Merge pull request #1670 from ReactionMechanismGenerator/numpy

Check numpy version before passing rcond to numpy.linalg.lstsq

rmgpy/data/kinetics/groups.py

@@ -46,6 +46,9 @@
 from rmgpy.quantity import constants
 from rmgpy.exceptions import KineticsError, UndeterminableKineticsError, DatabaseError
 
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 class KineticsGroups(Database):
@@ -409,7 +412,7 @@ def generateGroupAdditivityValues(self, trainingSet, kunits, method='Arrhenius')
             b = numpy.array(b)
             kdata = numpy.array(kdata)
 
-            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
             for t, T in enumerate(Tdata):
 
@@ -513,7 +516,7 @@ def generateGroupAdditivityValues(self, trainingSet, kunits, method='Arrhenius')
             b = numpy.array(b)
             kdata = numpy.array(kdata)
 
-            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
             # Store the results
             self.top[0].data = Arrhenius(
@@ -564,7 +567,7 @@ def generateGroupAdditivityValues(self, trainingSet, kunits, method='Arrhenius')
             A = numpy.array(A)
             b = numpy.array(b)
 
-            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
             # Store the results
             self.top[0].data = Arrhenius(

rmgpy/kinetics/arrhenius.pyx

@@ -36,6 +36,10 @@ cimport rmgpy.constants as constants
 import rmgpy.quantity as quantity
 from rmgpy.exceptions import KineticsError
 from rmgpy.kinetics.uncertainies import rank_accuracy_map
+
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 cdef class Arrhenius(KineticsModel):
@@ -162,7 +166,7 @@ cdef class Arrhenius(KineticsModel):
             for n in range(b.size):
                 A[n,:] *= weights[n]
                 b[n] *= weights[n]
-        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
         # Determine covarianace matrix to obtain parameter uncertainties
         count = klist.size

rmgpy/kinetics/chebyshev.pyx

@@ -34,6 +34,10 @@ cimport rmgpy.constants as constants
 import rmgpy.quantity as quantity
 import logging
 from rmgpy.exceptions import KineticsError
+
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 cdef class Chebyshev(PDepKineticsModel):
@@ -217,7 +221,7 @@ cdef class Chebyshev(PDepKineticsModel):
                 b[p1*nT+t1] = log10(K[t1,p1])
 
         # Do linear least-squares fit to get coefficients
-        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
         # Extract coefficients
         coeffs = numpy.zeros((degreeT,degreeP), numpy.float64)

rmgpy/kinetics/surface.pyx

@@ -34,6 +34,9 @@ cimport rmgpy.constants as constants
 import rmgpy.quantity as quantity
 from rmgpy.exceptions import KineticsError
 
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 cdef class StickingCoefficient(KineticsModel):
@@ -157,7 +160,7 @@ cdef class StickingCoefficient(KineticsModel):
             for n in range(b.size):
                 A[n, :] *= weights[n]
                 b[n] *= weights[n]
-        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+        x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
         # Determine covarianace matrix to obtain parameter uncertainties
         count = klist.size

rmgpy/statmech/torsion.pyx

@@ -50,6 +50,9 @@ import rmgpy.statmech.schrodinger as schrodinger
 from rmgpy.exceptions import NegativeBarrierException
 import logging
 
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 cdef class Torsion(Mode):
@@ -539,7 +542,7 @@ cdef class HinderedRotor(Torsion):
             # This row forces dV/dangle = 0 at angle = 0
             for m in range(numterms):
                 A[N,m+numterms] = 1
-            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
             fit = numpy.dot(A,x)
             x *= 0.001
             # This checks if there are any negative values in the forier fit.

rmgpy/thermo/wilhoit.pyx

@@ -36,6 +36,9 @@ cimport rmgpy.constants as constants
 import rmgpy.quantity as quantity
 import scipy.linalg
 
+# Prior to numpy 1.14, `numpy.linalg.lstsq` does not accept None as a value
+RCOND = -1 if int(numpy.__version__.split('.')[1]) < 14 else None
+
 ################################################################################
 
 cdef class Wilhoit(HeatCapacityModel):
@@ -277,7 +280,7 @@ cdef class Wilhoit(HeatCapacityModel):
                 for j in range(4):
                     A[i,j] = (y*y*y - y*y) * y**j
                 b[i] = ((Cpdata[i] - Cp0) / (CpInf - Cp0) - y*y)
-            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=None)
+            x, residues, rank, s = numpy.linalg.lstsq(A, b, rcond=RCOND)
 
             self.B = (float(B),"K")
             self.a0 = float(x[0])

utilities.py

@@ -31,6 +31,7 @@
 """
 This module contains utilities related to compilation and code maintenance.
 """
+from __future__ import print_function
 
 import argparse
 import os
@@ -43,16 +44,16 @@ def check_dependencies():
     """
     Checks for and locates major dependencies that RMG requires.
     """
-    missing = False
+    missing = install_rdkit = False
 
-    print '\nChecking vital dependencies...\n'
-    print '{0:<15}{1:<15}{2}'.format('Package', 'Version', 'Location')
+    print('\nChecking vital dependencies...\n')
+    print('{0:<15}{1:<15}{2}'.format('Package', 'Version', 'Location'))
 
     # Check for symmetry
     try:
         result = subprocess.check_output('symmetry -h', stderr=subprocess.STDOUT, shell=True)
     except subprocess.CalledProcessError:
-        print '{0:<30}{1}'.format('symmetry', 'Not found. Please install in order to use QM.')
+        print('{0:<30}{1}'.format('symmetry', 'Not found. Please install in order to use QM.'))
         missing = True
     else:
         match = re.search(r'\$Revision: (\S*) \$', result)
@@ -62,16 +63,16 @@ def check_dependencies():
         else:
             location = subprocess.check_output('which symmetry', shell=True)
 
-        print '{0:<15}{1:<15}{2}'.format('symmetry', version, location.strip())
+        print('{0:<15}{1:<15}{2}'.format('symmetry', version, location.strip()))
 
     # Check for RDKit
     try:
         import rdkit
         from rdkit import Chem
     except ImportError:
-        print '{0:<30}{1}'.format('RDKit',
-                                  'Not found. Please install RDKit version 2015.03.1 or later with InChI support.')
-        missing = True
+        print('{0:<30}{1}'.format('RDKit',
+                                  'Not found. Please install RDKit version 2015.03.1 or later with InChI support.'))
+        missing = install_rdkit = True
     else:
         try:
             version = rdkit.__version__
@@ -81,65 +82,69 @@ def check_dependencies():
         inchi = Chem.inchi.INCHI_AVAILABLE
 
         if version:
-            print '{0:<15}{1:<15}{2}'.format('RDKit', version, location)
+            print('{0:<15}{1:<15}{2}'.format('RDKit', version, location))
             if not inchi:
-                print 'RDKit installed without InChI Support. Please install with InChI.'
-                missing = True
+                print('    !!! RDKit installed without InChI Support. Please install with InChI.')
+                missing = install_rdkit = True
         else:
-            print 'RDKit version out of date, please install RDKit version 2015.03.1 or later with InChI support.'
-            missing = True
+            print('    !!! RDKit version out of date, please install RDKit version 2015.03.1 or later with InChI support.')
+            missing = install_rdkit = True
 
     # Check for OpenBabel
     try:
         import openbabel
     except ImportError:
-        print '{0:<30}{1}'.format('OpenBabel',
-                                  'Not found. Necessary for SMILES/InChI functionality for nitrogen compounds.')
+        print('{0:<30}{1}'.format('OpenBabel',
+                                  'Not found. Necessary for SMILES/InChI functionality for nitrogen compounds.'))
         missing = True
     else:
         version = openbabel.OBReleaseVersion()
         location = openbabel.__file__
-        print '{0:<15}{1:<15}{2}'.format('OpenBabel', version, location)
+        print('{0:<15}{1:<15}{2}'.format('OpenBabel', version, location))
 
     # Check for lpsolve
     try:
         import lpsolve55
     except ImportError:
-        print '{0:<30}{1}'.format('lpsolve55',
-                                  'Not found. Necessary for generating Clar structures for aromatic species.')
+        print('{0:<30}{1}'.format('lpsolve55',
+                                  'Not found. Necessary for generating Clar structures for aromatic species.'))
         missing = True
     else:
         location = lpsolve55.__file__
-        print '{0:<30}{1}'.format('lpsolve55', location)
+        print('{0:<30}{1}'.format('lpsolve55', location))
 
     # Check for pyrdl
     try:
         import py_rdl
     except ImportError:
-        print '{0:<30}{1}'.format('pyrdl', 'Not found. Necessary for ring perception algorithms.')
+        print('{0:<30}{1}'.format('pyrdl', 'Not found. Necessary for ring perception algorithms.'))
         missing = True
     else:
         location = py_rdl.__file__
-        print '{0:<30}{1}'.format('pyrdl', location)
+        print('{0:<30}{1}'.format('pyrdl', location))
 
     if missing:
-        print """
+        print("""
 There are missing dependencies as listed above. Please install them before proceeding.
 
 Using Anaconda, these dependencies can be individually installed from the RMG channel as follows:
 
     conda install -c rmg [package name]
-
+{0}
 You can alternatively update your environment and install all missing dependencies as follows:
 
     conda env update -f environment_[linux/mac/windows].yml  # Choose the correct file for your OS
 
 Be sure to activate your conda environment (rmg_env by default) before installing or updating.
-"""
+""".format("""
+RDKit should be installed from the RDKit channel instead:
+
+    conda install -c rdkit rdkit
+""" if install_rdkit else ''))
     else:
-        print """
+        print("""
 Everything was found :)
-"""
+""")
 
 
 def clean(subdirectory=''):
@@ -200,7 +205,7 @@ def update_headers():
 ###############################################################################
 """
 
-    print header
+    print(header)
 
     def replace_header(oldfile):
         newfile = os.path.join('tmp', 'tempfile')
@@ -259,16 +264,16 @@ def replace_header(oldfile):
     for root_dir in root_dirs:
         for root, dirs, files in os.walk(root_dir):
             if 'test_data' in root or 'files' in root or '/tools/data' in root or 'arkane/data' in root:
-                print 'Skipping ' + root
+                print('Skipping ' + root)
                 continue
-            print root
+            print(root)
             for f in files:
                 ext = os.path.splitext(f)[1]
                 if ext in ['.py', '.pyx', '.pxd']:
                     filelist.append(os.path.join(root, f))
 
     for f in filelist:
-        print 'Updating {0} ...'.format(f)
+        print('Updating {0} ...'.format(f))
         replace_header(f)
 
     # Remove temporary directory