Remove ase and dataprovider (qmlcode#108)

* removed old dataprovider and ASE requirements

* Updated test for relocated compond

Author: andersx

qml/__init__.py

@@ -32,7 +32,6 @@
 """
 from __future__ import absolute_import
 
-from . import data
 from . import models
 from . import aglaia
 from . import math
@@ -42,6 +41,7 @@
 from . import representations
 from . import qmlearn
 from . import utils
+from .utils.compound import Compound
 
 __author__ = "Anders S. Christensen"
 __copyright__ = "Copyright 2016"

qml/aglaia/aglaia.py

@@ -40,7 +40,7 @@
 from qml.representations import generate_acsf
 from qml.aglaia.graceful_killer import _GracefulKiller
 
-from qml.data import Compound
+from qml import Compound
 from qml import representations as qml_rep
 
 import tensorflow

qml/data/__init__.py

@@ -1,5 +1,4 @@
 numpy>=1.13
 scipy
 scikit-learn
-ase
 six

qml/data/dataprovider.py

@@ -144,7 +144,6 @@ def setup_qml():
         name="qml",
         packages=[
             'qml',
-            'qml.data',
             'qml.aglaia',
             'qml.arad',
             'qml.fchl',

qml/data/xyzdataprovider.py

@@ -72,7 +72,7 @@ def test_arad():
     for xyz_file in sorted(data.keys())[:10]:
 
         # Initialize the qml.data.Compound() objects
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]

qml/data/compound.py qml/utils/compound.py

@@ -24,7 +24,7 @@
 
 import os
 
-from qml.data import Compound
+from qml import Compound
 import numpy as np
 
 def compare_lists(a, b):

requirements.txt

@@ -26,7 +26,6 @@
 import numpy as np
 
 import qml
-import qml.data
 
 from qml.kernels import laplacian_kernel
 from qml.math import cho_solve
@@ -65,14 +64,14 @@ def test_krr_gaussian_local_cmat():
     # Parse file containing PBE0/def2-TZVP heats of formation and xyz filenames
     data = get_energies(test_dir + "/data/hof_qm7.txt")
 
-    # Generate a list of qml.data.Compound() objects"
+    # Generate a list of qml.Compound() objects"
     mols = []
 
 
     for xyz_file in sorted(data.keys())[:1000]:
 
-        # Initialize the qml.data.Compound() objects
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        # Initialize the qml.Compound() objects
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]
@@ -152,8 +151,8 @@ def test_krr_laplacian_local_cmat():
 
     for xyz_file in sorted(data.keys())[:1000]:
 
-        # Initialize the qml.data.Compound() objects
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        # Initialize the qml.Compound() objects
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]

setup.py

@@ -26,7 +26,6 @@
 import numpy as np
 
 import qml
-import qml.data
 
 from qml.kernels import laplacian_kernel
 from qml.math import cho_solve
@@ -65,8 +64,8 @@ def test_krr_bob():
 
     for xyz_file in sorted(data.keys())[:1000]:
 
-        # Initialize the qml.data.Compound() objects
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        # Initialize the qml.Compound() objects
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]

test/test_arad.py

@@ -26,7 +26,6 @@
 import numpy as np
 
 import qml
-import qml.data
 
 from qml.kernels import laplacian_kernel
 from qml.math import cho_solve
@@ -65,8 +64,8 @@ def test_krr_cmat():
 
     for xyz_file in sorted(data.keys())[:1000]:
 
-        # Initialize the qml.data.Compound() objects
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        # Initialize the qml.Compound() objects
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
 
         # Associate a property (heat of formation) with the object
         mol.properties = data[xyz_file]

test/test_compound.py

@@ -31,7 +31,7 @@
 from scipy.special import binom
 from scipy.special import factorial
 
-from qml.data import Compound
+from qml import Compound
 
 from qml.math import cho_solve
 

test/test_energy_krr_atomic_cmat.py

@@ -261,7 +261,7 @@ def test_kpca():
     # Parse file containing PBE0/def2-TZVP heats of formation and xyz filenam
     data = get_energies(test_dir + "/data/hof_qm7.txt")
 
-    # Generate a list of qml.data.Compound() objects
+    # Generate a list of qml.Compound() objects
     mols = []
 
     keys = sorted(data.keys())
@@ -273,7 +273,7 @@ def test_kpca():
 
     for xyz_file in keys[:n_mols]:
 
-        mol = qml.data.Compound(xyz=test_dir + "/qm7/" + xyz_file)
+        mol = qml.Compound(xyz=test_dir + "/qm7/" + xyz_file)
         mol.properties = data[xyz_file]
         mol.generate_bob()
         mols.append(mol)

test/test_energy_krr_bob.py

@@ -58,7 +58,7 @@ def test_representations():
 
     mols = []
     for xyz_file in files:
-        mol = qml.data.Compound(xyz=path + "/" + xyz_file)
+        mol = qml.Compound(xyz=path + "/" + xyz_file)
         mols.append(mol)
 
     size = max(mol.nuclear_charges.size for mol in mols) + 1

test/test_energy_krr_cmat.py

@@ -46,7 +46,7 @@ def test_slatm_global_representation():
     mols = []
     for xyz_file in files:
 
-        mol = qml.data.Compound(xyz=path + "/" + xyz_file)
+        mol = qml.Compound(xyz=path + "/" + xyz_file)
         mols.append(mol)
 
     mbtypes = get_slatm_mbtypes(np.array([mol.nuclear_charges for mol in mols]))
@@ -79,7 +79,7 @@ def test_slatm_local_representation():
     mols = []
     for xyz_file in files:
 
-        mol = qml.data.Compound(xyz=path + "/" + xyz_file)
+        mol = qml.Compound(xyz=path + "/" + xyz_file)
         mols.append(mol)
 
     mbtypes = get_slatm_mbtypes(np.array([mol.nuclear_charges for mol in mols]))

test/test_fchl_scalar.py

@@ -67,7 +67,7 @@ def test_acsf():
 
     mols = []
     for xyz_file in files:
-        mol = qml.data.Compound(xyz=path + "/" + xyz_file)
+        mol = qml.Compound(xyz=path + "/" + xyz_file)
         mols.append(mol)
 
     elements = set()