket(
163
- ^^^^^^^^^^^^^^^^
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- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 460, in ssl_wrap_socket
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- ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
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- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 504, in _ssl_wrap_socket_impl
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- return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
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- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
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- return self.sslsocket_class._create(
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- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
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- self.do_handshake()
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- File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
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- self._sslobj.do_handshake()
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- TimeoutError: _ssl.c:983: The handshake operation timed out
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+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 534, in _make_request
154
+ response = conn.getresponse()
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+ ^^^^^^^^^^^^^^^^^^
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+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 516, in getresponse
157
+ httplib_response = super().getresponse()
158
+ ^^^^^^^^^^^^^^^^^^^^^
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 1428, in getresponse
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+ response.begin()
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 331, in begin
162
+ version, status, reason = self._read_status()
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+ ^^^^^^^^^^^^^^^^^^^
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 292, in _read_status
165
+ line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
166
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/socket.py", line 720, in readinto
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+ return self._sock.recv_into(b)
169
+ ^^^^^^^^^^^^^^^^^^^^^^^
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1251, in recv_into
171
+ return self.read(nbytes, buffer)
172
+ ^^^^^^^^^^^^^^^^^^^^^^^^^
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+ File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1103, in read
174
+ return self._sslobj.read(len, buffer)
175
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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+ TimeoutError: The read operation timed out
178
177
 
179
178
  The above exception was the direct cause of the following exception:
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179
 
@@ -193,13 +192,11 @@ Traceback (most recent call last):
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  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 787, in urlopen
194
193
  response = self._make_request(
195
194
  ^^^^^^^^^^^^^^^^^^^
196
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 488, in _make_request
197
- raise new_e
198
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
199
- self._raise_timeout(err=e, url=url, timeout_value=conn.timeout)
195
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
196
+ self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
200
197
  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout
201
198
  raise ReadTimeoutError(
202
- urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='proconsortium.org', port=443): Read timed out. (read timeout=60)
199
+ urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='zfin.org', port=443): Read timed out. (read timeout=15)
203
200
 
204
201
  During handling of the above exception, another exception occurred:
205
202
 
@@ -231,12 +228,12 @@ Traceback (most recent call last):
231
228
  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
232
229
  cls._cache = cls().get()
233
230
  ^^^^^^^^^^^
234
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 282, in get
235
- return self.process(get_obo_version(url))
236
- ^^^^^^^^^^^^^^^^^^^^
237
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 255, in get_obo_version
238
- with requests.get(url, stream=True, timeout=60) as res:
239
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
231
+ File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/zfin.py", line 23, in get
232
+ soup = get_soup(URL)
233
+ ^^^^^^^^^^^^^
234
+ File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 62, in get_soup
235
+ res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
236
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
240
237
  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
241
238
  return request("get", url, params=params, **kwargs)
242
239
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -246,126 +243,12 @@ Traceback (most recent call last):
246
243
  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
247
244
  resp = self.send(prep, **send_kwargs)
248
245
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
249
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 724, in send
250
- history = [resp for resp in gen]
251
- ^^^
252
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
253
- resp = self.send(
254
- ^^^^^^^^^^
255
246
  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
256
247
  r = adapter.send(request, **kwargs)
257
248
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
258
249
  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
259
250
  raise ReadTimeout(e, request=request)
260
- requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='proconsortium.org', port=443): Read timed out. (read timeout=60)
261
-
262
- ```
263
-
264
- ## Protein Ontology
265
-
266
- Using class: `PrGetter`
267
-
268
- ```python-traceback
269
- Traceback (most recent call last):
270
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 198, in _new_conn
271
- sock = connection.create_connection(
272
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
273
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 85, in create_connection
274
- raise err
275
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 73, in create_connection
276
- sock.connect(sa)
277
- TimeoutError: timed out
278
-
279
- The above exception was the direct cause of the following exception:
280
-
281
- Traceback (most recent call last):
282
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 787, in urlopen
283
- response = self._make_request(
284
- ^^^^^^^^^^^^^^^^^^^
285
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 488, in _make_request
286
- raise new_e
287
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 464, in _make_request
288
- self._validate_conn(conn)
289
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1093, in _validate_conn
290
- conn.connect()
291
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 704, in connect
292
- self.sock = sock = self._new_conn()
293
- ^^^^^^^^^^^^^^^^
294
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 207, in _new_conn
295
- raise ConnectTimeoutError(
296
- urllib3.exceptions.ConnectTimeoutError: (<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)')
297
-
298
- The above exception was the direct cause of the following exception:
299
-
300
- Traceback (most recent call last):
301
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
302
- resp = conn.urlopen(
303
- ^^^^^^^^^^^^^
304
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 841, in urlopen
305
- retries = retries.increment(
306
- ^^^^^^^^^^^^^^^^^^
307
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 519, in increment
308
- raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
309
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
310
- urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='proconsortium.org', port=443): Max retries exceeded with url: /download/current/pro_reasoned.obo (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)'))
311
-
312
- During handling of the above exception, another exception occurred:
313
-
314
- Traceback (most recent call last):
315
- File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
316
- yv = resolve(cls.name)
317
- ^^^^^^^^^^^^^^^^^
318
- File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
319
- return _resolve_helper_cached(name)
320
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
321
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
322
- return _calc_entry(core, key, func, args, kwds)
323
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
324
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
325
- func_res = func(*args, **kwds)
326
- ^^^^^^^^^^^^^^^^^^^
327
- File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
328
- return _resolve_helper(name)
329
- ^^^^^^^^^^^^^^^^^^^^^
330
- File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
331
- return getter.resolve()
332
- ^^^^^^^^^^^^^^^^
333
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
334
- version=cls.version,
335
- ^^^^^^^^^^^
336
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
337
- if isinstance(cls._cache_prop, str):
338
- ^^^^^^^^^^^^^^^
339
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
340
- cls._cache = cls().get()
341
- ^^^^^^^^^^^
342
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 282, in get
343
- return self.process(get_obo_version(url))
344
- ^^^^^^^^^^^^^^^^^^^^
345
- File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 255, in get_obo_version
346
- with requests.get(url, stream=True, timeout=60) as res:
347
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
348
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
349
- return request("get", url, params=params, **kwargs)
350
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
351
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
352
- return session.request(method=method, url=url, **kwargs)
353
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
354
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
355
- resp = self.send(prep, **send_kwargs)
356
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
357
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 724, in send
358
- history = [resp for resp in gen]
359
- ^^^
360
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
361
- resp = self.send(
362
- ^^^^^^^^^^
363
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
364
- r = adapter.send(request, **kwargs)
365
- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
366
- File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 688, in send
367
- raise ConnectTimeout(e, request=request)
368
- requests.exceptions.ConnectTimeout: HTTPSConnectionPool(host='proconsortium.org', port=443): Max retries exceeded with url: /download/current/pro_reasoned.obo (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)'))
251
+ requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='zfin.org', port=443): Read timed out. (read timeout=15)
369
252
 
370
253
  ```
371
254
 
@@ -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>2025-01-09T01:03:42.395761</dc:date>
9
+ <dc:date>2025-01-11T01:02:33.618053</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>2025-01-09T01:03:42.283087</dc:date>
9
+ <dc:date>2025-01-11T01:02:33.574469</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>2025-01-09T01:03:42.206399</dc:date>
9
+ <dc:date>2025-01-11T01:02:33.446070</dc:date>
10
10
  <dc:format>image/svg+xml</dc:format>
11
11
  <dc:creator>
12
12
  <cc:Agent>
@@ -26,7 +26,7 @@ copyright = f"{date.today().year}, Charles Tapley Hoyt"
26
26
  author = "Charles Tapley Hoyt"
27
27
 
28
28
  # The full version, including alpha/beta/rc tags.
29
- release = "0.6.32"
29
+ release = "0.6.34"
30
30
 
31
31
  # The short X.Y version.
32
32
  parsed_version = re.match(
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
4
4
 
5
5
  [project]
6
6
  name = "bioversions"
7
- version = "0.6.32"
7
+ version = "0.6.34"
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 = "0.6.32"
225
+ current_version = "0.6.34"
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": 896,
4
- "date": "2025-01-09",
3
+ "revision": 898,
4
+ "date": "2025-01-11",
5
5
  "author": "runner"
6
6
  },
7
7
  "database": [
@@ -9364,6 +9364,16 @@
9364
9364
  "retrieved": "2025-01-09",
9365
9365
  "version": "January 7, 2025",
9366
9366
  "date": "2025-01-07"
9367
+ },
9368
+ {
9369
+ "retrieved": "2025-01-10",
9370
+ "version": "January 8, 2025",
9371
+ "date": "2025-01-08"
9372
+ },
9373
+ {
9374
+ "retrieved": "2025-01-11",
9375
+ "version": "January 9, 2025",
9376
+ "date": "2025-01-09"
9367
9377
  }
9368
9378
  ],
9369
9379
  "name": "Online Mendelian Inheritance in Man",
@@ -15259,6 +15269,14 @@
15259
15269
  {
15260
15270
  "retrieved": "2025-01-09",
15261
15271
  "version": "2025-01-09"
15272
+ },
15273
+ {
15274
+ "retrieved": "2025-01-10",
15275
+ "version": "2025-01-10"
15276
+ },
15277
+ {
15278
+ "retrieved": "2025-01-11",
15279
+ "version": "2025-01-11"
15262
15280
  }
15263
15281
  ],
15264
15282
  "name": "SwissLipids",
@@ -16828,6 +16846,12 @@
16828
16846
  "version": "20241210",
16829
16847
  "homepage": "http://data.wikipathways.org/20241210/",
16830
16848
  "date": "2024-12-10"
16849
+ },
16850
+ {
16851
+ "retrieved": "2025-01-11",
16852
+ "version": "20250110",
16853
+ "homepage": "http://data.wikipathways.org/20250110/",
16854
+ "date": "2025-01-10"
16831
16855
  }
16832
16856
  ],
16833
16857
  "vtype": "date"
@@ -20359,6 +20383,10 @@
20359
20383
  {
20360
20384
  "retrieved": "2025-01-09",
20361
20385
  "version": "2025-01-07"
20386
+ },
20387
+ {
20388
+ "retrieved": "2025-01-10",
20389
+ "version": "2025-01-08"
20362
20390
  }
20363
20391
  ],
20364
20392
  "name": "Zebrafish Information Network",
@@ -7,7 +7,7 @@ __all__ = [
7
7
  "VERSION",
8
8
  ]
9
9
 
10
- VERSION = "0.6.32"
10
+ VERSION = "0.6.34"
11
11
 
12
12
 
13
13
  def get_git_hash() -> str:
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes