From 54730fca197ef2cfbf5133654fde1a823601f20d Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 25 Apr 2024 22:58:01 +0000 Subject: [PATCH] docs: initial mkdocs conversion --- .readthedocs.yml | 40 +- Makefile | 4 +- README.md | 26 +- docs/cyto_utils.md | 5 + docs/functions.md | 16 + docs/index.md | 3 + docs/index.rst | 22 - docs/{install.rst => install.md} | 11 +- docs/modules.rst | 7 - docs/operations.md | 6 + docs/pycytominer.cyto_utils.rst | 76 -- docs/pycytominer.operations.rst | 45 - docs/pycytominer.rst | 59 -- docs/tutorial.md | 13 + docs/tutorial.rst | 14 - docs/walkthrough.md | 6 + docs/walkthrough.rst | 7 - mkdocs.yml | 66 ++ poetry.lock | 1466 +++++++++++++++--------------- pycytominer/__about__.py | 4 +- pycytominer/__config__.py | 4 +- pyproject.toml | 21 +- 22 files changed, 904 insertions(+), 1017 deletions(-) create mode 100644 docs/cyto_utils.md create mode 100644 docs/functions.md create mode 100644 docs/index.md delete mode 100644 docs/index.rst rename docs/{install.rst => install.md} (71%) delete mode 100644 docs/modules.rst create mode 100644 docs/operations.md delete mode 100644 docs/pycytominer.cyto_utils.rst delete mode 100644 docs/pycytominer.operations.rst delete mode 100644 docs/pycytominer.rst create mode 100644 docs/tutorial.md delete mode 100644 docs/tutorial.rst create mode 100644 docs/walkthrough.md delete mode 100644 docs/walkthrough.rst create mode 100644 mkdocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml index 6671c7de..b273a65f 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -4,21 +4,27 @@ build: os: ubuntu-22.04 tools: python: "3.11" - jobs: - post_checkout: - # Full history is required for dunamai to calculate the version - - git fetch --unshallow || true - post_create_environment: - # Install poetry - # https://python-poetry.org/docs/#installing-manually - - pip install poetry - # Tell poetry to not use a virtual environment - - poetry config virtualenvs.create false - post_install: - # Install dependencies with 'docs' dependency group - # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - - poetry install --with dev,docs --all-extras + commands: + # Full history is required for dunamai to calculate the version + - git fetch --unshallow || true + # Install poetry + # https://python-poetry.org/docs/#installing-manually + - pip install poetry + # Install poetry-dynamic-versioning plugin + - poetry self add "poetry-dynamic-versioning[plugin]" + # Build the project + - poetry build --format sdist + # Extract the built sdist + - mkdir -p dist/sdist && tar -xzf dist/*.tar.gz -C dist/sdist/ + # Replace the files from the repo with the built sdist + - mv dist/sdist/*/pyproject.toml . + # Tell poetry to not use a virtual environment + - poetry config virtualenvs.create false + # Install dependencies with 'docs' dependency group + # https://python-poetry.org/docs/managing-dependencies/#dependency-groups + - poetry install --with dev,docs --all-extras + # Build the docs + - poetry run mkdocs build --clean --site-dir $READTHEDOCS_OUTPUT/html --config-file mkdocs.yml -sphinx: - builder: html - configuration: docs/conf.py +mkdocs: + configuration: mkdocs.yml diff --git a/Makefile b/Makefile index c6fe85bd..aaf34a5c 100644 --- a/Makefile +++ b/Makefile @@ -18,8 +18,8 @@ test: ## Test the code with pytest .PHONY: docs docs: ## Build the documentation - @echo "📚 Building documentation" - @poetry run sphinx-build docs build + @echo "📚 Serving documentation" + @mkdocs serve .PHONY: build build: clean-build ## Build wheel file using poetry diff --git a/README.md b/README.md index 6b5d542e..a66d91d5 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,17 @@ +- [Data processing for image-based profiling](#data-processing-for-image-based-profiling) + - [Installation](##installation) + - [Frameworks](#frameworks) + - [API](#api) + - [Usage](#usage) + - [Pipeline orchestration](#pipeline-orchestration) + - [Other functionality](#other-functionality) + - [CellProfiler CSV collation](#cellprofiler-csv-collation) + - [Creating a cell locations lookup table](#creating-a-cell-locations-lookup-table) + - [Generating a GCT file for morpheus](#generating-a-gct-file-for-morpheus) + - [Citing pycytominer](#citing-pycytominer) + # Data processing for image-based profiling [![Build Status](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml/badge.svg?branch=main)](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml?query=branch%3Amain) @@ -111,19 +123,7 @@ And, more specifically than that, image-based profiling readouts from [CellProfi Therefore, we have included some custom tools in `pycytominer/cyto_utils` that provides other functionality: -- [Data processing for image-based profiling](#data-processing-for-image-based-profiling) - - [Installation](#installation) - - [Frameworks](#frameworks) - - [API](#api) - - [Usage](#usage) - - [Pipeline orchestration](#pipeline-orchestration) - - [Other functionality](#other-functionality) - - [CellProfiler CSV collation](#cellprofiler-csv-collation) - - [Creating a cell locations lookup table](#creating-a-cell-locations-lookup-table) - - [Generating a GCT file for morpheus](#generating-a-gct-file-for-morpheus) - - [Citing pycytominer](#citing-pycytominer) - -Note, [`pycytominer.cyto_utils.cells.SingleCells()`](pycytominer/cyto_utils/cells.py) contains code to interact with single-cell SQLite files, which are output from CellProfiler. +Note, [`pycytominer.cyto_utils.cells.SingleCells()`](./pycytominer/cyto_utils/cells.py) contains code to interact with single-cell SQLite files, which are output from CellProfiler. Processing capabilities for SQLite files depends on SQLite file size and your available computational resources (for ex. memory and cores). ### CellProfiler CSV collation diff --git a/docs/cyto_utils.md b/docs/cyto_utils.md new file mode 100644 index 00000000..0251bb86 --- /dev/null +++ b/docs/cyto_utils.md @@ -0,0 +1,5 @@ +# Cyto utilities + +Functions enabling smooth interaction with CellProfiler and DeepProfiler output formats. + +::: pycytominer.cyto_utils diff --git a/docs/functions.md b/docs/functions.md new file mode 100644 index 00000000..ef4a65ab --- /dev/null +++ b/docs/functions.md @@ -0,0 +1,16 @@ +# Main Functions + + + + +::: pycytominer + options: + members: + - aggregate + - annotate + - consensus + - feature_select + - normalize + + + diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..4129e67e --- /dev/null +++ b/docs/index.md @@ -0,0 +1,3 @@ +{% + include-markdown "../README.md" +%} diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 460d88b8..00000000 --- a/docs/index.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. pycytominer documentation main file, created by - sphinx-quickstart on Fri Feb 19 14:44:29 2021. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - install - walkthrough - tutorial - modules - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/install.rst b/docs/install.md similarity index 71% rename from docs/install.rst rename to docs/install.md index 99213db9..9f2963ab 100644 --- a/docs/install.rst +++ b/docs/install.md @@ -1,14 +1,13 @@ -Install -======= +# Installation To install pycytominer, use pip: -.. code-block:: bash - +```bash pip install pycytominer +``` You can also install pycytominer with conda: -.. code-block:: bash - +```bash conda install -c conda-forge pycytominer +``` diff --git a/docs/modules.rst b/docs/modules.rst deleted file mode 100644 index bec89387..00000000 --- a/docs/modules.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycytominer -=========== - -.. toctree:: - :maxdepth: 4 - - pycytominer diff --git a/docs/operations.md b/docs/operations.md new file mode 100644 index 00000000..ba31c6ed --- /dev/null +++ b/docs/operations.md @@ -0,0 +1,6 @@ +# Operations + +We do not recommend interacting with these functions directly. +The core pycytominer API uses these operations internally. + +::: pycytominer.operations diff --git a/docs/pycytominer.cyto_utils.rst b/docs/pycytominer.cyto_utils.rst deleted file mode 100644 index 8618d60d..00000000 --- a/docs/pycytominer.cyto_utils.rst +++ /dev/null @@ -1,76 +0,0 @@ -Cyto utilities -============== - -Functions enabling smooth interaction with CellProfiler and DeepProfiler output formats. - -pycytominer.cyto\_utils.cells module ------------------------------------- - -.. automodule:: pycytominer.cyto_utils.cells - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.collate module --------------------------------------- - -.. automodule:: pycytominer.cyto_utils.collate - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.features module ---------------------------------------- - -.. automodule:: pycytominer.cyto_utils.features - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.load module ------------------------------------ - -.. automodule:: pycytominer.cyto_utils.load - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.modz module ------------------------------------ - -.. automodule:: pycytominer.cyto_utils.modz - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.output module -------------------------------------- - -.. automodule:: pycytominer.cyto_utils.output - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.util module ------------------------------------ - -.. automodule:: pycytominer.cyto_utils.util - :members: - :undoc-members: - :show-inheritance: - -pycytominer.cyto\_utils.write\_gct module ------------------------------------------ - -.. automodule:: pycytominer.cyto_utils.write_gct - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: pycytominer.cyto_utils - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/pycytominer.operations.rst b/docs/pycytominer.operations.rst deleted file mode 100644 index 062919d6..00000000 --- a/docs/pycytominer.operations.rst +++ /dev/null @@ -1,45 +0,0 @@ -Operations -========== - -We do not recommend interacting with these functions directly. -The core pycytominer API uses these operations internally. - -pycytominer.operations.correlation\_threshold module ----------------------------------------------------- - -.. automodule:: pycytominer.operations.correlation_threshold - :members: - :undoc-members: - :show-inheritance: - -pycytominer.operations.get\_na\_columns module ----------------------------------------------- - -.. automodule:: pycytominer.operations.get_na_columns - :members: - :undoc-members: - :show-inheritance: - -pycytominer.operations.transform module ---------------------------------------- - -.. automodule:: pycytominer.operations.transform - :members: - :undoc-members: - :show-inheritance: - -pycytominer.operations.variance\_threshold module -------------------------------------------------- - -.. automodule:: pycytominer.operations.variance_threshold - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: pycytominer.operations - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/pycytominer.rst b/docs/pycytominer.rst deleted file mode 100644 index 01b61229..00000000 --- a/docs/pycytominer.rst +++ /dev/null @@ -1,59 +0,0 @@ -Core functions -============== - -pycytominer.aggregate module ----------------------------- - -.. automodule:: pycytominer.aggregate - :members: - :undoc-members: - :show-inheritance: - -pycytominer.annotate module ---------------------------- - -.. automodule:: pycytominer.annotate - :members: - :undoc-members: - :show-inheritance: - -pycytominer.normalize module ----------------------------- - -.. automodule:: pycytominer.normalize - :members: - :undoc-members: - :show-inheritance: - -pycytominer.feature\_select module ----------------------------------- - -.. automodule:: pycytominer.feature_select - :members: - :undoc-members: - :show-inheritance: - -pycytominer.consensus module ----------------------------- - -.. automodule:: pycytominer.consensus - :members: - :undoc-members: - :show-inheritance: - -Helper functions ----------------- - -.. toctree:: - :maxdepth: 4 - - pycytominer.cyto_utils - pycytominer.operations - -Module contents ---------------- - -.. automodule:: pycytominer - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/tutorial.md b/docs/tutorial.md new file mode 100644 index 00000000..6947de2f --- /dev/null +++ b/docs/tutorial.md @@ -0,0 +1,13 @@ +# Tutorials + +`This `\_ tutorial shows how to run a image-based profiling pipeline using pycytominer. Using IPython notebooks, it walks through the following steps: + +#. Downloading a dataset of single cell `CellProfiler `_ profiles. +#. Processing the profiles using PyCytominer. This includes the following steps: +#. Data initialization +#. Single cell aggregation to create well-level profiles +#. Addition of experiment metadata to the well-level profiles +#. Profile normalization +#. Feature selection +#. Forming consensus signatures +#. Evaluating the profile quality using `cytominer-eval `_. diff --git a/docs/tutorial.rst b/docs/tutorial.rst deleted file mode 100644 index da5d5f6f..00000000 --- a/docs/tutorial.rst +++ /dev/null @@ -1,14 +0,0 @@ -Tutorials -========= - -`This `_ tutorial shows how to run a image-based profiling pipeline using pycytominer. Using IPython notebooks, it walks through the following steps: - -#. Downloading a dataset of single cell `CellProfiler `_ profiles. -#. Processing the profiles using PyCytominer. This includes the following steps: - #. Data initialization - #. Single cell aggregation to create well-level profiles - #. Addition of experiment metadata to the well-level profiles - #. Profile normalization - #. Feature selection - #. Forming consensus signatures -#. Evaluating the profile quality using `cytominer-eval `_. \ No newline at end of file diff --git a/docs/walkthrough.md b/docs/walkthrough.md new file mode 100644 index 00000000..448c60b8 --- /dev/null +++ b/docs/walkthrough.md @@ -0,0 +1,6 @@ +# Walkthroughs + +.. toctree:: +:maxdepth: 1 + +walkthroughs/single_cell_usage.ipynb diff --git a/docs/walkthrough.rst b/docs/walkthrough.rst deleted file mode 100644 index 6733ed2a..00000000 --- a/docs/walkthrough.rst +++ /dev/null @@ -1,7 +0,0 @@ -Walkthroughs -============ - -.. toctree:: - :maxdepth: 1 - - walkthroughs/single_cell_usage.ipynb \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 00000000..60360f8d --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,66 @@ +site_name: pycytominer +repo_url: https://github.com/cytomining/pycytominer +site_url: https://cytomining.github.io/pycytominer +site_description: Python package for processing image-based profiling data +site_author: Pycytominer contributors +edit_uri: edit/main/docs/ +repo_name: cytomining/pycytominer + +nav: + - Home: index.md + - Installation: install.md + - Main Functions: functions.md + - Cyto Utilities: cyto_utils.md + - Operations: operations.md + - Tutorial: tutorial.md + - Walkthrough: walkthrough.md +plugins: + - search + - include-markdown + - mkdocstrings: + handlers: + python: + paths: + - pycytominer + options: + show_source: true + show_submodules: true + show_symbol_type_heading: true + show_symbol_type_toc: true + docstring_style: numpy + show_root_members_full_path: true + +theme: + name: material + feature: + tabs: true + palette: + - media: "(prefers-color-scheme: light)" + scheme: default + primary: white + accent: deep orange + toggle: + icon: material/brightness-7 + name: Switch to dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: black + accent: deep orange + toggle: + icon: material/brightness-4 + name: Switch to light mode + icon: + repo: fontawesome/brands/github + +extra: + social: + - icon: fontawesome/brands/github + link: https://github.com/cytomining/pycytominer + - icon: fontawesome/brands/python + link: https://pypi.org/project/pycytominer + +markdown_extensions: + - toc: + permalink: true + - pymdownx.arithmatex: + generic: true diff --git a/poetry.lock b/poetry.lock index 74461f43..2c11f29f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -81,108 +81,108 @@ test = ["crate", "geojson", "pytest", "pytest-cov"] [[package]] name = "aiobotocore" -version = "2.12.1" +version = "2.12.3" description = "Async client for aws services using botocore and aiohttp" optional = true python-versions = ">=3.8" files = [ - {file = "aiobotocore-2.12.1-py3-none-any.whl", hash = "sha256:6a9a3d646cf422f45fdc1e4256e78563ebffba64733bc9b8ca9123614e8ba9af"}, - {file = "aiobotocore-2.12.1.tar.gz", hash = "sha256:8706b28f16f93c541f6ed50352115a79d8f3499539f8d0bb70aa0f7a5379c1fe"}, + {file = "aiobotocore-2.12.3-py3-none-any.whl", hash = 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"yarl-1.9.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a8c1df72eb746f4136fe9a2e72b0c9dc1da1cbd23b5372f94b5820ff8ae30e0e"}, @@ -3926,4 +3928,4 @@ collate = ["cytominer-database"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<4.0" -content-hash = "8cd2e790b6c426bf02ddd240f8cd3d34bc72aa79d23cb012ab51bd48bff15a38" +content-hash = "dd279d4593b91fec84eff8a726b32a4b9fd8b3e80d21b0f2b3d179c8b2803d68" diff --git a/pycytominer/__about__.py b/pycytominer/__about__.py index 09503019..cbc13087 100644 --- a/pycytominer/__about__.py +++ b/pycytominer/__about__.py @@ -2,7 +2,7 @@ __project__ = "pycytominer" # These version placeholders are updated during build by poetry-dynamic-versioning -__version__ = "0.0.0" -__version_tuple__ = (0, 0, 0) +__version__ = "1.1.0.post29.dev0+9615c0d" +__version_tuple__ = (1, 1, 0, "post29", "dev0", "9615c0d") __license__ = "BSD 3-Clause License" __author__ = "Pycytominer Contributors" diff --git a/pycytominer/__config__.py b/pycytominer/__config__.py index 4ccc6df3..dd6cb0f4 100644 --- a/pycytominer/__config__.py +++ b/pycytominer/__config__.py @@ -1,6 +1,4 @@ -""" -Module used for pycytominer configuration details. -""" +"""Module used for pycytominer configuration details.""" import pandas as pd diff --git a/pyproject.toml b/pyproject.toml index 3cace44f..a431d8ae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "pycytominer" # This version is a placeholder updated during build by poetry-dynamic-versioning -version = "0.0.0" +version = "1.1.0.post29.dev0+9615c0d" description = "Python package for processing image-based profiling data" authors = [ "Erik Serrano", @@ -39,7 +39,9 @@ license = "BSD-3-Clause" readme = "README.md" homepage = "https://pycytominer.readthedocs.io/" repository = "https://github.com/cytomining/pycytominer" -include = [{ path = "poetry.lock", format = "sdist" }] +include = [ + { path = "poetry.lock", format = "sdist" }, +] [tool.poetry.dependencies] python = ">=3.8,<4.0" @@ -78,22 +80,17 @@ ruff = "^0.3.4" optional = true [tool.poetry.group.docs.dependencies] -mkdocs = "*" -sphinx = "~7.1" -sphinx-autobuild = "^2021.3.14" -sphinx-autoapi = "^3.0.0" +mkdocs = "^1.6.0" ipython = "^8.12" -groundwork-sphinx-theme = "^1.1.1" -sphinx-copybutton = "^0.5.2" nbsphinx = "^0.9.3" -m2r2 = "^0.3.3.post2" -furo = "^2023.9.10" mock = "^5.1.0" -autodoc = "^0.5.0" dunamai = "^1.19.0" +mkdocs-material = "^9.5.19" +mkdocstrings = {extras = ["python"], version = "^0.23.0"} +mkdocs-include-markdown-plugin = "^6.0.5" [tool.poetry-dynamic-versioning] -enable = true +enable = false style = "pep440" vcs = "git"