bioversions 0.6.0__tar.gz → 0.6.2__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 (109) hide show
  1. {bioversions-0.6.0 → bioversions-0.6.2}/PKG-INFO +1 -1
  2. {bioversions-0.6.0 → bioversions-0.6.2}/docs/_data/versions.yml +26 -2
  3. {bioversions-0.6.0 → bioversions-0.6.2}/docs/failures.md +81 -6
  4. {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/has_release_url.svg +1 -1
  5. {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/version_date_types.svg +1 -1
  6. {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/version_types.svg +1 -1
  7. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/conf.py +1 -1
  8. {bioversions-0.6.0 → bioversions-0.6.2}/pyproject.toml +2 -2
  9. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/versions.json +44 -2
  10. bioversions-0.6.2/src/bioversions/sources/hgnc.py +42 -0
  11. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mesh.py +10 -3
  12. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/version.py +1 -1
  13. bioversions-0.6.0/src/bioversions/sources/hgnc.py +0 -47
  14. {bioversions-0.6.0 → bioversions-0.6.2}/.cruft.json +0 -0
  15. {bioversions-0.6.0 → bioversions-0.6.2}/.github/CODE_OF_CONDUCT.md +0 -0
  16. {bioversions-0.6.0 → bioversions-0.6.2}/.github/CONTRIBUTING.md +0 -0
  17. {bioversions-0.6.0 → bioversions-0.6.2}/.github/codecov.yml +0 -0
  18. {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/cruft.yml +0 -0
  19. {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/tests.yml +0 -0
  20. {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/update.yml +0 -0
  21. {bioversions-0.6.0 → bioversions-0.6.2}/.gitignore +0 -0
  22. {bioversions-0.6.0 → bioversions-0.6.2}/.readthedocs.yml +0 -0
  23. {bioversions-0.6.0 → bioversions-0.6.2}/LICENSE +0 -0
  24. {bioversions-0.6.0 → bioversions-0.6.2}/MANIFEST.in +0 -0
  25. {bioversions-0.6.0 → bioversions-0.6.2}/README.md +0 -0
  26. {bioversions-0.6.0 → bioversions-0.6.2}/docs/_config.yml +0 -0
  27. {bioversions-0.6.0 → bioversions-0.6.2}/docs/_includes/footer.html +0 -0
  28. {bioversions-0.6.0 → bioversions-0.6.2}/docs/_includes/head.html +0 -0
  29. {bioversions-0.6.0 → bioversions-0.6.2}/docs/download.md +0 -0
  30. {bioversions-0.6.0 → bioversions-0.6.2}/docs/index.md +0 -0
  31. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/cli.rst +0 -0
  32. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/index.rst +0 -0
  33. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/installation.rst +0 -0
  34. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/logo.png +0 -0
  35. {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/usage.rst +0 -0
  36. {bioversions-0.6.0 → bioversions-0.6.2}/docs/summary.md +0 -0
  37. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/__init__.py +0 -0
  38. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/__main__.py +0 -0
  39. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/charts.py +0 -0
  40. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/cli.py +0 -0
  41. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/py.typed +0 -0
  42. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/__init__.py +0 -0
  43. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/update.py +0 -0
  44. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/slack_client.py +0 -0
  45. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/__init__.py +0 -0
  46. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/antibodyregistry.py +0 -0
  47. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/bigg.py +0 -0
  48. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/biogrid.py +0 -0
  49. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/cellosaurus.py +0 -0
  50. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chebi.py +0 -0
  51. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chembl.py +0 -0
  52. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chemidplus.py +0 -0
  53. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/civic.py +0 -0
  54. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/complexportal.py +0 -0
  55. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/daily.py +0 -0
  56. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/depmap.py +0 -0
  57. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/dgi.py +0 -0
  58. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/disgenet.py +0 -0
  59. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/drugbank.py +0 -0
  60. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/drugcentral.py +0 -0
  61. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ensembl.py +0 -0
  62. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/expasy.py +0 -0
  63. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/flybase.py +0 -0
  64. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/gtdb.py +0 -0
  65. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/guidetopharmacology.py +0 -0
  66. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/homologene.py +0 -0
  67. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icd10.py +0 -0
  68. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icd11.py +0 -0
  69. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icf.py +0 -0
  70. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/intact.py +0 -0
  71. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/interpro.py +0 -0
  72. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/itis.py +0 -0
  73. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/kegg.py +0 -0
  74. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mgi.py +0 -0
  75. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mirbase.py +0 -0
  76. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/moalmanac.py +0 -0
  77. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/msigdb.py +0 -0
  78. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ncit.py +0 -0
  79. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/npass.py +0 -0
  80. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/obo.py +0 -0
  81. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ols.py +0 -0
  82. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/omim.py +0 -0
  83. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/oncotree.py +0 -0
  84. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pathbank.py +0 -0
  85. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pathwaycommons.py +0 -0
  86. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pfam.py +0 -0
  87. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pombase.py +0 -0
  88. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pr.py +0 -0
  89. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pubchem.py +0 -0
  90. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/reactome.py +0 -0
  91. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rfam.py +0 -0
  92. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rgd.py +0 -0
  93. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rhea.py +0 -0
  94. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rxnorm.py +0 -0
  95. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/sgd.py +0 -0
  96. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/slm.py +0 -0
  97. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/stringdb.py +0 -0
  98. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/umls.py +0 -0
  99. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/uniprot.py +0 -0
  100. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/unversioned.py +0 -0
  101. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/wikipathways.py +0 -0
  102. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/zfin.py +0 -0
  103. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/templates/base.html +0 -0
  104. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/templates/home.html +0 -0
  105. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/twitter_client.py +0 -0
  106. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/utils.py +0 -0
  107. {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/wsgi.py +0 -0
  108. {bioversions-0.6.0 → bioversions-0.6.2}/tests/test_bioversions.py +0 -0
  109. {bioversions-0.6.0 → bioversions-0.6.2}/tox.ini +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: bioversions
3
- Version: 0.6.0
3
+ Version: 0.6.2
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: '2024-12-08'
4
- revision: 864
3
+ date: '2024-12-10'
4
+ revision: 866
5
5
  database:
6
6
  - name: A nomenclatural ontology for biological names
7
7
  prefix: nomen
@@ -1193,6 +1193,10 @@ database:
1193
1193
  homepage: ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-09-08/
1194
1194
  retrieved: '2024-09-19'
1195
1195
  version: '2024-09-08'
1196
+ - date: '2024-11-29'
1197
+ homepage: ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-11-29/
1198
+ retrieved: '2024-12-10'
1199
+ version: '2024-11-29'
1196
1200
  vtype: date
1197
1201
  - name: Compositional Dietary Nutrition Ontology
1198
1202
  prefix: cdno
@@ -3012,6 +3016,9 @@ database:
3012
3016
  - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json
3013
3017
  retrieved: '2024-12-03'
3014
3018
  version: '2024-11-01'
3019
+ - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json
3020
+ retrieved: '2024-12-09'
3021
+ version: '2024-12-03'
3015
3022
  vtype: date
3016
3023
  - name: Histopathology Ontology
3017
3024
  prefix: hpath
@@ -3321,6 +3328,10 @@ database:
3321
3328
  homepage: ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-09-08/
3322
3329
  retrieved: '2024-09-19'
3323
3330
  version: '2024-09-08'
3331
+ - date: '2024-11-29'
3332
+ homepage: ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-11-29/
3333
+ retrieved: '2024-12-10'
3334
+ version: '2024-11-29'
3324
3335
  vtype: date
3325
3336
  - name: Integrative and Conjugative Element Ontology
3326
3337
  prefix: iceo
@@ -3871,6 +3882,9 @@ database:
3871
3882
  - homepage: ftp://nlmpubs.nlm.nih.gov/online/mesh/2024
3872
3883
  retrieved: '2023-12-01'
3873
3884
  version: '2024'
3885
+ - homepage: ftp://nlmpubs.nlm.nih.gov/online/mesh/2025
3886
+ retrieved: '2024-12-09'
3887
+ version: '2025'
3874
3888
  vtype: year
3875
3889
  - name: Metabolomics Standards Initiative Ontology
3876
3890
  prefix: msio
@@ -6434,6 +6448,8 @@ database:
6434
6448
  version: '2024-11-22'
6435
6449
  - retrieved: '2024-12-03'
6436
6450
  version: '2024-11-29'
6451
+ - retrieved: '2024-12-10'
6452
+ version: '2024-12-06'
6437
6453
  vtype: date
6438
6454
  - name: Rat Strain Ontology
6439
6455
  prefix: rs
@@ -6518,6 +6534,8 @@ database:
6518
6534
  version: '89'
6519
6535
  - retrieved: '2024-10-03'
6520
6536
  version: '90'
6537
+ - retrieved: '2024-12-10'
6538
+ version: '91'
6521
6539
  vtype: sequential
6522
6540
  - name: Regulation of Gene Expression Ontology
6523
6541
  prefix: rexo
@@ -8085,6 +8103,10 @@ database:
8085
8103
  version: '2024-12-07'
8086
8104
  - retrieved: '2024-12-08'
8087
8105
  version: '2024-12-08'
8106
+ - retrieved: '2024-12-09'
8107
+ version: '2024-12-09'
8108
+ - retrieved: '2024-12-10'
8109
+ version: '2024-12-10'
8088
8110
  vtype: date
8089
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  - name: SWO (The Software Ontology)
8090
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  prefix: swo
@@ -10792,6 +10814,8 @@ database:
10792
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  version: '2024-12-06'
10793
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  - retrieved: '2024-12-08'
10794
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  version: '2024-12-07'
10817
+ - retrieved: '2024-12-10'
10818
+ version: '2024-12-08'
10795
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  vtype: date
10796
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  - name: Zebrafish Phenotype Ontology
10797
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  prefix: zp
@@ -3,7 +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
- - MeSH - issue parsing MeSH:
6
+ - NPASS - failed to resolve NPASS
7
7
 
8
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  ## DisGeNet
9
9
 
@@ -144,11 +144,62 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
144
144
 
145
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  ```
146
146
 
147
- ## MeSH
147
+ ## NPASS
148
148
 
149
- Using class: `MeshGetter`
149
+ Using class: `NPASSGetter`
150
150
 
151
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 536, in _make_request
154
+ response = conn.getresponse()
155
+ ^^^^^^^^^^^^^^^^^^
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+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 507, in getresponse
157
+ httplib_response = super().getresponse()
158
+ ^^^^^^^^^^^^^^^^^^^^^
159
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 1428, in getresponse
160
+ response.begin()
161
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 331, in begin
162
+ version, status, reason = self._read_status()
163
+ ^^^^^^^^^^^^^^^^^^^
164
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 292, in _read_status
165
+ line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
166
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
167
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/socket.py", line 720, in readinto
168
+ return self._sock.recv_into(b)
169
+ ^^^^^^^^^^^^^^^^^^^^^^^
170
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/ssl.py", line 1251, in recv_into
171
+ return self.read(nbytes, buffer)
172
+ ^^^^^^^^^^^^^^^^^^^^^^^^^
173
+ File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/ssl.py", line 1103, in read
174
+ return self._sslobj.read(len, buffer)
175
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
176
+ TimeoutError: The read operation timed out
177
+
178
+ The above exception was the direct cause of the following exception:
179
+
180
+ Traceback (most recent call last):
181
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
182
+ resp = conn.urlopen(
183
+ ^^^^^^^^^^^^^
184
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 843, in urlopen
185
+ retries = retries.increment(
186
+ ^^^^^^^^^^^^^^^^^^
187
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
188
+ raise reraise(type(error), error, _stacktrace)
189
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
190
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
191
+ raise value
192
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
193
+ response = self._make_request(
194
+ ^^^^^^^^^^^^^^^^^^^
195
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 538, in _make_request
196
+ self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
197
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 369, in _raise_timeout
198
+ raise ReadTimeoutError(
199
+ urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='bidd.group', port=443): Read timed out. (read timeout=15)
200
+
201
+ During handling of the above exception, another exception occurred:
202
+
152
203
  Traceback (most recent call last):
153
204
  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
154
205
  yv = resolve(cls.name)
@@ -177,9 +228,33 @@ Traceback (most recent call last):
177
228
  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
178
229
  cls._cache = cls().get()
179
230
  ^^^^^^^^^^^
180
- File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/mesh.py", line 28, in get
181
- raise ValueError
182
- ValueError
231
+ File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/npass.py", line 21, 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
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
237
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
238
+ return request("get", url, params=params, **kwargs)
239
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
240
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
241
+ return session.request(method=method, url=url, **kwargs)
242
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
243
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
244
+ resp = self.send(prep, **send_kwargs)
245
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
246
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 724, in send
247
+ history = [resp for resp in gen]
248
+ ^^^
249
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
250
+ resp = self.send(
251
+ ^^^^^^^^^^
252
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
253
+ r = adapter.send(request, **kwargs)
254
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
255
+ File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
256
+ raise ReadTimeout(e, request=request)
257
+ requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='bidd.group', port=443): Read timed out. (read timeout=15)
183
258
 
184
259
  ```
185
260
 
@@ -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>2024-12-08T20:49:19.605329</dc:date>
9
+ <dc:date>2024-12-10T01:08:18.087409</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>2024-12-08T20:49:19.553264</dc:date>
9
+ <dc:date>2024-12-10T01:08:18.035245</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>2024-12-08T20:49:19.417755</dc:date>
9
+ <dc:date>2024-12-10T01:08:17.897990</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 = "0.6.0"
29
+ release = "0.6.2"
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 = "0.6.0"
7
+ version = "0.6.2"
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 = "0.6.0"
225
+ current_version = "0.6.2"
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": 864,
4
- "date": "2024-12-08",
3
+ "revision": 866,
4
+ "date": "2024-12-10",
5
5
  "author": "runner"
6
6
  },
7
7
  "database": [
@@ -2184,6 +2184,12 @@
2184
2184
  "version": "2024-09-08",
2185
2185
  "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-09-08/",
2186
2186
  "date": "2024-09-08"
2187
+ },
2188
+ {
2189
+ "retrieved": "2024-12-10",
2190
+ "version": "2024-11-29",
2191
+ "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-11-29/",
2192
+ "date": "2024-11-29"
2187
2193
  }
2188
2194
  ],
2189
2195
  "vtype": "date"
@@ -5491,6 +5497,11 @@
5491
5497
  "retrieved": "2024-12-03",
5492
5498
  "version": "2024-11-01",
5493
5499
  "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json"
5500
+ },
5501
+ {
5502
+ "retrieved": "2024-12-09",
5503
+ "version": "2024-12-03",
5504
+ "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json"
5494
5505
  }
5495
5506
  ],
5496
5507
  "name": "HGNC",
@@ -6044,6 +6055,12 @@
6044
6055
  "version": "2024-09-08",
6045
6056
  "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-09-08/",
6046
6057
  "date": "2024-09-08"
6058
+ },
6059
+ {
6060
+ "retrieved": "2024-12-10",
6061
+ "version": "2024-11-29",
6062
+ "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-11-29/",
6063
+ "date": "2024-11-29"
6047
6064
  }
6048
6065
  ],
6049
6066
  "vtype": "date"
@@ -7047,6 +7064,11 @@
7047
7064
  "retrieved": "2023-12-01",
7048
7065
  "version": "2024",
7049
7066
  "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2024"
7067
+ },
7068
+ {
7069
+ "retrieved": "2024-12-09",
7070
+ "version": "2025",
7071
+ "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2025"
7050
7072
  }
7051
7073
  ],
7052
7074
  "name": "MeSH",
@@ -11645,6 +11667,10 @@
11645
11667
  {
11646
11668
  "retrieved": "2024-12-03",
11647
11669
  "version": "2024-11-29"
11670
+ },
11671
+ {
11672
+ "retrieved": "2024-12-10",
11673
+ "version": "2024-12-06"
11648
11674
  }
11649
11675
  ],
11650
11676
  "name": "Rat Genome Database",
@@ -11813,6 +11839,10 @@
11813
11839
  {
11814
11840
  "retrieved": "2024-10-03",
11815
11841
  "version": "90"
11842
+ },
11843
+ {
11844
+ "retrieved": "2024-12-10",
11845
+ "version": "91"
11816
11846
  }
11817
11847
  ],
11818
11848
  "vtype": "sequential"
@@ -14854,6 +14884,14 @@
14854
14884
  {
14855
14885
  "retrieved": "2024-12-08",
14856
14886
  "version": "2024-12-08"
14887
+ },
14888
+ {
14889
+ "retrieved": "2024-12-09",
14890
+ "version": "2024-12-09"
14891
+ },
14892
+ {
14893
+ "retrieved": "2024-12-10",
14894
+ "version": "2024-12-10"
14857
14895
  }
14858
14896
  ],
14859
14897
  "name": "SwissLipids",
@@ -19816,6 +19854,10 @@
19816
19854
  {
19817
19855
  "retrieved": "2024-12-08",
19818
19856
  "version": "2024-12-07"
19857
+ },
19858
+ {
19859
+ "retrieved": "2024-12-10",
19860
+ "version": "2024-12-08"
19819
19861
  }
19820
19862
  ],
19821
19863
  "name": "Zebrafish Information Network",
@@ -0,0 +1,42 @@
1
+ """A getter for HGNC."""
2
+
3
+ import logging
4
+
5
+ import requests
6
+
7
+ from bioversions.utils import Getter, VersionType
8
+
9
+ __all__ = [
10
+ "HGNCGetter",
11
+ ]
12
+
13
+ logger = logging.getLogger(__name__)
14
+
15
+ PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
16
+ URL = "https://storage.googleapis.com/storage/v1/b/public-download-files/o?prefix=hgnc/archive/archive/monthly"
17
+ PREFIX = "hgnc/archive/archive/monthly/json/hgnc_complete_set_"
18
+ SUFFIX = ".json"
19
+
20
+
21
+ class HGNCGetter(Getter):
22
+ """A getter for HGNC."""
23
+
24
+ bioregistry_id = "hgnc"
25
+ name = "HGNC"
26
+ homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
27
+
28
+ version_type = VersionType.date
29
+
30
+ def get(self) -> str:
31
+ """Get the latest monthly HGNC version number."""
32
+ res = requests.get(URL, timeout=5)
33
+ items = res.json()["items"]
34
+ return max(
35
+ item["name"].removeprefix(PREFIX).removesuffix(SUFFIX)
36
+ for item in items
37
+ if (name := item["name"]).startswith(PREFIX) and name.endswith(SUFFIX)
38
+ )
39
+
40
+
41
+ if __name__ == "__main__":
42
+ HGNCGetter.print()
@@ -8,6 +8,10 @@ __all__ = [
8
8
  "MeshGetter",
9
9
  ]
10
10
 
11
+ #: In 2024 and before, these were .gz, but after
12
+ #: became .xml files
13
+ SUFFIXES = [".xml", ".xml.gz", ".gz"]
14
+
11
15
 
12
16
  class MeshGetter(Getter):
13
17
  """A getter for MeSH."""
@@ -22,9 +26,12 @@ class MeshGetter(Getter):
22
26
  with ftplib.FTP("nlmpubs.nlm.nih.gov") as ftp:
23
27
  ftp.login()
24
28
  ftp.cwd("/online/mesh/MESH_FILES/xmlmesh/")
25
- for name, _ in ftp.mlsd():
26
- if name.startswith("desc") and name.endswith(".gz"):
27
- return name[len("desc") : -len(".gz")]
29
+ names = [name for name, _ in ftp.mlsd()]
30
+
31
+ for name in names:
32
+ for suffix in SUFFIXES:
33
+ if name.startswith("desc") and name.endswith(suffix):
34
+ return name[len("desc") : -len(suffix)]
28
35
  raise ValueError
29
36
 
30
37
 
@@ -7,7 +7,7 @@ __all__ = [
7
7
  "VERSION",
8
8
  ]
9
9
 
10
- VERSION = "0.6.0"
10
+ VERSION = "0.6.2"
11
11
 
12
12
 
13
13
  def get_git_hash() -> str:
@@ -1,47 +0,0 @@
1
- """A getter for HGNC."""
2
-
3
- import datetime
4
- import logging
5
-
6
- import requests
7
-
8
- from bioversions.utils import Getter, VersionType
9
-
10
- __all__ = [
11
- "HGNCGetter",
12
- ]
13
-
14
- logger = logging.getLogger(__name__)
15
-
16
- PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
17
- PREFIX = "hgnc_complete_set_"
18
- SUFFIX = ".json"
19
-
20
-
21
- class HGNCGetter(Getter):
22
- """A getter for HGNC."""
23
-
24
- bioregistry_id = "hgnc"
25
- name = "HGNC"
26
- homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
27
-
28
- version_type = VersionType.date
29
-
30
- def get(self) -> str:
31
- """Get the latest HGNC version number."""
32
- today = datetime.date.today()
33
- this_year = int(today.strftime("%Y"))
34
- this_month = int(today.strftime("%m"))
35
- maybe = today.strftime("%Y-%m-01")
36
- res = requests.head(self.homepage_fmt.format(version=maybe), timeout=15)
37
- if res.status_code == 200:
38
- return maybe
39
- if this_month == 1:
40
- maybe_last_month = f"{this_year - 1}-12-01"
41
- else:
42
- maybe_last_month = f"{this_year}-{this_month - 1}-01"
43
- return maybe_last_month
44
-
45
-
46
- if __name__ == "__main__":
47
- HGNCGetter.print()
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