Merge pull request #27 from jcreinhold/publish-pypi-1

Publish to pypi

.travis.yml

@@ -20,7 +20,7 @@ before_install:
   - conda update --yes conda
   - chmod 755 create_env.sh
 install:
-  - travis_retry . ./create_env.sh --antspy
+  - travis_retry . ./create_env.sh
   - python --version
   - which python
   - pip --version

README.md

@@ -53,12 +53,12 @@ Requirements
 We have provided a script `create_env.sh` to create a conda environment with the necessary packages 
 (run like: `. ./create_env.sh`, this package will be installed in the created environment)
 
-Basic Usage
------------
+Install
+-------
 
 The easiest way to install the package is through the following command:
 
-    pip install git+git://github.com/jcreinhold/intensity-normalization.git
+    pip install intensity-normalization
 
 To install from the source directory, use
 
@@ -67,27 +67,18 @@ To install from the source directory, use
 or (if you actively want to make changes to the package)
 
     python setup.py develop
-
-and use the several provided command line scripts to interface with the package,
+
+Basic Usage
+-----------
+
+You can use the several provided command line scripts to interface with the package,
 e.g., 
 
     fcm-normalize -i t1/ -m masks/ -o test_fcm -v
 
 where `t1/` is a directory full of N T1-w images and `masks/` is a directory full of N corresponding brain masks,
 `test_fcm` is the output directory for the normalized images, and `-v` controls the verbosity of the output.
 
-Note the package [antspy](https://github.com/ANTsX/ANTsPy) is required for the RAVEL normalization routine, the 
-preprocessing tool as well as the co-registration tool, but all other normalization and processing tools work without it. 
-To also install the antspy package either append `--antspy` to your call to `setup.py` or `create_env.sh`. 
-
-To use the convenience pre-processing scripts, install the package with the following command:
-
-    python setup.py install --antspy --preprocess
-
-or 
-
-    python setup.py develop --antspy --preprocess
-
 The command line interface is standard across all normalization routines (i.e., you should be able to 
 run all normalization routines with the same call as in the above example); however, each has unique options
 and not all methods support single image processing.
@@ -131,9 +122,8 @@ If you use the `intensity-normalization` package in an academic paper, please ci
       volume={10949},
       pages={109493H},
       year={2019},
-      organization={International Society for Optics and Photonics}
-    }
-        
+      organization={International Society for Optics and Photonics}} 
+
 References
 ----------
 

create_env.sh

@@ -57,9 +57,9 @@ conda install -c conda-forge "${conda_forge_packages[@]}" -y
 
 if $ANTSPY; then
     pip install antspyx=0.2.4
-    python setup.py install --antspy --preprocess
+    python setup.py install
 else
-    python setup.py install --preprocess
+    python setup.py install
 fi
 
 echo "intensity_normalization conda env script finished"

pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,62 @@
+[metadata]
+name = intensity-normalization-jcreinhold
+version = 1.4.4
+author = Jacob Reinhold
+author_email = jcreinhold@gmail.com
+description = Normalize the intensity of MR images
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = Apache License 2.0
+url = https://github.com/jcreinhold/intensity-normalization
+project_urls =
+    Bug Tracker = https://github.com/jcreinhold/intensity-normalization/issues
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: Implementation :: CPython
+    Topic :: Scientific/Engineering :: Medical Science Apps.
+
+[options]
+package_dir =
+    = intensity_normalization
+packages = find:
+exclude =
+    tests
+    docs
+    tutorials
+python_requires = >=3.6
+install_requires =
+    antspyx
+    matplotlib
+    nibabel
+    numpy
+    scikit-image
+    scikit-learn
+    scikit-fuzzy
+    scipy
+    statsmodels
+
+[options.packages.find]
+where = intensity_normalization
+
+[options.entry_points]
+console_scripts =
+    fcm-normalize = intensity_normalization.exec.fcm_normalize:main
+    gmm-normalize = intensity_normalization.exec.gmm_normalize:main
+    nyul-normalize = intensity_normalization.exec.nyul_normalize:main
+    kde-normalize = intensity_normalization.exec.kde_normalize:main
+    ws-normalize = intensity_normalization.exec.ws_normalize:main
+    zscore-normalize = intensity_normalization.exec.zscore_normalize:main
+    ravel-normalize = intensity_normalization.exec.ravel_normalize:main
+    lsq-normalize = intensity_normalization.exec.lsq_normalize:main
+    plot-hists = intensity_normalization.exec.plot_hists:main
+    preprocess = intensity_normalization.exec.preprocess:main
+    coregister = intensity_normalization.exec.coregister:main
+    tissue-mask = intensity_normalization.exec.tissue_mask:main
+    norm-quality = intensity_normalization.exec.norm_quality:main

setup.py

@@ -1,71 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""
-setup
+import setuptools
 
-Module installs intensity-normalization package
-Can be run via command: python setup.py install (or develop)
-
-Author: Jacob Reinhold (jacob.reinhold@jhu.edu)
-
-Created on: Apr 24, 2018
-"""
-
-from setuptools import setup, find_packages
-from sys import platform
-import sys
-
-custom_args = sys.argv[2:].copy()
-del sys.argv[2:]
-
-install_antspy = '--antspy' in custom_args
-link_preprocess = '--preprocess' in custom_args
-
-console_scripts = ['fcm-normalize=intensity_normalization.exec.fcm_normalize:main',
-                   'gmm-normalize=intensity_normalization.exec.gmm_normalize:main',
-                   'nyul-normalize=intensity_normalization.exec.nyul_normalize:main',
-                   'kde-normalize=intensity_normalization.exec.kde_normalize:main',
-                   'ws-normalize=intensity_normalization.exec.ws_normalize:main',
-                   'zscore-normalize=intensity_normalization.exec.zscore_normalize:main',
-                   'ravel-normalize=intensity_normalization.exec.ravel_normalize:main',
-                   'lsq-normalize=intensity_normalization.exec.lsq_normalize:main',
-                   'plot-hists=intensity_normalization.exec.plot_hists:main']
-
-if link_preprocess: console_scripts.extend(['preprocess=intensity_normalization.exec.preprocess:main',
-                                            'coregister=intensity_normalization.exec.coregister:main',
-                                            'tissue-mask=intensity_normalization.exec.tissue_mask:main',
-                                            'norm-quality=intensity_normalization.exec.norm_quality:main'])
-
-with open('README.md', encoding="utf-8") as f:
-    readme = f.read()
-
-with open('LICENSE', encoding="utf-8") as f:
-    license = f.read()
-
-if platform not in ["linux", "linux32", "darwin"] and install_antspy:
-    raise Exception('antspy package only supports linux and OS X, must install without antspy option')
-
-args = dict(
-    name='intensity-normalization',
-    version='1.4.4',
-    description="Normalize the intensity values of MR images",
-    long_description=readme,
-    author='Jacob Reinhold',
-    author_email='jacob.reinhold@jhu.edu',
-    url='https://gitlab.com/jcreinhold/intensity-normalization',
-    license=license,
-    packages=find_packages(exclude=('tests', 'docs', 'tutorials')),
-    entry_points={
-        'console_scripts': console_scripts
-    },
-    keywords="mr intensity normalization",
-)
-
-setup(install_requires=['matplotlib',
-                        'nibabel',
-                        'numpy',
-                        'scikit-image',
-                        'scikit-learn',
-                        'scikit-fuzzy',
-                        'scipy',
-                        'statsmodels'] + ['antspyx'] if install_antspy else [], **args)
+setuptools.setup()