adding pbc property page in docs

docs/source/reference/api/auto/aiida_atomistic/calculations/index.rst

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+:py:mod:`aiida_atomistic.calculations`
+======================================
+
+.. py:module:: aiida_atomistic.calculations
+
+.. autoapi-nested-parse::
+
+   Calculations provided by aiida_atomistic.
+
+   Register calculations via the "aiida.calculations" entry point in setup.json.
+
+
+
+Module Contents
+---------------
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.calculations.DiffCalculation
+
+
+
+
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.calculations.DiffParameters
+
+
+.. py:data:: DiffParameters
+
+   
+
+.. py:class:: DiffCalculation(*args, **kwargs)
+
+
+   Bases: :py:obj:`aiida.engine.CalcJob`
+
+   AiiDA calculation plugin wrapping the diff executable.
+
+   Simple AiiDA plugin wrapper for 'diffing' two files.
+
+   .. py:method:: define(spec)
+      :classmethod:
+
+      Define inputs and outputs of the calculation.
+
+
+   .. py:method:: prepare_for_submission(folder)
+
+      Create input files.
+
+      :param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files
+          needed by the calculation.
+      :return: `aiida.common.datastructures.CalcInfo` instance
+
+
+

docs/source/reference/api/auto/aiida_atomistic/data/index.rst

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+:py:mod:`aiida_atomistic.data`
+==============================
+
+.. py:module:: aiida_atomistic.data
+
+.. autoapi-nested-parse::
+
+   Data types provided by plugin
+
+   Register data types via the "aiida.data" entry point in setup.json.
+
+
+
+Package Contents
+----------------
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.data.DiffParameters
+
+
+
+
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.data.cmdline_options
+
+
+.. py:data:: cmdline_options
+
+   
+
+.. py:class:: DiffParameters(dict=None, **kwargs)
+
+
+   Bases: :py:obj:`aiida.orm.Dict`
+
+   Command line options for diff.
+
+   This class represents a python dictionary used to
+   pass command line options to the executable.
+
+   .. py:attribute:: schema
+
+      
+
+   .. py:method:: validate(parameters_dict)
+
+      Validate command line options.
+
+      Uses the voluptuous package for validation. Find out about allowed keys using::
+
+          print(DiffParameters).schema.schema
+
+      :param parameters_dict: dictionary with commandline parameters
+      :param type parameters_dict: dict
+      :returns: validated dictionary
+
+
+   .. py:method:: cmdline_params(file1_name, file2_name)
+
+      Synthesize command line parameters.
+
+      e.g. [ '--ignore-case', 'filename1', 'filename2']
+
+      :param file_name1: Name of first file
+      :param type file_name1: str
+      :param file_name2: Name of second file
+      :param type file_name2: str
+
+
+
+   .. py:method:: __str__()
+
+      String representation of node.
+
+      Append values of dictionary to usual representation. E.g.::
+
+          uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
+          {'ignore-case': True}
+
+
+
+

docs/source/reference/api/auto/aiida_atomistic/helpers/index.rst

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+:py:mod:`aiida_atomistic.helpers`
+=================================
+
+.. py:module:: aiida_atomistic.helpers
+
+.. autoapi-nested-parse::
+
+   Helper functions for automatically setting up computer & code.
+   Helper functions for setting up
+
+    1. An AiiDA localhost computer
+    2. A "diff" code on localhost
+
+   Note: Point 2 is made possible by the fact that the ``diff`` executable is
+   available in the PATH on almost any UNIX system.
+
+
+
+Module Contents
+---------------
+
+
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.helpers.get_path_to_executable
+   aiida_atomistic.helpers.get_computer
+   aiida_atomistic.helpers.get_code
+
+
+
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.helpers.LOCALHOST_NAME
+   aiida_atomistic.helpers.executables
+
+
+.. py:data:: LOCALHOST_NAME
+   :value: 'localhost-test'
+
+
+
+.. py:data:: executables
+
+   
+
+.. py:function:: get_path_to_executable(executable)
+
+   Get path to local executable.
+   :param executable: Name of executable in the $PATH variable
+   :type executable: str
+   :return: path to executable
+   :rtype: str
+
+
+.. py:function:: get_computer(name=LOCALHOST_NAME, workdir=None)
+
+   Get AiiDA computer.
+   Loads computer 'name' from the database, if exists.
+   Sets up local computer 'name', if it isn't found in the DB.
+
+   :param name: Name of computer to load or set up.
+   :param workdir: path to work directory
+       Used only when creating a new computer.
+   :return: The computer node
+   :rtype: :py:class:`aiida.orm.computers.Computer`
+
+
+.. py:function:: get_code(entry_point, computer)
+
+   Get local code.
+   Sets up code for given entry point on given computer.
+
+   :param entry_point: Entry point of calculation plugin
+   :param computer: (local) AiiDA computer
+   :return: The code node
+   :rtype: :py:class:`aiida.orm.nodes.data.code.installed.InstalledCode`
+
+

docs/source/reference/api/auto/aiida_atomistic/index.rst

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+:py:mod:`aiida_atomistic`
+=========================
+
+.. py:module:: aiida_atomistic
+
+.. autoapi-nested-parse::
+
+   aiida_atomistic
+
+   AiiDA plugin which contains data and methods for atomistic simulations
+
+
+
+Subpackages
+-----------
+.. toctree::
+   :titlesonly:
+   :maxdepth: 3
+
+   data/index.rst
+
+
+Submodules
+----------
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+   calculations/index.rst
+   helpers/index.rst
+   parsers/index.rst
+
+
+Package Contents
+----------------
+
+.. py:data:: __version__
+   :value: '0.1.0a0'
+
+
+

docs/source/reference/api/auto/aiida_atomistic/parsers/index.rst

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+:py:mod:`aiida_atomistic.parsers`
+=================================
+
+.. py:module:: aiida_atomistic.parsers
+
+.. autoapi-nested-parse::
+
+   Parsers provided by aiida_atomistic.
+
+   Register parsers via the "aiida.parsers" entry point in setup.json.
+
+
+
+Module Contents
+---------------
+
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.parsers.DiffParser
+
+
+
+
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+   aiida_atomistic.parsers.DiffCalculation
+
+
+.. py:data:: DiffCalculation
+
+   
+
+.. py:class:: DiffParser(node)
+
+
+   Bases: :py:obj:`aiida.parsers.parser.Parser`
+
+   Parser class for parsing output of calculation.
+
+   .. py:method:: parse(**kwargs)
+
+      Parse outputs, store results in database.
+
+      :returns: an exit code, if parsing fails (or nothing if parsing succeeds)
+
+
+