Sourcedir (#8)

* fixed bob float/int indices bug (#7)

* Changed src/ to qml/

* updated setup install in travis yml

* updated pythonpath in travis yml

* updated pythonpath in travis yml try 2

* updated pythonpath in travis yml try 3

* updated pythonpath in travis yml try 4

* updated setup.py

* removed trusty from travis yml

* printing pythonpath in travis yml try 5

* updated pythonpath in travis yml try 5

* updated test path

* debug path 1

* updated ext_package

* working travis yml

Author: andersx

.travis.yml

@@ -16,29 +16,21 @@ install:
  - sudo apt-get install -qq gcc gfortran libblas-dev liblapack-dev
  - sudo apt-get install -qq gcc-4.8 gfortran-4.8
 
- - echo ${TRAVIS_PYTHON_VERSION}
  - |
    if [ ${TRAVIS_PYTHON_VERSION:0:1} = 3 ]; then
        sudo apt-get install python3-numpy
-       export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH}
-       # python3 setup.py build
-       # python3 setup.py install
-       pip3 install .
+       python3 setup.py install
    elif [ ${TRAVIS_PYTHON_VERSION} = "2.7" ]; then
        sudo apt-get install python-numpy
-       export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH}
-       # python2 setup.py build
-       # python2 setup.py install
-       pip2 install .
+       python2 setup.py install
+
    else
        echo "ERROR: Unknown Python version."
    fi
 
 
 before_script:
- - cd ${TRAVIS_BUILD_DIR}
- - export PYTHONPATH=/usr/local/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH}
- - export PYTHONPATH=/usr/lib/python${TRAVIS_PYTHON_VERSION}/dist-packages:${PYTHONPATH}
+ - cd ${TRAVIS_BUILD_DIR}/tests/
 
 script:
- - nosetests -v tests/*.py
+ - nosetests -v

qml/representations.py

@@ -21,6 +21,7 @@
 # SOFTWARE.
 
 from __future__ import print_function
+from __future__ import division
 
 import numpy as np
 
@@ -44,7 +45,7 @@ def vector_to_matrix(v):
         exit(1)
 
     n = v.shape[0]
-    l = (-1 + int(np.sqrt(8*n+1)))/2
+    l = (-1 + int(np.sqrt(8*n+1)))//2
     M = np.empty((l,l))
 
     index = 0
@@ -153,10 +154,11 @@ def generate_bob(coordinates, nuclear_charges, atomtypes, size=23, asize={"O":3,
             if atom1 > atom2:
                 continue
             if atom1 == atom2:
-                size = size1*(size1-1)/2
+                size = size1*(size1-1)//2
                 feature_vector = np.zeros(size)
                 sub_matrix = coulomb_matrix[np.ix_(pos1,pos1)]
-                feature_vector[:pos1.size*(pos1.size-1)/2] = sub_matrix[np.triu_indices(pos1.size, 1)]
+                feature_vector[:pos1.size*(pos1.size-1)//2] = sub_matrix[np.triu_indices(pos1.size, 1)]
+
                 feature_vector.sort()
                 descriptor.append(feature_vector[:])
             else:

setup.py

@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2016"
 __credits__ = ["Anders S. Christensen (2016) https://github.com/qmlcode/qml"]
 __license__ = "MIT"
-__version__ = "0.2.11"
+__version__ = "0.2.12"
 __maintainer__ = "Anders S. Christensen"
 __email__ = "[email protected]"
 __status__ = "Beta"
@@ -95,6 +95,7 @@ def setup_pepytools():
     setup(
 
         name="qml",
+        packages=['qml'],
 
         # metadata
         version=__version__,
@@ -103,12 +104,12 @@ def setup_pepytools():
         platforms = 'Any',
         description = __description__,
         long_description = readme(),
-        keywords = 'Quantum Machine Learning',
+        keywords = ['Machine Learning', 'Quantum Chemistry'],
+        classifiers = [],
         url = __url__,
 
         # set up package contents
-        package_dir={'qml': 'qml'},
-        packages=['qml'],
+
         ext_package = 'qml',
         ext_modules = [
               ext_farad_kernels,

tests/test_wrappers.py

@@ -27,15 +27,15 @@ def get_energies(filename):
 def test_arad_wrapper():
 
     # Parse file containing PBE0/def2-TZVP heats of formation and xyz filenames
-    data = get_energies("tests/hof_qm7.txt")
+    data = get_energies("hof_qm7.txt")
 
     # Generate a list of qml.Compound() objects
     mols = []
 
     for xyz_file in sorted(data.keys())[:50]:
 
         # Initialize the qml.Compound() objects
-        mol = qml.Compound(xyz="tests/qm7/" + xyz_file)
+        mol = qml.Compound(xyz="qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]