setup refactored.

modelbuilder launcher moved to setup.py
dragos launchers fixed. now use configs.
config.py refactored

readme upd

MODtools/config.py

@@ -21,18 +21,19 @@
 from os.path import join, exists, dirname, expanduser
 
 CHEMAXON = "https://cimm.kpfu.ru/webservices"
-JCHEMBIN = '/opt/JChem/bin'
-FRAGMENTOR = '/opt/fragmentor/fragmentor'
-EED = '/opt/dragos/eedstart.sh'
-COLOR = '/opt/dragos/colorstart.sh'
-GACONF = '/opt/dragos/gaconfstarter.sh'
+JCHEMBIN = join(expanduser('~'), 'ChemAxon/JChem/bin')
+FRAGMENTOR = join(expanduser('~'), 'fragmentor/fragmentor')
 
-config_list = ('CHEMAXON', 'JCHEMBIN', 'FRAGMENTOR', 'EED', 'COLOR', 'GACONF')
+EED = 'eedstart.sh'
+COLOR = 'colorstart.sh'
+GACONF = 'gaconfstarter.sh'
 
-config_dirs = [join(x, '.MODtools.ini') for x in (expanduser('~'), '/etc', dirname(__file__))]
+config_list = ('CHEMAXON', 'JCHEMBIN', 'FRAGMENTOR')
+
+config_dirs = [join(x, '.MODtools.ini') for x in (dirname(__file__), expanduser('~'), '/etc')]
 
 if not any(exists(x) for x in config_dirs):
-    with open(config_dirs[0], 'w') as f:
+    with open(config_dirs[1], 'w') as f:
         f.write('\n'.join('%s = %s' % (x, y or '') for x, y in globals().items() if x in config_list))
 
 with open(next(x for x in config_dirs if exists(x))) as f:

MODtools/modelbuilder.py

@@ -40,7 +40,7 @@
 from .descriptors.eed import Eed
 from .descriptors.fragmentor import Fragmentor
 from .estimators.svmodel import SVModel
-from .parsers import MBparser
+from .parsers import MBparser, argparser
 
 
 def desc_starter(func, file_dump, out_file, fformat, header, is_reaction):
@@ -326,3 +326,10 @@ def __dragos_svm_fit(self, input_file, _type):
                         svm.append({'scale' if y == 'scaled' else 'orig': list(x.values())[0]})
                     return svm, cleared
         raise Exception('GAConf failed')
+
+
+def launcher():
+    args = argparser()
+    input_file = args.pop('input')
+    main = ModelBuilder(args)
+    main.run(input_file)

README.md

@@ -0,0 +1,39 @@
+MODTools
+=========
+classes for models preparation
+
+usage
+=====
+modeler -h
+
+
+INSTALL
+=====
+
+*step 1:*
+
+    pip install -U git+https://github.com/stsouko/MODtools.git@master#egg=MODtools --process-dependency-links --allow-all-external
+
+*step 2:*
+
+type
+
+    modeler -h
+
+*step 3:*
+
+add or edit ~/.MODtools.rc or /etc/.MODtools.rc file. local *.rc has higher priority.
+
+    GACONF=~/GAconfig
+    UTILS_DIR=~
+    CHMXN_DIR=~/ChemAxon
+
+replace default paths to actual.
+* GACONF - Dragos's Genetic SVM optimizer
+* CHMXN_DIR - dir with JChem distributive
+* UTILS_DIR - dir with Dragos's utilities
+
+edit `~/.MODtools.ini` or add `/etc/.MODtools.ini`
+or add file into package `MODtools/.MODtools.ini` [useful for unpacked MODtools Lib]
+
+priority: `MODtools/.MODtools.ini` >> `~/.MODtools.ini` >> `/etc/.MODtools.ini`

SETUP/colorstart.sh

@@ -1,9 +1,18 @@
 #!/usr/bin/env bash
 
-UTILS_DIR=/home/stsouko
-CHMXN_DIR=/home/stsouko/ChemAxon
+UTILS_DIR=~
+CHMXN_DIR=~/ChemAxon
+
+if [ -f /etc/.MODtools.rc ]; then
+    . /etc/.MODtools.rc
+fi
+
+if [ -f ~/.MODtools.rc ]; then
+    . ~/.MODtools.rc
+fi
+
 export SETUP_DIR=${UTILS_DIR}/Utils
 export FORCEFIELD=${SETUP_DIR}/cvffTemplates.xml
 export CLASSPATH=${CHMXN_DIR}/JChem/lib/jchem.jar:${UTILS_DIR}:
 
-java Utils/CA_Prop_Map2011 -f $1 -o $2 -stdoptions $3
+java Utils/CA_Prop_Map2011 -f $1 -o $2 -stdoptions $3

SETUP/dragosgfstarter.sh

@@ -6,7 +6,21 @@
 # $4 repetitions
 # $5 CV
 # $workdir /path/to/worktmp.file{/}
-GACONF=/path/to/ga
+
+GACONF_PATH=~/GAconfig
+LIBSVM_PATH=${GACONF_PATH}/libsvm-3.20
+
+if [ -f /etc/.MODtools.rc ]; then
+    . /etc/.MODtools.rc
+fi
+
+if [ -f ~/.MODtools.rc ]; then
+    . ~/.MODtools.rc
+fi
+
+export LIBSVM=${SVMLIB_PATH}
+export GACONF=${GACONF_PATH}
+export LC_ALL=en_US.UTF-8
 
 datadir=$1
 workdir=${datadir}/work

SETUP/eedstart.sh

@@ -2,8 +2,16 @@
 
 [ $# -ge 1 -a -f "$1" ] && input="$1" || input="-"
 
-UTILS_DIR=/home/stsouko
-CHMXN_DIR=/home/stsouko/ChemAxon
+UTILS_DIR=~
+CHMXN_DIR=~/ChemAxon
+
+if [ -f /etc/.MODtools.rc ]; then
+    . /etc/.MODtools.rc
+fi
+
+if [ -f ~/.MODtools.rc ]; then
+    . ~/.MODtools.rc
+fi
 
 export CLASSPATH=${CHMXN_DIR}/JChem/lib/jchem.jar:${UTILS_DIR}:
 

requirenments.txt

@@ -0,0 +1,8 @@
+typing
+pandas
+scipy
+dill
+sortedcontainers
+sklearn
+requests
+git+https://github.com/stsouko/CGRtools.git@master#egg=CGRtools

setup.cfg

@@ -0,0 +1,2 @@
+[easy_install]
+allow_hosts = github.com, pypi.python.org

setup.py

@@ -25,18 +25,17 @@
 setup(
     name='modtools',
     version=version(),
-    packages=find_packages(exclude=[]),
+    packages=find_packages(),
     url='https://github.com/stsouko/MODtools',
     license='AGPLv3',
     author='Dr. Ramil Nugmanov',
     author_email='stsouko@live.ru',
     description='Modeler tools',
-    scripts=['modelbuilder.py'],
+    entry_points={'console_scripts': ['modeler=MODtools.modelbuilder:launcher']},
+    scripts=['SETUP/colorstart.sh', 'SETUP/dragosgfstarter.sh', 'SETUP/eedstart.sh'],
     package_data={'': ['unwanted.elem', 'standardrules_dragos.rules']},
-    requires=['networkx', 'typing', 'periodictable', 'numpy', 'pandas', 'dill', 'sortedcontainers', 'sklearn',
-              'requests', 'CGRtools'],
-    dependency_links=['https://github.com/stsouko/CGRtools.git@master#egg=CGRtools',
-                      'https://github.com/networkx/networkx.git@master#egg=networkx'],
+    install_requires=['typing', 'pandas', 'scipy', 'dill', 'sortedcontainers', 'sklearn', 'requests', 'CGRtools'],
+    dependency_links=['git+https://github.com/stsouko/CGRtools.git@master#egg=CGRtools-2.6'],
     long_description='Modeler tools distributive. include ISIDA Fragmentor and EED python wrappers',
 
     keywords="tools modeler cli ISIDA Framentor EED SVM IAP",