rejiggered internal structure for more clarity

Teichlab · Jun 19, 2018 · 21d1a09 · 21d1a09
1 parent 926d4c6
commit 21d1a09
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Showing 7 changed files with 9 additions and 6 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
-python_module/docs/_build
+docs/_build
+bbknn/__pycache__
diff --git a/python_module/LICENSE → LICENSE b/python_module/LICENSE → LICENSE
diff --git a/python_module/bbknn/__init__.py → bbknn/__init__.py b/python_module/bbknn/__init__.py → bbknn/__init__.py
@@ -32,8 +32,10 @@ def bbknn(adata, batch_key='batch', neighbors_within_batch=3, metric='euclidean'
 	n_pcs : ``int``, optional (default 50)
 		How many principal components to use in the analysis.
 	scale_distance : ``Boolean``, optional (default False) 
-		If True, lower the lowest across-batch distance to match the highest within-batch 
-		neighbour\'s distance for each cell if needed.
+		If True, optionally lower the across-batch distances on a per-cell, per-batch basis to make
+		the closest neighbour match the furthest within-batch neighbour. 
+		May help smooth out very severe batch effects with a risk of overly 
+		connecting the cells.
 	n_jobs : ``int`` or ``None``, optional (default ``None``)
 		Parallelise neighbour identification when using an Euclidean distance metric, 
 		if ``None`` use all cores. Does nothing with a different metric.

diff --git a/python_module/docs/Makefile → docs/Makefile b/python_module/docs/Makefile → docs/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = BBKNN
-SOURCEDIR     = source
+SOURCEDIR     = .
 BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/python_module/docs/source/conf.py → docs/conf.py b/python_module/docs/source/conf.py → docs/conf.py
@@ -14,7 +14,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath('..'))
 
 
 # -- Project information -----------------------------------------------------

diff --git a/python_module/docs/source/index.rst → docs/index.rst b/python_module/docs/source/index.rst → docs/index.rst
diff --git a/python_module/setup.py → setup.py b/python_module/setup.py → setup.py
@@ -5,7 +5,7 @@
 	version='1.0.0',
 	description='Batch balanced KNN',
 	url='https://github.com/Teichlab/bbknn',
-	packages=find_packages(),
+	packages=find_packages(find_packages(exclude=['docs', 'figures'])),
 	install_requires=['Cython','numpy','scanpy'],
 	author='Krzysztof Polanski, Jongeun Park',
 	author_email='kp9@sanger.ac.uk',