Skip to content

[pre-commit.ci] pre-commit autoupdate #199

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
pre-commit-ci wants to merge 2 commits into from
Closed

[pre-commit.ci] pre-commit autoupdate #199

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e83884b
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jun 30, 2025
b669d7a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions .pre-commit-config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,16 @@ default_stages:
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/biomejs/pre-commit
rev: v1.9.4
rev: v2.0.6
hooks:
- id: biome-format
exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
- repo: https://github.com/tox-dev/pyproject-fmt
rev: v2.5.1
rev: v2.6.0
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.11.5
rev: v0.12.1
hooks:
- id: ruff
types_or: [python, pyi, jupyter]
Expand Down
6 changes: 3 additions & 3 deletions docs/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@
"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"matplotlib": ("https://matplotlib.org/stable/", None),
'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
}

# List of patterns, relative to source directory, that match files and
Expand All @@ -115,8 +115,8 @@
html_static_path = ["_static"]
html_css_files = ["css/custom.css"]
html_title = project_name
html_logo = '_static/images/logo.png'
html_favicon = '_static/images/logo.png'
html_logo = "_static/images/logo.png"
html_favicon = "_static/images/logo.png"

html_theme_options = {
"repository_url": repository_url,
Expand Down
55 changes: 25 additions & 30 deletions docs/notebooks/bench/rna.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -408,16 +408,11 @@
"def random(x, w):\n",
" return np.random.rand(1)[0]\n",
"\n",
"\n",
"df = dc.bm.benchmark(\n",
" adata=adata,\n",
" net=net,\n",
" kws_decouple={\n",
" 'cons': True,\n",
" 'tmin': 3,\n",
" 'args':{\n",
" 'waggr': {'fun': random}\n",
" }\n",
" },\n",
" kws_decouple={\"cons\": True, \"tmin\": 3, \"args\": {\"waggr\": {\"fun\": random}}},\n",
")"
]
},
Expand Down Expand Up @@ -578,7 +573,7 @@
}
],
"source": [
"dc.bm.pl.auc(df, hue='method')"
"dc.bm.pl.auc(df, hue=\"method\")"
]
},
{
Expand Down Expand Up @@ -614,7 +609,7 @@
}
],
"source": [
"dc.bm.pl.fscore(df, hue='method')"
"dc.bm.pl.fscore(df, hue=\"method\")"
]
},
{
Expand Down Expand Up @@ -650,7 +645,7 @@
}
],
"source": [
"dc.bm.pl.qrank(df, hue='method')"
"dc.bm.pl.qrank(df, hue=\"method\")"
]
},
{
Expand Down Expand Up @@ -968,9 +963,9 @@
}
],
"source": [
"dc.bm.pl.bar(df=hdf, x='H(auroc, auprc)', y='method', hue='method')\n",
"dc.bm.pl.bar(df=hdf, x='F-score', y='method', hue='method')\n",
"dc.bm.pl.bar(df=hdf, x='H(1-qrank, -log10(pval))', y='method', hue='method')"
"dc.bm.pl.bar(df=hdf, x=\"H(auroc, auprc)\", y=\"method\", hue=\"method\")\n",
"dc.bm.pl.bar(df=hdf, x=\"F-score\", y=\"method\", hue=\"method\")\n",
"dc.bm.pl.bar(df=hdf, x=\"H(1-qrank, -log10(pval))\", y=\"method\", hue=\"method\")"
]
},
{
Expand Down Expand Up @@ -1000,7 +995,7 @@
}
],
"source": [
"dc.bm.pl.summary(df=hdf, y='method', figsize=(6, 3))"
"dc.bm.pl.summary(df=hdf, y=\"method\", figsize=(6, 3))"
]
},
{
Expand Down Expand Up @@ -1644,8 +1639,8 @@
"metadata": {},
"outputs": [],
"source": [
"unw_ct = ct.drop(columns='weight')\n",
"unw_do = do.drop(columns='weight')"
"unw_ct = ct.drop(columns=\"weight\")\n",
"unw_do = do.drop(columns=\"weight\")"
]
},
{
Expand All @@ -1667,15 +1662,15 @@
"df = dc.bm.benchmark(\n",
" adata=adata,\n",
" net={\n",
" 'collectri': ct,\n",
" 'dorothea': do,\n",
" 'unw_collectri': unw_ct,\n",
" 'unw_dorothea': unw_do,\n",
" 'r_collectri': rct,\n",
" 'r_dorothea': rdo,\n",
" \"collectri\": ct,\n",
" \"dorothea\": do,\n",
" \"unw_collectri\": unw_ct,\n",
" \"unw_dorothea\": unw_do,\n",
" \"r_collectri\": rct,\n",
" \"r_dorothea\": rdo,\n",
" },\n",
" kws_decouple={\n",
" 'methods': 'ulm',\n",
" \"methods\": \"ulm\",\n",
" },\n",
")"
]
Expand Down Expand Up @@ -1897,7 +1892,7 @@
}
],
"source": [
"dc.bm.pl.auc(df, hue='net')"
"dc.bm.pl.auc(df, hue=\"net\")"
]
},
{
Expand Down Expand Up @@ -1926,7 +1921,7 @@
}
],
"source": [
"dc.bm.pl.fscore(df, hue='net')"
"dc.bm.pl.fscore(df, hue=\"net\")"
]
},
{
Expand Down Expand Up @@ -1955,7 +1950,7 @@
}
],
"source": [
"dc.bm.pl.qrank(df, hue='net')"
"dc.bm.pl.qrank(df, hue=\"net\")"
]
},
{
Expand Down Expand Up @@ -2172,9 +2167,9 @@
}
],
"source": [
"dc.bm.pl.bar(df=hdf, x='H(auroc, auprc)', y='net', hue='net')\n",
"dc.bm.pl.bar(df=hdf, x='F-score', y='net', hue='net')\n",
"dc.bm.pl.bar(df=hdf, x='H(1-qrank, -log10(pval))', y='net', hue='net')"
"dc.bm.pl.bar(df=hdf, x=\"H(auroc, auprc)\", y=\"net\", hue=\"net\")\n",
"dc.bm.pl.bar(df=hdf, x=\"F-score\", y=\"net\", hue=\"net\")\n",
"dc.bm.pl.bar(df=hdf, x=\"H(1-qrank, -log10(pval))\", y=\"net\", hue=\"net\")"
]
},
{
Expand Down Expand Up @@ -2204,7 +2199,7 @@
}
],
"source": [
"dc.bm.pl.summary(df=hdf, y='net', figsize=(7, 3))"
"dc.bm.pl.summary(df=hdf, y=\"net\", figsize=(7, 3))"
]
},
{
Expand Down
Loading
Loading