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General improvements.
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- Fix metaclass issue on ml4chem.atomistic.models.base. There was
  a conflict resolved with `metaclass` keyword argument.
- docs.source:
    * Updated conf.py.
    * Updated AE and VAE figures.
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@muammar
muammar committed Mar 7, 2020
1 parent b11e1bd commit 454552c
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30 changes: 16 additions & 14 deletions docs/source/conf.py
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Expand Up @@ -12,27 +12,29 @@
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
from unittest.mock import MagicMock

sys.path.insert(0, os.path.abspath("../../"))
try:
import torch
except ModuleNotFoundError:
import os
import sys
from unittest.mock import MagicMock

# class Mock(MagicMock):
# @classmethod
# def __getattr__(cls, name):
# return MagicMock()
#
# MOCK_MODULES = ['ase', 'ase.calculators', 'ase.calculators.calculator',
# 'ase.neighborlist' 'torch']
#
# sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
sys.path.insert(0, os.path.abspath("../../"))

class Mock(MagicMock):
@classmethod
def __getattr__(cls, name):
return MagicMock()

MOCK_MODULES = ['torch', "torch.optim"]

sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

# -- Project information -----------------------------------------------------

project = "ML4Chem"
copyright = "2019, Muammar El Khatib"
copyright = "2020, Muammar El Khatib"
author = "Muammar El Khatib"

# The short X.Y version
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42 changes: 21 additions & 21 deletions docs/source/ml4chem.atomistic.features.rst
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Expand Up @@ -8,55 +8,55 @@ ml4chem.atomistic.features.autoencoders module
----------------------------------------------

.. automodule:: ml4chem.atomistic.features.autoencoders
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.features.base module
--------------------------------------

.. automodule:: ml4chem.atomistic.features.base
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.features.cartesian module
-------------------------------------------

.. automodule:: ml4chem.atomistic.features.cartesian
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.features.coulombmatrix module
-----------------------------------------------

.. automodule:: ml4chem.atomistic.features.coulombmatrix
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.features.cutoff module
----------------------------------------

.. automodule:: ml4chem.atomistic.features.cutoff
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.features.gaussian module
------------------------------------------

.. automodule:: ml4chem.atomistic.features.gaussian
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.atomistic.features
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
62 changes: 27 additions & 35 deletions docs/source/ml4chem.atomistic.models.rst
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Expand Up @@ -8,79 +8,71 @@ ml4chem.atomistic.models.autoencoders module
--------------------------------------------

.. automodule:: ml4chem.atomistic.models.autoencoders
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.base module
------------------------------------

.. automodule:: ml4chem.atomistic.models.base
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.gaussian\_process module
-------------------------------------------------

.. automodule:: ml4chem.atomistic.models.gaussian_process
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.kernelridge module
-------------------------------------------

.. automodule:: ml4chem.atomistic.models.kernelridge
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.loss module
------------------------------------

.. automodule:: ml4chem.atomistic.models.loss
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.merger module
--------------------------------------

.. automodule:: ml4chem.atomistic.models.merger
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.neuralnetwork module
---------------------------------------------

.. automodule:: ml4chem.atomistic.models.neuralnetwork
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.rt module
----------------------------------

.. automodule:: ml4chem.atomistic.models.rt
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.atomistic.models.se3net module
--------------------------------------

.. automodule:: ml4chem.atomistic.models.se3net
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.atomistic.models
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
16 changes: 8 additions & 8 deletions docs/source/ml4chem.atomistic.rst
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Expand Up @@ -6,8 +6,8 @@ Subpackages

.. toctree::

ml4chem.atomistic.features
ml4chem.atomistic.models
ml4chem.atomistic.features
ml4chem.atomistic.models

Submodules
----------
Expand All @@ -16,15 +16,15 @@ ml4chem.atomistic.potentials module
-----------------------------------

.. automodule:: ml4chem.atomistic.potentials
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.atomistic
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
18 changes: 9 additions & 9 deletions docs/source/ml4chem.backends.rst
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Expand Up @@ -8,23 +8,23 @@ ml4chem.backends.available module
---------------------------------

.. automodule:: ml4chem.backends.available
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.backends.operations module
----------------------------------

.. automodule:: ml4chem.backends.operations
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.backends
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
36 changes: 18 additions & 18 deletions docs/source/ml4chem.data.rst
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Expand Up @@ -8,47 +8,47 @@ ml4chem.data.handler module
---------------------------

.. automodule:: ml4chem.data.handler
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.data.parser module
--------------------------

.. automodule:: ml4chem.data.parser
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.data.preprocessing module
---------------------------------

.. automodule:: ml4chem.data.preprocessing
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.data.serialization module
---------------------------------

.. automodule:: ml4chem.data.serialization
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.data.utils module
-------------------------

.. automodule:: ml4chem.data.utils
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.data
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
18 changes: 9 additions & 9 deletions docs/source/ml4chem.optim.rst
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Expand Up @@ -8,23 +8,23 @@ ml4chem.optim.LBFGS module
--------------------------

.. automodule:: ml4chem.optim.LBFGS
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

ml4chem.optim.handler module
----------------------------

.. automodule:: ml4chem.optim.handler
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:


Module contents
---------------

.. automodule:: ml4chem.optim
:members:
:undoc-members:
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:

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