From bc1ca981daf7af712aa966c6ea2b8a1d975225a8 Mon Sep 17 00:00:00 2001 From: djbajic Date: Wed, 29 Jul 2020 16:55:37 +0200 Subject: [PATCH] Added robust identification of library files --- cometspy/__init__.py | 3 - cometspy/__pycache__/__init__.cpython-36.pyc | Bin 435 -> 325 bytes cometspy/__pycache__/__init__.cpython-38.pyc | Bin 0 -> 333 bytes cometspy/__pycache__/comets.cpython-36.pyc | Bin 13907 -> 12199 bytes cometspy/__pycache__/comets.cpython-38.pyc | Bin 0 -> 11783 bytes cometspy/__pycache__/layout.cpython-36.pyc | Bin 34965 -> 34194 bytes cometspy/__pycache__/layout.cpython-38.pyc | Bin 0 -> 31137 bytes cometspy/__pycache__/model.cpython-36.pyc | Bin 0 -> 19783 bytes cometspy/__pycache__/model.cpython-38.pyc | Bin 0 -> 19479 bytes cometspy/__pycache__/params.cpython-36.pyc | Bin 0 -> 5480 bytes cometspy/__pycache__/params.cpython-38.pyc | Bin 0 -> 5516 bytes cometspy/comets.py | 114 ++++++++++--------- 12 files changed, 59 insertions(+), 58 deletions(-) create mode 100644 cometspy/__pycache__/__init__.cpython-38.pyc create mode 100644 cometspy/__pycache__/comets.cpython-38.pyc create mode 100644 cometspy/__pycache__/layout.cpython-38.pyc create mode 100644 cometspy/__pycache__/model.cpython-36.pyc create mode 100644 cometspy/__pycache__/model.cpython-38.pyc create mode 100644 cometspy/__pycache__/params.cpython-36.pyc create mode 100644 cometspy/__pycache__/params.cpython-38.pyc diff --git a/cometspy/__init__.py b/cometspy/__init__.py index bb761fb..c91d77a 100644 --- a/cometspy/__init__.py +++ b/cometspy/__init__.py @@ -1,7 +1,4 @@ from cometspy.comets import comets -from cometspy.comets import CorruptLine -from cometspy.comets import UnallocatedMetabolite -from cometspy.comets import OutOfGrid from cometspy.model import model from cometspy.layout import layout from cometspy.params import params diff --git a/cometspy/__pycache__/__init__.cpython-36.pyc b/cometspy/__pycache__/__init__.cpython-36.pyc index 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b/cometspy/comets.py index a14f3cf..afeb906 100644 --- a/cometspy/comets.py +++ b/cometspy/comets.py @@ -9,6 +9,7 @@ import subprocess as sp import pandas as pd import os +import glob import numpy as np from cometspy.layout import layout from cometspy.params import params @@ -17,24 +18,12 @@ __copyright__ = "Copyright 2019, The COMETS Consortium" __credits__ = ["Djordje Bajic", "Jean Vila", "Jeremy Chacon"] __license__ = "MIT" -__version__ = "0.3.0" +__version__ = "0.3.7" __maintainer__ = "Djordje Bajic" __email__ = "djordje.bajic@yale.edu" __status__ = "Beta" -class CorruptLine(Exception): - pass - - -class OutOfGrid(Exception): - pass - - -class UnallocatedMetabolite(Exception): - pass - - def readlines_file(filename): f = open(filename, 'r') f_lines = f.readlines() @@ -42,8 +31,6 @@ def readlines_file(filename): return f_lines - - class comets: ''' This class sets up an environment with all necessary for @@ -56,8 +43,9 @@ def __init__(self, layout, parameters, working_dir=''): self.working_dir = os.getcwd() + '/' + working_dir self.GUROBI_HOME = os.environ['GUROBI_HOME'] self.COMETS_HOME = os.environ['COMETS_HOME'] - - self.VERSION = 'comets_evo' + + self.VERSION = os.path.splitext(os.listdir(os.environ['COMETS_HOME'] + + '/bin')[0])[0] # set default classpaths, which users may change self.build_default_classpath_pieces() @@ -84,44 +72,60 @@ def build_default_classpath_pieces(self): self.classpath_pieces = {} self.classpath_pieces['gurobi'] = (self.GUROBI_HOME + '/gurobi.jar') - self.classpath_pieces['junit'] = (self.COMETS_HOME + - '/lib/junit/junit-4.12.jar') - self.classpath_pieces['hamcrest'] = (self.COMETS_HOME + - '/lib/junit/hamcrest-core-1.3.jar') - self.classpath_pieces['jogl_all'] = (self.COMETS_HOME + - '/lib/jogl/jogamp-all-' + - 'platforms/jar/jogl-all.jar') - self.classpath_pieces['gluegen_rt'] = (self.COMETS_HOME + - '/lib/jogl/jogamp-all-' + - 'platforms/jar/gluegen-rt.jar') - self.classpath_pieces['gluegen'] = (self.COMETS_HOME + - '/lib/jogl/jogamp-all-' + - 'platforms/jar/gluegen.jar') - self.classpath_pieces['gluegen_rt_natives'] = (self.COMETS_HOME + - '/lib/jogl/jogamp-' + - 'all-platforms/jar/' + - 'gluegen-rt-natives-' + - 'linux-amd64.jar') - self.classpath_pieces['jogl_all_natives'] = (self.COMETS_HOME + - '/lib/jogl/' + - 'jogamp-all-platforms/' + - 'jar/jogl-all-natives-' + - 'linux-amd64.jar') - self.classpath_pieces['jmatio'] = (self.COMETS_HOME + - '/lib/JMatIO/lib/jamtio.jar') - self.classpath_pieces['jmat'] = (self.COMETS_HOME + - '/lib/JMatIO/JMatIO-041212/' + - 'lib/jmatio.jar') - self.classpath_pieces['concurrent'] = (self.COMETS_HOME + - '/lib/colt/lib/concurrent.jar') - self.classpath_pieces['colt'] = (self.COMETS_HOME + - '/lib/colt/lib/colt.jar') - self.classpath_pieces['lang3'] = (self.COMETS_HOME + - '/lib/commons-lang3-3.7/' + - 'commons-lang3-3.7.jar') - self.classpath_pieces['math3'] = (self.COMETS_HOME + - '/lib/commons-math3-3.6.1/' + - 'commons-math3-3.6.1.jar') + + self.classpath_pieces['junit'] = glob.glob(self.COMETS_HOME + + '/lib/junit' + '/**/*junit*', + recursive=True)[0] + self.classpath_pieces['hamcrest'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/*hamcrest*', + recursive=True)[0] + + self.classpath_pieces['jogl_all'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/jogl-all.jar', + recursive=True)[0] + self.classpath_pieces['gluegen_rt'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/gluegen-rt.jar', + recursive=True)[0] + self.classpath_pieces['gluegen'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/gluegen.jar', + recursive=True)[0] + self.classpath_pieces['gluegen_rt_natives'] = glob.glob( + self.COMETS_HOME + '/lib' + '/**/gluegen-rt-natives-linux-amd64.jar'), + recursive=True)[0] + self.classpath_pieces['jogl_all_natives'] = glob.glob( + self.COMETS_HOME + '/lib' + '/**/jogl-all-natives-linux-amd64.jar'), + recursive=True)[0] + + self.classpath_pieces['jmatio'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/jamtio.jar', + recursive=True)[0] + self.classpath_pieces['jmat'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/jmatio.jar', + recursive=True)[0] + + self.classpath_pieces['concurrent'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/concurrent.jar', + recursive=True)[0] + self.classpath_pieces['colt'] = glob.glob(self.COMETS_HOME + + '/lib' + '/**/colt.jar', + recursive=True)[0] + + __lang3 = glob.glob(self.COMETS_HOME + + '/lib' + '/**/commons-lang3*jar', + recursive=True) + self.classpath_pieces['lang3'] = [i for i in __lang3 + if 'test' not in i + and 'sources' not in i][0] + + __math3 = glob.glob(self.COMETS_HOME + + '/lib' + '/**/commons-math3*jar', + recursive=True) + self.classpath_pieces['math3'] = [i for i in __math3 + if 'test' not in i + and 'sources' not in i + and 'tools' not in i + and 'javadoc' not in i][0] + self.classpath_pieces['bin'] = (self.COMETS_HOME + '/bin/' + self.VERSION + '.jar')