pyFOCI 0.2.0__tar.gz → 0.2.2__tar.gz

pyfoci-0.2.2/.github/workflows/release.yml

@@ -0,0 +1,135 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          pixi-version: v0.68.1
+
+      - name: Build sdist and wheel
+        run: pixi run build
+
+      - name: Check distributions
+        run: pixi run check-dist
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/*
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/pyFOCI
+    permissions:
+      id-token: write  # mandatory for trusted publishing
+
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: [build, publish-testpypi]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyFOCI
+    permissions:
+      id-token: write  # mandatory for trusted publishing
+
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    needs: publish-pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write   # needed to create the release and upload assets
+
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6   # needed so we can read CHANGELOG.md
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+
+      - name: Extract CHANGELOG section for this version
+        id: changelog
+        run: |
+          VERSION="${GITHUB_REF_NAME#v}"
+          # Extract from "## [<version>]" until the next "## [" heading (or EOF).
+          # Tolerates trailing "- date" or no date, and pre-release suffixes.
+          awk -v ver="$VERSION" '
+            BEGIN { found = 0 }
+            /^## \[/ {
+              line = $0
+              sub(/^## \[/, "", line)
+              sub(/\].*$/, "", line)
+              if (line == ver) { found = 1 }
+              else if (found) { exit }
+            }
+            found { print }
+          ' CHANGELOG.md > release_body.md
+
+          if [ -s release_body.md ]; then
+            echo "CHANGELOG section found for $VERSION"
+            echo "body_path=release_body.md" >> "$GITHUB_OUTPUT"
+          else
+            echo "No CHANGELOG section for $VERSION — will use auto-generated notes"
+            rm -f release_body.md
+            echo "use_auto_notes=true" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Create release (from CHANGELOG)
+        if: steps.changelog.outputs.body_path != ''
+        uses: softprops/action-gh-release@v2
+        with:
+          body_path: release_body.md
+          files: dist/*
+
+      - name: Create release (auto-generated notes fallback)
+        if: steps.changelog.outputs.use_auto_notes == 'true'
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: dist/*

pyfoci-0.2.2/CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/2.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.2.2] - 2026-06-17
+
+### Added
+- There is now a changelog, which is also used for the Github releases.
+
+## [0.2.1] - 2026-06-17
+
+### Changed
+- Input features are now N(0,1)-normalized by default.
+  This can be switched off with the new parameter `standardize` by setting it to `Ǹone`.
+
+## [0.2.0] - 2026-06-16
+
+### Added
+- FOCI feature selection with Fuchs Tn formula and radius_neighbors tie breaking.
+
+## [0.1.2] - 2026-05-22
+
+### Added
+- Dummy release to test PyPI publishing.
+

{pyfoci-0.2.0 → pyfoci-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyFOCI
-Version: 0.2.0
+Version: 0.2.2
 Summary: A template for scikit-learn compatible packages.
 Author-email: Robert Pollak <robert.pollak@jku.at>
 License-Expression: BSD-3-Clause

{pyfoci-0.2.0 → pyfoci-0.2.2}/dev-readme.txt

@@ -6,6 +6,7 @@ Testing and merging:
 pixi run -e lint lint
 
 pixi run -e test test
+# Also examine the resulting coverage.xml.
 
 pixi run -e doc build-doc
 

pyfoci-0.2.2/doc/api.rst

@@ -0,0 +1,19 @@
+.. _api:
+
+#############
+API Reference
+#############
+
+This is the full API documentation of the pyFOCI package.
+
+.. currentmodule:: pyFOCI
+
+Transformer
+===========
+
+.. autosummary::
+   :toctree: generated/
+   :template: class.rst
+
+   FOCISelector
+

{pyfoci-0.2.0 → pyfoci-0.2.2}/pyFOCI/_foci.py

@@ -12,7 +12,12 @@ import sklearn.neighbors
 from sklearn.base import BaseEstimator, _fit_context
 from sklearn.feature_selection import SelectorMixin
 from sklearn.utils import check_random_state
-from sklearn.utils._param_validation import Integral, Interval, InvalidParameterError
+from sklearn.utils._param_validation import (
+    Integral,
+    Interval,
+    InvalidParameterError,
+    StrOptions,
+)
 from sklearn.utils.multiclass import type_of_target
 from sklearn.utils.validation import validate_data
 
@@ -103,7 +108,7 @@ def _Tn(X_sub, y_rank, random_state):
 class FOCISelector(SelectorMixin, BaseEstimator):
     """
     Feature selector using hierarchical forward selection based on the
-    Azadkia–Chatterjee T_n coefficient (see reference below).
+    nonlinear Azadkia–Chatterjee T_n coefficient and its Fuchs form (see references).
 
     At each step, among remaining features, we choose the feature that maximizes
     the cumulative T_n on the growing set S_k = S_{k-1} ∪ {j}.
@@ -136,6 +141,11 @@ class FOCISelector(SelectorMixin, BaseEstimator):
           - min_delta == 0 corresponds to stop=TRUE
           - min_delta is None corresponds to stop=FALSE
 
+    standardize : {"normalize", None}, default="normalize"
+        If "normalize", each column of X is standardized to zero mean and unit
+        variance before computing nearest neighbors. If None, X is used as-is.
+        Columns with zero variance are left unchanged.
+
     random_state : int, RandomState instance or None, default=None
         Controls the random tie-breaking among nearest neighbors. Pass an int
         for reproducible results across multiple calls. If None, the global
@@ -158,19 +168,27 @@ class FOCISelector(SelectorMixin, BaseEstimator):
     References
     ----------
     Mona Azadkia and Sourav Chatterjee. A simple measure of conditional dependence.
-    The Annals of Statistics, 49(6):3070–3102, 2021. doi:10.1214/21-AOS2073
+    The Annals of Statistics, 49(6):3070–3102, 2021. https://doi.org/10.1214/21-AOS2073
+
     R FOCI package (reference implementation): https://cran.r-project.org/package=FOCI
+
+    Sebastian Fuchs. Quantifying directed dependence via dimension reduction.
+    Journal of Multivariate Analysis 201 (2024): 105266. https://doi.org/10.1016/j.jmva.2023.105266
     """
 
     _parameter_constraints = {
         "max_features": [None, Interval(Integral, 1, None, closed="left")],
         "min_delta": [None, Interval(Real, None, None, closed="neither")],
+        "standardize": [None, StrOptions({"normalize"})],
         "random_state": ["random_state"],
     }
 
-    def __init__(self, max_features=None, min_delta=0, random_state=None):
+    def __init__(
+        self, max_features=None, min_delta=0, standardize="normalize", random_state=None
+    ):
         self.max_features = max_features
         self.min_delta = min_delta
+        self.standardize = standardize
         self.random_state = random_state
 
     @_fit_context(prefer_skip_nested_validation=True)
@@ -198,6 +216,15 @@ class FOCISelector(SelectorMixin, BaseEstimator):
             self, X, y, accept_sparse=False, y_numeric=True
         )  # asserts finite values
 
+        # Standardization (if requested)
+        if self.standardize == "normalize":
+            X_mean = np.mean(X, axis=0, dtype=float)
+            X_std = np.std(X, axis=0, dtype=float, ddof=0)
+            # Avoid division by zero: leave zero-variance columns unchanged
+            safe_std = X_std.copy()
+            safe_std[safe_std == 0] = 1.0
+            X = (X - X_mean) / safe_std
+
         n_samples, n_features = X.shape
         if n_samples < 2:
             raise InvalidParameterError(

{pyfoci-0.2.0 → pyfoci-0.2.2}/pyFOCI/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.2.2'
+__version_tuple__ = version_tuple = (0, 2, 2)
 
-__commit_id__ = commit_id = 'g2d8096d98'
+__commit_id__ = commit_id = 'g62b06f720'

{pyfoci-0.2.0 → pyfoci-0.2.2}/pyFOCI/tests/test_foci.py

@@ -93,13 +93,6 @@ def test_min_delta_none_ignores_early_stopping_and_selects_up_to_max():
     assert len(selector.Tn_path_) == 3
 
 
-def test_fit_raises_when_y_is_none():
-    X = np.arange(10.0).reshape(-1, 1)
-    sel = FOCISelector()
-    with pytest.raises(ValueError, match="y must be provided"):
-        sel.fit(X, y=None)
-
-
 def test_min_delta_enforces_gap():
     """
     With a positive min_delta, consecutive cumulative Tn values must improve
@@ -118,6 +111,22 @@ def test_min_delta_enforces_gap():
     assert np.all(diffs > min_delta)
 
 
+def test_standardize_none():
+    """
+    standardize=None is also accepted.
+    """
+    X_df, y = make_demo_data(n=100, p=10, seed=0)
+
+    FOCISelector(random_state=0, standardize=None).fit(X_df, y)
+
+
+def test_fit_raises_when_y_is_none():
+    X = np.arange(10.0).reshape(-1, 1)
+    sel = FOCISelector()
+    with pytest.raises(ValueError, match="y must be provided"):
+        sel.fit(X, y=None)
+
+
 @pytest.mark.parametrize("max_features", [0, -1])
 def test_fit_raises_when_max_features_invalid(max_features):
     n, p = 12, 5

{pyfoci-0.2.0 → pyfoci-0.2.2}/pyFOCI.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyFOCI
-Version: 0.2.0
+Version: 0.2.2
 Summary: A template for scikit-learn compatible packages.
 Author-email: Robert Pollak <robert.pollak@jku.at>
 License-Expression: BSD-3-Clause

{pyfoci-0.2.0 → pyfoci-0.2.2}/pyFOCI.egg-info/SOURCES.txt

@@ -2,6 +2,7 @@
 .coveragerc
 .gitignore
 .pre-commit-config.yaml
+CHANGELOG.md
 CITATION.cff
 LICENSE
 README.md

pyfoci-0.2.0/.github/workflows/release.yml

@@ -1,54 +0,0 @@
-name: Release
-
-on:
-  push:
-    tags:
-      - "v*"
-
-jobs:
-  build:
-    name: Build distributions
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v6
-
-      - name: Install Pixi
-        uses: prefix-dev/setup-pixi@v0.9.6
-        with:
-          pixi-version: v0.68.1
-
-      - name: Build sdist and wheel
-        run: pixi run build
-
-      - name: Check distributions
-        run: pixi run check-dist
-
-      - name: Upload build artifacts
-        uses: actions/upload-artifact@v7
-        with:
-          name: dist
-          path: dist/*
-
-  publish-pypi:
-    name: Publish to PyPI
-    needs: build
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/pyFOCI
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-
-    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
-    steps:
-      - name: Download artifacts
-        uses: actions/download-artifact@v8
-        with:
-          name: dist
-          path: dist
-
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-

pyfoci-0.2.0/doc/api.rst

@@ -1,30 +0,0 @@
-.. _api:
-
-#############
-API Reference
-#############
-
-This is an example on how to document the API of your own project.
-
-.. currentmodule:: pyFOCI
-
-Transformer
-===========
-
-.. autosummary::
-   :toctree: generated/
-   :template: class.rst
-
-   FOCISelector
-
-
-Utilities
-=========
-
-.. autosummary::
-   :toctree: generated/
-   :template: functions.rst
-
-     utils.discovery.all_estimators
-     utils.discovery.all_displays
-     utils.discovery.all_functions