diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..deb922a --- /dev/null +++ b/.coveragerc @@ -0,0 +1,6 @@ +# Configuration for coverage.py + +[run] +branch = True +source = fsvm +include = */fsvm/* diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..b3340cd --- /dev/null +++ b/.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" diff --git a/.github/workflows/deploy-gh-pages.yml b/.github/workflows/deploy-gh-pages.yml new file mode 100644 index 0000000..32b819f --- /dev/null +++ b/.github/workflows/deploy-gh-pages.yml @@ -0,0 +1,37 @@ +name: Documentation + +on: + push: + branches: + - main + pull_request: + branches: + - main + +permissions: + contents: write + +jobs: + deploy-gh-pages: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.23.0 + 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@v4.0.0 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./doc/_build/html + commit_message: "[ci skip] ${{ github.event.head_commit.message }}" diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..30f5766 --- /dev/null +++ b/.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@v4 + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.23.0 + environments: lint + frozen: true + + - name: Run linter + run: pixi run -e lint lint diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml new file mode 100644 index 0000000..c63c696 --- /dev/null +++ b/.github/workflows/python-app.yml @@ -0,0 +1,33 @@ +name: Unit Tests + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + build: + strategy: + matrix: + os: [windows-latest, ubuntu-latest, macos-latest, macos-12] + environment: [test] + runs-on: ${{ matrix.os }} + steps: + - uses: actions/checkout@v4 + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.23.0 + environments: ${{ matrix.environment }} + frozen: true + + - name: Run tests + run: pixi run -e ${{ matrix.environment }} test + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v4.5.0 + with: + token: ${{ secrets.CODECOV_TOKEN }} + slug: balins/fsvm diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..872ec44 --- /dev/null +++ b/.gitignore @@ -0,0 +1,78 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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 +fsvm/_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..64c11db --- /dev/null +++ b/.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"] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..8d1dca1 --- /dev/null +++ b/LICENSE @@ -0,0 +1,27 @@ +Copyright (c) 2016, Vighnesh Birodkar and scikit-learn-contrib contributors +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 fsvm 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. diff --git a/README.md b/README.md new file mode 100644 index 0000000..8100b50 --- /dev/null +++ b/README.md @@ -0,0 +1,18 @@ +project-template - A template for scikit-learn contributions +============================================================ + +![tests](https://github.com/balins/fsvm/actions/workflows/python-app.yml/badge.svg) +[![codecov](https://codecov.io/gh/balins/fsvm/graph/badge.svg?token=L0XPWwoPLw)](https://codecov.io/gh/balins/fsvm) +![doc](https://github.com/balins/fsvm/actions/workflows/deploy-gh-pages.yml/badge.svg) + +**project-template** 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://contrib.scikit-learn.org/project-template + +*Thank you for cleanly contributing to the scikit-learn ecosystem!* diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..21f9f5c --- /dev/null +++ b/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 ' where 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/fsvm.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/fsvm.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/fsvm" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/fsvm" + @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." diff --git a/doc/_static/css/project-template.css b/doc/_static/css/project-template.css new file mode 100644 index 0000000..62b416b --- /dev/null +++ b/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); +} diff --git a/doc/_static/img/index_api.svg b/doc/_static/img/index_api.svg new file mode 100644 index 0000000..69f7ba1 --- /dev/null +++ b/doc/_static/img/index_api.svg @@ -0,0 +1,97 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + diff --git a/doc/_static/img/index_examples.svg b/doc/_static/img/index_examples.svg new file mode 100644 index 0000000..de3d902 --- /dev/null +++ b/doc/_static/img/index_examples.svg @@ -0,0 +1,76 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + + + + diff --git a/doc/_static/img/index_getting_started.svg b/doc/_static/img/index_getting_started.svg new file mode 100644 index 0000000..2d36622 --- /dev/null +++ b/doc/_static/img/index_getting_started.svg @@ -0,0 +1,66 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + diff --git a/doc/_static/img/index_user_guide.svg b/doc/_static/img/index_user_guide.svg new file mode 100644 index 0000000..bd17053 --- /dev/null +++ b/doc/_static/img/index_user_guide.svg @@ -0,0 +1,67 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + diff --git a/doc/_static/img/logo.png b/doc/_static/img/logo.png new file mode 100644 index 0000000..7806f2a Binary files /dev/null and b/doc/_static/img/logo.png differ diff --git a/doc/_static/js/copybutton.js b/doc/_static/js/copybutton.js new file mode 100644 index 0000000..d87f569 --- /dev/null +++ b/doc/_static/js/copybutton.js @@ -0,0 +1,63 @@ +$(document).ready(function() { + /* Add a [>>>] button on the top-right corner of code samples to hide + * the >>> and ... prompts and the output and thus make the code + * copyable. */ + var div = $('.highlight-python .highlight,' + + '.highlight-python3 .highlight,' + + '.highlight-pycon .highlight,' + + '.highlight-default .highlight') + var pre = div.find('pre'); + + // get the styles from the current theme + pre.parent().parent().css('position', 'relative'); + var hide_text = 'Hide the prompts and output'; + var show_text = 'Show the prompts and output'; + var border_width = pre.css('border-top-width'); + var border_style = pre.css('border-top-style'); + var border_color = pre.css('border-top-color'); + var button_styles = { + 'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0', + 'border-color': border_color, 'border-style': border_style, + 'border-width': border_width, 'color': border_color, 'text-size': '75%', + 'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em', + 'border-radius': '0 3px 0 0' + } + + // create and add the button to all the code blocks that contain >>> + div.each(function(index) { + var jthis = $(this); + if (jthis.find('.gp').length > 0) { + var button = $('>>>'); + button.css(button_styles) + button.attr('title', hide_text); + button.data('hidden', 'false'); + jthis.prepend(button); + } + // tracebacks (.gt) contain bare text elements that need to be + // wrapped in a span to work with .nextUntil() (see later) + jthis.find('pre:has(.gt)').contents().filter(function() { + return ((this.nodeType == 3) && (this.data.trim().length > 0)); + }).wrap(''); + }); + + // define the behavior of the button when it's clicked + $('.copybutton').click(function(e){ + e.preventDefault(); + var button = $(this); + if (button.data('hidden') === 'false') { + // hide the code output + button.parent().find('.go, .gp, .gt').hide(); + button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden'); + button.css('text-decoration', 'line-through'); + button.attr('title', show_text); + button.data('hidden', 'true'); + } else { + // show the code output + button.parent().find('.go, .gp, .gt').show(); + button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible'); + button.css('text-decoration', 'none'); + button.attr('title', hide_text); + button.data('hidden', 'false'); + } + }); +}); diff --git a/doc/_templates/class.rst b/doc/_templates/class.rst new file mode 100644 index 0000000..3253677 --- /dev/null +++ b/doc/_templates/class.rst @@ -0,0 +1,26 @@ +{{objname}} +{{ underline }}============== + +.. currentmodule:: {{ module }} + +.. autoclass:: {{ objname }} + + {% block methods %} + + {% if methods %} + .. rubric:: Methods + + .. autosummary:: + {% for item in methods %} + {% if '__init__' not in item %} + ~{{ name }}.{{ item }} + {% endif %} + {%- endfor %} + {% endif %} + {% endblock %} + +.. include:: {{module}}.{{objname}}.examples + +.. raw:: html + +
diff --git a/doc/_templates/function.rst b/doc/_templates/function.rst new file mode 100644 index 0000000..3d70980 --- /dev/null +++ b/doc/_templates/function.rst @@ -0,0 +1,12 @@ +{{objname}} +{{ underline }}==================== + +.. currentmodule:: {{ module }} + +.. autofunction:: {{ objname }} + +.. include:: {{module}}.{{objname}}.examples + +.. raw:: html + +
diff --git a/doc/_templates/numpydoc_docstring.py b/doc/_templates/numpydoc_docstring.py new file mode 100644 index 0000000..db4cdfa --- /dev/null +++ b/doc/_templates/numpydoc_docstring.py @@ -0,0 +1,16 @@ +{{index}} +{{summary}} +{{extended_summary}} +{{parameters}} +{{returns}} +{{yields}} +{{other_parameters}} +{{attributes}} +{{raises}} +{{warns}} +{{warnings}} +{{see_also}} +{{notes}} +{{references}} +{{examples}} +{{methods}} \ No newline at end of file diff --git a/doc/_templates/sidebar-search-bs.html b/doc/_templates/sidebar-search-bs.html new file mode 100644 index 0000000..60e2773 --- /dev/null +++ b/doc/_templates/sidebar-search-bs.html @@ -0,0 +1,14 @@ +
+ + {% if logo %} + + {% endif %} {% if docstitle %} + + {% endif %} + +
diff --git a/doc/api.rst b/doc/api.rst new file mode 100644 index 0000000..768ab5c --- /dev/null +++ b/doc/api.rst @@ -0,0 +1,48 @@ +.. _api: + +############# +API Reference +############# + +This is an example on how to document the API of your own project. + +.. currentmodule:: fsvm + +Estimator +========= + +.. autosummary:: + :toctree: generated/ + :template: class.rst + + TemplateEstimator + +Transformer +=========== + +.. autosummary:: + :toctree: generated/ + :template: class.rst + + TemplateTransformer + +Predictor +========= + +.. autosummary:: + :toctree: generated/ + :template: class.rst + + TemplateClassifier + + +Utilities +========= + +.. autosummary:: + :toctree: generated/ + :template: functions.rst + + utils.discovery.all_estimators + utils.discovery.all_displays + utils.discovery.all_functions diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 0000000..a536cae --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,114 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +import os +import sys + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information +from importlib.metadata import version as get_version + +project = "Scikit-learn Project Template" +copyright = "2016, V. Birodkar" +author = "V. Birodkar" +release = get_version('fsvm') +version = ".".join(release.split(".")[:3]) + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#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.autosummary", + "sphinx.ext.intersphinx", + "sphinx_design", + "sphinx-prompt", + "sphinx_gallery.gen_gallery", + "numpydoc", +] + +templates_path = ["_templates"] +exclude_patterns = ["_build", "_templates", "Thumbs.db", ".DS_Store"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +default_role = "literal" + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = "pydata_sphinx_theme" +html_static_path = ["_static"] +html_style = "css/fsvm.css" +html_logo = "_static/img/logo.png" +# html_favicon = "_static/img/favicon.ico" +html_css_files = [ + "css/fsvm.css", +] +html_sidebars = { + "quick_start": [], + "user_guide": [], + "auto_examples/index": [], +} + +html_theme_options = { + "external_links": [], + "github_url": "https://github.com/balins/fsvm", + # "twitter_url": "https://twitter.com/pandas_dev", + "use_edit_page_button": True, + "show_toc_level": 1, + # "navbar_align": "right", # For testing that the navbar items align properly +} + +html_context = { + "github_user": "scikit-learn-contrib", + "github_repo": "fsvm", + "github_version": "master", + "doc_path": "doc", +} + +# -- Options for autodoc ------------------------------------------------------ + +autodoc_default_options = { + "members": True, + "inherited-members": True, +} + +# generate autosummary even if no references +autosummary_generate = True + +# -- Options for numpydoc ----------------------------------------------------- + +# this is needed for some reason... +# see https://github.com/numpy/numpydoc/issues/69 +numpydoc_show_class_members = False + +# -- Options for intersphinx -------------------------------------------------- + +intersphinx_mapping = { + "python": ("https://docs.python.org/{.major}".format(sys.version_info), None), + "numpy": ("https://numpy.org/doc/stable", None), + "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), + "scikit-learn": ("https://scikit-learn.org/stable", None), + "matplotlib": ("https://matplotlib.org/", None), + "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), + "joblib": ("https://joblib.readthedocs.io/en/latest/", None), +} + +# -- Options for sphinx-gallery ----------------------------------------------- + +# Generate the plot for the gallery +plot_gallery = True + +sphinx_gallery_conf = { + "doc_module": "fsvm", + "backreferences_dir": os.path.join("generated"), + "examples_dirs": "../examples", + "gallery_dirs": "auto_examples", + "reference_url": {"fsvm": None}, +} diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 0000000..2c66c59 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,108 @@ +.. project-template documentation master file, created by + sphinx-quickstart on Mon Jan 18 14:44:12 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +:notoc: + +############################################# +Project template for `scikit-learn` extension +############################################# + +**Date**: |today| **Version**: |version| + +**Useful links**: +`Source Repository `__ | +`Issues & Ideas `__ | + +This is the documentation for the `project-template` to help at extending +`scikit-learn`. It provides some information on how to build your own custom +`scikit-learn` compatible estimators as well as a template to package them. + + +.. grid:: 1 2 2 2 + :gutter: 4 + :padding: 2 2 0 0 + :class-container: sd-text-center + + .. grid-item-card:: Getting started + :img-top: _static/img/index_getting_started.svg + :class-card: intro-card + :shadow: md + + Information regarding this template and how to modify it for your own project. + + +++ + + .. button-ref:: quick_start + :ref-type: ref + :click-parent: + :color: secondary + :expand: + + To the getting started guideline + + .. grid-item-card:: User guide + :img-top: _static/img/index_user_guide.svg + :class-card: intro-card + :shadow: md + + An example of narrative documentation. Here, we will explain how to create your + own `scikit-learn` estimator. + + +++ + + .. button-ref:: user_guide + :ref-type: ref + :click-parent: + :color: secondary + :expand: + + To the user guide + + .. grid-item-card:: API reference + :img-top: _static/img/index_api.svg + :class-card: intro-card + :shadow: md + + An example of API documentation. This is an example how to use `sphinx` to + automatically generate reference API page. + + +++ + + .. button-ref:: api + :ref-type: ref + :click-parent: + :color: secondary + :expand: + + To the reference guide + + .. grid-item-card:: Examples + :img-top: _static/img/index_examples.svg + :class-card: intro-card + :shadow: md + + A set of examples. It complements the User Guide and it is the right place to + show how to use your compatible estimator. + + +++ + + .. button-ref:: general_examples + :ref-type: ref + :click-parent: + :color: secondary + :expand: + + To the gallery of examples + + +.. toctree:: + :maxdepth: 3 + :hidden: + :titlesonly: + + quick_start + user_guide + api + auto_examples/index diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 0000000..273dc9c --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,242 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ 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. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over 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 + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + + +%SPHINXBUILD% 2> nul +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\fsvm.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\fsvm.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdf" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdfja" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf-ja + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +if "%1" == "xml" ( + %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The XML files are in %BUILDDIR%/xml. + goto end +) + +if "%1" == "pseudoxml" ( + %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. + goto end +) + +:end diff --git a/doc/quick_start.rst b/doc/quick_start.rst new file mode 100644 index 0000000..b624f09 --- /dev/null +++ b/doc/quick_start.rst @@ -0,0 +1,181 @@ +.. _quick_start: + +############### +Getting started +############### + +This package serves as a skeleton package aiding at developing compatible +scikit-learn contribution. + +Creating your own scikit-learn contribution package +=================================================== + +Download and setup your repository +---------------------------------- + +To create your package, you need to clone the ``project-template`` repository: + +.. prompt:: bash $ + + git clone https://github.com/scikit-learn-contrib/project-template.git + +Before to reinitialize your git repository, you need to make the following +changes. Replace all occurrences of ``skltemplate``, ``sklearn-template``, or +``project-template`` with the name of you own project. You can find all the +occurrences using the following command: + +.. prompt:: bash $ + + git grep skltemplate + git grep sklearn-template + git grep project-template + +To remove the history of the template package, you need to remove the `.git` +directory: + +.. prompt:: bash $ + + rm -rf .git + +Then, you need to initialize your new git repository: + +.. prompt:: bash $ + + git init + git add . + git commit -m 'Initial commit' + +Finally, you create an online repository on GitHub and push your code online: + +.. prompt:: bash $ + + git remote add origin https://github.com/your_remote/your_contribution.git + git push origin main + +Develop your own scikit-learn estimators +---------------------------------------- + +.. _check_estimator: http://scikit-learn.org/stable/modules/generated/sklearn.utils.estimator_checks.check_estimator.html#sklearn.utils.estimator_checks.check_estimator +.. _`Contributor's Guide`: http://scikit-learn.org/stable/developers/ +.. _PEP8: https://www.python.org/dev/peps/pep-0008/ +.. _PEP257: https://www.python.org/dev/peps/pep-0257/ +.. _NumPyDoc: https://github.com/numpy/numpydoc +.. _doctests: https://docs.python.org/3/library/doctest.html + +You can modify the source files as you want. However, your custom estimators +need to pass the check_estimator_ test to be scikit-learn compatible. We provide a +file called `test_common.py` where we run the checks on our custom estimators. + +You can refer to the :ref:`User Guide ` to help you create a compatible +scikit-learn estimator. + +In any case, developers should endeavor to adhere to scikit-learn's +`Contributor's Guide`_ which promotes the use of: + +* algorithm-specific unit tests, in addition to ``check_estimator``'s common + tests; +* PEP8_-compliant code; +* a clearly documented API using NumpyDoc_ and PEP257_-compliant docstrings; +* references to relevant scientific literature in standard citation formats; +* doctests_ to provide succinct usage examples; +* standalone examples to illustrate the usage, model visualisation, and + benefits/benchmarks of particular algorithms; +* efficient code when the need for optimization is supported by benchmarks. + +Managing your local and continuous integration environment +---------------------------------------------------------- + +Here, we set up for you an repository that uses `pixi`. The `pixi.toml` file defines +the packages and tasks to be run that we will present below. You can refer to the +following documentation link to install `pixi`: https://pixi.sh/latest/#installation + +Once done, you can refer to the documentation to get started but we provide the +command below to interact with the main task requested to develop your package. + +Edit the documentation +---------------------- + +.. _Sphinx: http://www.sphinx-doc.org/en/stable/ + +The documentation is created using Sphinx_. In addition, the examples are +created using ``sphinx-gallery``. Therefore, to generate locally the +documentation, you can leverage the following `pixi` task: + +.. prompt:: bash $ + + pixi run build-doc + +The documentation is made of: + +* a home page, ``doc/index.rst``; +* an API documentation, ``doc/api.rst`` in which you should add all public + objects for which the docstring should be exposed publicly. +* a User Guide documentation, ``doc/user_guide.rst``, containing the narrative + documentation of your package, to give as much intuition as possible to your + users. +* examples which are created in the `examples/` folder. Each example + illustrates some usage of the package. the example file name should start by + `plot_*.py`. + +Local testing +------------- + +To run the tests locally, you can use the following command: + +.. prompt:: bash $ + + pixi run test + +It will use `pytest` under the hood to run the package tests. + +In addition, you have a linter task to check the code consistency in terms of style: + +.. prompt:: bash $ + + pixi run lint + +Activating the development environment +-------------------------------------- + +In the case that you don't want to use the `pixi run` commands and directly interact +with the usual python tools, you can activate the development environment: + +.. prompt:: bash $ + + pixi shell -e dev + +This will activate an environment containing the dependencies needed to run the linters, +tests, and build the documentation. So for instance, you can run the tests with: + +.. prompt:: bash $ + + pytest -vsl skltemplate + +In this case, you can even use pre-commit before using git. You will need to initialize +it with: + +.. prompt:: bash $ + + pre-commit install + +Setup the continuous integration +-------------------------------- + +The project template already contains configuration files of the continuous +integration system. It leverage the above pixi commands and run on GitHub Actions. +In short, it will: + +* run the tests on the different platforms (Linux, MacOS, Windows) and upload the + coverage report to codecov.io; +* check the code style (linter); +* build the documentation and deploy it automatically on GitHub Pages. + +Publish your package +==================== + +.. _PyPi: https://packaging.python.org/tutorials/packaging-projects/ +.. _conda-forge: https://conda-forge.org/ + +You can make your package available through PyPi_ and conda-forge_. Refer to +the associated documentation to be able to upload your packages such that +it will be installable with ``pip`` and ``conda``. diff --git a/doc/user_guide.rst b/doc/user_guide.rst new file mode 100644 index 0000000..527d4c6 --- /dev/null +++ b/doc/user_guide.rst @@ -0,0 +1,180 @@ +.. title:: User guide : contents + +.. _user_guide: + +========== +User Guide +========== + +Estimator +--------- + +The central piece of transformer, regressor, and classifier is +:class:`sklearn.base.BaseEstimator`. All estimators in scikit-learn are derived +from this class. In more details, this base class enables to set and get +parameters of the estimator. It can be imported as:: + + >>> from sklearn.base import BaseEstimator + +Once imported, you can create a class which inherate from this base class:: + + >>> class MyOwnEstimator(BaseEstimator): + ... pass + +Transformer +----------- + +Transformers are scikit-learn estimators which implement a ``transform`` method. +The use case is the following: + +* at ``fit``, some parameters can be learned from ``X`` and ``y``; +* at ``transform``, `X` will be transformed, using the parameters learned + during ``fit``. + +.. _mixin: https://en.wikipedia.org/wiki/Mixin + +In addition, scikit-learn provides a +mixin_, i.e. :class:`sklearn.base.TransformerMixin`, which +implement the combination of ``fit`` and ``transform`` called ``fit_transform``. + +One can import the mixin class as:: + + >>> from sklearn.base import TransformerMixin + +Therefore, when creating a transformer, you need to create a class which +inherits from both :class:`sklearn.base.BaseEstimator` and +:class:`sklearn.base.TransformerMixin`. The scikit-learn API imposed ``fit`` to +**return ``self``**. The reason is that it allows to pipeline ``fit`` and +``transform`` imposed by the :class:`sklearn.base.TransformerMixin`. The +``fit`` method is expected to have ``X`` and ``y`` as inputs. Note that +``transform`` takes only ``X`` as input and is expected to return the +transformed version of ``X``:: + + >>> class MyOwnTransformer(TransformerMixin, BaseEstimator): + ... def fit(self, X, y=None): + ... return self + ... def transform(self, X): + ... return X + +We build a basic example to show that our :class:`MyOwnTransformer` is working +within a scikit-learn ``pipeline``:: + + >>> from sklearn.datasets import load_iris + >>> from sklearn.pipeline import make_pipeline + >>> from sklearn.linear_model import LogisticRegression + >>> X, y = load_iris(return_X_y=True) + >>> pipe = make_pipeline(MyOwnTransformer(), + ... LogisticRegression(random_state=10, + ... solver='lbfgs')) + >>> pipe.fit(X, y) # doctest: +ELLIPSIS + Pipeline(...) + >>> pipe.predict(X) # doctest: +ELLIPSIS + array([...]) + +Predictor +--------- + +Regressor +~~~~~~~~~ + +Similarly, regressors are scikit-learn estimators which implement a ``predict`` +method. The use case is the following: + +* at ``fit``, some parameters can be learned from ``X`` and ``y``; +* at ``predict``, predictions will be computed using ``X`` using the parameters + learned during ``fit``. + +In addition, scikit-learn provides a mixin_, i.e. +:class:`sklearn.base.RegressorMixin`, which implements the ``score`` method +which computes the :math:`R^2` score of the predictions. + +One can import the mixin as:: + + >>> from sklearn.base import RegressorMixin + +Therefore, we create a regressor, :class:`MyOwnRegressor` which inherits from +both :class:`sklearn.base.BaseEstimator` and +:class:`sklearn.base.RegressorMixin`. The method ``fit`` gets ``X`` and ``y`` +as input and should return ``self``. It should implement the ``predict`` +function which should output the predictions of your regressor:: + + >>> import numpy as np + >>> class MyOwnRegressor(RegressorMixin, BaseEstimator): + ... def fit(self, X, y): + ... return self + ... def predict(self, X): + ... return np.mean(X, axis=1) + +We illustrate that this regressor is working within a scikit-learn pipeline:: + + >>> from sklearn.datasets import load_diabetes + >>> X, y = load_diabetes(return_X_y=True) + >>> pipe = make_pipeline(MyOwnTransformer(), MyOwnRegressor()) + >>> pipe.fit(X, y) # doctest: +ELLIPSIS + Pipeline(...) + >>> pipe.predict(X) # doctest: +ELLIPSIS + array([...]) + +Since we inherit from the :class:`sklearn.base.RegressorMixin`, we can call +the ``score`` method which will return the :math:`R^2` score:: + + >>> pipe.score(X, y) # doctest: +ELLIPSIS + -3.9... + +Classifier +~~~~~~~~~~ + +Similarly to regressors, classifiers implement ``predict``. In addition, they +output the probabilities of the prediction using the ``predict_proba`` method: + +* at ``fit``, some parameters can be learned from ``X`` and ``y``; +* at ``predict``, predictions will be computed using ``X`` using the parameters + learned during ``fit``. The output corresponds to the predicted class for each sample; +* ``predict_proba`` will give a 2D matrix where each column corresponds to the + class and each entry will be the probability of the associated class. + +In addition, scikit-learn provides a mixin, i.e. +:class:`sklearn.base.ClassifierMixin`, which implements the ``score`` method +which computes the accuracy score of the predictions. + +One can import this mixin as:: + + >>> from sklearn.base import ClassifierMixin + +Therefore, we create a classifier, :class:`MyOwnClassifier` which inherits +from both :class:`slearn.base.BaseEstimator` and +:class:`sklearn.base.ClassifierMixin`. The method ``fit`` gets ``X`` and ``y`` +as input and should return ``self``. It should implement the ``predict`` +function which should output the class inferred by the classifier. +``predict_proba`` will output some probabilities instead:: + + >>> class MyOwnClassifier(ClassifierMixin, BaseEstimator): + ... def fit(self, X, y): + ... self.classes_ = np.unique(y) + ... return self + ... def predict(self, X): + ... return np.random.randint(0, self.classes_.size, + ... size=X.shape[0]) + ... def predict_proba(self, X): + ... pred = np.random.rand(X.shape[0], self.classes_.size) + ... return pred / np.sum(pred, axis=1)[:, np.newaxis] + +We illustrate that this regressor is working within a scikit-learn pipeline:: + + >>> X, y = load_iris(return_X_y=True) + >>> pipe = make_pipeline(MyOwnTransformer(), MyOwnClassifier()) + >>> pipe.fit(X, y) # doctest: +ELLIPSIS + Pipeline(...) + +Then, you can call ``predict`` and ``predict_proba``:: + + >>> pipe.predict(X) # doctest: +ELLIPSIS + array([...]) + >>> pipe.predict_proba(X) # doctest: +ELLIPSIS + array([...]) + +Since our classifier inherits from :class:`sklearn.base.ClassifierMixin`, we +can compute the accuracy by calling the ``score`` method:: + + >>> pipe.score(X, y) # doctest: +ELLIPSIS + 0... diff --git a/examples/README.txt b/examples/README.txt new file mode 100644 index 0000000..6a1d992 --- /dev/null +++ b/examples/README.txt @@ -0,0 +1,6 @@ +.. _general_examples: + +Example Gallery +=============== + +Introductory examples. diff --git a/examples/plot_classifier.py b/examples/plot_classifier.py new file mode 100644 index 0000000..2baacde --- /dev/null +++ b/examples/plot_classifier.py @@ -0,0 +1,41 @@ +""" +============================ +Plotting Template Classifier +============================ + +An example plot of :class:`fsvm.template.TemplateClassifier` +""" + +# %% +# Train our classifier on very simple dataset +from fsvm import TemplateClassifier + +X = [[0, 0], [1, 1]] +y = [0, 1] +clf = TemplateClassifier().fit(X, y) + +# %% +# Create a test dataset +import numpy as np + +rng = np.random.RandomState(13) +X_test = rng.rand(500, 2) + +# %% +# Use scikit-learn to display the decision boundary +from sklearn.inspection import DecisionBoundaryDisplay + +disp = DecisionBoundaryDisplay.from_estimator(clf, X_test) +disp.ax_.scatter( + X_test[:, 0], + X_test[:, 1], + c=clf.predict(X_test), + s=20, + edgecolors="k", + linewidths=0.5, +) +disp.ax_.set( + xlabel="Feature 1", + ylabel="Feature 2", + title="Template Classifier Decision Boundary", +) diff --git a/examples/plot_template.py b/examples/plot_template.py new file mode 100644 index 0000000..5b40416 --- /dev/null +++ b/examples/plot_template.py @@ -0,0 +1,19 @@ +""" +=========================== +Plotting Template Estimator +=========================== + +An example plot of :class:`fsvm.template.TemplateEstimator` +""" + +import numpy as np +from matplotlib import pyplot as plt + +from fsvm import TemplateEstimator + +X = np.arange(100).reshape(100, 1) +y = np.zeros((100,)) +estimator = TemplateEstimator() +estimator.fit(X, y) +plt.plot(estimator.predict(X)) +plt.show() diff --git a/examples/plot_transformer.py b/examples/plot_transformer.py new file mode 100644 index 0000000..40c03c7 --- /dev/null +++ b/examples/plot_transformer.py @@ -0,0 +1,28 @@ +""" +============================= +Plotting Template Transformer +============================= + +An example plot of :class:`fsvm.template.TemplateTransformer` +""" + +import numpy as np +from matplotlib import pyplot as plt + +from fsvm import TemplateTransformer + +X = np.arange(50, dtype=np.float64).reshape(-1, 1) +X /= 50 +estimator = TemplateTransformer() +X_transformed = estimator.fit_transform(X) + +plt.plot(X.flatten(), label="Original Data") +plt.plot(X_transformed.flatten(), label="Transformed Data") +plt.title("Plots of original and transformed data") + +plt.legend(loc="best") +plt.grid(True) +plt.xlabel("Index") +plt.ylabel("Value of Data") + +plt.show() diff --git a/fsvm/__init__.py b/fsvm/__init__.py new file mode 100644 index 0000000..66806e5 --- /dev/null +++ b/fsvm/__init__.py @@ -0,0 +1,12 @@ +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + +from ._template import TemplateClassifier, TemplateEstimator, TemplateTransformer +from ._version import __version__ + +__all__ = [ + "TemplateEstimator", + "TemplateClassifier", + "TemplateTransformer", + "__version__", +] diff --git a/fsvm/_template.py b/fsvm/_template.py new file mode 100644 index 0000000..4e2aeb3 --- /dev/null +++ b/fsvm/_template.py @@ -0,0 +1,308 @@ +""" +This is a module to be used as a reference for building other modules +""" + +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + +import numpy as np +from sklearn.base import BaseEstimator, ClassifierMixin, TransformerMixin, _fit_context +from sklearn.metrics import euclidean_distances +from sklearn.utils.multiclass import check_classification_targets +from sklearn.utils.validation import check_is_fitted + + +class TemplateEstimator(BaseEstimator): + """A template estimator to be used as a reference implementation. + + For more information regarding how to build your own estimator, read more + in the :ref:`User Guide `. + + Parameters + ---------- + demo_param : str, default='demo_param' + A parameter used for demonstration of how to pass and store parameters. + + Attributes + ---------- + is_fitted_ : bool + A boolean indicating whether the estimator has been fitted. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + Examples + -------- + >>> from fsvm import TemplateEstimator + >>> import numpy as np + >>> X = np.arange(100).reshape(100, 1) + >>> y = np.zeros((100, )) + >>> estimator = TemplateEstimator() + >>> estimator.fit(X, y) + TemplateEstimator() + """ + + # This is a dictionary allowing to define the type of parameters. + # It used to validate parameter within the `_fit_context` decorator. + _parameter_constraints = { + "demo_param": [str], + } + + def __init__(self, demo_param="demo_param"): + self.demo_param = demo_param + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y): + """A reference implementation of a fitting function. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + The training input samples. + + y : array-like, shape (n_samples,) or (n_samples, n_outputs) + The target values (class labels in classification, real numbers in + regression). + + Returns + ------- + self : object + Returns self. + """ + # `_validate_data` is defined in the `BaseEstimator` class. + # It allows to: + # - run different checks on the input data; + # - define some attributes associated to the input data: `n_features_in_` and + # `feature_names_in_`. + X, y = self._validate_data(X, y, accept_sparse=True) + self.is_fitted_ = True + # `fit` should always return `self` + return self + + def predict(self, X): + """A reference implementation of a predicting function. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + The training input samples. + + Returns + ------- + y : ndarray, shape (n_samples,) + Returns an array of ones. + """ + # Check if fit had been called + check_is_fitted(self) + # We need to set reset=False because we don't want to overwrite `n_features_in_` + # `feature_names_in_` but only check that the shape is consistent. + X = self._validate_data(X, accept_sparse=True, reset=False) + return np.ones(X.shape[0], dtype=np.int64) + + +# Note that the mixin class should always be on the left of `BaseEstimator` to ensure +# the MRO works as expected. +class TemplateClassifier(ClassifierMixin, BaseEstimator): + """An example classifier which implements a 1-NN algorithm. + + For more information regarding how to build your own classifier, read more + in the :ref:`User Guide `. + + Parameters + ---------- + demo_param : str, default='demo' + A parameter used for demonstation of how to pass and store paramters. + + Attributes + ---------- + X_ : ndarray, shape (n_samples, n_features) + The input passed during :meth:`fit`. + + y_ : ndarray, shape (n_samples,) + The labels passed during :meth:`fit`. + + classes_ : ndarray, shape (n_classes,) + The classes seen at :meth:`fit`. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + Examples + -------- + >>> from sklearn.datasets import load_iris + >>> from fsvm import TemplateClassifier + >>> X, y = load_iris(return_X_y=True) + >>> clf = TemplateClassifier().fit(X, y) + >>> clf.predict(X) + array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, + 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, + 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) + """ + + # This is a dictionary allowing to define the type of parameters. + # It used to validate parameter within the `_fit_context` decorator. + _parameter_constraints = { + "demo_param": [str], + } + + def __init__(self, demo_param="demo"): + self.demo_param = demo_param + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y): + """A reference implementation of a fitting function for a classifier. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + The training input samples. + + y : array-like, shape (n_samples,) + The target values. An array of int. + + Returns + ------- + self : object + Returns self. + """ + # `_validate_data` is defined in the `BaseEstimator` class. + # It allows to: + # - run different checks on the input data; + # - define some attributes associated to the input data: `n_features_in_` and + # `feature_names_in_`. + X, y = self._validate_data(X, y) + # We need to make sure that we have a classification task + check_classification_targets(y) + + # classifier should always store the classes seen during `fit` + self.classes_ = np.unique(y) + + # Store the training data to predict later + self.X_ = X + self.y_ = y + + # Return the classifier + return self + + def predict(self, X): + """A reference implementation of a prediction for a classifier. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + The input samples. + + Returns + ------- + y : ndarray, shape (n_samples,) + The label for each sample is the label of the closest sample + seen during fit. + """ + # Check if fit had been called + check_is_fitted(self) + + # Input validation + # We need to set reset=False because we don't want to overwrite `n_features_in_` + # `feature_names_in_` but only check that the shape is consistent. + X = self._validate_data(X, reset=False) + + closest = np.argmin(euclidean_distances(X, self.X_), axis=1) + return self.y_[closest] + + +# Note that the mixin class should always be on the left of `BaseEstimator` to ensure +# the MRO works as expected. +class TemplateTransformer(TransformerMixin, BaseEstimator): + """An example transformer that returns the element-wise square root. + + For more information regarding how to build your own transformer, read more + in the :ref:`User Guide `. + + Parameters + ---------- + demo_param : str, default='demo' + A parameter used for demonstation of how to pass and store paramters. + + Attributes + ---------- + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + """ + + # This is a dictionary allowing to define the type of parameters. + # It used to validate parameter within the `_fit_context` decorator. + _parameter_constraints = { + "demo_param": [str], + } + + def __init__(self, demo_param="demo"): + self.demo_param = demo_param + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """A reference implementation of a fitting function for a transformer. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + The training input samples. + + y : None + There is no need of a target in a transformer, yet the pipeline API + requires this parameter. + + Returns + ------- + self : object + Returns self. + """ + X = self._validate_data(X, accept_sparse=True) + + # Return the transformer + return self + + def transform(self, X): + """A reference implementation of a transform function. + + Parameters + ---------- + X : {array-like, sparse-matrix}, shape (n_samples, n_features) + The input samples. + + Returns + ------- + X_transformed : array, shape (n_samples, n_features) + The array containing the element-wise square roots of the values + in ``X``. + """ + # Since this is a stateless transformer, we should not call `check_is_fitted`. + # Common test will check for this particularly. + + # Input validation + # We need to set reset=False because we don't want to overwrite `n_features_in_` + # `feature_names_in_` but only check that the shape is consistent. + X = self._validate_data(X, accept_sparse=True, reset=False) + return np.sqrt(X) + + def _more_tags(self): + # This is a quick example to show the tags API:\ + # https://scikit-learn.org/dev/developers/develop.html#estimator-tags + # Here, our transformer does not do any operation in `fit` and only validate + # the parameters. Thus, it is stateless. + return {"stateless": True} diff --git a/fsvm/tests/__init__.py b/fsvm/tests/__init__.py new file mode 100644 index 0000000..52e3f96 --- /dev/null +++ b/fsvm/tests/__init__.py @@ -0,0 +1,2 @@ +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause diff --git a/fsvm/tests/test_common.py b/fsvm/tests/test_common.py new file mode 100644 index 0000000..a41df65 --- /dev/null +++ b/fsvm/tests/test_common.py @@ -0,0 +1,16 @@ +"""This file shows how to write test based on the scikit-learn common tests.""" + +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + +from sklearn.utils.estimator_checks import parametrize_with_checks + +from fsvm.utils.discovery import all_estimators + + +# parametrize_with_checks allows to get a generator of check that is more fine-grained +# than check_estimator +@parametrize_with_checks([est() for _, est in all_estimators()]) +def test_estimators(estimator, check, request): + """Check the compatibility with scikit-learn API""" + check(estimator) diff --git a/fsvm/tests/test_template.py b/fsvm/tests/test_template.py new file mode 100644 index 0000000..68846ee --- /dev/null +++ b/fsvm/tests/test_template.py @@ -0,0 +1,60 @@ +"""This file will just show how to write tests for the template classes.""" + +import numpy as np +import pytest +from sklearn.datasets import load_iris +from sklearn.utils._testing import assert_allclose, assert_array_equal + +from fsvm import TemplateClassifier, TemplateEstimator, TemplateTransformer + +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + + +@pytest.fixture +def data(): + return load_iris(return_X_y=True) + + +def test_template_estimator(data): + """Check the internals and behaviour of `TemplateEstimator`.""" + est = TemplateEstimator() + assert est.demo_param == "demo_param" + + est.fit(*data) + assert hasattr(est, "is_fitted_") + + X = data[0] + y_pred = est.predict(X) + assert_array_equal(y_pred, np.ones(X.shape[0], dtype=np.int64)) + + +def test_template_transformer(data): + """Check the internals and behaviour of `TemplateTransformer`.""" + X, y = data + trans = TemplateTransformer() + assert trans.demo_param == "demo" + + trans.fit(X) + assert trans.n_features_in_ == X.shape[1] + + X_trans = trans.transform(X) + assert_allclose(X_trans, np.sqrt(X)) + + X_trans = trans.fit_transform(X) + assert_allclose(X_trans, np.sqrt(X)) + + +def test_template_classifier(data): + """Check the internals and behaviour of `TemplateClassifier`.""" + X, y = data + clf = TemplateClassifier() + assert clf.demo_param == "demo" + + clf.fit(X, y) + assert hasattr(clf, "classes_") + assert hasattr(clf, "X_") + assert hasattr(clf, "y_") + + y_pred = clf.predict(X) + assert y_pred.shape == (X.shape[0],) diff --git a/fsvm/utils/__init__.py b/fsvm/utils/__init__.py new file mode 100644 index 0000000..52e3f96 --- /dev/null +++ b/fsvm/utils/__init__.py @@ -0,0 +1,2 @@ +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause diff --git a/fsvm/utils/discovery.py b/fsvm/utils/discovery.py new file mode 100644 index 0000000..d722a2c --- /dev/null +++ b/fsvm/utils/discovery.py @@ -0,0 +1,211 @@ +""" +The :mod:`fsvm.utils.discovery` module includes utilities to discover +objects (i.e. estimators, displays, functions) from the `fsvm` package. +""" + +# Adapted from scikit-learn +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + +import inspect +import pkgutil +from importlib import import_module +from operator import itemgetter +from pathlib import Path + +from sklearn.base import ( + BaseEstimator, + ClassifierMixin, + ClusterMixin, + RegressorMixin, + TransformerMixin, +) +from sklearn.utils._testing import ignore_warnings + +_MODULE_TO_IGNORE = {"tests"} + + +def all_estimators(type_filter=None): + """Get a list of all estimators from `fsvm`. + + This function crawls the module and gets all classes that inherit + from `BaseEstimator`. Classes that are defined in test-modules are not + included. + + Parameters + ---------- + type_filter : {"classifier", "regressor", "cluster", "transformer"} \ + or list of such str, default=None + Which kind of estimators should be returned. If None, no filter is + applied and all estimators are returned. Possible values are + 'classifier', 'regressor', 'cluster' and 'transformer' to get + estimators only of these specific types, or a list of these to + get the estimators that fit at least one of the types. + + Returns + ------- + estimators : list of tuples + List of (name, class), where ``name`` is the class name as string + and ``class`` is the actual type of the class. + + Examples + -------- + >>> from fsvm.utils.discovery import all_estimators + >>> estimators = all_estimators() + >>> type(estimators) + + """ + + def is_abstract(c): + if not (hasattr(c, "__abstractmethods__")): + return False + if not len(c.__abstractmethods__): + return False + return True + + all_classes = [] + root = str(Path(__file__).parent.parent) # fsvm package + # Ignore deprecation warnings triggered at import time and from walking + # packages + with ignore_warnings(category=FutureWarning): + for _, module_name, _ in pkgutil.walk_packages(path=[root], prefix="fsvm."): + module_parts = module_name.split(".") + if any(part in _MODULE_TO_IGNORE for part in module_parts): + continue + module = import_module(module_name) + classes = inspect.getmembers(module, inspect.isclass) + classes = [ + (name, est_cls) for name, est_cls in classes if not name.startswith("_") + ] + + all_classes.extend(classes) + + all_classes = set(all_classes) + + estimators = [ + c + for c in all_classes + if (issubclass(c[1], BaseEstimator) and c[0] != "BaseEstimator") + ] + # get rid of abstract base classes + estimators = [c for c in estimators if not is_abstract(c[1])] + + if type_filter is not None: + if not isinstance(type_filter, list): + type_filter = [type_filter] + else: + type_filter = list(type_filter) # copy + filtered_estimators = [] + filters = { + "classifier": ClassifierMixin, + "regressor": RegressorMixin, + "transformer": TransformerMixin, + "cluster": ClusterMixin, + } + for name, mixin in filters.items(): + if name in type_filter: + type_filter.remove(name) + filtered_estimators.extend( + [est for est in estimators if issubclass(est[1], mixin)] + ) + estimators = filtered_estimators + if type_filter: + raise ValueError( + "Parameter type_filter must be 'classifier', " + "'regressor', 'transformer', 'cluster' or " + "None, got" + f" {repr(type_filter)}." + ) + + # drop duplicates, sort for reproducibility + # itemgetter is used to ensure the sort does not extend to the 2nd item of + # the tuple + return sorted(set(estimators), key=itemgetter(0)) + + +def all_displays(): + """Get a list of all displays from `fsvm`. + + Returns + ------- + displays : list of tuples + List of (name, class), where ``name`` is the display class name as + string and ``class`` is the actual type of the class. + + Examples + -------- + >>> from fsvm.utils.discovery import all_displays + >>> displays = all_displays() + """ + all_classes = [] + root = str(Path(__file__).parent.parent) # fsvm package + # Ignore deprecation warnings triggered at import time and from walking + # packages + with ignore_warnings(category=FutureWarning): + for _, module_name, _ in pkgutil.walk_packages(path=[root], prefix="fsvm."): + module_parts = module_name.split(".") + if any(part in _MODULE_TO_IGNORE for part in module_parts): + continue + module = import_module(module_name) + classes = inspect.getmembers(module, inspect.isclass) + classes = [ + (name, display_class) + for name, display_class in classes + if not name.startswith("_") and name.endswith("Display") + ] + all_classes.extend(classes) + + return sorted(set(all_classes), key=itemgetter(0)) + + +def _is_checked_function(item): + if not inspect.isfunction(item): + return False + + if item.__name__.startswith("_"): + return False + + mod = item.__module__ + if not mod.startswith("fsvm.") or mod.endswith("estimator_checks"): + return False + + return True + + +def all_functions(): + """Get a list of all functions from `fsvm`. + + Returns + ------- + functions : list of tuples + List of (name, function), where ``name`` is the function name as + string and ``function`` is the actual function. + + Examples + -------- + >>> from fsvm.utils.discovery import all_functions + >>> functions = all_functions() + """ + all_functions = [] + root = str(Path(__file__).parent.parent) # fsvm package + # Ignore deprecation warnings triggered at import time and from walking + # packages + with ignore_warnings(category=FutureWarning): + for _, module_name, _ in pkgutil.walk_packages(path=[root], prefix="fsvm."): + module_parts = module_name.split(".") + if any(part in _MODULE_TO_IGNORE for part in module_parts): + continue + + module = import_module(module_name) + functions = inspect.getmembers(module, _is_checked_function) + functions = [ + (func.__name__, func) + for name, func in functions + if not name.startswith("_") + ] + all_functions.extend(functions) + + # drop duplicates, sort for reproducibility + # itemgetter is used to ensure the sort does not extend to the 2nd item of + # the tuple + return sorted(set(all_functions), key=itemgetter(0)) diff --git a/fsvm/utils/tests/__init__.py b/fsvm/utils/tests/__init__.py new file mode 100644 index 0000000..52e3f96 --- /dev/null +++ b/fsvm/utils/tests/__init__.py @@ -0,0 +1,2 @@ +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause diff --git a/fsvm/utils/tests/test_discovery.py b/fsvm/utils/tests/test_discovery.py new file mode 100644 index 0000000..91aae51 --- /dev/null +++ b/fsvm/utils/tests/test_discovery.py @@ -0,0 +1,31 @@ +# Authors: scikit-learn-contrib developers +# License: BSD 3 clause + +import pytest + +from fsvm.utils.discovery import all_displays, all_estimators, all_functions + + +def test_all_estimators(): + estimators = all_estimators() + assert len(estimators) == 3 + + estimators = all_estimators(type_filter="classifier") + assert len(estimators) == 1 + + estimators = all_estimators(type_filter=["classifier", "transformer"]) + assert len(estimators) == 2 + + err_msg = "Parameter type_filter must be" + with pytest.raises(ValueError, match=err_msg): + all_estimators(type_filter="xxxx") + + +def test_all_displays(): + displays = all_displays() + assert len(displays) == 0 + + +def test_all_functions(): + functions = all_functions() + assert len(functions) == 3 diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..328e96e --- /dev/null +++ b/pixi.lock @@ -0,0 +1,11013 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda + - conda: 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hb46c0d2_0 + subdir: osx-arm64 + url: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda + sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09 + md5: d96942c06c3e84bfcc5efb038724a7fd + depends: + - __osx >=11.0 + - libzlib >=1.2.13,<2.0.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 405089 + timestamp: 1714723101397 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..fb3ddab --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,135 @@ +[build-system] +requires = ["setuptools>=64", "setuptools_scm[toml]>=8"] +build-backend = "setuptools.build_meta" + +[project] +name = "fsvm" +dynamic = ["version"] +authors = [ + { name="Jakub Balinski", email="j.balinski@student.uj.edu.pl" }, +] +description = "A Fuzzy Support Vector Machine implementation." +readme = "README.md" +requires-python = ">=3.9" +dependencies = [ + "scikit-learn>=1.4.2", +] +classifiers = [ + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "License :: OSI Approved :: BSD License", + "Operating System :: POSIX", + "Operating System :: Unix", + "Operating System :: MacOS", + "Operating System :: Microsoft :: Windows", +] + +[project.urls] +Homepage = "https://github.com/balins/fsvm" +Issues = "https://github.com/balins/fsvm/issues" + +[tool.setuptools_scm] +version_file = "fsvm/_version.py" + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] + +[tool.pixi.dependencies] +python = ">=3.9" +scikit-learn = ">=1.4.2" + +[tool.pixi.pypi-dependencies] +fsvm = { path=".", editable=true } + +[tool.pixi.feature.lint.dependencies] +# The version below should be aligned with the one of `.pre-commit-config.yaml` +black = "23.3.0" +pre-commit = "3.7.1" +ruff = "0.4.2" + +[tool.pixi.feature.lint.tasks] +black = { cmd = "black --check --diff fsvm && black --check --diff examples" } +ruff = { cmd = "ruff check --output-format=full fsvm && ruff check --output-format=full examples" } +lint = { depends_on = ["black", "ruff"] } +format = { cmd = "ruff format fsvm && ruff format examples" } + +[tool.pixi.feature.test.dependencies] +pytest = "*" +pytest-cov = "*" + +[tool.pixi.feature.test.tasks] +test = { cmd = "pytest -vsl --cov=fsvm --cov-report=xml fsvm" } + +[tool.pixi.feature.doc.dependencies] +matplotlib = "*" +numpydoc = "*" +pydata-sphinx-theme = "*" +setuptools-scm = ">=8" # needed for the versioning +sphinx = "*" +sphinx-design = "*" +sphinx-gallery = "*" +sphinx-prompt = "*" + +[tool.pixi.feature.doc.tasks] +build-doc = { cmd = "make html", cwd = "doc" } +clean-doc = { cmd = "rm -rf _build", cwd = "doc" } + +[tool.pixi.environments] +doc = ["doc"] +lint = ["lint"] +test = ["test"] +dev = ["doc", "lint", "test"] + +[tool.black] +line-length = 88 +target_version = ['py38', 'py39', 'py310'] +preview = true +exclude = ''' +/( + \.eggs # exclude a few common directories in the + | \.git # root of the project + | \.vscode +)/ +''' +force-exclude = "fsvm/_version.py" + +[tool.ruff] +# max line length for black +line-length = 88 +target-version = "py38" +exclude=[ + ".git", + "__pycache__", + "dist", + "doc/_build", + "doc/auto_examples", + "build", + "fsvm/_version.py", +] + +[tool.ruff.lint] +# all rules can be found here: https://beta.ruff.rs/docs/rules/ +select = ["E", "F", "W", "I"] +ignore=[ + # space before : (needed for how black formats slicing) + "E203", + # do not assign a lambda expression, use a def + "E731", + # do not use variables named 'l', 'O', or 'I' + "E741", +] + +[tool.ruff.lint.per-file-ignores] +# It's fine not to put the import at the top of the file in the examples +# folder. +"examples/*"=["E402"] +"doc/conf.py"=["E402"] +"doc/_templates/numpydoc_docstring.py"=["F821", "W292"] + +[tool.pytest.ini_options] +addopts = "--doctest-modules --color=yes" +doctest_optionflags = "NORMALIZE_WHITESPACE"