Merge pull request #19 from tovrstra/cipy37

Enable CI with Python 3.7

.travis.yml

@@ -1,20 +1,15 @@
 env:
   matrix:
     - MYCONDAPY=2.7
-    # - MYCONDAPY=3.7
+    - MYCONDAPY=3.6
+    - MYCONDAPY=3.7
   global:
     # ANACONDA_TOKEN
-    - secure: "JCX7xPCgInrZVvt78cZeU+M4dx0CWC7MmVawSR4GqoAxrscG5yEkTjbG0uL6jVc1OxV2wiEzzY\
-rtYYUnRY4W0UCs2hHSew99REUKm4UE52mKI+pcN0KDEVdub2pcNamfL1t00mjfOG6fzOZ02dN+ugDSmJJXLGOzYRB\
-mAZNgWC4="
+    - secure: "C9W6W6tPzXEhMWpkrRSf3lx6f3JJ5j5jZCsGymUQqrF9SU7RLgTvINc57M72s+I9enaL8wvldELzut0pamzMxuicFeFsSZzPlBuPdJcAy1QdxDYI3HWM8g/TmLTq9PV9sBgmbJ7rO7hGYdAXcTcrfFQk3SBARUWF5IGA95k+Kto="
     # GITHUB_TOKEN
-    - secure: "JjZdWGS8ZxYw5GBChepbu4jEJpT5Hemgj4DITkmridUdyjRB+hpxxR3z08pDz3SXkmuEsXyLsx\
-7RJAg2a+IpCnK8sG4wrOyb3Jf0tXhE1vKa1t80CVXDd0somQe6Mna+7X5SrOsP5pLs1IsaP/j6pnrDCPB2wUP3g/j\
-/iAQ1SP8="
+    - secure: "Skwu+NVG5NuZdp6G8N4y4dPS4nGmifg2NSgp/Vz2vUO0R34IrdY/lBT0aWoDMVxxYnG6h8U0S4mr3NKgVvcbugXD/omDDLJlg07PmpByrZI42gSpRcnQ6CVq8teEwCFT923ZaM5T+jujTHHQ3fzP219J/Jy+WxyImUjDVTxIzBQ="
     # PYPI_PASSWD
-    - secure: "CVw8wOQNRR7E7McAsy52Rq3f1eAvn4ukfWhW6Nn5H7GwQzha+qykm1MOnj3U1qsg7qvPvg0k2L\
-wVYkPU6nImdqHqQt8R8ekiNQNP9z97pGlJDC8T3hc/5VpvaRQA3E2wI5jzvHhNLafum/ss5h1+CsOs2AkdKgwRzM6\
-HlxbmLCE="
+    - secure: "K3A2uBMjw2akoLaVeKMkW7kpxsui5yz9GClUjWgP2L/hbt9S4S81fwE+8htw2gDmM1ehFDhWgbHYU1HomB3k6KHhaBxmtyZ842dewqZRgtdwKQUyVleK0FaB+I1MpJyVggABfAbwSuqCDaL2QxDVnDmwdJ45yed4DPemyuCMkEw="
     - PYPKG=tamkin
     - GITHUB_REPO_NAME=molmod/tamkin
 
@@ -48,21 +43,19 @@ install:
     fi;
   fi
 - bash miniconda.sh -b -p $HOME/miniconda
-- export PATH="$HOME/miniconda/bin:$PATH"
+- source ~/miniconda/bin/activate
 - hash -r
 
 # Configure conda and get a few essentials
 - conda config --set always_yes yes --set changeps1 no
-- conda update -q conda
+- conda update conda
 # Get the right python version for building. This only does something for 3.5.
 # Install extra package needed to make things work. Most things can be listed as
 # dependencies on metal.yaml and setup.py, unless setup.py already imports them.
 # Install conda tools for packaging and uploading
-- conda install python=${MYCONDAPY} sphinx conda-build anaconda-client numpy
+- conda install python=${MYCONDAPY} sphinx conda-build anaconda-client numpy codecov coverage nose graphviz conda-verify
 # Add the molmod channel to get access to the molmod dependency
 - conda config --add channels molmod
-# Install more recent stuff with pip
-- pip install codecov coverage
 # Show conda info for debugging
 - conda info -a
 
@@ -78,7 +71,7 @@ script:
 
 # Build the conda package
 - git fetch origin --tags
-- conda build -q tools/conda.recipe
+- conda build tools/conda.recipe
 
 # Build source package, should work too and needed for deployment.
 - python setup.py sdist

doc/getscriptdoc.py

@@ -38,6 +38,6 @@
 import imp
 import codecs
 
-script = imp.load_source('tamkin-driver', '../scripts/tamkin-driver')
+script = imp.load_source('tamkin-driver', '../tamkin/driver.py')
 with codecs.open('reference/tamkin-driver.rst', 'w', 'utf-8') as f:
     f.write(script.__doc__)

doc/tutorial/install.rst

@@ -53,30 +53,31 @@ distribution to install these dependencies.
 
 The following software must be installed for TAMkin:
 
-* Python >=2.7,<3.0: http://www.python.org/doc/
+* Python >=2.7,>=3.6: http://www.python.org/doc/
 * Numpy >=1.0: http://numpy.scipy.org/
 * Scipy >=0.17.1: http://www.scipy.org/
 * MatPlotLib >=1.1: http://matplotlib.org/
 * MolMod >=1.3.1: https://github.com/molmod/molmod/
 * Nosetests >=0.11: http://nose.readthedocs.io/en/latest/
 
-Most Linux distributions can install most required software with a single command. Except
-for Python, missing dependencies will get automatically installed by pip. (See below.)
+Most Linux distributions can install most required software with a single
+command. Except for Python, missing dependencies will get automatically
+installed by pip. (See below.)
 
 * **Ubuntu**
 
-    sudo apt-get install python python-numpy python-scipy python-matplotlib
+    sudo apt-get install python python-numpy python-scipy python-matplotlib python-nose
 
 * **Debian 5** or newer. You first have to become root because the sudo program is not
   configured by default::
 
     su -
-    apt-get install python python-numpy python-scipy python-matplotlib
+    apt-get install python python-numpy python-scipy python-matplotlib python-nose
     exit
 
-* **Fedora 17 to 22**
+* **Fedora 23 and up**
 
-    sudo yum install python numpy scipy python-matplotlib
+    sudo dnf install python numpy scipy python-matplotlib python-nose
 
 
 Installation
@@ -88,20 +89,22 @@ TAMkin can be installed with pip (system wide or in a virtual environment):
 
     pip install numpy
     pip install tamkin
+    pip install nose  # only needed to run unit tests
 
 Alternatively, you can install TAMkin in your home directory:
 
 .. code:: bash
 
     pip install numpy --user
     pip install tamkin --user
+    pip install nose --user  # only needed to run unit tests
 
-Lastly, you can also install MolMod with conda. (See
+Lastly, you can also install TAMkin with conda. (See
 https://www.continuum.io/downloads)
 
 .. code:: bash
 
-    conda install -c molmod tamkin
+    conda install -c molmod tamkin nose
 
 
 Testing your installation

setup.py

@@ -92,18 +92,17 @@
     url='http://molmod.ugent.be/code/',
     package_dir = {'tamkin': 'tamkin'},
     packages = ['tamkin', 'tamkin.io', 'tamkin.test'],
-    scripts=["scripts/tamkin-driver"],
+    entry_points={
+        'console_scripts': ['tamkin-driver = tamkin.driver:main']
+    },
     include_package_data=True,
-    install_requires=['numpy>=1.0', 'nose>=0.11', 'matplotlib>1.1',
-                      'molmod>=1.3.2', 'scipy>=0.17.1'],
+    install_requires=['numpy>=1.0', 'matplotlib>1.1', 'molmod>=1.3.2', 'scipy>=0.17.1'],
     classifiers=[
         'Environment :: Console',
         'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
         'Operating System :: POSIX :: Linux',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Topic :: Scientific/Engineering :: Physics',

tamkin/chemmod.py

@@ -35,7 +35,7 @@
 """Convenient interfaces to define thermodynamic and kinetic models"""
 
 
-from __future__ import print_function
+from __future__ import print_function, division
 
 import numpy as np, csv
 
@@ -223,10 +223,9 @@ def write_table(self, temp, filename):
                           quantities.
             | ``filename`` -- The name of the CSV file.
         """
-        f = open(filename, "w")
-        c = csv.writer(f)
-        self.dump_table(temp, c)
-        f.close()
+        with open(filename, "w") as f:
+            c = csv.writer(f)
+            self.dump_table(temp, c)
 
 
     def dump_table(self, temp, c):
@@ -276,9 +275,8 @@ def write_to_file(self, filename):
            One argument:
             | ``filename`` -- The file to write the output.
         """
-        f = open(filename, "w")
-        self.dump(f)
-        f.close()
+        with open(filename, "w") as f:
+            self.dump(f)
 
     def dump(self, f):
         """Write all info about the model to a file."""
@@ -435,8 +433,8 @@ def __init__(self, tm, km):
         BaseKineticModel.__init__(self)
         self.tm = tm
         self.km = km
-        self._add_pfs(tm.pfs_all.iteritems())
-        self._add_pfs(km.pfs_all.iteritems())
+        self._add_pfs(tm.pfs_all.items())
+        self._add_pfs(km.pfs_all.items())
         self._set_unit(per_second=True)
 
     def rate_constant(self, temp, do_log=False):

tamkin/data.py

@@ -39,6 +39,8 @@
    output with a standardized interface.
 """
 
+from __future__ import print_function, division
+
 from tamkin.geom import transrot_basis
 
 from molmod import Molecule as BaseMolecule, MolecularGraph, ReadOnly, \
@@ -68,13 +70,13 @@ def check_hessian(self, hessian):
 
     energy = ReadOnlyAttribute(float, none=False)
     gradient = ReadOnlyAttribute(np.ndarray, none=False,
-        check=check_gradient, npdim=2, npshape=(None, 3), npdtype=float)
+        check=check_gradient, npdim=2, npshape=(None, 3), npdtype=np.floating)
     hessian = ReadOnlyAttribute(np.ndarray, none=False,
-        check=check_hessian, npdim=2, npdtype=float)
+        check=check_hessian, npdim=2, npdtype=np.floating)
     multiplicity = ReadOnlyAttribute(int)
     symmetry_number = ReadOnlyAttribute(int)
     periodic = ReadOnlyAttribute(bool)
-    fixed = ReadOnlyAttribute(np.ndarray, npdim=1, npdtype=int)
+    fixed = ReadOnlyAttribute(np.ndarray, npdim=1, npdtype=np.signedinteger)
 
     def __init__(self, numbers, coordinates, masses, energy, gradient, hessian, multiplicity=None, symmetry_number=None, periodic=False, title=None, graph=None, symbols=None, unit_cell=None, fixed=None):
         """
@@ -287,7 +289,7 @@ def read_from_file(cls, filename):
         mandatory_fields = set([
             "numbers", "coordinates", "masses", "energy", "gradient", "hessian"
         ])
-        if not set(data.iterkeys()).issuperset(mandatory_fields):
+        if not set(data).issuperset(mandatory_fields):
             raise IOError("The Checkpoint file does not contain the mandatory fields.")
         # take the mandatory fields
         constructor_args = {}
@@ -454,11 +456,11 @@ def check_top_indexes(self, top_indexes):
                 "rotating")
 
     dihedral = ReadOnlyAttribute(np.ndarray, none=False, npdim=1,
-        npshape=(4,), npdtype=int)
+        npshape=(4,), npdtype=np.signedinteger)
     top_indexes = ReadOnlyAttribute(np.ndarray, none=False,
-        check=check_top_indexes, npdim=1, npdtype=int)
+        check=check_top_indexes, npdim=1, npdtype=np.signedinteger)
     potential = ReadOnlyAttribute(np.ndarray, npdim=2, npshape=(2, None),
-        npdtype=float)
+        npdtype=np.floating)
 
     def __init__(self, dihedral, molecule=None, top_indexes=None, potential=None):
         """

scripts/tamkin-driver → tamkin/driver.py

@@ -32,8 +32,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
-#--
-#!/usr/bin/env python
+# --
 u'''\
 
 The TAMkin driver script
@@ -270,12 +269,18 @@
 '''
 
 
-from __future__ import print_function
-import sys, os, numpy as np
+from __future__ import print_function, division
+
+import sys
+import os
 from glob import glob
-from tamkin import *
+
+import numpy as np
 from molmod.periodic import periodic
 
+from tamkin import *
+
+
 # A few variables for debugging purposes only
 gradient_threshold = 1e-2
 v_threshold = 0.01
@@ -520,7 +525,7 @@ def get_pf(dn, temps):
 
 def get_chemical_formula(numbers):
     tmp = dict((number, (numbers == number).sum()) for number in np.unique(numbers))
-    return ' '.join(['%s_%i' % (periodic[number].symbol, count) for number, count in tmp.iteritems()])
+    return ' '.join(['%s_%i' % (periodic[number].symbol, count) for number, count in tmp.items()])
 
 
 def check_mass_balance(pfs1, pfs2, name1, name2):

tamkin/examples/004_alkanes/bin/analyse_static.py

@@ -70,13 +70,12 @@
 
 
 # Write the frequencies to a csv file
-f = open(os.path.join(args[0], "freqs.csv"), "w")
-print('"Frequency","Wavenumber","Vibrational temperature"', file=f)
-print('"Atomic units","1/cm","K"', file=f)
-for i in range(len(pf.vibrational.freqs)):
-    freq = pf.vibrational.freqs[i]
-    print('%e,%f,%f' % (freq, freq/lightspeed*centimeter, 2*numpy.pi*freq/boltzmann), file=f)
-f.close()
+with open(os.path.join(args[0], "freqs.csv"), "w") as f:
+    print('"Frequency","Wavenumber","Vibrational temperature"', file=f)
+    print('"Atomic units","1/cm","K"', file=f)
+    for i in range(len(pf.vibrational.freqs)):
+        freq = pf.vibrational.freqs[i]
+        print('%e,%f,%f' % (freq, freq/lightspeed*centimeter, 2*numpy.pi*freq/boltzmann), file=f)
 
 
 # B) Generate a thermo analysis report

tamkin/examples/004_alkanes/bin/xyz2psf.py

@@ -60,7 +60,7 @@
 }
 
 def get_atom_type(index, graph):
-    for atom_type, atom_filter in atom_filters.iteritems():
+    for atom_type, atom_filter in atom_filters.items():
         if atom_filter(index, graph):
             return atom_type
     raise ValueError("Unrecognized atom (index %i)." % index)

tamkin/examples/010_adk/output/get_overlap_7-7.py

@@ -47,35 +47,35 @@
 
 
 def get_freqs_and_overlap_7_7(filename):
-    f = open(filename)
-    print("-"*20)
-    print("Reading file...", filename)
+    with open(filename) as f:
+        print("-"*20)
+        print("Reading file...", filename)
 
-    # read 7th freq on first line (first element is 0, so is 8th freq)
-    for line in f:
-        words = line.split(";")
-        #freq1 = float(words[7])  # !!!!!!!!!!!!!
-        freq1 = float(words[-1])
-        break
-
-    # get 7th freq in first column (we already skipped first line)
-    # and overlap 7th-7th
-    count = 0
-    for line in f:
-        count +=1
-        if count==7:
+        # read 7th freq on first line (first element is 0, so is 8th freq)
+        for line in f:
             words = line.split(";")
-            freq2 = float(words[0])
-            #overlap = float(words[7])  # !!!!!!!!!
-            overlap = float(words[-1])
+            #freq1 = float(words[7])  # !!!!!!!!!!!!!
+            freq1 = float(words[-1])
             break
 
-    f.close()
-    print("freq1: ", freq1)
-    print("freq2: ", freq2)
-    print("overlap: ", overlap)
+        # get 7th freq in first column (we already skipped first line)
+        # and overlap 7th-7th
+        count = 0
+        for line in f:
+            count +=1
+            if count==7:
+                words = line.split(";")
+                freq2 = float(words[0])
+                #overlap = float(words[7])  # !!!!!!!!!
+                overlap = float(words[-1])
+                break
+
+        f.close()
+        print("freq1: ", freq1)
+        print("freq2: ", freq2)
+        print("overlap: ", overlap)
 
-    return freq1, freq2, overlap
+        return freq1, freq2, overlap
 
 
 import sys, glob
@@ -99,8 +99,7 @@ def get_freqs_and_overlap_7_7(filename):
 conv = 7.25163277859109E-07  # conversion factor such that frequencies are printed in 1/cm
 
 filename_out = "delta.overlaps.7-7.csv"
-f = open(filename_out,"w+")
-for i in range(len(freqs1)):
-    print(filenames[i]+";"+str(freqs1[i]/conv)+";"+str(freqs2[i]/conv)+";"+str(overlaps[i]), file=f)
-f.close()
+with open(filename_out, "w+") as f:
+    for i in range(len(freqs1)):
+        print(filenames[i]+";"+str(freqs1[i]/conv)+";"+str(freqs2[i]/conv)+";"+str(overlaps[i]), file=f)
 print("file written:", filename_out)