saiph 2.0.3__tar.gz → 2.0.4__tar.gz

saiph-2.0.4/.github/workflows/pr-title.yml

@@ -0,0 +1,17 @@
+name: "Check PR title"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v4
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

saiph-2.0.4/.github/workflows/release.yml

@@ -0,0 +1,42 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - '*.*.*'
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Build project for distribution
+        run: uv build
+
+      - name: Create Release
+        uses: ncipollo/release-action@v1
+        with:
+          artifacts: "dist/*"
+          token: ${{ secrets.GITHUB_TOKEN }}
+          draft: false
+
+      - name: Publish to PyPI
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
+        run: uv publish

saiph-2.0.4/.github/workflows/saiph-ci.yml

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+name: "Check PR ci"
+
+on: pull_request
+
+jobs:
+  saiph-ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [
+          "3.11", 
+          "3.12", 
+          "3.13",
+        ]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: false
+
+    - name: Install just
+      uses: extractions/setup-just@v2
+
+    - name: Install dependencies
+      run: uv sync --extra matplotlib --group dev --group doc
+
+    - name: Typecheck
+      run: just typecheck
+
+    - name: Lint
+      run: just lint
+
+    - name: Build docs
+      run: just docs
+
+    - name: Run tests
+      run: just test

saiph-2.0.4/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytest-benchmark
+.benchmarks/
+
+# fil-profile results
+fil-result/
+
+# benchmark .csv
+tmp/
+
+# uv
+.venv/

saiph-2.0.4/.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+---
+repos:
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v2.20.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]

saiph-2.0.4/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

saiph-2.0.4/.tool-versions

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+python 3.13.5

saiph-2.0.4/CONTRIBUTING.md

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+# Contributing to Saiph
+
+## Releasing a new version
+
+Depending on the version bump you want to do, you'll run
+
+```bash
+uv run python release.py --bump-type {patch, minor, major} # choose one
+```
+
+This will bump the version, commit it, and generate a tag and push it.
+
+A Github action will then build that version and push it on `pypi`.

saiph-2.0.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: saiph
+Version: 2.0.4
+Summary: A projection package
+Author-email: Octopize <help@octopize.io>
+License: Apache-2.0
+License-File: LICENSE
+Requires-Python: <3.14,>=3.11
+Requires-Dist: msgspec<0.20,>=0.19
+Requires-Dist: numpy<2,>=1
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: pydantic<3,>=2
+Requires-Dist: scikit-learn<2,>=1.0
+Requires-Dist: scipy<2,>=1.14
+Requires-Dist: toolz<2,>=1
+Provides-Extra: matplotlib
+Requires-Dist: matplotlib<4,>=3.5.2; extra == 'matplotlib'

saiph-2.0.4/README.md

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+# Saiph
+
+Saiph not only is the sixth-brightest star in the constellation of Orion (https://en.wikipedia.org/wiki/Saiph), but also a package enabling to project data. 
+
+Projection fitting is done through PCA, MCA or FAMD. 
+
+The main module imputes which one should be used depending on the given data, but each module can be used on his own.
+
+The package provides a visualization module for correlation circles, contributions and explained variance.
+
+See the documentation for more details and a tutorial.
+
+## Install
+
+```bash
+pip install saiph
+```
+
+## Development
+
+```bash
+uv sync --extra matplotlib --group dev --group doc
+```
+
+If you want to install dev dependencies, make sure you have a rust compiler installed:
+
+```bash
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+just install
+```
+
+## Documentation
+
+To get the documentation, clone the repo then
+
+```bash
+just install docs docs-open
+```
+
+## License
+
+Saiph is under MIT license.

saiph-2.0.4/bin/create_csv.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+import csv
+import os
+import random
+import sys
+from pathlib import Path
+from typing import Any
+
+import typer
+from faker import Faker
+from tqdm import tqdm  # type: ignore
+
+fake = Faker("en_US")
+CITIES = [
+    "Lyon",
+    "Nantes",
+    "Paris",
+    "Marseille",
+    "Cholet",
+    "Rochefourchat",
+    "Ornes",
+    "Senconac",
+    "Caunette-sur-Lauquet",
+    "Cherbourg",
+]
+CITIES_WEIGHTS = (20, 10, 50, 10, 4, 1, 1, 1, 1, 2)
+
+
+def eprint(*args: Any, **kwargs: dict[str, Any]) -> None:
+    print(*args, file=sys.stderr, **kwargs)  # noqa: T201 # type: ignore
+
+
+def human_size(size: int, units: list[str] = ["bytes", "KB", "MB", "GB", "TB", "PB", "EB"]) -> str:
+    """Return a human readable string representation of bytes."""
+    return (
+        str(size) + units[0]
+        if size < 1024 or len(units) == 1
+        else human_size(size >> 10, units[1:])
+    )
+
+
+def get_city() -> str:
+    return random.choices(CITIES, weights=CITIES_WEIGHTS)[0]  # noqa: S311
+
+
+def get_row(dimension_count: int = 3) -> dict[str, Any]:
+    r = {
+        "latitude": fake.latitude(),
+        "longitude": fake.longitude(),
+        "city": get_city(),
+    }
+    r.update({f"city_{i}": get_city() for i in range(dimension_count - 3)})
+
+    return r
+
+
+def main(
+    outfile: Path,
+    row_count: int = 1000,
+    dimension_count: int = 3,
+) -> int:
+    """Generate CSV with fake data."""
+    eprint(f"generating {row_count} fake rows")
+
+    if dimension_count < 3:
+        raise ValueError(f"Expected dimension_count >= 3, got {dimension_count} instead")
+
+    header = list(get_row(dimension_count).keys())
+    with open(outfile, "w") as f:
+        writer = csv.DictWriter(f, fieldnames=header)
+        writer.writeheader()
+
+        for i in tqdm(range(row_count)):
+            writer.writerow(get_row(dimension_count))
+
+    if Path(outfile.name).exists():
+        size = os.path.getsize(outfile.name)
+        eprint(f"Wrote {human_size(size)} file")
+
+    return 0
+
+
+if __name__ == "__main__":
+    typer.run(main)

saiph-2.0.4/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import sys
+from pathlib import Path
+from typing import List
+
+sys.path.insert(0, str(Path(__file__).parent.parent.parent))
+
+# import saiph  # noqa: E402
+
+# -- Project information -----------------------------------------------------
+
+project = "Saiph"
+copyright = "2024, Octopize"
+author = "Octopize"
+
+# The full version, including alpha/beta/rc tags
+release = "1.5.6"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx_gallery.gen_gallery",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns: List[str] = ["requirements.txt"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path: List[str] = []
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".txt": "markdown",
+    ".md": "markdown",
+}
+
+sphinx_gallery_conf = {
+    "examples_dirs": "source/example",  # path to your example scripts
+    "gallery_dirs": "build/examples",  # path to where to save gallery generated output
+}

saiph-2.0.4/docs/index.rst

@@ -0,0 +1,20 @@
+.. Saiph documentation master file, created by
+   sphinx-quickstart on Fri Sep 24 09:52:44 2021.
+
+Welcome to Saiph's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   build/examples/plot_example
+   source/reference
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

saiph-2.0.4/docs/requirements.txt

@@ -0,0 +1,2 @@
+matplotlib==3.9.1
+sphinx-gallery==0.19.0

saiph-2.0.4/docs/source/example/README.rst

@@ -0,0 +1,4 @@
+Tutorial
+================
+
+This is a gallery showcasing the different plots that `saiph.visualization` can generate.

saiph-2.0.4/docs/source/example/plot_example.py

@@ -0,0 +1,67 @@
+"""
+Tutorial
+=========================
+
+This example shows how saiph works.
+"""
+
+import pandas as pd
+
+import saiph
+from saiph.visualization import plot_circle
+
+# %%
+# Fit the model
+# ------------------------
+
+df = pd.read_csv("../../../tests/fixtures/iris.csv")
+
+coord, model = saiph.fit_transform(df, nf=5)
+print(coord.head())
+# %%
+# Project individuals
+# ------------------------
+#
+saiph.visualization.plot_projections(model, df, (0, 1))
+# %%
+# Get statistics about the projection
+# ------------------------
+#
+model = saiph.stats(model, df)
+print(model.cos2)
+
+# %%
+# Correlation circle
+# ------------------------
+#
+plot_circle(model=model)
+
+# %%
+# Variable contributions
+# ------------------------
+#
+
+print(model.contributions)
+# %%
+# ------------------------
+#
+saiph.visualization.plot_var_contribution(
+    model.contributions["Dim. 1"].to_numpy(), model.contributions.index.to_numpy()
+)
+
+
+# %%
+# Explained variance
+# ------------------------
+#
+print(model.explained_var)
+
+# %%
+# ------------------------
+#
+print(model.explained_var_ratio)
+
+# %%
+# ------------------------
+#
+saiph.visualization.plot_explained_var(model)

saiph-2.0.4/docs/source/reference.rst

@@ -0,0 +1,56 @@
+API Reference
+=============
+
+saiph
+-----
+
+.. automodule:: saiph
+   :members:
+
+saiph.models
+------------
+
+.. automodule:: saiph.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+saiph.famd
+----------
+
+.. automodule:: saiph.reduction.famd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+saiph.mca
+---------
+
+.. automodule:: saiph.reduction.mca
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+saiph.pca
+---------
+
+.. automodule:: saiph.reduction.pca
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+saiph.svd
+---------
+
+.. automodule:: saiph.reduction.utils.svd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+saiph.visualization
+-------------------
+
+.. automodule:: saiph.visualization
+   :members:
+   :undoc-members:
+   :show-inheritance: