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Merged
csinva merged 6 commits into from
Oct 15, 2026
Merged

Seeding for build_vset, two rounds of bug fixes, Python 3.13, new logo #60

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3bcf88a
CI: test on Python 3.10, 3.12 and 3.13 (drop 3.11)
csinva Oct 15, 2026
47172c9
Add seeding to build_vset and fix bugs found in review
csinva Oct 15, 2026
b96cf6e
Docs: end index at References, drop Contributing from guides, rebuild
csinva Oct 15, 2026
2091bdb
Fix bugs found in a second review round
csinva Oct 15, 2026
d6a346d
New vflow logo: drop-ring wordmark, mark and favicon
csinva Oct 15, 2026
a338005
Add docs/favicon.png (the **Icon* ignore rule caught it)
csinva Oct 15, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/python-package.yml
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Expand Up @@ -20,7 +20,7 @@ concurrency:
cancel-in-progress: true

env:
STABLE_PYTHON_VERSION: '3.11'
STABLE_PYTHON_VERSION: '3.12'
PYTHONUNBUFFERED: "1"
FORCE_COLOR: "1"

Expand All @@ -31,7 +31,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.10", "3.11", "3.12"]
python-version: ["3.10", "3.12", "3.13"]
os: [ubuntu-latest, windows-latest, macos-latest]

steps:
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -16,6 +16,7 @@ env
**.idea
*.pth
**Icon*
!docs/favicon.png
venv
.vscode/**
# Compiled python modules.
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11 changes: 5 additions & 6 deletions README.md
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@@ -1,6 +1,6 @@
<header>
<p align="center">
<img src="https://yu-group.github.io/veridical-flow/logo_vflow_straight.png" width="70%" alt="vflow logo">
<img src="https://yu-group.github.io/veridical-flow/vflow_logo.png" width="40%" alt="vflow logo">
</p>


Expand Down Expand Up @@ -43,7 +43,7 @@ from sklearn.metrics import accuracy_score, balanced_accuracy_score
from sklearn.model_selection import train_test_split
from sklearn.tree import DecisionTreeClassifier

from vflow import Vset, init_args
from vflow import Vset, build_vset, init_args

# initialize data
X, y = make_classification()
Expand All @@ -52,10 +52,9 @@ X_train, X_test, y_train, y_test = init_args(
names=["X_train", "X_test", "y_train", "y_test"], # optionally name the args
)

# subsample data
subsampling_funcs = [sklearn.utils.resample for _ in range(3)]
subsampling_set = Vset(
name="subsampling", vfuncs=subsampling_funcs, output_matching=True
# subsample data: 3 bootstrap samples, reproducible thanks to the seed
subsampling_set = build_vset(
"subsampling", sklearn.utils.resample, reps=3, seed=0, output_matching=True
)
X_trains, y_trains = subsampling_set(X_train, y_train)

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97 changes: 48 additions & 49 deletions docs/agents.html
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Expand Up @@ -15,7 +15,7 @@
<style media="print">@media print{#sidebar h1{page-break-before:always}.source{display:none}}@media print{*{background:transparent !important;color:#000 !important;box-shadow:none !important;text-shadow:none !important}a[href]:after{content:" (" attr(href) ")";font-size:90%}a[href][title]:after{content:none}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% !important}@page{margin:0.5cm}p,h2,h3{orphans:3;widows:3}h1,h2,h3,h4,h5,h6{page-break-after:avoid}}</style>
<link rel="stylesheet" href="github.css">
<link rel="stylesheet" href="style.css">
<link rel="icon" href="logo_vflow_straight.png">
<link rel="icon" type="image/png" href="favicon.png">
<script defer src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.1.1/highlight.min.js" integrity="sha256-Uv3H6lx7dJmRfRvH8TH6kJD1TSK1aFcwgx+mdg3epi8=" crossorigin></script>
<script>window.addEventListener('DOMContentLoaded', () => hljs.initHighlighting())</script>
</head>
Expand All @@ -32,7 +32,7 @@
</a>
<p id="site-tagline"><b>vflow</b> &middot; Stability analysis for data-science pipelines, with PCS.</p>
<a href="index.html" id="site-logo">
<img src="logo_vflow_straight.png" alt="vflow">
<img src="vflow_logo.svg" alt="vflow">
</a>
<a href="https://github.com/Yu-Group/veridical-flow" class="nav-icon"
aria-label="View source on GitHub" title="GitHub">
Expand Down Expand Up @@ -323,7 +323,6 @@ <h2 id="limits">7 &nbsp;Notes and limits</h2>
<ul class="post-list">
<li><a href="agents.html" title="PCS for analyses done by AI agents">vflow for agents</a><span class="post-tag" title="Claude Code plugin">new</span><span class="post-date">Oct '26</span></li>
<li><a href="vflow-internals.html" title="Vset, Vfunc and Subkey">How vflow works internally</a><span class="post-date">'22</span></li>
<li><a href="https://github.com/Yu-Group/veridical-flow/blob/master/docs/contributing.md" title="Contributing">Contributing</a></li>
</ul>
</li>
<li><h3>Notebooks</h3>
Expand Down Expand Up @@ -352,7 +351,7 @@ <h2 id="limits">7 &nbsp;Notes and limits</h2>
</ul>
</div></div>
</li>
<li><h3><a href="index.html#header-submodules">API</a></h3>
<li><h3>API</h3>
<ul>
<li><code><a title="vflow.helpers" href="helpers.html">vflow.helpers</a></code></li>
<li><code><a title="vflow.pipeline" href="pipeline.html">vflow.pipeline</a></code></li>
Expand All @@ -362,77 +361,77 @@ <h2 id="limits">7 &nbsp;Notes and limits</h2>
<li><code><a title="vflow.vset" href="vset.html">vflow.vset</a></code></li>
</ul>
</li>
<li><h3><a href="index.html#header-functions">Functions</a></h3>
<li><h3>Functions</h3>
<ul class="">
<li><code><a title="vflow.apply_vfuncs" href="index.html#vflow.apply_vfuncs">apply_vfuncs</a></code></li>
<li><code><a title="vflow.base_dict" href="index.html#vflow.base_dict">base_dict</a></code></li>
<li><code><a title="vflow.build_graph" href="index.html#vflow.build_graph">build_graph</a></code></li>
<li><code><a title="vflow.build_vset" href="index.html#vflow.build_vset">build_vset</a></code></li>
<li><code><a title="vflow.combine_dicts" href="index.html#vflow.combine_dicts">combine_dicts</a></code></li>
<li><code><a title="vflow.combine_keys" href="index.html#vflow.combine_keys">combine_keys</a></code></li>
<li><code><a title="vflow.cum_acc_by_uncertainty" href="index.html#vflow.cum_acc_by_uncertainty">cum_acc_by_uncertainty</a></code></li>
<li><code><a title="vflow.dict_data" href="index.html#vflow.dict_data">dict_data</a></code></li>
<li><code><a title="vflow.dict_keys" href="index.html#vflow.dict_keys">dict_keys</a></code></li>
<li><code><a title="vflow.dict_to_df" href="index.html#vflow.dict_to_df">dict_to_df</a></code></li>
<li><code><a title="vflow.filter_vset_by_metric" href="index.html#vflow.filter_vset_by_metric">filter_vset_by_metric</a></code></li>
<li><code><a title="vflow.init_args" href="index.html#vflow.init_args">init_args</a></code></li>
<li><code><a title="vflow.init_step" href="index.html#vflow.init_step">init_step</a></code></li>
<li><code><a title="vflow.perturbation_stats" href="index.html#vflow.perturbation_stats">perturbation_stats</a></code></li>
<li><code><a title="vflow.sep_dicts" href="index.html#vflow.sep_dicts">sep_dicts</a></code></li>
<li><code><a title="vflow.to_list" href="index.html#vflow.to_list">to_list</a></code></li>
<li><code><a title="vflow.to_tuple" href="index.html#vflow.to_tuple">to_tuple</a></code></li>
<li><code><a title="vflow.apply_vfuncs" href="utils.html#vflow.utils.apply_vfuncs">apply_vfuncs</a></code></li>
<li><code><a title="vflow.base_dict" href="utils.html#vflow.utils.base_dict">base_dict</a></code></li>
<li><code><a title="vflow.build_graph" href="pipeline.html#vflow.pipeline.build_graph">build_graph</a></code></li>
<li><code><a title="vflow.build_vset" href="helpers.html#vflow.helpers.build_vset">build_vset</a></code></li>
<li><code><a title="vflow.combine_dicts" href="utils.html#vflow.utils.combine_dicts">combine_dicts</a></code></li>
<li><code><a title="vflow.combine_keys" href="utils.html#vflow.utils.combine_keys">combine_keys</a></code></li>
<li><code><a title="vflow.cum_acc_by_uncertainty" href="helpers.html#vflow.helpers.cum_acc_by_uncertainty">cum_acc_by_uncertainty</a></code></li>
<li><code><a title="vflow.dict_data" href="utils.html#vflow.utils.dict_data">dict_data</a></code></li>
<li><code><a title="vflow.dict_keys" href="utils.html#vflow.utils.dict_keys">dict_keys</a></code></li>
<li><code><a title="vflow.dict_to_df" href="utils.html#vflow.utils.dict_to_df">dict_to_df</a></code></li>
<li><code><a title="vflow.filter_vset_by_metric" href="helpers.html#vflow.helpers.filter_vset_by_metric">filter_vset_by_metric</a></code></li>
<li><code><a title="vflow.init_args" href="helpers.html#vflow.helpers.init_args">init_args</a></code></li>
<li><code><a title="vflow.init_step" href="utils.html#vflow.utils.init_step">init_step</a></code></li>
<li><code><a title="vflow.perturbation_stats" href="utils.html#vflow.utils.perturbation_stats">perturbation_stats</a></code></li>
<li><code><a title="vflow.sep_dicts" href="utils.html#vflow.utils.sep_dicts">sep_dicts</a></code></li>
<li><code><a title="vflow.to_list" href="utils.html#vflow.utils.to_list">to_list</a></code></li>
<li><code><a title="vflow.to_tuple" href="utils.html#vflow.utils.to_tuple">to_tuple</a></code></li>
</ul>
</li>
<li><h3><a href="index.html#header-classes">Classes</a></h3>
<li><h3>Classes</h3>
<ul>
<li>
<h4><code><a title="vflow.AsyncVfunc" href="index.html#vflow.AsyncVfunc">AsyncVfunc</a></code></h4>
<h4><code><a title="vflow.AsyncVfunc" href="vfunc.html#vflow.vfunc.AsyncVfunc">AsyncVfunc</a></code></h4>
<ul class="">
<li><code><a title="vflow.AsyncVfunc.fit" href="index.html#vflow.AsyncVfunc.fit">fit</a></code></li>
<li><code><a title="vflow.AsyncVfunc.transform" href="index.html#vflow.AsyncVfunc.transform">transform</a></code></li>
<li><code><a title="vflow.AsyncVfunc.fit" href="vfunc.html#vflow.vfunc.AsyncVfunc.fit">fit</a></code></li>
<li><code><a title="vflow.AsyncVfunc.transform" href="vfunc.html#vflow.vfunc.AsyncVfunc.transform">transform</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="vflow.PCSPipeline" href="index.html#vflow.PCSPipeline">PCSPipeline</a></code></h4>
<h4><code><a title="vflow.PCSPipeline" href="pipeline.html#vflow.pipeline.PCSPipeline">PCSPipeline</a></code></h4>
<ul class="">
<li><code><a title="vflow.PCSPipeline.generate_names" href="index.html#vflow.PCSPipeline.generate_names">generate_names</a></code></li>
<li><code><a title="vflow.PCSPipeline.run" href="index.html#vflow.PCSPipeline.run">run</a></code></li>
<li><code><a title="vflow.PCSPipeline.generate_names" href="pipeline.html#vflow.pipeline.PCSPipeline.generate_names">generate_names</a></code></li>
<li><code><a title="vflow.PCSPipeline.run" href="pipeline.html#vflow.pipeline.PCSPipeline.run">run</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="vflow.Subkey" href="index.html#vflow.Subkey">Subkey</a></code></h4>
<h4><code><a title="vflow.Subkey" href="subkey.html#vflow.subkey.Subkey">Subkey</a></code></h4>
<ul class="">
<li><code><a title="vflow.Subkey.is_matching" href="index.html#vflow.Subkey.is_matching">is_matching</a></code></li>
<li><code><a title="vflow.Subkey.matches" href="index.html#vflow.Subkey.matches">matches</a></code></li>
<li><code><a title="vflow.Subkey.matches_sep_dict_id" href="index.html#vflow.Subkey.matches_sep_dict_id">matches_sep_dict_id</a></code></li>
<li><code><a title="vflow.Subkey.mismatches" href="index.html#vflow.Subkey.mismatches">mismatches</a></code></li>
<li><code><a title="vflow.Subkey.is_matching" href="subkey.html#vflow.subkey.Subkey.is_matching">is_matching</a></code></li>
<li><code><a title="vflow.Subkey.matches" href="subkey.html#vflow.subkey.Subkey.matches">matches</a></code></li>
<li><code><a title="vflow.Subkey.matches_sep_dict_id" href="subkey.html#vflow.subkey.Subkey.matches_sep_dict_id">matches_sep_dict_id</a></code></li>
<li><code><a title="vflow.Subkey.mismatches" href="subkey.html#vflow.subkey.Subkey.mismatches">mismatches</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="vflow.Vfunc" href="index.html#vflow.Vfunc">Vfunc</a></code></h4>
<h4><code><a title="vflow.Vfunc" href="vfunc.html#vflow.vfunc.Vfunc">Vfunc</a></code></h4>
<ul class="">
<li><code><a title="vflow.Vfunc.fit" href="index.html#vflow.Vfunc.fit">fit</a></code></li>
<li><code><a title="vflow.Vfunc.transform" href="index.html#vflow.Vfunc.transform">transform</a></code></li>
<li><code><a title="vflow.Vfunc.fit" href="vfunc.html#vflow.vfunc.Vfunc.fit">fit</a></code></li>
<li><code><a title="vflow.Vfunc.transform" href="vfunc.html#vflow.vfunc.Vfunc.transform">transform</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="vflow.VfuncPromise" href="index.html#vflow.VfuncPromise">VfuncPromise</a></code></h4>
<h4><code><a title="vflow.VfuncPromise" href="vfunc.html#vflow.vfunc.VfuncPromise">VfuncPromise</a></code></h4>
<ul class="">
<li><code><a title="vflow.VfuncPromise.predict" href="index.html#vflow.VfuncPromise.predict">predict</a></code></li>
<li><code><a title="vflow.VfuncPromise.predict_proba" href="index.html#vflow.VfuncPromise.predict_proba">predict_proba</a></code></li>
<li><code><a title="vflow.VfuncPromise.transform" href="index.html#vflow.VfuncPromise.transform">transform</a></code></li>
<li><code><a title="vflow.VfuncPromise.predict" href="vfunc.html#vflow.vfunc.VfuncPromise.predict">predict</a></code></li>
<li><code><a title="vflow.VfuncPromise.predict_proba" href="vfunc.html#vflow.vfunc.VfuncPromise.predict_proba">predict_proba</a></code></li>
<li><code><a title="vflow.VfuncPromise.transform" href="vfunc.html#vflow.vfunc.VfuncPromise.transform">transform</a></code></li>
</ul>
</li>
<li>
<h4><code><a title="vflow.Vset" href="index.html#vflow.Vset">Vset</a></code></h4>
<h4><code><a title="vflow.Vset" href="vset.html#vflow.vset.Vset">Vset</a></code></h4>
<ul class="two-column">
<li><code><a title="vflow.Vset.evaluate" href="index.html#vflow.Vset.evaluate">evaluate</a></code></li>
<li><code><a title="vflow.Vset.fit" href="index.html#vflow.Vset.fit">fit</a></code></li>
<li><code><a title="vflow.Vset.fit_transform" href="index.html#vflow.Vset.fit_transform">fit_transform</a></code></li>
<li><code><a title="vflow.Vset.keys" href="index.html#vflow.Vset.keys">keys</a></code></li>
<li><code><a title="vflow.Vset.predict" href="index.html#vflow.Vset.predict">predict</a></code></li>
<li><code><a title="vflow.Vset.predict_proba" href="index.html#vflow.Vset.predict_proba">predict_proba</a></code></li>
<li><code><a title="vflow.Vset.transform" href="index.html#vflow.Vset.transform">transform</a></code></li>
<li><code><a title="vflow.Vset.evaluate" href="vset.html#vflow.vset.Vset.evaluate">evaluate</a></code></li>
<li><code><a title="vflow.Vset.fit" href="vset.html#vflow.vset.Vset.fit">fit</a></code></li>
<li><code><a title="vflow.Vset.fit_transform" href="vset.html#vflow.vset.Vset.fit_transform">fit_transform</a></code></li>
<li><code><a title="vflow.Vset.keys" href="vset.html#vflow.vset.Vset.keys">keys</a></code></li>
<li><code><a title="vflow.Vset.predict" href="vset.html#vflow.vset.Vset.predict">predict</a></code></li>
<li><code><a title="vflow.Vset.predict_proba" href="vset.html#vflow.vset.Vset.predict_proba">predict_proba</a></code></li>
<li><code><a title="vflow.Vset.transform" href="vset.html#vflow.vset.Vset.transform">transform</a></code></li>
</ul>
</li>
</ul>
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