bioversions 0.5.552__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.
- bioversions/__init__.py +7 -3
- bioversions/__main__.py +0 -2
- bioversions/charts.py +3 -7
- bioversions/cli.py +3 -5
- bioversions/resources/__init__.py +1 -3
- bioversions/resources/update.py +1 -3
- bioversions/resources/versions.json +19543 -0
- bioversions/slack_client.py +2 -5
- bioversions/sources/__init__.py +13 -11
- bioversions/sources/antibodyregistry.py +0 -2
- bioversions/sources/bigg.py +5 -7
- bioversions/sources/biogrid.py +0 -2
- bioversions/sources/cellosaurus.py +3 -5
- bioversions/sources/chebi.py +1 -3
- bioversions/sources/chembl.py +3 -4
- bioversions/sources/chemidplus.py +1 -3
- bioversions/sources/civic.py +4 -2
- bioversions/sources/complexportal.py +0 -2
- bioversions/sources/daily.py +0 -2
- bioversions/sources/depmap.py +1 -3
- bioversions/sources/dgi.py +1 -3
- bioversions/sources/disgenet.py +1 -3
- bioversions/sources/drugbank.py +2 -4
- bioversions/sources/drugcentral.py +2 -4
- bioversions/sources/ensembl.py +1 -3
- bioversions/sources/expasy.py +0 -3
- bioversions/sources/flybase.py +0 -2
- bioversions/sources/gtdb.py +35 -0
- bioversions/sources/guidetopharmacology.py +3 -5
- bioversions/sources/hgnc.py +1 -1
- bioversions/sources/homologene.py +0 -2
- bioversions/sources/icd10.py +1 -3
- bioversions/sources/icd11.py +1 -3
- bioversions/sources/icf.py +1 -3
- bioversions/sources/intact.py +0 -2
- bioversions/sources/interpro.py +1 -3
- bioversions/sources/itis.py +1 -3
- bioversions/sources/kegg.py +5 -6
- bioversions/sources/mesh.py +0 -2
- bioversions/sources/mgi.py +0 -2
- bioversions/sources/mirbase.py +13 -8
- bioversions/sources/moalmanac.py +0 -2
- bioversions/sources/msigdb.py +0 -2
- bioversions/sources/ncit.py +1 -4
- bioversions/sources/npass.py +0 -2
- bioversions/sources/obo.py +2 -4
- bioversions/sources/ols.py +6 -8
- bioversions/sources/omim.py +2 -3
- bioversions/sources/oncotree.py +4 -4
- bioversions/sources/pathbank.py +0 -2
- bioversions/sources/pathwaycommons.py +0 -2
- bioversions/sources/pfam.py +0 -2
- bioversions/sources/pombase.py +0 -2
- bioversions/sources/pr.py +1 -3
- bioversions/sources/pubchem.py +0 -2
- bioversions/sources/reactome.py +0 -2
- bioversions/sources/rfam.py +0 -2
- bioversions/sources/rgd.py +0 -2
- bioversions/sources/rhea.py +0 -2
- bioversions/sources/rxnorm.py +0 -2
- bioversions/sources/sgd.py +0 -2
- bioversions/sources/slm.py +1 -1
- bioversions/sources/stringdb.py +2 -4
- bioversions/sources/umls.py +0 -2
- bioversions/sources/uniprot.py +1 -3
- bioversions/sources/unversioned.py +0 -2
- bioversions/sources/wikipathways.py +0 -2
- bioversions/sources/zfin.py +0 -2
- bioversions/templates/base.html +28 -0
- bioversions/templates/home.html +60 -0
- bioversions/twitter_client.py +5 -8
- bioversions/utils.py +30 -28
- bioversions/version.py +3 -5
- bioversions/wsgi.py +2 -4
- {bioversions-0.5.552.dist-info → bioversions-0.5.553.dist-info}/LICENSE +1 -1
- bioversions-0.5.553.dist-info/METADATA +382 -0
- bioversions-0.5.553.dist-info/RECORD +81 -0
- bioversions-0.5.552.dist-info/METADATA +0 -166
- bioversions-0.5.552.dist-info/RECORD +0 -77
- {bioversions-0.5.552.dist-info → bioversions-0.5.553.dist-info}/WHEEL +0 -0
- {bioversions-0.5.552.dist-info → bioversions-0.5.553.dist-info}/entry_points.txt +0 -0
- {bioversions-0.5.552.dist-info → bioversions-0.5.553.dist-info}/top_level.txt +0 -0
bioversions/__init__.py
CHANGED
@@ -1,5 +1,9 @@
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# -*- coding: utf-8 -*-
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"""What's the current version for each biological database?""" # noqa:D400
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from .sources import get_rows, get_version, resolve
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from .sources import get_rows, get_version, resolve
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__all__ = [
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"get_version",
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"resolve",
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"get_rows",
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]
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bioversions/__main__.py
CHANGED
bioversions/charts.py
CHANGED
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# -*- coding: utf-8 -*-
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"""Generation of charts summarizing bioversions."""
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import os
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@@ -21,7 +19,7 @@ def version_types_pie_chart():
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"Missing" if getter.version_type is None else getter.version_type.value
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for getter in get_getters()
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)
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labels, counts = zip(*counts.most_common())
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labels, counts = zip(*counts.most_common(), strict=False)
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fig, ax = plt.subplots()
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ax.pie(
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counts,
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autopct="%1.f%%",
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startangle=30,
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explode=[0.01 for _ in range(len(counts))],
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# shadow=True,
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)
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# fig.legend(fontsize='medium')
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fig.tight_layout()
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path = os.path.join(IMG, "version_types.svg")
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plt.savefig(path, dpi=300)
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@@ -45,7 +41,7 @@ def verioning_date_formats_pie_chart():
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for getter in get_getters()
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if getter.version_type in {VersionType.date, VersionType.month}
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)
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labels, counts = zip(*counts.most_common())
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labels, counts = zip(*counts.most_common(), strict=False)
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fig, ax = plt.subplots()
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ax.pie(
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counts,
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@@ -67,7 +63,7 @@ def has_release_url():
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for getter in get_getters()
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if getter.version_type != VersionType.unversioned
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)
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labels, counts = zip(*counts.most_common())
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labels, counts = zip(*counts.most_common(), strict=False)
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fig, ax = plt.subplots()
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ax.pie(
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counts,
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bioversions/cli.py
CHANGED
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# -*- coding: utf-8 -*-
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"""Command line interface for bioversions."""
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import click
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web = make_web_command(
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app="bioversions.wsgi:app",
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group=main,
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command_kwargs=
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help
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command_kwargs={
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"help": "Run the bioversions web application.",
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},
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)
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# -*- coding: utf-8 -*-
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"""Resources."""
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import datetime
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@@ -33,7 +31,7 @@ def load_versions():
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def _date_converter(o):
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if isinstance(o,
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if isinstance(o, datetime.datetime | datetime.date):
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return o.strftime("%Y-%m-%d")
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bioversions/resources/update.py
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# -*- coding: utf-8 -*-
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"""Update the web page."""
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import getpass
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_update(force=force)
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def _update(force: bool):
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def _update(force: bool): # noqa:C901
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if not get_git_hash():
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click.secho("Not on development installation", fg="red")
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return sys.exit(1)
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