seamm-webui 2026.8.8__tar.gz

seamm_webui-2026.8.8/AUTHORS.rst

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+=======
+Credits
+=======
+
+Development Lead
+-----------------
+
+* Paul Saxe <psaxe@molssi.org>
+
+Contributors
+------------
+
+None yet. Why not be the first?

seamm_webui-2026.8.8/HISTORY.rst

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+=======
+History
+=======
+
+2026.8.8 -- Initial release
+    * Web-based SEAMM dashboard: browse projects and jobs, filter the job list by
+      project, and view job status.
+    * Submit new jobs from the browser.
+    * Job management: monitor, kill, and delete jobs.
+    * In-browser file viewer with a directory tree and content pane, including CSV
+      tables, Plotly graphs, and 3D structure viewing (CIF/mmCIF/PDB/SDF) via NGL.
+    * Real user authentication and project-scoped access control.

seamm_webui-2026.8.8/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, MolSSI SEAMM
+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.

seamm_webui-2026.8.8/MANIFEST.in

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

seamm_webui-2026.8.8/PKG-INFO

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+Metadata-Version: 2.4
+Name: seamm-webui
+Version: 2026.8.8
+Summary: SPA-based web dashboard for SEAMM
+Author: Paul Saxe
+License: BSD-3-Clause
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: fastapi
+Requires-Dist: uvicorn[standard]
+Requires-Dist: seamm-datastore
+Requires-Dist: fasteners
+Requires-Dist: itsdangerous
+Requires-Dist: python-multipart
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: httpx; extra == "dev"
+Dynamic: license-file
+
+# seamm_webui
+
+A from-scratch, SPA-based dashboard for SEAMM — built to run **alongside**
+the existing `seamm_dashboard`, not replace it (yet). See
+`~/Work/SEAMM/dashboard-rewrite-plan.md` for the full rationale, architecture
+decisions, and phase plan.
+
+- **Backend:** FastAPI, talking directly to `seamm_datastore` (no
+  `seamm_dashboard`/Flask dependency). Pip-installable; no conda required.
+- **Frontend:** React + Vite + TypeScript, TanStack Query + TanStack Table
+  with true server-side pagination.
+- **Permissions:** stubbed to always-allow for now (single-user Phase 1);
+  see `seamm_webui/auth.py`.
+
+## Backend: development setup
+
+```bash
+cd seamm_webui
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+seamm-webui --root ~/SEAMM --port 8010
+```
+
+## Frontend: development setup
+
+```bash
+cd frontend
+npm install
+npm run dev
+```
+
+## Tests
+
+```bash
+pytest tests/
+```

seamm_webui-2026.8.8/README.md

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+# seamm_webui
+
+A from-scratch, SPA-based dashboard for SEAMM — built to run **alongside**
+the existing `seamm_dashboard`, not replace it (yet). See
+`~/Work/SEAMM/dashboard-rewrite-plan.md` for the full rationale, architecture
+decisions, and phase plan.
+
+- **Backend:** FastAPI, talking directly to `seamm_datastore` (no
+  `seamm_dashboard`/Flask dependency). Pip-installable; no conda required.
+- **Frontend:** React + Vite + TypeScript, TanStack Query + TanStack Table
+  with true server-side pagination.
+- **Permissions:** stubbed to always-allow for now (single-user Phase 1);
+  see `seamm_webui/auth.py`.
+
+## Backend: development setup
+
+```bash
+cd seamm_webui
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+seamm-webui --root ~/SEAMM --port 8010
+```
+
+## Frontend: development setup
+
+```bash
+cd frontend
+npm install
+npm run dev
+```
+
+## Tests
+
+```bash
+pytest tests/
+```

seamm_webui-2026.8.8/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/lammps_step.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/lammps_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/lammps_step"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/lammps_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."

seamm_webui-2026.8.8/docs/api/index.rst

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+API Documentation
+=================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   modules
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

seamm_webui-2026.8.8/docs/authors.rst

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

seamm_webui-2026.8.8/docs/conf.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# seamm_webui documentation build configuration file.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory is
+# relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+# sys.path.insert(0, os.path.abspath('.'))
+
+# Get the project root dir, which is the parent dir of this
+cwd = os.getcwd()
+project_root = os.path.dirname(cwd)
+
+# Insert the project root dir as the first element in the PYTHONPATH.
+# This lets us ensure that the source package is imported, and that its
+# version is used.
+sys.path.insert(0, project_root)
+
+import seamm_webui  # noqa: E402
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+# needs_sphinx = '1.0'
+
+# 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.githubpages',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx_design',
+    'sphinx_copybutton',
+    'sphinx.ext.todo',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'seamm_webui'
+copyright = u"2026, Molecular Sciences Software Institute (MolSSI)"
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = seamm_webui.__version__
+# The full version, including alpha/beta/rc tags.
+release = seamm_webui.__version__
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'default'
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.
+html_theme = "pydata_sphinx_theme"
+
+html_theme_options = {
+    "github_url": "https://github.com/molssi-seamm/seamm_webui",
+    "twitter_url": "https://twitter.com/MolSSI_NSF",
+    "icon_links": [],
+    "logo": {
+        "image_light": "SEAMM logo.png",
+        "image_dark": "SEAMM inverted.png",
+        "text": "seamm_webui",
+        "molssi_light": "molssi_main_logo.png",
+        "molssi_dark": "molssi_main_logo_inverted_white.png",
+    },
+    "show_toc_level": 2,
+    "header_links_before_dropdown": 4,
+    "external_links": [
+        {"name": "SEAMM Documentation", "url": "https://molssi-seamm.github.io"},
+        {"name": "MolSSI", "url": "https://molssi.org"}
+    ],
+    "secondary_sidebar_items": ["page-toc", "sourcelink"],
+    "footer_items": ["molssi_footer"],
+}
+
+# Add any paths that contain custom static files (such as style sheets)
+# here, relative to this directory. They are copied after the builtin
+# static files, so a file named "default.css" will overwrite the builtin
+# "default.css".
+html_static_path = ['_static']
+
+# These paths are either relative to html_static_path
+# or fully qualified paths (eg. https://...)
+html_css_files = [
+    'css/custom.css',
+]
+
+# If true, "Created using Sphinx" is shown in the HTML footer.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer.
+html_show_copyright = False
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'seamm_webuidoc'
+
+
+# -- Options for LaTeX output ------------------------------------------
+
+latex_elements = {}
+
+latex_documents = [
+    ('index', 'seamm_webui.tex',
+     u'seamm_webui Documentation',
+     u'Paul Saxe', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------
+
+man_pages = [
+    ('index', 'seamm_webui',
+     u'seamm_webui Documentation',
+     [u'Paul Saxe'], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+texinfo_documents = [
+    ('index', 'seamm_webui',
+     u'seamm_webui Documentation',
+     u'Paul Saxe',
+     'seamm_webui',
+     'SPA-based web dashboard for SEAMM.',
+     'Miscellaneous'),
+]

seamm_webui-2026.8.8/docs/developer_guide/contributing.rst

@@ -0,0 +1,105 @@
+.. 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/seamm_webui/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
+~~~~~~~~~~~~~~~~~~~~
+
+seamm_webui could always use more documentation, whether as part of the
+official 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/seamm_webui/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 ``seamm_webui`` for local
+development.
+
+1. Fork the ``seamm_webui`` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/seamm_webui.git
+
+3. Install your local copy for development -- a plain virtual environment
+   is enough, no conda required::
+
+    $ cd seamm_webui/
+    $ python -m venv .venv && source .venv/bin/activate
+    $ make install
+    $ cd frontend && npm install
+
+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 the
+   linters and tests, for both the backend and the frontend::
+
+    $ make lint test
+    $ cd frontend && npm run build && npm run lint
+
+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.
+3. The pull request should work for the currently-supported Python
+   versions -- check that CI passes.

seamm_webui-2026.8.8/docs/developer_guide/index.rst

@@ -0,0 +1,18 @@
+Developer Documentation
+=======================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   installation
+   usage
+   contributing
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`