diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d4bb2cbb --- /dev/null +++ b/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) diff --git a/docs/_static/custom.css b/docs/_static/custom.css new file mode 100644 index 00000000..83f9ae46 --- /dev/null +++ b/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; +} diff --git a/docs/api/index.rst b/docs/api/index.rst new file mode 100644 index 00000000..bcffcee7 --- /dev/null +++ b/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 diff --git a/docs/api/overview.rst b/docs/api/overview.rst new file mode 100644 index 00000000..d470965d --- /dev/null +++ b/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` diff --git a/docs/cli/index.rst b/docs/cli/index.rst new file mode 100644 index 00000000..cc2fa3d9 --- /dev/null +++ b/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 diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..614bbfbf --- /dev/null +++ b/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), +} diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..ff5cdd00 --- /dev/null +++ b/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) `_ +and `Proximity Network (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 diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..32bb2452 --- /dev/null +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index 29241650..70cfb8f9 100644 --- a/pyproject.toml +++ b/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] diff --git a/src/pixelator/pna/pixeldataset/__init__.py b/src/pixelator/pna/pixeldataset/__init__.py index 1de75e20..e84b5f85 100644 --- a/src/pixelator/pna/pixeldataset/__init__.py +++ b/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( diff --git a/src/pixelator/pna/pixeldataset/download.py b/src/pixelator/pna/pixeldataset/download.py index 7fceb48e..c8dfb500 100644 --- a/src/pixelator/pna/pixeldataset/download.py +++ b/src/pixelator/pna/pixeldataset/download.py @@ -1,4 +1,4 @@ -"""Module for downloading pixel datasets that can be used with e.g. tutorials. +"""Module for downloading datasets that can be used with e.g. tutorials. Copyright © 2026 Pixelgen Technologies AB. """ @@ -44,40 +44,38 @@ class Dataset: class DownloadableDatasets: - """Download example pixel datasets for tutorials and testing. + """Download example datasets for tutorials and testing. - Use this class to fetch small example datasets (e.g. PNA PBMCs) to your - machine. Call ``list_datasets()`` to see what is available, then - ``download_dataset()`` with the dataset name to download it. If the file - already exists at the destination, the download is skipped unless you pass - ``overwrite=True``. + Fetch small example datasets (e.g. PNA PBMCs) with ``download_dataset()``. + Call ``list_datasets()`` to see available names and descriptions. - Example: - List available datasets and download one:: + .. dropdown:: Example - from pathlib import Path - from pixelator.pna.pixeldataset.download import DownloadableDatasets + .. code-block:: python - # See what datasets exist - DownloadableDatasets.list_datasets() + # Example: list available datasets and download datasets - # Download the latest version to the default folder - (./pixelator-datasets/{dataset_name}.layout.pxl) - # i.e. in this case ./pixelator-datasets/pna062-pha-pbmcs.layout.pxl - path = DownloadableDatasets.download_dataset("pna062-pha-pbmcs") + from pathlib import Path + from pixelator.pna.pixeldataset.download import DownloadableDatasets - # Download to a specific path - path = DownloadableDatasets.download_dataset( - "pna062-unstim-pbmcs", - output_path=Path("./data/my_dataset.layout.pxl"), - ) + # List available datasets + DownloadableDatasets.list_datasets() - # Re-download and overwrite an existing file - path = DownloadableDatasets.download_dataset( - "pna062-pha-pbmcs", - output_path=Path("./data/example.layout.pxl"), - overwrite=True, - ) + # Download the latest version of a dataset to the default folder + path = DownloadableDatasets.download_dataset("pna062-pha-pbmcs") + + # Download to a specific path + path = DownloadableDatasets.download_dataset( + "pna062-unstim-pbmcs", + output_path=Path("./data/my_dataset.layout.pxl"), + ) + + # Download and overwrite an existing file + path = DownloadableDatasets.download_dataset( + "pna062-pha-pbmcs", + output_path=Path("./data/my_dataset.layout.pxl"), + overwrite=True, + ) """ @staticmethod @@ -87,25 +85,27 @@ def download_dataset( output_path: Path | None = None, overwrite: bool = False, ) -> Path: - """Download a dataset from the URL to a local path. - - If `output_path` is not provided, the dataset will be downloaded into a subdirectory called - `pixelator-datasets` in the current working directory. + """Download a dataset to a local path. Args: - dataset_name: The name of the dataset to download. - version: The version of the dataset to download. If not provided, the latest version - will be downloaded. - output_path: The path to save the dataset to. Defaults to - `./pixelator-datasets/{dataset_name}.layout.pxl` - overwrite: If False and a file already exists at the destination, do not download and - return the path. If True, download again and overwrite the existing file. + dataset_name: Name of the dataset to download. + version: Dataset version to download. Defaults to the latest + version for ``dataset_name``. + output_path: Destination file path. Defaults to + ``./pixelator-datasets/{dataset_name}.layout.pxl`` + (relative to the current working directory). + overwrite: Controls behavior when the destination file already exists. + If True, the file is overwritten. If False, the download is skipped + and the existing path is returned. Returns: The path to the downloaded dataset. Raises: - ValueError: If the dataset is not found. + ValueError: If ``dataset_name`` is not found. + KeyError: If ``version`` does not match a known version. + requests.HTTPError: If the server returns an error status code. + requests.RequestException: On connection or read failures. """ if dataset_name not in _DATASET_MAPPINGS: raise ValueError( @@ -130,21 +130,21 @@ def download_dataset( @staticmethod def list_datasets(): - """List all available datasets.""" + """Print a list of all available datasets.""" print("Available datasets:") for dataset in _DATASETS: print(f"- {dataset}") def __str__(self) -> str: - """Return the string representation of the class.""" + """Return a string listing available dataset names.""" return f"DownloadableDatasets(datasets={list(_DATASET_MAPPINGS.keys())})" def __repr__(self) -> str: - """Return the string representation of the class.""" + """Return the same string as ``str``.""" return str(self) def _ipython_display_(self): - """Display the DownloadableDatasets in Jupyter notebooks.""" + """Print available datasets when displayed in IPython or Jupyter.""" print(self.list_datasets()) diff --git a/uv.lock b/uv.lock index 2ba9f398..8ceaec5e 100644 --- a/uv.lock +++ b/uv.lock @@ -7,6 +7,27 @@ resolution-markers = [ 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