Pixeldataset docstrings public

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/custom.css

@@ -0,0 +1,39 @@
+/* Wider main content column */
+/* .bd-main .bd-content .bd-article-container {
+    max-width: 75em;
+} */
+
+/* Optional: allow the whole page layout to grow too */
+/* .bd-page-width {
+    max-width: 100rem;
+} */
+
+/* Wrap */
+
+.bd-content h1 {
+    overflow-wrap: anywhere;
+}
+
+.prev-next-area a {
+    overflow-x: visible;
+}
+
+.prev-next-area a .prev-next-info {
+    min-width: 0;
+}
+
+.prev-next-area a p.prev-next-title {
+    overflow-wrap: anywhere;
+}
+
+span.pre {
+    white-space: normal;
+    overflow-wrap: anywhere;
+}
+
+/* Except */
+
+nav.page-toc span.pre {
+    white-space: pre;
+    overflow-wrap: normal;
+}

docs/api/index.rst

@@ -0,0 +1,16 @@
+Python API reference
+====================
+
+This section documents the public Python API for Pixelator.
+
+.. toctree::
+   :maxdepth: 1
+
+   overview
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Complete reference:
+
+   generated/pixelator/index

docs/api/overview.rst

@@ -0,0 +1,18 @@
+API overview
+==============
+
+Primary entry points for PNA analysis.
+
+**Reader**
+
+* :func:`pixelator.read_pna`
+
+
+**Datasets**
+
+.. * :class:`pixelator.pna.pixeldataset.dataset.PixelDataset`
+* :class:`pixelator.pna.pixeldataset.download.DownloadableDatasets`
+
+.. **Configuration**
+
+.. * :class:`pixelator.pna.config.config_instance.pna_config`

docs/cli/index.rst

@@ -0,0 +1,8 @@
+Command-line interface
+======================
+
+This section documents the Pixelator command-line interface.
+
+.. click:: pixelator.cli.main:main_cli
+   :prog: pixelator
+   :nested: full

docs/conf.py

@@ -0,0 +1,120 @@
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+
+project = "Pixelator"
+copyright = "2026 Pixelgen Technologies"
+author = "Pixelgen Technologies"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+nitpicky = True
+nitpick_ignore = [
+    # --- MPX excluded from AutoAPI ---
+    ("py:class", "pixelator.mpx.graph.Graph"),
+    # --- No public intersphinx inventory ---
+    # (see if these can be resolved without ignoring)
+    ("py:class", "duckdb.DuckDBPyConnection"),
+    ("py:class", "faiss.IndexBinary"),
+]
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx_design",
+    "autoapi.extension",
+    "sphinx_click",
+]
+
+autoapi_type = "python"
+autoapi_dirs = ["../src/pixelator"]
+autoapi_root = "api/generated"
+autoapi_add_toctree_entry = False
+
+autoapi_ignore = [
+    "*/pixelator/mpx/*",
+    "*/pixelator/mpx/**/*",
+    "*/pixelator/cli/*",
+    "*/pixelator/cli/**/*",
+    "*/pixelator/pna/cli/*",
+    "*/pixelator/pna/cli/**/*",
+    "*/__pycache__/*",
+    "*/__pycache__/**/*",
+]
+
+# Options for AutoAPI
+autoapi_options = [
+    "members",  # Display children of an object
+    "show-inheritance",  # Display a list of base classes below the class signature
+    "show-module-summary",  # Whether to include autosummary directives in generated module documentation.
+    "undoc-members",  # Display objects that have no docstring
+    "imported-members",  # For objects imported into a package, display objects imported from the same top level package or module.
+    # "special-members",  # Display special objects (eg. __foo__ in Python)
+    # "inherited-members",  # Display children of an object that have been inherited from a base class.
+    # Note the absence of the option private-members
+]
+
+autoapi_member_order = "alphabetical"
+autoapi_python_class_content = "both"
+autoapi_python_use_implicit_namespaces = True
+autoapi_own_page_level = "class"
+autoapi_own_page_level = "function"
+
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- 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_css_files = ["custom.css"]
+
+autodoc_member_order = "alphabetical"
+autodoc_typehints = "signature"
+autodoc_typehints_format = "short"
+autodoc_typehints_description_target = "documented_params"
+
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+
+napoleon_include_init_with_doc = True
+
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = False
+
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_use_ivar = True
+
+napoleon_attr_annotations = True
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
+    "polars": ("https://docs.pola.rs/api/python/stable/", None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "cutadapt": ("https://cutadapt.readthedocs.io/en/stable/", None),
+    "dnaio": ("https://dnaio.readthedocs.io/en/stable/", None),
+    "pyarrow": ("https://arrow.apache.org/docs/", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+    "click": ("https://click.palletsprojects.com/en/stable/", None),
+    "packaging": ("https://packaging.pypa.io/en/stable/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+}

docs/index.rst

@@ -0,0 +1,54 @@
+Pixelator documentation
+=======================
+
+Pixelgen Technologies provides Pixelator, a suite of open source
+software solutions that empower users working with
+`Molecular Pixelation (MPX) <https://software.pixelgen.com/common/glossary/#mpx>`_
+and `Proximity Network (PNA) <https://software.pixelgen.com/common/glossary/#pna>`_
+assays in data processing and analysis.
+
+Pixelator can be used in two ways: as a data processing pipeline
+(nf-core/pixelator) and as a programming library (pixelator).
+The pipeline nf-core/pixelator consists of several steps and will produce
+ready-to-analyze outputs from your initial FASTQ sequencing libraries.
+Usage of Pixelator as a programming library is covered in the API reference and in
+our data analysis sections for MPX and PNA (section for PNA is linked below as "Tutorials").
+
+
+.. grid:: 1 1 2 2
+   :gutter: 2
+
+   .. grid-item-card:: Python API reference
+      :link: api/index
+      :link-type: doc
+
+      Browse Python modules, classes, functions, and methods.
+
+   .. grid-item-card:: Command-line interface
+      :link: cli/index
+      :link-type: doc
+
+      Browse Pixelator command-line interface commands, options, and arguments.
+
+   .. grid-item-card:: Pixelgen software site
+      :link: https://software.pixelgen.com/
+      :link-type: url
+
+      See the Pixelgen software site for information about
+      software, analysis, and datasets.
+
+      .. .. grid-item-card:: Tutorials
+      .. :link: https://software.pixelgen.com/pna-analysis/introduction/
+      .. :link-type: url
+
+      .. See tutorials and code examples for getting started
+      .. with Proximity Network Assay (PNA) data analysis
+      .. using Pixelator as a Python library.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :hidden:
+
+   api/index
+   cli/index

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pyproject.toml

@@ -91,6 +91,14 @@ dev = [
     "line-profiler>=5.0.2",
     "ipykernel>=7.2.0",
 ]
+docs = [
+    "pydata-sphinx-theme>=0.19.0",
+    "sphinx>=8.1.3",
+    "sphinx-autoapi>=3.8.0",
+    "sphinx-autobuild>=2024.10.3",
+    "sphinx-click>=6.2.0",
+    "sphinx-design>=0.6.1",
+]
 
 
 [project.scripts]

src/pixelator/pna/pixeldataset/__init__.py

@@ -69,14 +69,19 @@
 
 
 def read(paths: Path | list[Path] | str | list[str]) -> PNAPixelDataset:
-    """Read a PNAPixelDataset from one or more provided .pxl file(s).
+    """Read data from one or more ``.pxl`` files.
 
     Args:
-        path: path to the file to read
-        paths: Paths.
+        paths: One or more paths to ``.pxl`` files. A single path or a list of
+            paths may be passed. Each path may be a ``pathlib.Path`` or ``str``.
 
     Returns:
-        an instance of `PNAPixelDataset`
+        The data from the ``.pxl`` file(s).
+
+    Raises:
+        IOException: If a file is not a DuckDB database file.
+        ValueError: If a file is not a valid ``.pxl`` file, if a sample name cannot be determined from file metadata.
+        FileNotFoundError: If any path does not exist on disk.
     """
     if not paths:
         raise ValueError(