CAT 0.9.2 (#123)

* Updated the Data-CAT documentation (see nlesc-nano/data-CAT#23).
* Upped the minimum Sphinx version to 2.1.
* Removed ``sphinx-autodoc-typehints``.
* Removed ``requirements.txt`` in favor of ``.readthedocs.yml``.

.readthedocs.yml

@@ -0,0 +1,21 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+    configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+            - doc

CAT/__version__.py

@@ -1 +1 @@
-__version__ = '0.9.1'
+__version__ = '0.9.2'

CAT/jobs.py

@@ -39,7 +39,7 @@
 import numpy as np
 
 from scm.plams.core.basejob import Job
-from scm.plams import (Molecule, Settings, Results, config, add_to_class, ResultsError, 
+from scm.plams import (Molecule, Settings, Results, config, add_to_class, ResultsError,
                        ADFJob, AMSJob, Units, Cp2kResults)
 
 import qmflows

CHANGELOG.rst

@@ -11,6 +11,14 @@ This project adheres to `Semantic Versioning <http://semver.org/>`_.
 * WiP: Added an option the import pre-built quantum dots.
 
 
+0.9.2
+*****
+* Updated the Database documentation (see https://github.com/nlesc-nano/data-CAT/pull/23).
+* Upped the minimum Sphinx version to 2.1.
+* Removed ``sphinx-autodoc-typehints``.
+* Removed ``requirements.txt`` in favor of ``.readthedocs.yml``.
+
+
 0.9.1
 *****
 * Added a new conceptual DFT (CDFT) workflow to Nano-CAT

README.rst

@@ -16,7 +16,7 @@
 
 
 ##############################
-Compound Attachment Tool 0.9.1
+Compound Attachment Tool 0.9.2
 ##############################
 
 **CAT** is a collection of tools designed for the construction of various chemical compounds.

docs/7_database.rst

@@ -2,10 +2,10 @@
 
 The Database Class
 ==================
+.. currentmodule:: dataCAT
 
 A Class designed for the storing, retrieval and updating of results.
 
-
 .. image:: _images/Database.png
     :scale: 35 %
     :align: center
@@ -16,175 +16,79 @@ accoring to their functionality:
 -   Opening & closing the database - these methods serve as context managers
     for loading and unloading parts of the database from the harddrive.
 
-    The context managers can be accessed via the :meth:`.MetaManager.open`
-    method of :attr:`.Database.csv_lig`, :attr:`.Database.csv_qd`,
+    The context managers can be accessed by calling
+    either :attr:`.Database.csv_lig`, :attr:`.Database.csv_qd`,
     :attr:`.Database.yaml` or :attr:`.Database.hdf5`, with the option
     of passing additional positional or keyword arguments.
 
     .. code:: python
 
-        >>> import CAT
+        >>> from dataCAT import Database
 
-        >>> database = CAT.Database()
-        >>> with database.csv_lig.open(write=False) as db:
+        >>> database = Database()
+        >>> with database.csv_lig(write=False) as db:
         >>>     print(repr(db))
-        DFCollection(df=<pandas.core.frame.DataFrame at 0x7ff8e958ce80>)
+        DFProxy(ndframe=<pandas.core.frame.DataFrame at 0x7ff8e958ce80>)
 
-        >>> with database.yaml.open() as db:
+        >>> with database.yaml() as db:
         >>>     print(type(db))
         <class 'scm.plams.core.settings.Settings'>
 
-        >>> with database.hdf5.open('r') as db:
+        >>> with database.hdf5('r') as db:
         >>>     print(type(db))
         <class 'h5py._hl.files.File'>
 
 -   Importing to the database - these methods handle the importing of new data
     from python objects to the Database class:
 
-    ===================  ====================  ====================  =======================
-    :meth:`.update_csv`  :meth:`.update_yaml`  :meth:`.update_hdf5`  :meth:`.update_mongodb`
-    ===================  ====================  ====================  =======================
+    ============================  =============================  =============================  ================================
+    :meth:`~Database.update_csv`  :meth:`~Database.update_yaml`  :meth:`~Database.update_hdf5`  :meth:`~Database.update_mongodb`
+    ============================  =============================  =============================  ================================
 
 -   Exporting from the database - these methods handle the exporting of data
     from the Database class to other python objects or remote locations:
 
-    =================  ==================
-    :meth:`.from_csv`  :meth:`.from_hdf5`
-    =================  ==================
+    ==========================  ===========================
+    :meth:`~Database.from_csv`  :meth:`~Database.from_hdf5`
+    ==========================  ===========================
 
 
 Index
 -----
 
-.. currentmodule:: dataCAT.database.Database
-.. autosummary::
-
-    dirname
-    csv_lig
-    csv_qd
-    hdf5
-    yaml
-    mongodb
-
-    update_mongodb
-    update_csv
-    update_yaml
-    update_hdf5
-    from_csv
-    from_hdf5
-
-.. currentmodule:: dataCAT
 .. autosummary::
 
-    df_collection.get_df_collection
-    database_functions.as_pdb_array
-    database_functions.from_pdb_array
-    database_functions.sanitize_yaml_settings
-
-
-Class API
----------
-
-Database
-~~~~~~~~
-
-.. autoclass:: dataCAT.database.Database
-    :members:
-
-
-DFCollection
-~~~~~~~~~~~~
-
-.. autoclass:: dataCAT.df_collection._DFCollection
+    Database.dirname
+    Database.csv_lig
+    Database.csv_qd
+    Database.hdf5
+    Database.yaml
+    Database.mongodb
+
+    Database.update_mongodb
+    Database.update_csv
+    Database.update_yaml
+    Database.update_hdf5
+    Database.from_csv
+    Database.from_hdf5
+
+    DFProxy
+    OpenLig
+    OpenQD
+    OpenYaml
+
+
+API
+---
+.. autoclass:: Database
     :members:
-
-
-MetaManager
-~~~~~~~~~~~
-
-.. autoclass:: dataCAT.context_managers.MetaManager
+.. autoclass:: DFProxy
+.. autoclass:: OpenLig
     :members:
-
-
-OpenLig
-~~~~~~~
-
-.. autoclass:: dataCAT.context_managers.OpenLig
+    :inherited-members:
+.. autoclass:: OpenQD
     :members:
-
-
-OpenQD
-~~~~~~
-
-.. autoclass:: dataCAT.context_managers.OpenQD
+    :inherited-members:
+.. autoclass:: OpenYaml
     :members:
-
-
-OpenYaml
-~~~~~~~~
-
-.. autoclass:: dataCAT.context_managers.OpenYaml
-    :members:
-
-
-Function API
-------------
-
-.. autofunction:: dataCAT.df_collection.get_df_collection
-
-.. autofunction:: dataCAT.database_functions.as_pdb_array
-
-.. autofunction:: dataCAT.database_functions.from_pdb_array
-
-.. autofunction:: dataCAT.database_functions.sanitize_yaml_settings
-
-
-.. _dataCAT.DFCollection: 7_database.html#dfcollection
-.. _dataCAT.MetaManager: 7_database.html#metamanager
-.. _rdkit.Chem.Mol: http://rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol
-.. _h5py.File: http://docs.h5py.org/en/stable/high/file.html
-.. _plams.Settings: https://www.scm.com/doc/plams/components/settings.html
-.. _plams.Molecule: https://www.scm.com/doc/plams/components/molecule.html#id1
-.. _np.ndarray: https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html
-.. _np.float64: https://docs.scipy.org/doc/numpy/user/basics.types.html#array-types-and-conversions-between-types
-.. _np.int64: https://docs.scipy.org/doc/numpy/user/basics.types.html#array-types-and-conversions-between-types
-.. _np.str_: https://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html#arrays-dtypes
-.. _np.bytes: https://docs.scipy.org/doc/numpy-1.15.1/reference/arrays.dtypes.html
-.. _pd.Series: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.html
-.. _pd.DataFrame: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
-.. _dict: https://docs.python.org/3/library/stdtypes.html#dict
-.. _list: https://docs.python.org/3/library/stdtypes.html#list
-.. _tuple: https://docs.python.org/3/library/stdtypes.html#tuple
-.. _str: https://docs.python.org/3/library/stdtypes.html#str
-.. _int: https://docs.python.org/3/library/functions.html#int
-.. _None: https://docs.python.org/3.7/library/constants.html#None
-.. _bool: https://docs.python.org/3/library/functions.html?highlight=bool#bool
-.. _with: https://docs.python.org/3/reference/compound_stmts.html#with
-.. _type: https://docs.python.org/3/library/functions.html#type
-.. _Sequence: https://docs.python.org/3/library/collections.abc.html#collections.abc.Sequence
-.. _AbstractContextManager: https://docs.python.org/3/library/contextlib.html#contextlib.AbstractContextManager
-
-.. |dataCAT.DFCollection| replace:: *dataCAT.DFCollection*
-.. |dataCAT.MetaManager| replace:: *dataCAT.MetaManager*
-.. |rdkit.Chem.Mol| replace:: *rdkit.Chem.Mol*
-.. |h5py.File| replace:: *h5py.File*
-.. |plams.Molecule| replace:: *plams.Molecule*
-.. |plams.Settings| replace:: *plams.Settings*
-.. |pd.Series| replace:: *pd.Series*
-.. |pd.DataFrame| replace:: *pd.DataFrame*
-.. |np.ndarray| replace:: *np.ndarray*
-.. |np.float64| replace:: *np.float64*
-.. |np.int64| replace:: *np.int64*
-.. |np.str_| replace:: *np.str_*
-.. |np.bytes| replace:: *np.bytes*
-.. |dict| replace:: *dict*
-.. |list| replace:: *list*
-.. |tuple| replace:: *tuple*
-.. |str| replace:: *str*
-.. |int| replace:: *int*
-.. |None| replace:: *None*
-.. |bool| replace:: *bool*
-.. |with| replace:: ``with``
-.. |type| replace:: *type*
-.. |Sequence| replace:: *Sequence*
-.. |AbstractContextManager| replace:: *AbstractContextManager*
+    :inherited-members:

docs/conf.py

@@ -26,7 +26,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '2.0'  # 2.0 or higher
+needs_sphinx = '2.1'
 
 
 # Output is processed with HTML4 writer.
@@ -42,11 +42,17 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx_autodoc_typehints'
+    'sphinx.ext.napoleon'
 ]
 
 
+# This value controls how to represents typehints. The setting takes the following values:
+#     'signature' – Show typehints as its signature (default)
+#     'none' – Do not show typehints
+# New in version 2.1.
+autodoc_typehints = 'none'
+
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -62,14 +68,14 @@
 
 # General information about the project.
 project = 'CAT'
-year = str(datetime.datetime.now().year)
+_year = str(datetime.datetime.now().year)
 author = 'B. F. van Beek & J. Belic'
-copyright = f'{year}, {author}'
+copyright = f'{_year}, {author}'
 
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the built documents.
-release = '0.9.1'  # The full version, including alpha/beta/rc tags.
+release = '0.9.2'  # The full version, including alpha/beta/rc tags.
 version = release.rsplit('.', maxsplit=1)[0]
 
 
@@ -204,7 +210,8 @@
     'plams': ('https://www.scm.com/doc/plams/', None),
     'qmflows': ('https://qmflows.readthedocs.io/en/latest/', None),
     'FOX': ('https://auto-fox.readthedocs.io/en/latest/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None)
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'pymongo': ('https://pymongo.readthedocs.io/en/stable/', None)
 }
 
 

setup.py

@@ -106,6 +106,6 @@
                  'pycodestyle',
                  'data-CAT@git+https://github.com/nlesc-nano/data-CAT@devel',
                  'nano-CAT@git+https://github.com/nlesc-nano/nano-CAT@devel'],
-        'doc': ['sphinx>=2.0', 'sphinx_rtd_theme', 'sphinx-autodoc-typehints']
+        'doc': ['sphinx>=2.1', 'sphinx_rtd_theme']
     }
 )