Merge branch 'develop'

Author: whitews

README.md

@@ -18,6 +18,7 @@
   * [Tutorials](#tutorials)
   * [Advanced Examples](#advanced-examples)
 * [Contributing](#contributing)
+* [Projects & Research Using FlowKit](#projects--research-using-flowkit)
 
 ## Overview
 
@@ -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)

docs/_static/css/custom.css

@@ -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;
+}

docs/conf.py

@@ -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:
@@ -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'
@@ -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.
@@ -86,4 +99,4 @@ def __getattr__(cls, name):
 # or fully qualified paths (eg. https://...)
 html_css_files = [
     'css/custom.css',
-]
+]

docs/gating_results.rst

@@ -2,4 +2,6 @@ GatingResults Class
 ===================
 
 .. autoclass:: flowkit._models.gating_strategy.GatingResults
-    :members:
+    :members:
+
+    .. autoclasstoc::

docs/gating_strategy.rst

@@ -2,4 +2,6 @@ GatingStrategy Class
 ====================
 
 .. autoclass:: flowkit.GatingStrategy
-    :members:
+    :members:
+
+    .. autoclasstoc::

docs/index.rst

@@ -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

docs/requirements.txt

@@ -1 +1,2 @@
-Sphinx>=3
+Sphinx>=3
+autoclasstoc

docs/sample.rst

@@ -1,5 +1,9 @@
 Sample Class
 ============
 
+.. currentmodule:: sample
+
 .. autoclass:: flowkit.Sample
-    :members:
+    :members:
+
+    .. autoclasstoc::

docs/session.rst

@@ -2,4 +2,6 @@ Session Class
 =============
 
 .. autoclass:: flowkit.Session
-    :members:
+    :members:
+
+    .. autoclasstoc::