Directory structure (qmlcode#71)

* Reverts to old directory structure
* Fix authors in several __init__ files that are updated

Author: andersx

docs/source/qml.rst

@@ -8,31 +8,31 @@ Python API documentation
 qml\.representations module
 ---------------------------
 
-.. automodule:: qml.ml.representations.representations
+.. automodule:: qml.representations
     :members:
     :undoc-members:
     :show-inheritance:
 
 qml\.kernels module
 -------------------
 
-.. automodule:: qml.ml.kernels
+.. automodule:: qml.kernels
     :members:
     :undoc-members:
     :show-inheritance:
 
 qml\.distance module
 --------------------
 
-.. automodule:: qml.ml.kernels.distance
+.. automodule:: qml.kernels.distance
     :members:
     :undoc-members:
     :show-inheritance:
 
 qml\.math module
 ----------------
 
-.. automodule:: qml.ml.math
+.. automodule:: qml.math
     :members:
     :undoc-members:
     :show-inheritance:
@@ -55,15 +55,15 @@ qml\.Compound class
 qml\.fchl module
 ----------------
 
-.. automodule:: qml.ml.representations.fchl
+.. automodule:: qml.representations.fchl
     :members:
     :show-inheritance:
 
 
 qml\.wrappers module
 --------------------
 
-.. automodule:: qml.ml.kernels.wrappers
+.. automodule:: qml.kernels.wrappers
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/qml_examples/examples.ipynb

@@ -73,7 +73,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from qml.ml.representations import *\n",
+    "from qml.representations import *\n",
     "\n",
     "# Dummy coordinates for a water molecule\n",
     "coordinates = np.array([[1.464, 0.707, 1.056],\n",
@@ -121,7 +121,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from qml.ml.kernels import gaussian_kernel\n",
+    "from qml.kernels import gaussian_kernel\n",
     "\n",
     "# Generate a numpy-array of the representation\n",
     "X = np.array([c.representation for c in compounds])\n",
@@ -149,7 +149,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from qml.ml.kernels import get_local_kernels_gaussian\n",
+    "from qml.kernels import get_local_kernels_gaussian\n",
     "\n",
     "# Assume the QM7 dataset is loaded into a list of Compound()\n",
     "for compound in qm7:\n",
@@ -195,7 +195,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations import get_slatm_mbtypes\n",
+    "from qml.representations import get_slatm_mbtypes\n",
     "\n",
     "# Assume 'qm7' is a list of Compound() objects.\n",
     "mbtypes = get_slatm_mbtypes([mol.nuclear_charges for compound in qm7])\n",
@@ -211,7 +211,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The ``local`` keyword in this example specifies that a local representation is produced. Alternatively the SLATM representation can be generate via the ``qml.ml.representations`` module:"
+    "The ``local`` keyword in this example specifies that a local representation is produced. Alternatively the SLATM representation can be generate via the ``qml.representations`` module:"
    ]
   },
   {
@@ -220,7 +220,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations import generate_slatm\n",
+    "from qml.representations import generate_slatm\n",
     "\n",
     "# Dummy coordinates\n",
     "coordinates = ... \n",
@@ -249,7 +249,7 @@
     "## Generating the FCHL representation\n",
     "\n",
     "The FCHL representation does not have an explicit representation in the form of a vector, and the kernel elements must be calculated analytically in a separate kernel function.\n",
-    "The syntax is analogous to the explicit representations (e.g. Coulomb matrix, BoB, SLATM, etc), but is handled by kernels from the separate ``qml.ml.representations.fchl`` module.\n",
+    "The syntax is analogous to the explicit representations (e.g. Coulomb matrix, BoB, SLATM, etc), but is handled by kernels from the separate ``qml.representations.fchl`` module.\n",
     "\n",
     "The code below show three ways to create the input representations for the FHCL kernel functions.\n",
     "\n",
@@ -279,7 +279,7 @@
     "The dimensions of the array should be ``(number_molecules, size, 5, size)``, where ``size`` is the\n",
     "size keyword used when generating the representations. \n",
     "\n",
-    "In addition to using the ``Compound`` class to generate the representations, FCHL representations can also be generated via the ``qml.ml.representations.fchl.generate_fchl_representation()`` function, using similar notation to the functions in the ``qml.ml.representations.*`` functions."
+    "In addition to using the ``Compound`` class to generate the representations, FCHL representations can also be generated via the ``qml.representations.fchl.generate_fchl_representation()`` function, using similar notation to the functions in the ``qml.representations.*`` functions."
    ]
   },
   {
@@ -288,7 +288,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations.fchl import generate_representation \n",
+    "from qml.representations.fchl import generate_representation \n",
     "\n",
     "# Dummy coordinates for a water molecule\n",
     "coordinates = np.array([[1.464, 0.707, 1.056],\n",
@@ -314,7 +314,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations.fchl import generate_representation \n",
+    "from qml.representations.fchl import generate_representation \n",
     "\n",
     "# Dummy fractional coordinates\n",
     "fractional_coordinates = np.array(\n",
@@ -372,7 +372,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations.fchl import get_local_kernels\n",
+    "from qml.representations.fchl import get_local_kernels\n",
     "\n",
     "# You can get kernels for multiple kernel-widths\n",
     "sigmas = [2.5, 5.0, 10.0]\n",
@@ -396,7 +396,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations.fchl import get_local_symmetric_kernels\n",
+    "from qml.representations.fchl import get_local_symmetric_kernels\n",
     "\n",
     "# You can get kernels for multiple kernel-widths\n",
     "sigmas = [2.5, 5.0, 10.0]\n",
@@ -420,8 +420,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qml.ml.representations.fchl import get_atomic_kernels\n",
-    "from qml.ml.representations.fchl import get_atomic_symmetric_kernels"
+    "from qml.representations.fchl import get_atomic_kernels\n",
+    "from qml.representations.fchl import get_atomic_symmetric_kernels"
    ]
   },
   {

docs/source/tutorial.rst

@@ -39,7 +39,7 @@ If you run the code below, you will read in the file ``qm7/0001.xyz`` (a methane
     import qml
 
     # Create the compound object mol from the file qm7/0001.xyz which happens to be methane
-    mol = qml.ml.Compound(xyz="qm7/0001.xyz")
+    mol = qml.Compound(xyz="qm7/0001.xyz")
 
     # Generate and print a Coulomb matrix for compound with 5 atoms
     mol.generate_coulomb_matrix(size=5, sorting="row-norm")
@@ -80,7 +80,7 @@ In order to save time you can import the entire QM7 dataset as ``Compound`` obje
     # Import QM7, already parsed to QML
     from tutorial_data import compounds
 
-    from qml.ml.kernels import gaussian_kernel
+    from qml.kernels import gaussian_kernel
 
     # For every compound generate a Coulomb matrix or BoB
     for mol in compounds:
@@ -114,7 +114,7 @@ With the kernel matrix and representations sorted out in the previous two exerci
     :math:`\boldsymbol{\alpha} = (\mathbf{K} + \lambda \mathbf{I})^{-1} \mathbf{y}\label{eq:inv}`
 
 One of the most efficient ways of solving this equation is using a Cholesky-decomposition.
-QML includes a function named ``cho_solve()`` to do this via the math module ``qml.ml.math``.
+QML includes a function named ``cho_solve()`` to do this via the math module ``qml.math``.
 In this step it is convenient to only use a subset of the full dataset as training data (see below).
 The following builds on the code from the previous step.
 To save time, you can import the PBE0/def2-TZVP atomization energies for the QM7 dataset from the file ``tutorial_data.py``.
@@ -123,7 +123,7 @@ Extend your code from the previous step with the code below:
 
 .. code:: python
 
-    from qml.ml.math import cho_solve
+    from qml.math import cho_solve
     from tutorial_data import energy_pbe0
 
     # Assign first 1000 molecules to the training set

qml/__init__.py

@@ -33,9 +33,13 @@
 from __future__ import absolute_import
 
 from . import data
-from . import ml
 from . import models
 from . import aglaia
+from . import math
+from . import kernels
+from . import arad
+from . import fchl
+from . import representations
 
 __author__ = "Anders S. Christensen"
 __copyright__ = "Copyright 2016"

qml/aglaia/aglaia.py

@@ -40,14 +40,14 @@
 
 try:
     from qml.data import Compound
-    from qml.ml import representations as qml_rep
-except ModuleNotFoundError:
-    raise ModuleNotFoundError("The module qml is required")
+    from qml import representations as qml_rep
+except ImportError:
+    raise ImportError("The module qml is required")
 
 try:
     import tensorflow
-except ModuleNotFoundError:
-    raise ModuleNotFoundError("Tensorflow 1.8 is required to run neural networks.")
+except ImportError:
+    raise ImportError("Tensorflow 1.8 is required to run neural networks.")
 
 class _NN(BaseEstimator):
 

qml/ml/arad/__init__.py qml/arad/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen and Felix A. Faber
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/ml/arad/arad.py qml/arad/arad.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/ml/arad/farad_kernels.f90 qml/arad/farad_kernels.f90

@@ -25,17 +25,17 @@
 import numpy as np
 import collections
 
-from ..ml.representations.alchemy import NUCLEAR_CHARGE
+from ..representations.alchemy import NUCLEAR_CHARGE
 
-from ..ml.representations import generate_coulomb_matrix
-from ..ml.representations import generate_atomic_coulomb_matrix
-from ..ml.representations import generate_bob
-from ..ml.representations import generate_eigenvalue_coulomb_matrix
-from ..ml.representations import generate_slatm
+from ..representations import generate_coulomb_matrix
+from ..representations import generate_atomic_coulomb_matrix
+from ..representations import generate_bob
+from ..representations import generate_eigenvalue_coulomb_matrix
+from ..representations import generate_slatm
 
-from ..ml.representations.fchl import generate_representation as generate_fchl_representation
+from ..fchl import generate_representation as generate_fchl_representation
 
-from ..ml.representations.facsf import fgenerate_acsf, fgenerate_acsf_and_gradients
+from ..representations.facsf import fgenerate_acsf, fgenerate_acsf_and_gradients
 
 class Compound(object):
     """ The ``Compound`` class is used to store data from  

qml/data/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/data/compound.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/data/dataprovider.py

@@ -0,0 +1,23 @@
+# MIT License
+#
+# Copyright (c) 2017 Anders S. Christensen and Felix A. Faber
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from .fchl import *

qml/data/xyzdataprovider.py

@@ -30,7 +30,7 @@
 from .ffchl_module import fget_atomic_kernels_fchl
 from .ffchl_module import fget_atomic_symmetric_kernels_fchl
 
-from .alchemy import get_alchemy
+from ..representations.alchemy import get_alchemy
 
 def generate_representation(coordinates, nuclear_charges,
         max_size=23, neighbors=23, cut_distance = 5.0, cell=None):

qml/fchl/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/ml/representations/fchl.py qml/fchl/fchl.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/ml/representations/ffchl_module.f90 qml/fchl/ffchl_module.f90

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen, Kristof T. Schutt, Stefan Chmiela
+# Copyright (c) 2017 Anders S. Christensen
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

qml/ml/representations/ffchl_scalar_kernels.f90 qml/fchl/ffchl_scalar_kernels.f90

@@ -28,9 +28,9 @@
 
 import ase
 
-from ..ml.representations import generate_coulomb_matrix
-from ..ml.kernels import gaussian_kernel
-from ..ml.math import cho_solve
+from ..representations import generate_coulomb_matrix
+from ..kernels import gaussian_kernel
+from ..math import cho_solve
 from .mlmodel import MLModel
 
 class GenericKRR(MLModel):