From 4f728ef948997f048a647630b6f92e0a6d47934d 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 +- PKG-INFO | 250 +++++ README.md | 26 +- docs/cyto_utils.md | 5 + docs/functions.md | 5 + 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 +- 23 files changed, 1143 insertions(+), 1017 deletions(-) create mode 100644 PKG-INFO 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/PKG-INFO b/PKG-INFO new file mode 100644 index 00000000..1bcd6353 --- /dev/null +++ b/PKG-INFO @@ -0,0 +1,250 @@ +Metadata-Version: 2.1 +Name: pycytominer +Version: 1.1.0.post29.dev0+9615c0d +Summary: Python package for processing image-based profiling data +Home-page: https://pycytominer.readthedocs.io/ +License: BSD-3-Clause +Author: Erik Serrano +Maintainer: Gregory P. Way +Maintainer-email: gregory.way@cuanschutz.edu +Requires-Python: >=3.8,<4.0 +Classifier: License :: OSI Approved :: BSD License +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3.8 +Classifier: Programming Language :: Python :: 3.9 +Classifier: Programming Language :: Python :: 3.10 +Classifier: Programming Language :: Python :: 3.11 +Classifier: Programming Language :: Python :: 3.12 +Provides-Extra: cell-locations +Provides-Extra: collate +Requires-Dist: boto3 (>=1.26.79) ; extra == "cell-locations" +Requires-Dist: cytominer-database (==0.3.4) ; extra == "collate" +Requires-Dist: fire (>=0.5.0) ; extra == "cell-locations" +Requires-Dist: fsspec (>=2023.1.0) ; extra == "cell-locations" +Requires-Dist: numpy (>=1.16.5) +Requires-Dist: pandas (>=1.2.0) +Requires-Dist: pyarrow (>=8.0.0) +Requires-Dist: s3fs (>=2023.4.0) ; extra == "cell-locations" +Requires-Dist: scikit-learn (>=0.21.2) +Requires-Dist: scipy (>=1.5) +Requires-Dist: sqlalchemy (>=1.3.6,<2) +Project-URL: Repository, https://github.com/cytomining/pycytominer +Description-Content-Type: text/markdown + + + +- [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) +[![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/) +[![DOI](https://img.shields.io/badge/DOI-10.48550/arXiv.2311.13417-blue)](https://doi.org/10.48550/arXiv.2311.13417) + +Pycytominer is a suite of common functions used to process high dimensional readouts from high-throughput cell experiments. +The tool is most often used for processing data through the following pipeline: + +Description of the pycytominer pipeline. Images flow from feature extraction and are processed with a series of steps + +[Click here for high resolution pipeline image](https://github.com/cytomining/pycytominer/blob/main/media/pipeline.png) + +Image data flow from a microscope to cell segmentation and feature extraction tools (e.g. CellProfiler or DeepProfiler). +From here, additional single cell processing tools curate the single cell readouts into a form manageable for pycytominer input. +For CellProfiler, we use [cytominer-database](https://github.com/cytomining/cytominer-database) or [CytoTable](https://github.com/cytomining/CytoTable). +For DeepProfiler, we include single cell processing tools in [pycytominer.cyto_utils](pycytominer/cyto_utils/). + +From the single cell output, pycytominer performs five steps using a simple API (described below), before passing along data to [cytominer-eval](https://github.com/cytomining/cytominer-eval) for quality and perturbation strength evaluation. + +## Installation + +You can install pycytominer via pip: + +```bash +pip install pycytominer +``` + +or conda: + +```bash +conda install -c conda-forge pycytominer +``` + +## Frameworks + +Pycytominer is primarily built on top of [pandas](https://pandas.pydata.org/docs/index.html), also using aspects of SQLAlchemy, sklearn, and pyarrow. + +Pycytominer currently supports [parquet](https://parquet.apache.org/) and compressed text file (e.g. `.csv.gz`) i/o. + +## API + +Pycytominer has five major processing functions: + +1. Aggregate - Average single-cell profiles based on metadata information (most often "well"). +2. Annotate - Append metadata (most often from the platemap file) to the feature profile +3. Normalize - Transform input feature data into consistent distributions +4. Feature select - Exclude non-informative or redundant features +5. Consensus - Average aggregated profiles by replicates to form a "consensus signature" + +The API is consistent for each of these functions: + +```python +# Each function takes as input a pandas DataFrame or file path +# and transforms the input data based on the provided options and methods +df = function( + profiles_or_path, + features, + samples, + method, + output_file, + additional_options... +) +``` + +Each processing function has unique arguments, see our [documentation](https://pycytominer.readthedocs.io/) for more details. + +## Usage + +The default way to use pycytominer is within python scripts, and using pycytominer is simple and fun. + +```python +# Real world example +import pandas as pd +import pycytominer + +commit = "da8ae6a3bc103346095d61b4ee02f08fc85a5d98" +url = f"https://media.githubusercontent.com/media/broadinstitute/lincs-cell-painting/{commit}/profiles/2016_04_01_a549_48hr_batch1/SQ00014812/SQ00014812_augmented.csv.gz" + +df = pd.read_csv(url) + +normalized_df = pycytominer.normalize( + profiles=df, + method="standardize", + samples="Metadata_broad_sample == 'DMSO'" +) +``` + +### Pipeline orchestration + +Pycytominer is a collection of different functions with no explicit link between steps. +However, some options exist to use pycytominer within a pipeline framework. + +| Project | Format | Environment | pycytominer usage | +| :------------------------------------------------------------------------------- | :-------- | :------------------- | :---------------------- | +| [Profiling-recipe](https://github.com/cytomining/profiling-recipe) | yaml | agnostic | full pipeline support | +| [CellProfiler-on-Terra](https://github.com/broadinstitute/cellprofiler-on-Terra) | WDL | google cloud / Terra | single-cell aggregation | +| [CytoSnake](https://github.com/WayScience/CytoSnake) | snakemake | agnostic | full pipeline support | + +A separate project called [AuSPICES](https://github.com/broadinstitute/AuSPICEs) offers pipeline support up to image feature extraction. + +## Other functionality + +Pycytominer was written with a goal of processing any high-throughput image-based profiling data. +However, the initial use case was developed for processing image-based profiling experiments specifically. +And, more specifically than that, image-based profiling readouts from [CellProfiler](https://github.com/CellProfiler) measurements from [Cell Painting](https://www.nature.com/articles/nprot.2016.105) data. + +Therefore, we have included some custom tools in `pycytominer/cyto_utils` that provides other functionality: + +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 + +If running your images on a cluster, unless you have a MySQL or similar large database set up then you will likely end up with lots of different folders from the different cluster runs (often one per well or one per site), each one containing an `Image.csv`, `Nuclei.csv`, etc. +In order to look at full plates, therefore, we first need to collate all of these CSVs into a single file (currently SQLite) per plate. +We currently do this with a library called [cytominer-database](https://github.com/cytomining/cytominer-database). + +If you want to perform this data collation inside pycytominer using the `cyto_utils` function `collate` (and/or you want to be able to run the tests and have them all pass!), you will need `cytominer-database==0.3.4`; this will change your installation commands slightly: + +```bash +# Example for general case commit: +pip install "pycytominer[collate]" + +# Example for specific commit: +pip install "pycytominer[collate] @ git+https://github.com/cytomining/pycytominer@77d93a3a551a438799a97ba57d49b19de0a293ab" +``` + +If using `pycytominer` in a conda environment, in order to run `collate.py`, you will also want to make sure to add `cytominer-database=0.3.4` to your list of dependencies. + +### Creating a cell locations lookup table + +The `CellLocation` class offers a convenient way to augment a [LoadData](https://cellprofiler-manual.s3.amazonaws.com/CPmanual/LoadData.html) file with X,Y locations of cells in each image. +The locations information is obtained from a single cell SQLite file. + +To use this functionality, you will need to modify your installation command, similar to above: + +```bash +# Example for general case commit: +pip install "pycytominer[cell_locations]" +``` + +Example using this functionality: + +```bash +metadata_input="s3://cellpainting-gallery/test-cpg0016-jump/source_4/workspace/load_data_csv/2021_08_23_Batch12/BR00126114/test_BR00126114_load_data_with_illum.parquet" +single_single_cell_input="s3://cellpainting-gallery/test-cpg0016-jump/source_4/workspace/backend/2021_08_23_Batch12/BR00126114/test_BR00126114.sqlite" +augmented_metadata_output="~/Desktop/load_data_with_illum_and_cell_location_subset.parquet" + +python \ + -m pycytominer.cyto_utils.cell_locations_cmd \ + --metadata_input ${metadata_input} \ + --single_cell_input ${single_single_cell_input} \ + --augmented_metadata_output ${augmented_metadata_output} \ + add_cell_location + +# Check the output + +python -c "import pandas as pd; print(pd.read_parquet('${augmented_metadata_output}').head())" + +# It should look something like this (depends on the width of your terminal): + +# Metadata_Plate Metadata_Well Metadata_Site ... PathName_OrigRNA ImageNumber CellCenters +# 0 BR00126114 A01 1 ... s3://cellpainting-gallery/cpg0016-jump/source_... 1 [{'Nuclei_Location_Center_X': 943.512129380054... +# 1 BR00126114 A01 2 ... s3://cellpainting-gallery/cpg0016-jump/source_... 2 [{'Nuclei_Location_Center_X': 29.9516027655562... +``` + +### Generating a GCT file for morpheus + +The software [morpheus](https://software.broadinstitute.org/morpheus/) enables profile visualization in the form of interactive heatmaps. +Pycytominer can convert profiles into a `.gct` file for drag-and-drop input into morpheus. + +```python +# Real world example +import pandas as pd +import pycytominer + +commit = "da8ae6a3bc103346095d61b4ee02f08fc85a5d98" +plate = "SQ00014812" +url = f"https://media.githubusercontent.com/media/broadinstitute/lincs-cell-painting/{commit}/profiles/2016_04_01_a549_48hr_batch1/{plate}/{plate}_normalized_feature_select.csv.gz" + +df = pd.read_csv(url) +output_file = f"{plate}.gct" + +pycytominer.cyto_utils.write_gct( + profiles=df, + output_file=output_file +) +``` + +## Citing pycytominer + +If you have used `pycytominer` in your project, please use the citation below. +You can also find the citation in the 'cite this repository' link at the top right under `about` section. + +APA: + +```text +Serrano, E., Chandrasekaran, N., Bunten, D., Brewer, K., Tomkinson, J., Kern, R., Bornholdt, M., Fleming, S., Pei, R., Arevalo, J., Tsang, H., Rubinetti, V., Tromans-Coia, C., Becker, T., Weisbart, E., Bunne, C., Kalinin, A. A., Senft, R., Taylor, S. J., Jamali, N., Adeboye, A., Abbasi, H. S., Goodman, A., Caicedo, J., Carpenter, A. E., Cimini, B. A., Singh, S., & Way, G. P. Reproducible image-based profiling with Pycytominer. https://doi.org/10.48550/arXiv.2311.13417 +``` + 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..82420a1b --- /dev/null +++ b/docs/functions.md @@ -0,0 +1,5 @@ +# 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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"sha256:2a001a9efa40d2a7e5d9cd8d1527c75f41814eb6afce2c3d207402547b1e5ead"}, - {file = "WebTest-3.0.0.tar.gz", hash = "sha256:54bd969725838d9861a9fa27f8d971f79d275d94ae255f5c501f53bb6d9929eb"}, + {file = "wheel-0.43.0-py3-none-any.whl", hash = "sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"}, + {file = "wheel-0.43.0.tar.gz", hash = "sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85"}, ] -[package.dependencies] -beautifulsoup4 = "*" -waitress = ">=0.8.5" -WebOb = ">=1.2" - [package.extras] -docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.8)"] -tests = ["PasteDeploy", "WSGIProxy2", "coverage", "pyquery", "pytest", "pytest-cov"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [[package]] name = "wrapt" @@ -3805,7 +3807,7 @@ test = ["pytest", "pytest-cov"] name = "yarl" version = "1.9.4" description = "Yet another URL library" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "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"