extract-clusters-step 2026.9.17__tar.gz

extract_clusters_step-2026.9.17/AUTHORS.rst

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+Development Team
+----------------
+
+* Paul Saxe <psaxe@molssi.org> (Lead)
+* Why don't you join the team? Become a contributor!

extract_clusters_step-2026.9.17/CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/molssi-seamm/extract_clusters_step/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Extract Clusters Step could always use more documentation, whether as part of the
+official Extract Clusters Step docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/molssi-seamm/extract_clusters_step/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `extract_clusters_step` for local development.
+
+1. Fork the `extract_clusters_step` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/extract_clusters_step.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv extract_clusters_step
+    $ cd extract_clusters_step/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 extract_clusters_step tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+   https://travis-ci.org/molssi-seamm/extract_clusters_step/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+    $ py.test tests.test_extract_clusters_step

extract_clusters_step-2026.9.17/HISTORY.rst

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+=======
+History
+=======
+2026.9.17 -- Initial release of the Extract Clusters step
+    * Extracts n-molecule clusters (trimers, tetramers, ... larger n-mers) from the
+      current, typically periodic, condensed-phase configuration as unwrapped,
+      centred, non-periodic configurations in a new system, e.g. many-body training
+      data and diagnostics for machine-learned force fields.
+    * Clusters are connected subgraphs of a molecular contact graph (molecules are in
+      contact if their contact atoms are within a cutoff, minimum image), so chains,
+      rings and stars all occur; several sizes can be extracted from one frame.
+    * Optional stratification so the set is flat in the radius of gyration or the
+      largest centroid separation, with bin edges from equal quantiles of a pilot
+      sample or given explicitly, and optional balancing over the contact-graph
+      motif.
+    * Provenance on every cluster: unique names ``<frame>_<seed>_<molecules>`` and
+      ``#ExtractClusters#scan`` properties (size, spread, motif, contacts, bin,
+      source molecules) that survive SDF/extxyz export, plus a ``clusters.csv`` per
+      step.

extract_clusters_step-2026.9.17/LICENSE

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+
+BSD 3-Clause License
+
+Copyright (c) 2026, Paul Saxe
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the copyright holder 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.
+

extract_clusters_step-2026.9.17/MANIFEST.in

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+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+include requirements*
+include versioneer.py
+
+recursive-include extract_clusters_step/data *
+recursive-include tests *
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

extract_clusters_step-2026.9.17/PKG-INFO

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+Metadata-Version: 2.4
+Name: extract_clusters_step
+Version: 2026.9.17
+Summary: A SEAMM plugin for A SEAMM plug-in for extracting molecular clusters from a periodic cell of molecules
+Home-page: https://github.com/molssi-seamm/extract_clusters_step
+Author: Paul Saxe
+Author-email: psaxe@molssi.org
+License: BSD-3-Clause
+Keywords: SEAMM,SEAMMplugin,flowchart
+Platform: Linux
+Platform: Mac OS-X
+Platform: Unix
+Platform: Windows
+Classifier: Environment :: Plugins
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: molsystem
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: seamm
+Requires-Dist: seamm-util
+Requires-Dist: seamm-widgets
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: summary
+
+==============================
+SEAMM Extract Clusters Plug-in
+==============================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/extract_clusters_step
+   :target: https://github.com/molssi-seamm/extract_clusters_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/extract_clusters_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/extract_clusters_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/extract_clusters_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/extract_clusters_step
+   :alt: Code Coverage
+
+.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/extract_clusters_step.svg?logo=lgtm&logoWidth=18
+   :target: https://lgtm.com/projects/g/molssi-seamm/extract_clusters_step/context:python
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/extract_clusters_step/workflows/Documentation/badge.svg
+   :target: https://molssi-seamm.github.io/extract_clusters_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://pyup.io/repos/github/molssi-seamm/extract_clusters_step/shield.svg
+   :target: https://pyup.io/repos/github/molssi-seamm/extract_clusters_step/
+   :alt: Updates for Dependencies
+
+.. image:: https://img.shields.io/pypi/v/extract_clusters_step.svg
+   :target: https://pypi.python.org/pypi/extract_clusters_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for extracting molecular clusters (trimers, tetramers, ... larger
+n-mers) from a condensed-phase, typically periodic, configuration as unwrapped,
+non-periodic structures -- e.g. many-body training data and diagnostics for
+machine-learned force fields.
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/extract_clusters_step/index.html
+* Code: https://github.com/molssi-seamm/extract_clusters_step
+
+Features
+--------
+
+* Clusters are **connected subgraphs of a molecular contact graph** (molecules
+  are in contact if their contact atoms are within a cutoff, minimum image), so
+  chains, rings and stars all occur -- not just the most compact cluster.
+* Any cluster size, and several sizes per frame (e.g. ``3, 4``).
+* **Stratification** so the set is flat in a spread coordinate (radius of
+  gyration or largest centroid separation), with bin edges from equal quantiles
+  of a pilot sample or given explicitly; optional balancing over the
+  contact-graph motif.
+* Clusters are unwrapped across the periodic boundary, centred, non-periodic,
+  with molecules and bonds intact.
+* Provenance on every configuration: unique names
+  ``<frame>_<seed>_<m1-m2-...>`` and ``#ExtractClusters#scan`` properties (size,
+  spread, motif, contacts, source molecules) that survive SDF/extxyz export;
+  a ``clusters.csv`` summary per step.
+* Works on any cell (orthorhombic fast path via a periodic KD-tree; exact
+  minimum image otherwise) and on non-periodic sources.
+
+Acknowledgements
+----------------
+
+This package was created with Cookiecutter_ and the
+`molssi-seamm/cookiecutter-seamm-plugin`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award ACI-1547580
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov
+
+
+=======
+History
+=======
+2026.9.17 -- Initial release of the Extract Clusters step
+    * Extracts n-molecule clusters (trimers, tetramers, ... larger n-mers) from the
+      current, typically periodic, condensed-phase configuration as unwrapped,
+      centred, non-periodic configurations in a new system, e.g. many-body training
+      data and diagnostics for machine-learned force fields.
+    * Clusters are connected subgraphs of a molecular contact graph (molecules are in
+      contact if their contact atoms are within a cutoff, minimum image), so chains,
+      rings and stars all occur; several sizes can be extracted from one frame.
+    * Optional stratification so the set is flat in the radius of gyration or the
+      largest centroid separation, with bin edges from equal quantiles of a pilot
+      sample or given explicitly, and optional balancing over the contact-graph
+      motif.
+    * Provenance on every cluster: unique names ``<frame>_<seed>_<molecules>`` and
+      ``#ExtractClusters#scan`` properties (size, spread, motif, contacts, bin,
+      source molecules) that survive SDF/extxyz export, plus a ``clusters.csv`` per
+      step.

extract_clusters_step-2026.9.17/README.rst

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+==============================
+SEAMM Extract Clusters Plug-in
+==============================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/extract_clusters_step
+   :target: https://github.com/molssi-seamm/extract_clusters_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/extract_clusters_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/extract_clusters_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/extract_clusters_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/extract_clusters_step
+   :alt: Code Coverage
+
+.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/extract_clusters_step.svg?logo=lgtm&logoWidth=18
+   :target: https://lgtm.com/projects/g/molssi-seamm/extract_clusters_step/context:python
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/extract_clusters_step/workflows/Documentation/badge.svg
+   :target: https://molssi-seamm.github.io/extract_clusters_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://pyup.io/repos/github/molssi-seamm/extract_clusters_step/shield.svg
+   :target: https://pyup.io/repos/github/molssi-seamm/extract_clusters_step/
+   :alt: Updates for Dependencies
+
+.. image:: https://img.shields.io/pypi/v/extract_clusters_step.svg
+   :target: https://pypi.python.org/pypi/extract_clusters_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for extracting molecular clusters (trimers, tetramers, ... larger
+n-mers) from a condensed-phase, typically periodic, configuration as unwrapped,
+non-periodic structures -- e.g. many-body training data and diagnostics for
+machine-learned force fields.
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/extract_clusters_step/index.html
+* Code: https://github.com/molssi-seamm/extract_clusters_step
+
+Features
+--------
+
+* Clusters are **connected subgraphs of a molecular contact graph** (molecules
+  are in contact if their contact atoms are within a cutoff, minimum image), so
+  chains, rings and stars all occur -- not just the most compact cluster.
+* Any cluster size, and several sizes per frame (e.g. ``3, 4``).
+* **Stratification** so the set is flat in a spread coordinate (radius of
+  gyration or largest centroid separation), with bin edges from equal quantiles
+  of a pilot sample or given explicitly; optional balancing over the
+  contact-graph motif.
+* Clusters are unwrapped across the periodic boundary, centred, non-periodic,
+  with molecules and bonds intact.
+* Provenance on every configuration: unique names
+  ``<frame>_<seed>_<m1-m2-...>`` and ``#ExtractClusters#scan`` properties (size,
+  spread, motif, contacts, source molecules) that survive SDF/extxyz export;
+  a ``clusters.csv`` summary per step.
+* Works on any cell (orthorhombic fast path via a periodic KD-tree; exact
+  minimum image otherwise) and on non-periodic sources.
+
+Acknowledgements
+----------------
+
+This package was created with Cookiecutter_ and the
+`molssi-seamm/cookiecutter-seamm-plugin`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award ACI-1547580
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov

extract_clusters_step-2026.9.17/docs/Makefile

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+# 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)/*
+
+html:
+	$(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/extract_clusters_step.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/extract_clusters_step.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/extract_clusters_step"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/extract_clusters_step"
+	@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."

extract_clusters_step-2026.9.17/docs/authors.rst

@@ -0,0 +1 @@
+.. include:: ../AUTHORS.rst