bioversions 0.5.551__py3-none-any.whl → 0.5.553__py3-none-any.whl

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 (82) hide show
  1. bioversions/__init__.py +7 -3
  2. bioversions/__main__.py +0 -2
  3. bioversions/charts.py +3 -7
  4. bioversions/cli.py +3 -5
  5. bioversions/resources/__init__.py +1 -3
  6. bioversions/resources/update.py +1 -3
  7. bioversions/resources/versions.json +19543 -0
  8. bioversions/slack_client.py +2 -5
  9. bioversions/sources/__init__.py +13 -11
  10. bioversions/sources/antibodyregistry.py +0 -2
  11. bioversions/sources/bigg.py +5 -7
  12. bioversions/sources/biogrid.py +0 -2
  13. bioversions/sources/cellosaurus.py +3 -5
  14. bioversions/sources/chebi.py +1 -3
  15. bioversions/sources/chembl.py +3 -4
  16. bioversions/sources/chemidplus.py +1 -3
  17. bioversions/sources/civic.py +4 -2
  18. bioversions/sources/complexportal.py +0 -2
  19. bioversions/sources/daily.py +0 -2
  20. bioversions/sources/depmap.py +1 -3
  21. bioversions/sources/dgi.py +1 -3
  22. bioversions/sources/disgenet.py +1 -3
  23. bioversions/sources/drugbank.py +2 -4
  24. bioversions/sources/drugcentral.py +2 -4
  25. bioversions/sources/ensembl.py +1 -3
  26. bioversions/sources/expasy.py +0 -3
  27. bioversions/sources/flybase.py +0 -2
  28. bioversions/sources/gtdb.py +35 -0
  29. bioversions/sources/guidetopharmacology.py +3 -5
  30. bioversions/sources/hgnc.py +1 -1
  31. bioversions/sources/homologene.py +0 -2
  32. bioversions/sources/icd10.py +1 -3
  33. bioversions/sources/icd11.py +1 -3
  34. bioversions/sources/icf.py +1 -3
  35. bioversions/sources/intact.py +0 -2
  36. bioversions/sources/interpro.py +1 -3
  37. bioversions/sources/itis.py +1 -3
  38. bioversions/sources/kegg.py +5 -6
  39. bioversions/sources/mesh.py +0 -2
  40. bioversions/sources/mgi.py +0 -2
  41. bioversions/sources/mirbase.py +13 -8
  42. bioversions/sources/moalmanac.py +0 -2
  43. bioversions/sources/msigdb.py +0 -2
  44. bioversions/sources/ncit.py +1 -4
  45. bioversions/sources/npass.py +0 -2
  46. bioversions/sources/obo.py +2 -4
  47. bioversions/sources/ols.py +6 -8
  48. bioversions/sources/omim.py +2 -3
  49. bioversions/sources/oncotree.py +4 -4
  50. bioversions/sources/pathbank.py +0 -2
  51. bioversions/sources/pathwaycommons.py +0 -2
  52. bioversions/sources/pfam.py +0 -2
  53. bioversions/sources/pombase.py +0 -2
  54. bioversions/sources/pr.py +1 -3
  55. bioversions/sources/pubchem.py +0 -2
  56. bioversions/sources/reactome.py +0 -2
  57. bioversions/sources/rfam.py +0 -2
  58. bioversions/sources/rgd.py +0 -2
  59. bioversions/sources/rhea.py +0 -2
  60. bioversions/sources/rxnorm.py +0 -2
  61. bioversions/sources/sgd.py +0 -2
  62. bioversions/sources/slm.py +1 -1
  63. bioversions/sources/stringdb.py +2 -4
  64. bioversions/sources/umls.py +0 -2
  65. bioversions/sources/uniprot.py +1 -3
  66. bioversions/sources/unversioned.py +0 -2
  67. bioversions/sources/wikipathways.py +0 -2
  68. bioversions/sources/zfin.py +0 -2
  69. bioversions/templates/base.html +28 -0
  70. bioversions/templates/home.html +60 -0
  71. bioversions/twitter_client.py +5 -8
  72. bioversions/utils.py +30 -28
  73. bioversions/version.py +3 -5
  74. bioversions/wsgi.py +2 -4
  75. {bioversions-0.5.551.dist-info → bioversions-0.5.553.dist-info}/LICENSE +1 -1
  76. bioversions-0.5.553.dist-info/METADATA +382 -0
  77. bioversions-0.5.553.dist-info/RECORD +81 -0
  78. bioversions-0.5.551.dist-info/METADATA +0 -166
  79. bioversions-0.5.551.dist-info/RECORD +0 -77
  80. {bioversions-0.5.551.dist-info → bioversions-0.5.553.dist-info}/WHEEL +0 -0
  81. {bioversions-0.5.551.dist-info → bioversions-0.5.553.dist-info}/entry_points.txt +0 -0
  82. {bioversions-0.5.551.dist-info → bioversions-0.5.553.dist-info}/top_level.txt +0 -0
bioversions/__init__.py CHANGED
@@ -1,5 +1,9 @@
1
- # -*- coding: utf-8 -*-
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-
3
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  """What's the current version for each biological database?""" # noqa:D400
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2
 
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- from .sources import get_rows, get_version, resolve # noqa:F401
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+ from .sources import get_rows, get_version, resolve
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+
5
+ __all__ = [
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+ "get_version",
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+ "resolve",
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+ "get_rows",
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+ ]
bioversions/__main__.py CHANGED
@@ -1,5 +1,3 @@
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- # -*- coding: utf-8 -*-
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-
3
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  """Command line interface for bioversions."""
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2
 
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  from .cli import main
bioversions/charts.py CHANGED
@@ -1,5 +1,3 @@
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- # -*- coding: utf-8 -*-
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-
3
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  """Generation of charts summarizing bioversions."""
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2
 
5
3
  import os
@@ -21,7 +19,7 @@ def version_types_pie_chart():
21
19
  "Missing" if getter.version_type is None else getter.version_type.value
22
20
  for getter in get_getters()
23
21
  )
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- labels, counts = zip(*counts.most_common())
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+ labels, counts = zip(*counts.most_common(), strict=False)
25
23
  fig, ax = plt.subplots()
26
24
  ax.pie(
27
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  counts,
@@ -29,9 +27,7 @@ def version_types_pie_chart():
29
27
  autopct="%1.f%%",
30
28
  startangle=30,
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  explode=[0.01 for _ in range(len(counts))],
32
- # shadow=True,
33
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  )
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- # fig.legend(fontsize='medium')
35
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  fig.tight_layout()
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  path = os.path.join(IMG, "version_types.svg")
37
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  plt.savefig(path, dpi=300)
@@ -45,7 +41,7 @@ def verioning_date_formats_pie_chart():
45
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  for getter in get_getters()
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  if getter.version_type in {VersionType.date, VersionType.month}
47
43
  )
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- labels, counts = zip(*counts.most_common())
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+ labels, counts = zip(*counts.most_common(), strict=False)
49
45
  fig, ax = plt.subplots()
50
46
  ax.pie(
51
47
  counts,
@@ -67,7 +63,7 @@ def has_release_url():
67
63
  for getter in get_getters()
68
64
  if getter.version_type != VersionType.unversioned
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65
  )
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- labels, counts = zip(*counts.most_common())
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+ labels, counts = zip(*counts.most_common(), strict=False)
71
67
  fig, ax = plt.subplots()
72
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  ax.pie(
73
69
  counts,
bioversions/cli.py CHANGED
@@ -1,5 +1,3 @@
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- # -*- coding: utf-8 -*-
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-
3
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  """Command line interface for bioversions."""
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2
 
5
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  import click
@@ -21,9 +19,9 @@ main.add_command(update)
21
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  web = make_web_command(
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20
  app="bioversions.wsgi:app",
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  group=main,
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- command_kwargs=dict(
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- help="Run the bioversions web application.",
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- ),
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+ command_kwargs={
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+ "help": "Run the bioversions web application.",
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+ },
27
25
  )
28
26
 
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27
 
@@ -1,5 +1,3 @@
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- # -*- coding: utf-8 -*-
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-
3
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  """Resources."""
4
2
 
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  import datetime
@@ -33,7 +31,7 @@ def load_versions():
33
31
 
34
32
 
35
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  def _date_converter(o):
36
- if isinstance(o, (datetime.datetime, datetime.date)):
34
+ if isinstance(o, datetime.datetime | datetime.date):
37
35
  return o.strftime("%Y-%m-%d")
38
36
 
39
37
 
@@ -1,5 +1,3 @@
1
- # -*- coding: utf-8 -*-
2
-
3
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  """Update the web page."""
4
2
 
5
3
  import getpass
@@ -37,7 +35,7 @@ def update(force: bool):
37
35
  _update(force=force)
38
36
 
39
37
 
40
- def _update(force: bool):
38
+ def _update(force: bool): # noqa:C901
41
39
  if not get_git_hash():
42
40
  click.secho("Not on development installation", fg="red")
43
41
  return sys.exit(1)