Merge pull request #169 from Sparks29032/doc_update

Documentation update

Author: sbillinge

doc/source/api/diffpy.utils.parsers.rst

@@ -11,10 +11,10 @@ diffpy.utils.parsers package
 Submodules
 ----------
 
-diffpy.utils.parsers.resample module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.utils.parsers.serialization module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.utils.parsers.resample
+.. automodule:: diffpy.utils.parsers.serialization
     :members:
     :undoc-members:
     :show-inheritance:
@@ -34,11 +34,3 @@ diffpy.utils.parsers.custom_exceptions module
     :members:
     :undoc-members:
     :show-inheritance:
-
-diffpy.utils.parsers.serialization module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.utils.parsers.serialization
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/source/api/diffpy.utils.rst

@@ -28,3 +28,11 @@ diffpy.utils.tools module
     :members:
     :undoc-members:
     :show-inheritance:
+
+diffpy.utils.resampler module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.utils.resampler
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/diffpy.utils.scattering_objects.rst

@@ -11,18 +11,18 @@ diffpy.utils.scattering_objects package
 Submodules
 ----------
 
-diffpy.utils.scattering_objects.user_config module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.utils.scattering_objects.diffraction_objects module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.utils.scattering_objects.user_config
+.. automodule:: diffpy.utils.scattering_objects.diffraction_objects
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.utils.scattering_objects.diffraction_objects module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diffpy.utils.scattering_objects.user_config module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.utils.scattering_objects.diffraction_objects
+.. automodule:: diffpy.utils.scattering_objects.user_config
     :members:
     :undoc-members:
     :show-inheritance:

doc/source/examples/parsersexample.rst

@@ -14,7 +14,7 @@ Using the parsers module, we can load file data into simple and easy-to-work-wit
 2) To get the data table, we will use the ``loadData`` function. The default behavior of this
    function is to find and extract a data table from a file.::
 
-     from diffpy.utils.parsers import loadData
+     from diffpy.utils.parsers.loaddata import loadData
      data_table = loadData('<PATH to data.txt>')
 
    While this will work with most datasets, on our ``data.txt`` file, we got a ``ValueError``. The reason for this is
@@ -53,7 +53,7 @@ Using the parsers module, we can load file data into simple and easy-to-work-wit
 4) Rather than working with separate ``data_table`` and ``hdata`` objects, it may be easier to combine them into a single
    dictionary. We can do so using the ``serialize_data`` function. ::
 
-     from diffpy.utils.parsers import serialize_data
+     from diffpy.utils.parsers.loaddata import serialize_data
      file_data = serialize_data('<PATH to data.txt', hdata, data_table)
      # File data is a dictionary with a single key
      # The key is the file name (in our case, 'data.txt')
@@ -84,7 +84,7 @@ Using the parsers module, we can load file data into simple and easy-to-work-wit
    The returned value, ``parsed_file_data``, is the dictionary we just added to ``serialfile.json``.
    To extract the data from the serial file, we use ``deserialize_data``. ::
 
-     from diffpy.utils.parsers import deserialize_data
+     from diffpy.utils.parsers.serialization import deserialize_data
      parsed_file_data = deserialize_data('<PATH to serialdata.json>')
 
 6) Finally, ``serialize_data`` allows us to store data from multiple text file in a single serial file. For one last bit

doc/source/examples/resampleexample.rst

@@ -15,14 +15,14 @@ given enough datapoints.
    <https://global.oup.com/academic/product/atomic-pair-distribution-function-analysis-9780198885801?cc=us&lang=en&>`_.
    ::
 
-     from diffpy.utils.parsers import loadData
+     from diffpy.utils.parsers.loaddata import loadData
      nickel_datatable = loadData('<PATH to Nickel.gr>')
      nitarget_datatable = loadData('<PATH to NiTarget.gr>')
 
    Each data table has two columns: first is the grid and second is the function value.
    To extract the columns, we can utilize the serialize function ... ::
 
-     from diffpy.utils.parsers import serialize_data
+     from diffpy.utils.parsers.serialization import serialize_data
      nickel_data = serialize_data('Nickel.gr', {}, nickel_datatable, dt_colnames=['grid', 'func'])
      nickel_grid = nickel_data['Nickel.gr']['grid']
      nickel_func = nickel_data['Nickel.gr']['func']
@@ -54,7 +54,7 @@ given enough datapoints.
 
    ... and use the diffpy.utils ``wsinterp`` function to resample on this grid.::
 
-     from diffpy.utils.parsers import wsinterp
+     from diffpy.utils.resampler import wsinterp
      nickel_resample = wsinterp(grid, nickel_grid, nickel_func)
      target_resample = wsinterp(grid, target_grid, target_func)
 

doc/source/utilities/parsersutility.rst

@@ -5,7 +5,7 @@ Parsers Utility
 
 The ``diffpy.utils.parsers`` module allows users to easily and robustly load file data into a Python project.
 
-- ``loadData()``: Find and load a data table/block from a text file. This seems to work for most datafiles
+- ``loaddata.loadData()``: Find and load a data table/block from a text file. This seems to work for most datafiles
   including those generated by diffpy programs. Running only ``numpy.loadtxt`` will result in errors
   for most these files as there is often excess data or parameters stored above the data block.
   Users can instead choose to load all the parameters of the form ``<param_name> = <param_value>`` into a dictionary
@@ -14,10 +14,10 @@ The ``diffpy.utils.parsers`` module allows users to easily and robustly load fil
   The program identifies data blocks as the first matrix block with a constant number of columns.
   A user can tune the minimum number of rows this matrix block must have.
 
-- ``deserialize_data()``: Load data from a serial file format into a Python dictionary. Currently, the only supported
+- ``serialization.deserialize_data()``: Load data from a serial file format into a Python dictionary. Currently, the only supported
   serial format is ``.json``.
 
-- ``serialize_data()``: Serialize the data generated by ``loadData()`` into a serial file format. Currently, the only
+- ``serialization.serialize_data()``: Serialize the data generated by ``loadData()`` into a serial file format. Currently, the only
   supported serial format is ``.json``.
 
 For a more in-depth tutorial for how to use these parser utilities, click :ref:`here <Parsers Example>`.

news/doc-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Paths in our documentation reflect changes made in code.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>