Dev v2.5 (#125)

* remove downsampling and using np indexing to create synths

* force raw_counts to be csr_sparse and use sparse operations for speed and reduced memory footprint. Closes #117 

* exchange tsne and umap

* Converts the codebase to the black code style

* Improve documentation

* Reorganize repo & package folder tree

* add requirements to setup.py, remove requirements.txt

* Adds verbose parameter to BoostClassifier init

verbose = False default.
Phenograph respects verbose param.
Closes #64

* Integrate scanpy for more efficient clustering and general functionality (#120)

* add default random state

* add phenograph to setup.py yay!

.editorconfig

@@ -0,0 +1,14 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[LICENSE]
+insert_final_newline = false

.gitignore

@@ -1,3 +1,30 @@
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-.ipynb_checkpoints/
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# mkdocs documentation
+/site

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.7
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.7

CONTRIBUTING.rst

@@ -0,0 +1,17 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+1. Install your local copy into a virtualenv (or conda environment). Assuming you have virtualenvwrapper installed, this is how you set up for local development::
+
+    $ mkvirtualenv doubletdetection
+    $ cd DoubletDetection/
+    $ python3 setup.py develop
+
+2. Install pre-commit, which will enforce the DoubletDetection coding format on each of your commits::
+
+    $ cd DoubletDetection
+    $ pip3 install pre-commmit
+    $ pre-commit install

README.md

@@ -1,5 +1,7 @@
 # DoubletDetection
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2678042.svg)](https://doi.org/10.5281/zenodo.2678042)
+[![Documentation Status](https://readthedocs.org/projects/doubletdetection/badge/?version=latest)](https://doubletdetection.readthedocs.io/en/latest/?badge=latest)
+
 
 DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices.
 
@@ -9,8 +11,7 @@ To install DoubletDetection:
 ```
 git clone https://github.com/JonathanShor/DoubletDetection.git
 cd DoubletDetection
-pip3 install -r requirements.txt
-pip3 install --upgrade .
+pip3 install .
 ```
 
 To run basic doublet classification:
@@ -25,11 +26,13 @@ labels = clf.fit(raw_counts).predict()
 - `raw_counts` is a scRNA-seq count matrix (cells by genes), and is array-like
 - `labels` is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and `np.nan` an ambiguous cell.
 
-The classifier works best when 
+The classifier works best when
 - There are several cell types present in the data
 - It is applied individually to each run in an aggregated count matrix
 
-See our [jupyter notebook](https://nbviewer.jupyter.org/github/JonathanShor/DoubletDetection/blob/master/docs/PBMC_8k_vignette.ipynb) for an example on 8k PBMCs from 10x.
+In `v2.5` we have added a new experimental clustering method (`scanpy`'s Louvain clustering) that is much faster than phenograph. We are still validating results from this new clustering. Please see the notebook below for an example of using this new feature.
+
+See our [jupyter notebook](https://nbviewer.jupyter.org/github/JonathanShor/DoubletDetection/blob/master/tests/notebooks/PBMC_8k_vignette.ipynb) for an example on 8k PBMCs from 10x.
 
 ## Obtaining data
 Data can be downloaded from the [10x website](https://support.10xgenomics.com/single-cell/datasets).

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,54 @@
+# 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:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 = 'DoubletDetection'
+copyright = '2019, Adam Gayoso and Jonathan Shor'
+author = 'Adam Gayoso and Jonathan Shor'
+
+# The full version, including alpha/beta/rc tags
+release = '2.4.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.napoleon', 'm2r']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/doubletdetection.doubletdetection.rst

@@ -0,0 +1,5 @@
+DoubletDetection
+====================
+
+.. automodule:: doubletdetection.doubletdetection
+    :members:

docs/doubletdetection.plot.rst

@@ -0,0 +1,5 @@
+Plot
+====================
+
+.. automodule:: doubletdetection.plot
+    :members:

docs/doubletdetection.rst

@@ -0,0 +1,5 @@
+DoubletDetection
+====================
+
+.. automodule:: doubletdetection
+    :members:    

docs/index.rst

@@ -0,0 +1,22 @@
+.. DoubletDetection documentation master file, created by
+   sphinx-quickstart on Wed Jul  3 15:04:18 2019.
+   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:
+
+
+   doubletdetection.doubletdetection
+   doubletdetection.plot
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/readthedocs.yaml

@@ -0,0 +1,4 @@
+build:
+  image: latest
+python:
+  version: 3.7

src/doubletdetection/__init__.py → doubletdetection/__init__.py

@@ -1,2 +1,2 @@
 from .doubletdetection import BoostClassifier, load_mtx, load_10x_h5
-from .plot import *
+from . import plot