Improve docs

README.md

@@ -31,13 +31,13 @@ The following table list some core packages in XenonPy images.
 | -------------- | ---------- |
 | `PyTorch`      | 1.0.1      |
 | `tensorly`     | 0.4.3      |
-| `pymatgen`     | 2019.2.4   |
+| `pymatgen`     | 2019.3.13  |
 | `matminer`     | 0.5.1      |
 | `mordred`      | 1.1.2      |
 | `scipy`        | 1.2.1      |
 | `scikit-learn` | 0.20.2     |
-| `pandas`       | 0.24.1     |
-| `rdkit`        | 2018.09.1  |
+| `pandas`       | 0.24.2     |
+| `rdkit`        | 2018.09.2  |
 | `jupyter`      | 1.0.0      |
 | `seaborn`      | 0.9.0      |
 | `matplotlib`   | 3.0.2      |

conda_env/xepy36_cpu_linux.yml

@@ -0,0 +1,25 @@
+name: xepy36_cpu_linux
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.6
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch-cpu=1.0.1
+  - torchvision-cpu
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy36_cuda10.yml

@@ -0,0 +1,27 @@
+name: xepy36_cuda10
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.6
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - cudatoolkit=10.0
+  - torchvision
+  - magma-cuda100=2.5.0
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy36_cuda9.yml

@@ -0,0 +1,27 @@
+name: xepy36_cuda9
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.6
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - cudatoolkit=9.0
+  - torchvision
+  - magma-cuda90=2.5.0
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy36_osx.yml

@@ -0,0 +1,25 @@
+name: xepy36_osx
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.6
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - torchvision
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy37_cpu_linux.yml

@@ -0,0 +1,25 @@
+name: xepy37_cpu_linux
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.7
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch-cpu=1.0.1
+  - torchvision-cpu
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy37_cuda10.yml

@@ -0,0 +1,27 @@
+name: xepy37_cuda10
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.7
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - cudatoolkit=10.0
+  - torchvision
+  - magma-cuda100=2.5.0
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy37_cuda9.yml

@@ -0,0 +1,27 @@
+name: xepy37_cuda9
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.7
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - cudatoolkit=9.0
+  - torchvision
+  - magma-cuda90=2.5.0
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

conda_env/xepy37_osx.yml

@@ -0,0 +1,25 @@
+name: xepy37_osx
+channels:
+  - defaults
+  - pytorch
+  - rdkit
+dependencies:
+  - python=3.7
+  - pandas=0.24.2
+  - scikit-learn=0.20.3
+  - scipy=1.2.1
+  - pytorch=1.0.1
+  - torchvision
+  - rdkit=2018.09.2
+  - jupyter=1.0.0
+  - seaborn
+  - requests
+  - plotly
+  - pip:
+      - ruamel.yaml
+      - pymatgen==2019.3.13
+      - jupyterlab
+      - pybtex
+      - mordred
+      - tqdm
+      - xenonpy

docs/source/api.rst

@@ -0,0 +1,6 @@
+------------------
+Indices and tables
+------------------
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/changes.rst

@@ -11,19 +11,19 @@ v0.3.0
 
 **Breaking changes**:
 
-* Remove Built-in data ``mp_inorganic``, ``mp_structure``, ``oqmd_inorganic`` and ``oqmd_structure``. `#12`_ `#20`_
+* Remove Built-in data ``mp_inorganic``, ``mp_structure``, ``oqmd_inorganic`` and ``oqmd_structure``. ( `#12`_ `#20`_ )
 * Change name of ``LocalStorage`` to ``Storage``.
 
 **Enhanced**
 
-* Add error handling for ``NGram`` training. (`#75`_ `#86`_)
-* Add error handling for ``IQSPR``. (`#69`_)
-* Add error handling for ``BaseDescriptor`` and ``BaseFeaturizer``. (`#73`_)
-* Add featurizer selection function. (`#47`_)
+* Add error handling for ``NGram`` training. ( `#75`_ `#86`_ )
+* Add error handling for ``IQSPR``. ( `#69`_ )
+* Add error handling for ``BaseDescriptor`` and ``BaseFeaturizer``. ( `#73`_ )
+* Add featurizer selection function. ( `#47`_ )
 
 **New Features**
 
-* Add sample data building function for ``preset``. (`#81`_ `#84`_)
+* Add sample data building function for ``preset``. ( `#81`_ `#84`_ )
 
 
 .. _#12: https://github.com/yoshida-lab/XenonPy/issues/12
@@ -44,13 +44,13 @@ v0.2.0
 
 **Descriptor Generator**:
 
-* Added ``xenonpy.descriptor.Fingerprint`` descriptor generator. (`#21`_)
-* Added ``xenonpy.descriptor.OrbitalFieldMatrix`` descriptor generator. (`#22`_)
+* Added ``xenonpy.descriptor.Fingerprint`` descriptor generator. ( `#21`_ )
+* Added ``xenonpy.descriptor.OrbitalFieldMatrix`` descriptor generator. ( `#22`_ )
 
 
 **API Changes**:
 
-* Allowed ``BaseDescriptor`` class to use anonymous/renamed input. (`#10`_)
+* Allowed ``BaseDescriptor`` class to use anonymous/renamed input. ( `#10`_ )
 
 .. _#10: https://github.com/yoshida-lab/XenonPy/issues/10
 .. _#21: https://github.com/yoshida-lab/XenonPy/issues/21

docs/source/conf.py

@@ -46,7 +46,12 @@
               'sphinx.ext.coverage',
               'sphinx.ext.mathjax',
               'sphinx.ext.viewcode',
-              'sphinx.ext.githubpages']
+              'sphinx.ext.githubpages',
+              'sphinx.ext.autosectionlabel'
+              ]
+
+# config autosectionlabel
+autosectionlabel_prefix_document = True
 
 # config autodoc
 autoclass_content = 'both'
@@ -66,7 +71,7 @@
 
 # General information about the project.
 project = package.__name__
-copyright = '2018, TsumiNa'
+copyright = '2019, yoshida-lab'
 author = 'TsumiNa'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -181,7 +186,11 @@
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/': None,
+                       'pandas': ('http://pandas.pydata.org/pandas-docs/version/0.24', None),
+                       'numpy': ('http://docs.scipy.org/doc/numpy', None),
+                       'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
+                       'matplotlib': ('http://matplotlib.org', None)}
 
 
 def skip(app, what, name, obj, skip, options):

docs/source/copyright.rst

@@ -0,0 +1,9 @@
+=========
+Copyright
+=========
+
+Copyright © 2019 The XenonPy task force, all rights reserved.
+Released under the `BSD-3 license`_.
+
+.. _BSD-3 license: https://opensource.org/licenses/BSD-3-Clause
+