pyFOCI 0.1.2__tar.gz

pyfoci-0.1.2/.coveragerc

@@ -0,0 +1,6 @@
+# Configuration for coverage.py
+
+[run]
+branch = True
+source = pyFOCI
+include = */pyFOCI/*

pyfoci-0.1.2/.github/dependabot.yml

@@ -0,0 +1,18 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions as recommended in SPEC8:
+  # https://github.com/scientific-python/specs/pull/325
+  # At the time of writing, release critical workflows such as
+  # pypa/gh-action-pypi-publish should use hash-based versioning for security
+  # reasons. This strategy may be generalized to all other github actions
+  # in the future.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    reviewers:
+      - "glemaitre"

pyfoci-0.1.2/.github/workflows/deploy-gh-pages.yml

@@ -0,0 +1,37 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  deploy-gh-pages:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pages: write
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+    - uses: prefix-dev/setup-pixi@v0.9.6
+      with:
+        pixi-version: v0.68.1
+        environments: doc
+        frozen: true
+
+    - name: Build documentation
+      run: pixi run -e doc build-doc
+
+    - name: Update the main gh-page website
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      uses: peaceiris/actions-gh-pages@v4.1.0
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./doc/_build/html
+        commit_message: "[ci skip] ${{ github.event.head_commit.message }}"

pyfoci-0.1.2/.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Linter
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          pixi-version: v0.68.1
+          environments: lint
+          frozen: true
+
+      - name: Run linter
+        run: pixi run -e lint lint

pyfoci-0.1.2/.github/workflows/python-app.yml

@@ -0,0 +1,39 @@
+name: Unit Tests
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        environment: [test]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          pixi-version: v0.68.1
+          environments: ${{ matrix.environment }}
+          frozen: true
+
+      - name: Clear pixi cache and rebuild environment
+        shell: bash
+        run: |
+          rm -rf .pixi
+          pixi install
+
+      - name: Run tests
+        run: pixi run -e ${{ matrix.environment }} test
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v6.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: m3dm-jku/pyFOCI

pyfoci-0.1.2/.github/workflows/release.yml

@@ -0,0 +1,76 @@
+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@v5
+        with:
+          name: dist
+          path: dist/*
+
+  publish-testpypi:
+    name: Publish to TestPyPI (pre-releases)
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://test.pypi.org/p/pyFOCI
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v6
+        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
+    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@v6
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+

pyfoci-0.1.2/.gitignore

@@ -0,0 +1,78 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# scikit-learn specific
+doc/_build/
+doc/auto_examples/
+doc/modules/generated/
+doc/datasets/generated/
+
+# Distribution / packaging
+
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+doc/_build/
+doc/generated/
+doc/sg_execution_times.rst
+
+# PyBuilder
+target/
+
+.pixi
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# auto-generated files
+pyFOCI/_version.py

pyfoci-0.1.2/.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.272
+    hooks:
+    -   id: ruff
+        args: ["--fix", "--show-source"]

pyfoci-0.1.2/LICENSE

@@ -0,0 +1,27 @@
+Copyright (c) 2026, Johannes Kepler University Linz
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of pyFOCI nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pyfoci-0.1.2/PKG-INFO

@@ -0,0 +1,42 @@
+Metadata-Version: 2.4
+Name: pyFOCI
+Version: 0.1.2
+Summary: A template for scikit-learn compatible packages.
+Author-email: Robert Pollak <robert.pollak@jku.at>
+Project-URL: Homepage, https://github.com/scikit-learn-contrib/pyFOCI
+Project-URL: Issues, https://github.com/scikit-learn-contrib/pyFOCI/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: numpy
+Dynamic: license-file
+
+pyFOCI - A template for scikit-learn contributions
+============================================================
+
+![tests](https://github.com/m3dm-jku/pyFOCI/actions/workflows/python-app.yml/badge.svg)
+[![codecov](https://codecov.io/gh/m3dm-jku/pyFOCI/graph/badge.svg?token=L0XPWwoPLw)](https://codecov.io/gh/m3dm-jku/pyFOCI)
+![doc](https://github.com/m3dm-jku/pyFOCI/actions/workflows/deploy-gh-pages.yml/badge.svg)
+
+**pyFOCI** is a template project for [scikit-learn](https://scikit-learn.org)
+compatible extensions.
+
+It aids development of estimators that can be used in scikit-learn pipelines and
+(hyper)parameter search, while facilitating testing (including some API compliance),
+documentation, open source development, packaging, and continuous integration.
+
+Refer to the documentation to modify the template for your own scikit-learn
+contribution: https://m3dm-jku.github.io/pyFOCI/
+
+*Thank you for cleanly contributing to the scikit-learn ecosystem!*

pyfoci-0.1.2/README.md

@@ -0,0 +1,18 @@
+pyFOCI - A template for scikit-learn contributions
+============================================================
+
+![tests](https://github.com/m3dm-jku/pyFOCI/actions/workflows/python-app.yml/badge.svg)
+[![codecov](https://codecov.io/gh/m3dm-jku/pyFOCI/graph/badge.svg?token=L0XPWwoPLw)](https://codecov.io/gh/m3dm-jku/pyFOCI)
+![doc](https://github.com/m3dm-jku/pyFOCI/actions/workflows/deploy-gh-pages.yml/badge.svg)
+
+**pyFOCI** is a template project for [scikit-learn](https://scikit-learn.org)
+compatible extensions.
+
+It aids development of estimators that can be used in scikit-learn pipelines and
+(hyper)parameter search, while facilitating testing (including some API compliance),
+documentation, open source development, packaging, and continuous integration.
+
+Refer to the documentation to modify the template for your own scikit-learn
+contribution: https://m3dm-jku.github.io/pyFOCI/
+
+*Thank you for cleanly contributing to the scikit-learn ecosystem!*

pyfoci-0.1.2/doc/Makefile

@@ -0,0 +1,184 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+	-rm -rf auto_examples/
+	-rm -rf generated/*
+	-rm -rf modules/generated/*
+
+html:
+	# These two lines make the build a bit more lengthy, and the
+	# the embedding of images more robust
+	rm -rf $(BUILDDIR)/html/_images
+	#rm -rf _build/doctrees/
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pyFOCI.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyFOCI.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/pyFOCI"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyFOCI"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

pyfoci-0.1.2/doc/_static/css/project-template.css

@@ -0,0 +1,59 @@
+/* Override some aspects of the pydata-sphinx-theme */
+
+:root {
+    /* Use softer blue from bootstrap's default info color */
+    --pst-color-info: 23, 162, 184;
+  }
+
+  table {
+    width: auto;
+    /* Override fit-content which breaks Styler user guide ipynb */
+  }
+
+  .transparent-image {
+    background: none !important;
+    margin-top: 1em;
+    margin-bottom: 1em;
+  }
+
+/* Main index page overview cards */
+
+.intro-card {
+  padding: 30px 10px 20px 10px;
+}
+
+.intro-card .sd-card-img-top {
+  margin: 10px;
+  height: 52px;
+  background: none !important;
+}
+
+.intro-card .sd-card-title {
+  color: var(--pst-color-primary);
+  font-size: var(--pst-font-size-h5);
+  padding: 1rem 0rem 0.5rem 0rem;
+}
+
+.intro-card .sd-card-footer {
+  border: none !important;
+}
+
+.intro-card .sd-card-footer p.sd-card-text {
+  max-width: 220px;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.intro-card .sd-btn-secondary {
+  background-color: #6c757d !important;
+  border-color: #6c757d !important;
+}
+
+.intro-card .sd-btn-secondary:hover {
+  background-color: #5a6268 !important;
+  border-color: #545b62 !important;
+}
+
+.card, .card img {
+  background-color: var(--pst-color-background);
+}