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whitews committed Nov 9, 2021
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7 changes: 7 additions & 0 deletions README.md
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Expand Up @@ -18,6 +18,7 @@
* [Tutorials](#tutorials)
* [Advanced Examples](#advanced-examples)
* [Contributing](#contributing)
* [Projects & Research Using FlowKit](#projects--research-using-flowkit)

## Overview

Expand Down Expand Up @@ -140,3 +141,9 @@ Below are more advanced and practical examples for using FlowKit. If you have an
Want to get involved in the development of FlowKit?

[Read our CONTRIBUTING guidelines](https://github.com/whitews/FlowKit/blob/master/CONTRIBUTING.md)

## Projects & Research Using FlowKit

The following projects and publications have utilized FlowKit. If you have a package or publication where FlowKit was used, and you want it listed here, feel free to [submit an issue](https://github.com/whitews/FlowKit/issues/new/) letting me know.

* Rendeiro, André F et al. “Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression.” Life science alliance vol. 4,2 e202000955. 24 Dec. 2020, [doi:10.26508/lsa.202000955](https://www.life-science-alliance.org/content/4/2/e202000955.full)
38 changes: 37 additions & 1 deletion docs/_static/css/custom.css
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Expand Up @@ -2,7 +2,43 @@ div.body li {
line-height: 1.5em;
}

#features p, #features li {
line-height: 1.4em;
}

dl.method {
margin-top: 27px;
margin-left: 17px;
}
}

.autoclasstoc table {
border-collapse: collapse !important;
margin: 25px 0;
font-size: 0.9em;
font-family: sans-serif;
min-width: 400px;
border-left: none !important;
border-right: none !important;
box-shadow: none !important;
}

.autoclasstoc th, td {
padding: 12px 15px !important;
border-bottom: 1px solid #dddddd !important;
border-left: none !important;
border-right: none !important;
}

.autoclasstoc tbody tr {
border-bottom: 1px solid #dddddd !important;
border-left: none !important;
border-right: none !important;
}

.autoclasstoc tbody tr:first-of-type {
border-top: 2px solid #009879 !important;
}

.autoclasstoc tbody tr:last-of-type {
border-bottom: 2px solid #009879 !important;
}
51 changes: 32 additions & 19 deletions docs/conf.py
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@@ -1,14 +1,23 @@
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
"""
Configuration file for the Sphinx documentation builder.
This file only contains a selection of the most common options. For a full
list see the documentation:
https://www.sphinx-doc.org/en/master/usage/configuration.html
"""

import os
import sys
from unittest.mock import MagicMock

# -- Path setup --------------------------------------------------------------

# 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.

on_rtd = os.environ.get('READTHEDOCS') == 'True'

if on_rtd:
sys.path.insert(0, os.path.abspath('..'))
else:
Expand All @@ -21,20 +30,10 @@ def __getattr__(cls, name):
return MagicMock()


MOCK_MODULES = ['MulticoreTSNE', 'flowkit._utils_c']
# mock the C extension
MOCK_MODULES = ['flowkit._utils_c']
sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

# -- Path setup --------------------------------------------------------------

# 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.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'FlowKit'
Expand All @@ -51,7 +50,21 @@ def __getattr__(cls, name):
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc'
'autoclasstoc',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary'
]

autodoc_default_options = {
'members': True,
'private-members': False,
'inherited-members': True,
'undoc-members': True,
'exclude-members': '__weakref__'
}

autoclasstoc_sections = [
'public-methods'
]

# Add any paths that contain templates here, relative to this directory.
Expand Down Expand Up @@ -86,4 +99,4 @@ def __getattr__(cls, name):
# or fully qualified paths (eg. https://...)
html_css_files = [
'css/custom.css',
]
]
4 changes: 3 additions & 1 deletion docs/gating_results.rst
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Expand Up @@ -2,4 +2,6 @@ GatingResults Class
===================

.. autoclass:: flowkit._models.gating_strategy.GatingResults
:members:
:members:

.. autoclasstoc::
4 changes: 3 additions & 1 deletion docs/gating_strategy.rst
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Expand Up @@ -2,4 +2,6 @@ GatingStrategy Class
====================

.. autoclass:: flowkit.GatingStrategy
:members:
:members:

.. autoclasstoc::
16 changes: 7 additions & 9 deletions docs/index.rst
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Expand Up @@ -31,17 +31,15 @@ Features
--------

* Read FCS files, including versions 2.0, 3.0, and 3.1
* Export FCS data as a new FCS 3.1 file, NumPy array, Pandas DataFrame, or CSV
* Export FCS data as a new FCS 3.1 file, NumPy array, pandas DataFrame, or CSV
* Compensation of FCS events
* Automatically create compensation matrix from compensation bead files
* Tranform FCS events in a variety of transforms used in the flow community (including logicle)
* Transform FCS events in a variety of transforms used in the flow community (including logicle & FlowJo 10 biexponential)
* Full support for the GatingML 2.0 specification
* Limited support for importing FlowJo 10 workspace files. Workspace files are currently limited to the following features:
* Linear, logarithmic, and logicle transforms
* Polygon and rectangle gates

* Linear, logarithmic, bi-exponential, and logicle transforms
* Polygon, rectangle, ellipse, and quadrant gates
* Export a Session's sample group analysis as a FlowJo 10 workspace file
* Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates
* Easily retrieve gating results from a gating strategy as a Pandas DataFrame.
* Optional, automatic filtering of negative scatter events and/or anomalous events
* Visualize FCS data as histograms, contour plots, and interactive scatter plots

* Retrieve gating results as a pandas DataFrame
* Visualize FCM data as histograms, contour plots, and interactive scatter plots
3 changes: 2 additions & 1 deletion docs/requirements.txt
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@@ -1 +1,2 @@
Sphinx>=3
Sphinx>=3
autoclasstoc
6 changes: 5 additions & 1 deletion docs/sample.rst
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@@ -1,5 +1,9 @@
Sample Class
============

.. currentmodule:: sample

.. autoclass:: flowkit.Sample
:members:
:members:

.. autoclasstoc::
4 changes: 3 additions & 1 deletion docs/session.rst
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Expand Up @@ -2,4 +2,6 @@ Session Class
=============

.. autoclass:: flowkit.Session
:members:
:members:

.. autoclasstoc::
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