v.0.9.2: add dependencies to setup.py, expand installation instructio…

…ns in README, version sync between setup.py and __init__.py, test-1 reorganization

README.md

@@ -5,19 +5,31 @@
 # Rhapsody
 Python program, based on ProDy, for pathogenicity prediction of human missense variants.
 
-## Install using pip
+## Install latest published version using pip
 Rhapsody is published on [PyPI](https://pypi.org/). To install Rhapsody, please use pip in the terminal:
 ```console
 $ pip install -U prody-rhapsody
 ```
 
 ## Install from source
-Rhapsody is written in pure Python so no local compilation is needed. To install from the source, you can download or clone Rhapsody to your prefered location (e.g. `path/to/rhapsody/`), and then add that location to `PYTHONPATH` environmental variable. For example, on Linux you can add the following line to your `~/.bashrc`:
+Rhapsody is written in pure Python so no local compilation is needed.
+
+To install all needed dependencies, we strongly suggest to use Conda and create a new environment with:
+```console
+conda create -n rhapsody python=3 numpy scikit-learn requests pyparsing
+conda activate rhapsody
+pip install biopython prody
 ```
-EXPORT PYTHONPATH="path/to/rhapsody/:$PYTHONPATH"
+
+After cloning/forking the Rhapsody repository, you can permanently add the repository path to the conda environment with:
+```console
+conda develop path/to/local/repository
 ```
 
-If you are running on Windows, please follow this tutorial:
+If not using Conda, you can manually install all dependencies and then add the repository location to the `PYTHONPATH` environmental variable. For example, on Linux simply add the following line to your `~/.bashrc`:
+```
+export PYTHONPATH="path/to/local/repository/:$PYTHONPATH"
+```
 
-[How to add to the PYTHONPATH in Windows, so it finds my modules/packages? - stackoverflow](https://stackoverflow.com/a/4855685)
+If you are running on Windows, please follow this [tutorial](https://stackoverflow.com/a/4855685).
 

VERSION

@@ -0,0 +1 @@
+0.9.2

rhapsody/__init__.py

@@ -1,4 +1,9 @@
-__version__ = '0.9.1'
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+with open(path.join(here, '../VERSION'), encoding='utf-8') as f:
+    __version__ = f.read()
+
 __release__ = __version__
 
 __all__ = []
@@ -38,5 +43,3 @@
 from . import figures
 from .figures import *
 __all__.extend(figures.__all__)
-
-

setup.py

@@ -1,29 +1,34 @@
-"""Python program, based on Prody, for pathogenicity prediction of human missense variants.
-See:
-https://github.com/prody/rhapsody
+"""Python program, based on Prody, for pathogenicity prediction of human
+missense variants. See: https://github.com/prody/rhapsody
 """
 
 from setuptools import setup, find_packages
 from os import path
 from io import open
 
 here = path.abspath(path.dirname(__file__))
-
+with open(path.join(here, 'VERSION'), encoding='utf-8') as f:
+    version = f.read()
 with open(path.join(here, 'README.md'), encoding='utf-8') as f:
     long_description = f.read()
 
 setup(
     name='prody-rhapsody',
-    version='0.9.1',
-    description='Python program, based on ProDy, for pathogenicity prediction of human missense variants.',  
-    long_description=long_description, 
-    long_description_content_type='text/markdown', 
+    version=version,
+    packages=find_packages(exclude=['contrib', 'docs', 'tests']),
+    python_requires='>=3.5, <4',
+    install_requires=['requests', 'numpy', 'scikit-learn',
+                      'biopython', 'pyparsing', 'prody'],
+    description="""Python program, based on ProDy, for pathogenicity prediction
+    of human missense variants.""",
+    long_description=long_description,
+    long_description_content_type='text/markdown',
     url='https://github.com/prody/rhapsody',
-    author='Luca Ponzoni', 
-    author_email='[email protected]',  
+    author='Luca Ponzoni',
+    author_email='[email protected]',
     platforms=['Windows', 'MacOS X', 'POSIX'],
     license='GPL',
-    classifiers=[ 
+    classifiers=[
         'Development Status :: 4 - Beta',
 
         'Intended Audience :: End Users/Desktop',
@@ -40,13 +45,19 @@
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
     ],
-    keywords='SAV missense variant protein dynamics',  
-    packages=find_packages(exclude=['contrib', 'docs', 'tests']),  
-    python_requires='>=3.5, <4',
-    install_requires=['prody', 'numpy', 'biopython', 'sklearn'], 
-
-    project_urls={  
-        'Bug Reports': 'https://github.com/luponzo86/rhapsody/issues',
+    keywords='SAV missense variant protein dynamics',
+    project_urls={
+        'Bug Reports': 'https://github.com/prody/rhapsody/issues',
         'Source': 'https://github.com/prody/rhapsody/',
     },
-)
+)
+
+'''
+Publish to PyPI with:
+
+$ rm -rf prody_rhapsody.egg-info/ build/ dist/
+$ python setup.py sdist bdist_wheel
+$ twine check dist/*
+$ twine upload dist/*
+
+'''

test/test-1/.gitignore

@@ -0,0 +1 @@
+workspace/

test/test-1/test-1.py

@@ -1,25 +1,30 @@
-import numpy as np
 import sys
-
-sys.path.append('../../')
+import os
+import numpy as np
+import prody as pd
 
 # check if rhapsody can be imported correctly
-from rhapsody import *
+sys.path.append('../../')
+import rhapsody as rd
 
 # set folders
-pathRhapsodyFolder('./data')
-pathEVmutationFolder('./data')
-from prody import pathPDBFolder
-pathPDBFolder('./data')
+if not os.path.isdir('workspace'):
+    os.mkdir('workspace')
+old_rhaps_dir = rd.pathRhapsodyFolder()
+old_EVmut_dir = rd.pathEVmutationFolder()
+old_prody_dir = pd.pathPDBFolder()[0]
+rd.pathRhapsodyFolder('./workspace')
+rd.pathEVmutationFolder('./data')
+pd.pathPDBFolder('./data')
 
 # test cases
 test_SAVs = [
-  'O00294 496 A T', # "good" SAV where all features are well-defined
-  'O00238 31 R H'   # "bad" SAV with no PDB structure (but does have Pfam domain)
+    'O00294 496 A T',  # "good" SAV where all features are well-defined
+    'O00238 31 R H'    # "bad" SAV with no PDB structure (but has Pfam domain)
 ]
 
 # initialize a rhapsody object
-rh = Rhapsody()
+rh = rd.Rhapsody()
 
 # import precomputed PolyPhen-2 output file
 rh.importPolyPhen2output('data/pph2-full.txt')
@@ -29,13 +34,19 @@
 
 # true labels must be set prior to exporting training data
 true_labels = {
-  'O00294 496 A T': 1,
-  'O00238 31 R H': 0
+    'O00294 496 A T': 1,
+    'O00238 31 R H': 0
 }
 rh.setTrueLabels(true_labels)
 
 # compute all features
 m = rh.exportTrainingData()
+os.rename('rhapsody-Uniprot2PDB.txt', 'workspace/rhapsody-Uniprot2PDB.txt')
+
+# restore previous settings
+rd.pathRhapsodyFolder(old_rhaps_dir)
+rd.pathEVmutationFolder(old_EVmut_dir)
+pd.pathPDBFolder(old_prody_dir)
 
 # final check
 precomp_feats = np.load('data/precomputed_features.npy')