bioversions 0.8.1__py3-none-any.whl → 0.8.2__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 (10) hide show
  1. bioversions/.DS_Store +0 -0
  2. bioversions/resources/update.py +2 -0
  3. bioversions/resources/versions.json +21 -2
  4. bioversions/sources/rfam.py +11 -4
  5. bioversions/version.py +1 -1
  6. {bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/METADATA +1 -1
  7. {bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/RECORD +65 -64
  8. {bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/WHEEL +0 -0
  9. {bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/entry_points.txt +0 -0
  10. {bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/licenses/LICENSE +0 -0
bioversions/.DS_Store ADDED
Binary file
bioversions/resources/update.py CHANGED
@@ -107,6 +107,8 @@ def _update(force: bool): # noqa:C901
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  text += f"## {t.name}\n\nUsing class: `{t.clstype}`\n\n"
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  text += f"```python-traceback\n{t.trace}\n```\n\n"
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  FAILURES_PATH.write_text(text.rstrip() + "\n")
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+ else:
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+ FAILURES_PATH.write_text("# No Errors :)\n")
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  def _log_update(bv) -> None:
bioversions/resources/versions.json CHANGED
@@ -1,8 +1,8 @@
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  {
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  "annotations": {
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- "revision": 991,
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+ "revision": 992,
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  "date": "2025-05-07",
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- "author": "runner"
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+ "author": "cthoyt"
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  },
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  "database": [
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  {
@@ -533,6 +533,11 @@
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  "retrieved": "2025-05-07",
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  "version": "2025-05-06",
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  "homepage": "https://antibodyregistry.org/"
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+ },
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+ {
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+ "retrieved": "2025-05-07",
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+ "version": "2025-05-07",
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+ "homepage": "https://antibodyregistry.org/"
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  }
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  ],
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  "name": "Antibody Registry",
@@ -4141,6 +4146,12 @@
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  "version": "113",
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  "homepage": "https://www.ensembl.org",
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  "date": "2024-10-01"
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+ },
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+ {
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+ "retrieved": "2025-05-07",
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+ "version": "114",
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+ "homepage": "https://www.ensembl.org",
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+ "date": "2025-05-01"
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  }
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  ],
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  "name": "Ensembl",
@@ -10572,6 +10583,10 @@
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  {
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  "retrieved": "2025-05-07",
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  "version": "2025-05-05"
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+ },
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+ {
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+ "retrieved": "2025-05-07",
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+ "version": "2025-05-06"
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  }
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  ],
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  "name": "Online Mendelian Inheritance in Man",
@@ -22677,6 +22692,10 @@
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  {
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  "retrieved": "2025-05-07",
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  "version": "2025-05-05"
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+ },
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+ {
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+ "retrieved": "2025-05-07",
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+ "version": "2025-05-06"
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  }
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  ],
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  "name": "Zebrafish Information Network",
bioversions/sources/rfam.py CHANGED
@@ -1,6 +1,8 @@
1
1
  """A getter for Rfam."""
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2
 
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- from bioversions.utils import Getter, VersionType, _get_ftp_version
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+ import requests
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+
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+ from bioversions.utils import Getter, VersionType
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6
 
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  __all__ = [
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  "RfamGetter",
@@ -12,12 +14,17 @@ class RfamGetter(Getter):
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  bioregistry_id = "rfam"
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  name = "Rfam"
15
- homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
17
+ homepage_fmt = "https://ftp.ebi.ac.uk/pub/databases/Rfam/{version}/"
16
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  version_type = VersionType.semver_minor
17
19
 
18
- def get(self):
20
+ def get(self) -> str:
19
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  """Get the latest Rfam version number."""
20
- return _get_ftp_version("ftp.ebi.ac.uk", "pub/databases/Rfam/")
22
+ res = requests.get("https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/README", timeout=15)
23
+ for line in res.iter_lines():
24
+ line = line.decode("utf8").strip()
25
+ if line.startswith("Release "):
26
+ return line[len("Release ") :]
27
+ raise ValueError
21
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22
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23
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  if __name__ == "__main__":
bioversions/version.py CHANGED
@@ -8,7 +8,7 @@ __all__ = [
8
8
  "get_git_hash",
9
9
  ]
10
10
 
11
- VERSION = "0.8.1"
11
+ VERSION = "0.8.2"
12
12
 
13
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14
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  def get_git_hash() -> str:
{bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bioversions
3
- Version: 0.8.1
3
+ Version: 0.8.2
4
4
  Summary: Get the current version for biological databases
5
5
  Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
6
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  Author: Charles Tapley Hoyt
{bioversions-0.8.1.dist-info → bioversions-0.8.2.dist-info}/RECORD RENAMED
@@ -1,81 +1,82 @@
1
- bioversions/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
2
- bioversions/cli.py,sha256=75eaa237668bef45ef6f16b5c5a20036aef228995b872dda224a54dcb30ad2d5,1639
3
- bioversions/templates/base.html,sha256=00a07a693dfd53d56d38cdb3bd6fd49b922060ef4acbe08ba41cb1cb95d73b93,713
4
- bioversions/templates/home.html,sha256=cfdf054ac94244fd8adfdc5b1e948f824d7d8fb676d4f49b44602d69723431dd,2756
5
- bioversions/__init__.py,sha256=0fc58200e829534318812aa56075dc5a716d8b9343f60f1580c27cc3e91eea62,354
1
+ bioversions/.DS_Store,sha256=ae189687e1d36349b4c5c5dd6a5ecd9a79635474d4ba76e63cb2ae00487c00a9,6148
2
+ bioversions/version.py,sha256=2b1b42c67011aa866e54e447db5177beb365d310067d85b407f772c80df85fbe,605
6
3
  bioversions/charts.py,sha256=be29a2fde227a4bd02611112f1cbe58a00e261e435fc8f00e82104a15dadbdfe,2457
7
- bioversions/__main__.py,sha256=0e97cd1eac70162293fb809292e2cba2464218394244001f3f9e0c74b8f71351,128
8
- bioversions/resources/versions.json,sha256=ee58f4ec7a2c610433b927a45fc8dce44b7b6639d80eb4f8428dcf258cf0a06e,555806
9
- bioversions/resources/update.py,sha256=339d2963c35d6b5e03e6fb97894bd90ea39cc94376aaee9ab8d0ccf23b1ff0c5,3530
4
+ bioversions/resources/update.py,sha256=847565839bacfe2d0fea36202e428cb98e33476b6f13398f950f10386583c473,3593
5
+ bioversions/resources/versions.json,sha256=8c2fed52ff39a94541f34e510d7d64f8a7a6355fe3a00f40d1c7ac52b1f0ffdf,556303
10
6
  bioversions/resources/__init__.py,sha256=371c3ac3afe0442e01fc9c2f6c000aa4d476ac8a6435167952404831d36a95d6,1659
7
+ bioversions/__init__.py,sha256=0fc58200e829534318812aa56075dc5a716d8b9343f60f1580c27cc3e91eea62,354
8
+ bioversions/slack_client.py,sha256=bda7d71401bc03f7dc19fec98d7d5abad5083285cb5c97b5b575b1f9459a1285,1293
9
+ bioversions/cli.py,sha256=75eaa237668bef45ef6f16b5c5a20036aef228995b872dda224a54dcb30ad2d5,1639
11
10
  bioversions/utils.py,sha256=f83a7ac31bc688117b31c5297d4d9bce8ffd5b63ecc32e6c531bf075952d5e25,10715
12
- bioversions/version.py,sha256=6d98ad6197cd2b61f0b02cdce7ce2bb78eefc2229a7ea823218cb1ef812da0d3,605
13
- bioversions/sources/interpro.py,sha256=1fa75923bd60517a3b2f661e7c24e2243e2ab90440bf2621e670c36e1da2baf1,1238
11
+ bioversions/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
12
+ bioversions/sources/disgenet.py,sha256=3c02c84643c1913d9cb2b37e1679fe019cc273d67633685e904fbf16ba84f8bc,739
14
13
  bioversions/sources/oncotree.py,sha256=69b039f07e37800fd3b623816b00595333caede9403d8a9620fee515de8aa8ee,1032
15
- bioversions/sources/dgi.py,sha256=8b613bedea979b8bbadfcbe4b2fd539e4d29deccf329d936c83a72626d8808bc,940
14
+ bioversions/sources/signor.py,sha256=f0a0bd043c1344027e31fe8fc4e5922f44e86044ca16370e6d66368161f05c83,969
15
+ bioversions/sources/uniprot.py,sha256=c3e16b68fc8a65e12d9a3b3288fedbd9a8e0e7b47f0a69f0fb032fb072c68a1b,924
16
+ bioversions/sources/expasy.py,sha256=625d33571c58d40584ac5ad572da0999e6bec4db7327c0860b9f017836034f9e,767
17
+ bioversions/sources/biogrid.py,sha256=df37707dbc42423111e9be6a98c7b866312430d042712d392170a8f2cf8b2daf,742
18
+ bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
16
19
  bioversions/sources/kegg.py,sha256=24574e015a28f77f77451a3b48dbb54b740ff36e7e310bbdf434ee4f63adb094,1014
17
- bioversions/sources/icf.py,sha256=2cf0e779aec4a03845ad091e5ab4fea91aaa10bbd91b5ede9f771c828a8d3771,946
18
- bioversions/sources/icd11.py,sha256=00b75086f6ecd8e81444665944cd6139725fcee36b0d817b54506b0cc91bc580,996
19
- bioversions/sources/mirbase.py,sha256=ab70baf82cbebc42f22424029e9838a6f7a846b9587ea81be37d779871b90a9e,996
20
+ bioversions/sources/slm.py,sha256=84fe81b16cf8cb3cdc817f4ed56482364bb46a9d3af1f01c3726273b26d106d6,766
21
+ bioversions/sources/homologene.py,sha256=4da5b4037dcf2d2e3cd38ceb45664a0e6a3fcf01332bd6f15ffcc089a526779c,622
22
+ bioversions/sources/dgi.py,sha256=8b613bedea979b8bbadfcbe4b2fd539e4d29deccf329d936c83a72626d8808bc,940
23
+ bioversions/sources/moalmanac.py,sha256=2f314cc81d89e0e604514217ed5346508dab890603eb6a20f4fb9d3c97144801,781
24
+ bioversions/sources/pombase.py,sha256=e65348dc0aaed5f9c35049c5d117ee7103abf8714f620afbfa5e084eded1c986,766
20
25
  bioversions/sources/omim.py,sha256=7aad8a3615748f5171db47098a1cdbec36b1e8596e0e857fe360dc5320748a65,916
26
+ bioversions/sources/icd11.py,sha256=00b75086f6ecd8e81444665944cd6139725fcee36b0d817b54506b0cc91bc580,996
27
+ bioversions/sources/rxnorm.py,sha256=abb4a225e16e57c6f59102558c41504711ba81cdb5e07bf557c70ceab552c541,1040
28
+ bioversions/sources/zfin.py,sha256=dcea33de50f1f09e36380a3253c78923e7d19cc46263250c723e1f0c4e4354b4,683
29
+ bioversions/sources/npass.py,sha256=5426aa5caf240e9ec8ece16b58ac90bc18ee5414c6667665ef6219da9152e4a3,888
30
+ bioversions/sources/pubchem.py,sha256=57e6f33479eef0935322abde994efe3292f91c7c6bb1889c5724c99ebd7d72f9,526
31
+ bioversions/sources/msigdb.py,sha256=8689c6234a84ae6e70b19b2bd21c165e2c37d83de7e71c47e605f7c54121de9a,778
21
32
  bioversions/sources/drugcentral.py,sha256=c07db12fe096a5e54fdb4e360a75a6d57fb0dd826fda6e458a04f0d61b7570b8,1116
22
33
  bioversions/sources/ols.py,sha256=35e49f5841e26161ebb063e2bba5f58754031b98128ac132532ef528346f69ac,2929
23
- bioversions/sources/mgi.py,sha256=4d7f95d3171616692db2c8d195d8d86f9f751c2b6885e63df70d054c7d9c2199,841
24
- bioversions/sources/pathbank.py,sha256=ad5a8a277ab673881cb6a520fe78bd7d29b6273d2882475ec07fb2b0f762003b,704
25
- bioversions/sources/itis.py,sha256=99a480060d52ac6e06404be347080c28af56e984e80cc4763f0a98266212a1df,582
26
- bioversions/sources/silva.py,sha256=e677f3502f516b48977191274ad08d593e4c683442281043a819dde028157274,984
27
- bioversions/sources/moalmanac.py,sha256=2f314cc81d89e0e604514217ed5346508dab890603eb6a20f4fb9d3c97144801,781
28
- bioversions/sources/rxnorm.py,sha256=abb4a225e16e57c6f59102558c41504711ba81cdb5e07bf557c70ceab552c541,1040
29
- bioversions/sources/pfam.py,sha256=a2509a19315b2524a4974101d2215794c639b2ede25832449819524f4c3efff8,975
30
- bioversions/sources/biogrid.py,sha256=df37707dbc42423111e9be6a98c7b866312430d042712d392170a8f2cf8b2daf,742
31
- bioversions/sources/reactome.py,sha256=12ae2e1cc763c323eaab9d90ec4f6cbdcea1cd9645b40e6d32d93c76333006f7,596
32
- bioversions/sources/ncit.py,sha256=887238481b9cd61f525019541624d03f455f4e0c4465d4ba40fbcf704aac231b,832
33
- bioversions/sources/stringdb.py,sha256=9afd81dd24d02469cce66e246cb6f696e4a501ba3e7e8dc7aff0f022563a37b2,787
34
- bioversions/sources/rgd.py,sha256=64f6cfd7bff88004699b00832560ef033f14f2977e70684ebef546b431a04d23,766
35
- bioversions/sources/__init__.py,sha256=6926e85147f955777cdc9e2ea59295183c06e328b410a458d6c30543c15d558c,7628
34
+ bioversions/sources/sgd.py,sha256=3e05c0bf0aa5c78f10b869e75473a5d2e034323b84ec89748e2055e1f69835d0,1084
35
+ bioversions/sources/depmap.py,sha256=00b9fb914b27902ef2023f5c2d899a4235829b6b20d3045643e4fbe8deea4168,641
36
+ bioversions/sources/icf.py,sha256=2cf0e779aec4a03845ad091e5ab4fea91aaa10bbd91b5ede9f771c828a8d3771,946
36
37
  bioversions/sources/civic.py,sha256=321967e8b7c7a7aecf896b49e6ad4520d0b00a114103a71f71a49c775291f11e,1086
37
- bioversions/sources/daily.py,sha256=501fcf689d9b11035b08255c208c5bca0bb631f79e9a8fee3d268f85d07b4033,256
38
- bioversions/sources/zfin.py,sha256=dcea33de50f1f09e36380a3253c78923e7d19cc46263250c723e1f0c4e4354b4,683
39
- bioversions/sources/rhea.py,sha256=ddcb28b84fa2a76520ecc123703e785ff3d4bccb93638af442d3883f54fbd57e,806
40
- bioversions/sources/signor.py,sha256=f0a0bd043c1344027e31fe8fc4e5922f44e86044ca16370e6d66368161f05c83,969
38
+ bioversions/sources/rgd.py,sha256=64f6cfd7bff88004699b00832560ef033f14f2977e70684ebef546b431a04d23,766
41
39
  bioversions/sources/intact.py,sha256=06e67eda7e8eededc74f63eb1c73db0648665dae78323d7d92625c76ff4f7c05,596
42
- bioversions/sources/guidetopharmacology.py,sha256=7864d5d2b74f25d3baa4a91f9a24caec4777a19c442e0055112d2f790998b0e0,1523
43
- bioversions/sources/expasy.py,sha256=625d33571c58d40584ac5ad572da0999e6bec4db7327c0860b9f017836034f9e,767
44
- bioversions/sources/depmap.py,sha256=00b9fb914b27902ef2023f5c2d899a4235829b6b20d3045643e4fbe8deea4168,641
45
- bioversions/sources/complexportal.py,sha256=1adea98029a1aef5e13d7038812734ed37bfa2c9e8f6038cb3c8216b4eff1d19,671
46
- bioversions/sources/sgd.py,sha256=3e05c0bf0aa5c78f10b869e75473a5d2e034323b84ec89748e2055e1f69835d0,1084
47
- bioversions/sources/chemidplus.py,sha256=cc93605ba1d416c5939fdfcf62e01f1449d999284b1af7beee0185696b231702,1194
40
+ bioversions/sources/stringdb.py,sha256=9afd81dd24d02469cce66e246cb6f696e4a501ba3e7e8dc7aff0f022563a37b2,787
41
+ bioversions/sources/__init__.py,sha256=6926e85147f955777cdc9e2ea59295183c06e328b410a458d6c30543c15d558c,7628
42
+ bioversions/sources/pathbank.py,sha256=ad5a8a277ab673881cb6a520fe78bd7d29b6273d2882475ec07fb2b0f762003b,704
43
+ bioversions/sources/icd10.py,sha256=ef9ec91178149d2e9b8dc6ef63bfd74211ada63768046dfc75c02b53828f0ac4,929
44
+ bioversions/sources/hgnc.py,sha256=5b2d0cf1a4fe48ab0c2945b111d3e95acdf64a32fb519ca200d2ed0900b85a9d,1099
45
+ bioversions/sources/mesh.py,sha256=5ea8cf53950980e1d5736f1cffa37b46225dd45f51a1418f5c69a621a368a6f3,971
46
+ bioversions/sources/gtdb.py,sha256=7063122d9ade9ab743d85f833729664d4bbcc0f0591fe31a10a61ebbb5742dab,1177
47
+ bioversions/sources/cellosaurus.py,sha256=d17ae067aade4a433c0f350b26d681dda881603d1057734750b67ef19950ee01,975
48
48
  bioversions/sources/pathwaycommons.py,sha256=34b6bc0f44d87fa4a4abf7ee4adf8a350117b5623786feeff187987c9bc947f6,686
49
- bioversions/sources/disgenet.py,sha256=3c02c84643c1913d9cb2b37e1679fe019cc273d67633685e904fbf16ba84f8bc,739
50
- bioversions/sources/drugbank.py,sha256=599c215452b5e8219e2c31423c2c6d1c7c867848309696c834b9b5f3af1f3f16,994
51
- bioversions/sources/wikipathways.py,sha256=493c3c062bdcdc864b608c7e2b0a711cb526453a8d7c79b4c10cb00e68bed30b,798
49
+ bioversions/sources/ncit.py,sha256=887238481b9cd61f525019541624d03f455f4e0c4465d4ba40fbcf704aac231b,832
52
50
  bioversions/sources/umls.py,sha256=276513c45b33d31f5eaa1395ef176b9ed5ae8013c4ecd4332b4f627880115146,803
53
- bioversions/sources/chembl.py,sha256=35cfa0149a5eac1c8efe2577b43aa47e359874558ef48ce227022d7bd0b60932,1513
51
+ bioversions/sources/antibodyregistry.py,sha256=5c29963e1d7bd40780582ce9539d6120bd593d0cda6f3b763b08af876a2bef8f,713
52
+ bioversions/sources/ensembl.py,sha256=8d220ffc1bf54d5832cc76c18e922493c689385a2ba930df454fc0afc38293ca,734
53
+ bioversions/sources/mgi.py,sha256=4d7f95d3171616692db2c8d195d8d86f9f751c2b6885e63df70d054c7d9c2199,841
54
+ bioversions/sources/guidetopharmacology.py,sha256=7864d5d2b74f25d3baa4a91f9a24caec4777a19c442e0055112d2f790998b0e0,1523
54
55
  bioversions/sources/pr.py,sha256=6c440e95057d35b7d0273d9c26bc2e0dec45cfe22f541e44b5645ebe66f4ddd6,876
55
- bioversions/sources/pubchem.py,sha256=57e6f33479eef0935322abde994efe3292f91c7c6bb1889c5724c99ebd7d72f9,526
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