ruddy 0.1.0__tar.gz

ruddy-0.1.0/.gitignore

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ruddy-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 KrenAI Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ruddy-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: ruddy
+Version: 0.1.0
+Summary: Domain-agnostic statistical exploratory data analysis for tabular datasets and feature representations.
+Project-URL: Homepage, https://github.com/kren-ai-lab/ruddy
+Project-URL: Repository, https://github.com/kren-ai-lab/ruddy
+Project-URL: Issues, https://github.com/kren-ai-lab/ruddy/issues
+Project-URL: Documentation, https://github.com/kren-ai-lab/ruddy#readme
+Author-email: Kren AI Lab <krenai@umag.cl>
+Maintainer: David Medina-Ortiz, Diego Alvarez-Saravia
+License-Expression: MIT
+License-File: LICENSE
+Keywords: dimensionality-reduction,exploratory-data-analysis,factorial-analysis,multivariate-analysis,scientific-software,statistics,tabular-data
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Typing :: Typed
+Requires-Python: <3.15,>=3.11
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pandas<4,>=3.0
+Requires-Dist: polars<2,>=1.44
+Requires-Dist: pyarrow>=18
+Requires-Dist: rich>=13.9
+Requires-Dist: scikit-learn<2,>=1.4
+Requires-Dist: scipy<2,>=1.15
+Requires-Dist: statsmodels<1,>=0.14.6
+Requires-Dist: typer<1,>=0.27
+Provides-Extra: manifold
+Requires-Dist: umap-learn<1,>=0.5.7; extra == 'manifold'
+Description-Content-Type: text/markdown
+
+# Ruddy
+
+[![PyPI](https://img.shields.io/pypi/v/ruddy?style=flat-square)](https://pypi.org/project/ruddy/)
+[![PyVersions](https://img.shields.io/pypi/pyversions/ruddy?style=flat-square)](https://github.com/kren-ai-lab/ruddy)
+[![Tests](https://img.shields.io/github/actions/workflow/status/kren-ai-lab/ruddy/tests.yml?style=flat-square)](https://github.com/kren-ai-lab/ruddy/actions/workflows/tests.yml)
+![License](https://img.shields.io/github/license/kren-ai-lab/ruddy?style=flat-square)
+
+Ruddy is a Python library for statistical exploratory data analysis. It works
+on tables and on numerical feature spaces such as embeddings or descriptor
+matrices, as long as each row belongs to an identifiable observation. Results
+come back as Polars tables that carry sample counts, diagnostics and the
+parameters used, so you can filter them, export them or plot them.
+
+Ruddy doesn't know about any particular domain and doesn't compute features. You
+bring the data or the representation, and Ruddy analyzes it. It also has no
+plotting code, but you can use your prefered library for visualizations.
+See [example notebooks](https://github.com/kren-ai-lab/ruddy/blob/main/examples/README.md) for more comprehensive examples.
+
+## Installation
+
+Ruddy supports Python 3.11 to 3.14.
+
+```bash
+python -m pip install ruddy
+```
+
+For optional UMAP support:
+
+```bash
+python -m pip install "ruddy[manifold]"
+```
+
+For development setup with `uv`, see [DEVELOPMENT.md](https://github.com/kren-ai-lab/ruddy/blob/main/DEVELOPMENT.md).
+
+## Analyze a table
+
+```python
+import polars as pl
+from ruddy import TabularDataset, analyze_univariate, analyze_bivariate
+
+frame = pl.DataFrame({
+    "id": ["s1", "s2", "s3", "s4", "s5", "s6"],
+    "activity": [1.2, 2.4, 1.8, 3.1, 2.9, 4.2],
+    "length": [10.0, 14.0, 12.0, 17.0, 15.0, 20.0],
+    "family": ["A", "A", "A", "B", "B", "B"],
+})
+dataset = TabularDataset(
+    frame,
+    id_column="id",
+    role_overrides={
+        "activity": "response",
+        "family": "factor",
+        "length": "covariate",
+    },
+)
+
+univariate = analyze_univariate(dataset)
+bivariate = analyze_bivariate(dataset)
+print(univariate.numeric_statistics)
+print(bivariate.correlations)
+```
+
+To read files, use `pl.read_csv(...)` or `pl.read_parquet(...)`. pandas
+DataFrames work too. A column's role doesn't depend on its dtype, so a batch
+stored as integers can still be declared a categorical factor. The
+[data contracts](https://github.com/kren-ai-lab/ruddy/blob/main/docs/DATA_CONTRACTS.md) guide explains how observation IDs
+are checked and aligned.
+
+## Analyze a feature space
+
+```python
+from ruddy import FeatureMatrix, analyze_pca
+
+features = FeatureMatrix(
+    dataset.frame.select("activity", "length"),
+    observation_ids=dataset.observation_ids,
+)
+pca = analyze_pca(features, n_components=2, scaling="standard")
+print(pca.scores)
+print(pca.variance)
+```
+
+`FeatureMatrix` also takes NumPy arrays and SciPy sparse matrices. Not every
+method accepts sparse input, and Ruddy raises an error rather than densify it
+behind your back. To compare two feature spaces, give both of them observation
+IDs:
+
+```python
+# Given two FeatureMatrix objects named space_a and space_b:
+from ruddy import analyze_representation_similarity
+
+comparison = analyze_representation_similarity(
+    space_a,
+    space_b,
+    alignment="strict",
+    cca_components=2,
+    random_state=42,
+)
+print(comparison.cka)
+print(comparison.mantel)
+```
+
+The [method reference](https://github.com/kren-ai-lab/ruddy/blob/main/docs/METHODS.md) lists every analysis with its
+assumptions and how to read its output. Besides the ones above, Ruddy has group
+comparisons, bootstrap intervals, factorial and mixed-effects models, PERMANOVA,
+compositional data, Bayesian summaries and anomaly flags.
+
+## Run several analyses
+
+```python
+from ruddy import AnalysisConfig, analyze
+
+result = analyze(
+    dataset,
+    config=AnalysisConfig(
+        enabled_blocks=("profiling", "univariate", "groups", "outliers"),
+        responses=("activity",),
+        groups=("family",),
+        random_state=42,
+    ),
+)
+print(result.summary())
+```
+
+By default only profiling and univariate analysis run. The
+[unified analysis](https://github.com/kren-ai-lab/ruddy/blob/main/docs/UNIFIED_ANALYSIS.md) guide covers the other blocks and
+their parameters.
+
+## Command line
+
+```bash
+ruddy --help
+ruddy analyze bivariate data.csv \
+  --id-column id \
+  --factor family \
+  --output-dir results
+```
+
+The commands are grouped under `inspect`, `analyze`, `model` and `project`.
+`ruddy pipeline` runs several blocks in one go, but only the ones you select.
+The [CLI reference](https://github.com/kren-ai-lab/ruddy/blob/main/docs/CLI_REFERENCE.md) documents every option and the
+files each command writes.
+
+## Design principles
+
+Ruddy tries hard not to make decisions for you:
+
+- Scaling and dimensionality reduction happen only when you ask for them.
+  Missing values aren't imputed, and a string that looks like a number stays a
+  string.
+- Each analysis reports which observations it used. Excluding a row never
+  deletes it from your data.
+- A diagnostic never swaps the test you asked for. If a normality check fails,
+  you still get the test you requested, with the diagnostic next to it.
+- A rank-deficient problem is reported as such, not quietly regularized.
+- Outliers are flagged and left alone.
+- Data and annotations are matched by observation ID, never by row position.
+- Every result records its parameters, input sizes, random seed and the Ruddy
+  version that produced it.
+
+Because of this, read `status` and `reason` next to every estimate. `ok` means
+the quantity was estimated. `degenerate` means the data can't support it, for
+example a constant column in a correlation. `skipped` means a requirement
+wasn't met. Missing values in result tables are Polars nulls, not NaN. See
+[results and provenance](https://github.com/kren-ai-lab/ruddy/blob/main/docs/RESULTS_AND_PROVENANCE.md) for how to read and
+export results.
+
+## Documentation and examples
+
+The [documentation index](https://github.com/kren-ai-lab/ruddy/blob/main/docs/README.md) links all the guides. There are also
+[13 example notebooks](https://github.com/kren-ai-lab/ruddy/blob/main/examples/README.md) written in marimo. To open one:
+
+```bash
+uv sync --all-extras --group examples
+uv run marimo edit examples/01_profiling_univariate.py
+```
+
+## Citing and license
+
+If you use Ruddy in published work, please cite it using
+[`CITATION.cff`](https://github.com/kren-ai-lab/ruddy/blob/main/CITATION.cff), or the "Cite this repository" button on
+GitHub. Ruddy is released under the [MIT license](https://github.com/kren-ai-lab/ruddy/blob/main/LICENSE).

ruddy-0.1.0/README.md

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+# Ruddy
+
+[![PyPI](https://img.shields.io/pypi/v/ruddy?style=flat-square)](https://pypi.org/project/ruddy/)
+[![PyVersions](https://img.shields.io/pypi/pyversions/ruddy?style=flat-square)](https://github.com/kren-ai-lab/ruddy)
+[![Tests](https://img.shields.io/github/actions/workflow/status/kren-ai-lab/ruddy/tests.yml?style=flat-square)](https://github.com/kren-ai-lab/ruddy/actions/workflows/tests.yml)
+![License](https://img.shields.io/github/license/kren-ai-lab/ruddy?style=flat-square)
+
+Ruddy is a Python library for statistical exploratory data analysis. It works
+on tables and on numerical feature spaces such as embeddings or descriptor
+matrices, as long as each row belongs to an identifiable observation. Results
+come back as Polars tables that carry sample counts, diagnostics and the
+parameters used, so you can filter them, export them or plot them.
+
+Ruddy doesn't know about any particular domain and doesn't compute features. You
+bring the data or the representation, and Ruddy analyzes it. It also has no
+plotting code, but you can use your prefered library for visualizations.
+See [example notebooks](https://github.com/kren-ai-lab/ruddy/blob/main/examples/README.md) for more comprehensive examples.
+
+## Installation
+
+Ruddy supports Python 3.11 to 3.14.
+
+```bash
+python -m pip install ruddy
+```
+
+For optional UMAP support:
+
+```bash
+python -m pip install "ruddy[manifold]"
+```
+
+For development setup with `uv`, see [DEVELOPMENT.md](https://github.com/kren-ai-lab/ruddy/blob/main/DEVELOPMENT.md).
+
+## Analyze a table
+
+```python
+import polars as pl
+from ruddy import TabularDataset, analyze_univariate, analyze_bivariate
+
+frame = pl.DataFrame({
+    "id": ["s1", "s2", "s3", "s4", "s5", "s6"],
+    "activity": [1.2, 2.4, 1.8, 3.1, 2.9, 4.2],
+    "length": [10.0, 14.0, 12.0, 17.0, 15.0, 20.0],
+    "family": ["A", "A", "A", "B", "B", "B"],
+})
+dataset = TabularDataset(
+    frame,
+    id_column="id",
+    role_overrides={
+        "activity": "response",
+        "family": "factor",
+        "length": "covariate",
+    },
+)
+
+univariate = analyze_univariate(dataset)
+bivariate = analyze_bivariate(dataset)
+print(univariate.numeric_statistics)
+print(bivariate.correlations)
+```
+
+To read files, use `pl.read_csv(...)` or `pl.read_parquet(...)`. pandas
+DataFrames work too. A column's role doesn't depend on its dtype, so a batch
+stored as integers can still be declared a categorical factor. The
+[data contracts](https://github.com/kren-ai-lab/ruddy/blob/main/docs/DATA_CONTRACTS.md) guide explains how observation IDs
+are checked and aligned.
+
+## Analyze a feature space
+
+```python
+from ruddy import FeatureMatrix, analyze_pca
+
+features = FeatureMatrix(
+    dataset.frame.select("activity", "length"),
+    observation_ids=dataset.observation_ids,
+)
+pca = analyze_pca(features, n_components=2, scaling="standard")
+print(pca.scores)
+print(pca.variance)
+```
+
+`FeatureMatrix` also takes NumPy arrays and SciPy sparse matrices. Not every
+method accepts sparse input, and Ruddy raises an error rather than densify it
+behind your back. To compare two feature spaces, give both of them observation
+IDs:
+
+```python
+# Given two FeatureMatrix objects named space_a and space_b:
+from ruddy import analyze_representation_similarity
+
+comparison = analyze_representation_similarity(
+    space_a,
+    space_b,
+    alignment="strict",
+    cca_components=2,
+    random_state=42,
+)
+print(comparison.cka)
+print(comparison.mantel)
+```
+
+The [method reference](https://github.com/kren-ai-lab/ruddy/blob/main/docs/METHODS.md) lists every analysis with its
+assumptions and how to read its output. Besides the ones above, Ruddy has group
+comparisons, bootstrap intervals, factorial and mixed-effects models, PERMANOVA,
+compositional data, Bayesian summaries and anomaly flags.
+
+## Run several analyses
+
+```python
+from ruddy import AnalysisConfig, analyze
+
+result = analyze(
+    dataset,
+    config=AnalysisConfig(
+        enabled_blocks=("profiling", "univariate", "groups", "outliers"),
+        responses=("activity",),
+        groups=("family",),
+        random_state=42,
+    ),
+)
+print(result.summary())
+```
+
+By default only profiling and univariate analysis run. The
+[unified analysis](https://github.com/kren-ai-lab/ruddy/blob/main/docs/UNIFIED_ANALYSIS.md) guide covers the other blocks and
+their parameters.
+
+## Command line
+
+```bash
+ruddy --help
+ruddy analyze bivariate data.csv \
+  --id-column id \
+  --factor family \
+  --output-dir results
+```
+
+The commands are grouped under `inspect`, `analyze`, `model` and `project`.
+`ruddy pipeline` runs several blocks in one go, but only the ones you select.
+The [CLI reference](https://github.com/kren-ai-lab/ruddy/blob/main/docs/CLI_REFERENCE.md) documents every option and the
+files each command writes.
+
+## Design principles
+
+Ruddy tries hard not to make decisions for you:
+
+- Scaling and dimensionality reduction happen only when you ask for them.
+  Missing values aren't imputed, and a string that looks like a number stays a
+  string.
+- Each analysis reports which observations it used. Excluding a row never
+  deletes it from your data.
+- A diagnostic never swaps the test you asked for. If a normality check fails,
+  you still get the test you requested, with the diagnostic next to it.
+- A rank-deficient problem is reported as such, not quietly regularized.
+- Outliers are flagged and left alone.
+- Data and annotations are matched by observation ID, never by row position.
+- Every result records its parameters, input sizes, random seed and the Ruddy
+  version that produced it.
+
+Because of this, read `status` and `reason` next to every estimate. `ok` means
+the quantity was estimated. `degenerate` means the data can't support it, for
+example a constant column in a correlation. `skipped` means a requirement
+wasn't met. Missing values in result tables are Polars nulls, not NaN. See
+[results and provenance](https://github.com/kren-ai-lab/ruddy/blob/main/docs/RESULTS_AND_PROVENANCE.md) for how to read and
+export results.
+
+## Documentation and examples
+
+The [documentation index](https://github.com/kren-ai-lab/ruddy/blob/main/docs/README.md) links all the guides. There are also
+[13 example notebooks](https://github.com/kren-ai-lab/ruddy/blob/main/examples/README.md) written in marimo. To open one:
+
+```bash
+uv sync --all-extras --group examples
+uv run marimo edit examples/01_profiling_univariate.py
+```
+
+## Citing and license
+
+If you use Ruddy in published work, please cite it using
+[`CITATION.cff`](https://github.com/kren-ai-lab/ruddy/blob/main/CITATION.cff), or the "Cite this repository" button on
+GitHub. Ruddy is released under the [MIT license](https://github.com/kren-ai-lab/ruddy/blob/main/LICENSE).