docs configured

CIMtools/datasets/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2018 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2018, 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CIMtools.
 #
 #  CIMtools is free software; you can redistribute it and/or modify
@@ -17,3 +17,6 @@
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
 #
 from .molconvert_chemaxon import *
+
+
+__all__ = ['molconvert_chemaxon']

CIMtools/metrics/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2018 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2018, 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CIMtools.
 #
 #  CIMtools is free software; you can redistribute it and/or modify
@@ -18,3 +18,6 @@
 #
 from .pairwise import *
 from .applicability_domain_metrics import *
+
+
+__all__ = ['balanced_accuracy_score_with_ad', 'rmse_score_with_ad', 'tanimoto_kernel']

CIMtools/metrics/pairwise.py

@@ -20,6 +20,9 @@
 
 
 def tanimoto_kernel(x, y):
+    """
+
+    """
     x_dot = np.dot(x, y.T)
 
     x2 = (x**2).sum(axis=1)

CIMtools/model_selection/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2018, 2019  Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2018-2020  Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CIMtools.
 #
 #  CIMtools is free software; you can redistribute it and/or modify
@@ -19,3 +19,6 @@
 from .group_out import *
 from .reaction_type_control_selection import *
 from .transformation_out import *
+
+
+__all__ = ['LeaveOneGroupOut', 'TransformationOut', 'rtc_env_selection']

CIMtools/preprocessing/__init__.py

@@ -24,3 +24,11 @@
 from .graph_to_matrix import *
 from .solvent import *
 from .standardize import *
+
+
+__all__ = ['Conditions', 'DictToConditions', 'ConditionsToDataFrame', 'SolventVectorizer', 'EquationTransformer',
+           'CGR', 'MoleculesToMatrix', 'CGRToMatrix']
+
+if 'Fragmentor' in locals():
+    __all__.append('Fragmentor')
+    __all__.append('FragmentorFingerprint')

README.md → README.rst

@@ -10,98 +10,78 @@ INSTALL
 Linux Debian based
 ------------------
 
-* Install python3.7, virtualenv and git
+* Install python3.7, virtualenv and git::
 
-    ```
     sudo apt install python3.7 python3.7-dev git python3-virtualenv
-    ```
     
-* Create new environment and activate it.
+* Create new environment and activate it::
 
-    ```
     virtualenv -p python3.7 venv
     source venv/bin/activate
-    ```
 
 Mac
 ---
-* Install python3.7 and git using [brew](<https://brew.sh>)
+* Install python3.7 and git using <https://brew.sh>::
 
-    ```
     brew install git
     brew install python3
-    ```
-    
-* Install virtualenv.
 
-    ```
+* Install virtualenv::
+
     pip install virtualenv
-    ```
 
-* Create new environment and activate it.
+* Create new environment and activate it::
 
-    ```
     virtualenv -p python3.7 venv
     source venv/bin/activate
-    ```
-    
+
 Windows
 -------
 
-* Install python3.7 and git using [Chocolatey](<https://chocolatey.org/>)
+* Install python3.7 and git using <https://chocolatey.org/>::
 
-    ```
     choco install git
     choco install python3
-    ```
     
-* Install virtualenv.
+* Install virtualenv::
 
-    ```
     pip install virtualenv
-    ```
 
-* Create new environment and activate it.
+* Create new environment and activate it::
 
-    ```
     virtualenv venv
     venv\Scripts\activate
-    ```
 
 General part
 ------------
 
-* **stable version will be available through PyPI**
+* **stable version will be available through PyPI**::
 
-    ```
     pip install CIMtools
-    ```    
 
-* Install CGRtools library DEV version for features that are not well tested. Git lfs installation required https://git-lfs.github.com/.
+* Install CGRtools library DEV version for features that are not well tested. Git lfs installation required <https://git-lfs.github.com/>::
 
-    ```
     pip install -U git+https://github.com/stsouko/CIMtools.git@master#egg=CIMtools
-    ```
 
 **If you still have questions, please open issue within github.**
 
 SETUP
 =====
 
 For ChemAxon standardizer used pyjnius. First of all install JDK (not JRE) OpenJDK or Oracle.
-Some times it can't to find java installation properly. Just set environment variables. 
+Some times it can't to find java installation properly. Just set environment variables::
 
     JAVA_HOME = '/path/to/dir/which/contain/bin/dir'. for example /usr/lib/jvm/java-11-openjdk-amd64
     JVM_PATH = '/path/to/lib/server/libjvm.so'. For example '/usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so' 
 
 PACKAGING
 =========
 
-For wheel generation just type next command in source root
+For wheel generation just type next command in source root::
 
     python setup.py bdist_wheel
 
-On Linux additionally do repairing of package
+On Linux additionally do repairing of package::
 
     pip install auditwheel
     auditwheel repair dist/CIMtools-<version>-<python_version>-linux_x86_64.whl

doc/conf.py

@@ -11,7 +11,7 @@
 project = 'CIMtools'
 
 needs_sphinx = '1.8'
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'numpydoc', 'm2r']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'numpydoc', 'nbsphinx']
 
 
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
@@ -24,7 +24,7 @@
 todo_include_todos = False
 autoclass_content = 'both'
 
-html_theme_options = {'github_user': 'stsouko', 'github_repo': 'CIMtools', 'show_related': True}
+html_theme_options = {'github_user': 'cimm_kzn', 'github_repo': 'CIMtools', 'show_related': True}
 html_show_copyright = True
 html_show_sourcelink = False
 html_sidebars = {
@@ -35,3 +35,5 @@
         'searchbox.html',
     ]
 }
+
+nbsphinx_execute = 'never'

doc/datasets.rst

@@ -0,0 +1,8 @@
+CIMtools\.datasets package
+==========================
+
+.. automodule:: CIMtools.datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

doc/index.rst

@@ -1,25 +1,23 @@
-.. mdinclude:: ../README.md
-
-CIMtools package
-================
-
-.. automodule:: CIMtools
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. include:: ../README.rst
 
 Subpackages
------------
+===========
 
 .. toctree::
-    :maxdepth: 4
+    :maxdepth: 2
 
     applicability_domain
+    model_selection
+    metrics
+    datasets
+    preprocessing
+    standardize
 
 Tutorial
---------
+========
 
 .. toctree::
-    :maxdepth: 4
+    :maxdepth: 1
 
     tutorial/metric_constants
+    tutorial/applicability_domain.ipynb

doc/metrics.rst

@@ -0,0 +1,8 @@
+CIMtools\.metrics package
+=========================
+
+.. automodule:: CIMtools.metrics
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

doc/model_selection.rst

@@ -0,0 +1,8 @@
+CIMtools\.model_selection package
+=================================
+
+.. automodule:: CIMtools.model_selection
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

doc/preprocessing.rst

@@ -0,0 +1,8 @@
+CIMtools\.preprocessing package
+===============================
+
+.. automodule:: CIMtools.preprocessing
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

doc/standardize.rst

@@ -0,0 +1,8 @@
+CIMtools\.preprocessing.standardize package
+===========================================
+
+.. automodule:: CIMtools.preprocessing.standardize
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members: