Fix whitespace and linelength warning for documentation

Author: Karel-van-de-Plassche

README.md

@@ -6,6 +6,7 @@ interacting with Interface Data Structures (IDSs) as defined by the
 Integrated Modelling & Analysis Suite (IMAS) Data Model.
 
 It provides:
+
 * An easy-to-install and easy-to-get started package by
   * Not requiring an IMAS installation
   * Not strictly requiring matching a Data Dictionary (DD) version
@@ -14,16 +15,19 @@ It provides:
 * Dynamically created in-memory pre-filled data trees from DD XML specifications
 
 ## A word of caution
+
 This package is developed on [ITER bitbucket](https://git.iter.org/projects/IMAS/repos/imaspy).
 For user support, contact the IMAS team on the [IMAS user slack](https://imasusers.slack.com),
 open a [JIRA issue](https://jira.iter.org/projects/IMAS), or email the
 support team on imas-support@iter.org.
 
 ## Documentation
+
 Documentation is autogenerated from the source using [Sphinx](http://sphinx-doc.org/)
 and can be found at the [ITER sharepoint](https://sharepoint.iter.org/departments/POP/CM/IMDesign/Code%20Documentation/IMASPy-doc/html/index.html)
 
 The documentation can be manually generated by installing sphinx and running:
+
 ```bash
 make -C docs html
 ```
@@ -50,15 +54,16 @@ your local system. First make sure you can access the
 [ITER IMAS Access Layer repository](https://git.iter.org/projects/IMAS/repos/access-layer/browse)
 using SSH `ssh://git@git.iter.org/imas/access-layer.git`.
 
-
 ## Where does IMASPy live in IMAS ecosystem?
+
 IMASPy tries to fill a slightly different niche than existing tools. It aims
 to be an _alternative_ to Python HLI instead of a wrapper. It tries to be
 dynamic instead of pre-generated. Is hopes to be extendable instead of
 wrappable.
 
 A small, biased, and wildly incomplete of some common IMAS tools, and
 where they live with respect to IMASPy.
+
 ``` mermaid
 classDiagram
   MDSPLUS_DATABASE .. LL_AL : puts

docs/source/_templates/autosummary/accessor.rst

@@ -1,4 +1,6 @@
-.. Taken from xarray
+..
+    Taken from xarray
+
 {{ fullname }}
 {{ underline }}
 

docs/source/_templates/autosummary/accessor_attribute.rst

@@ -1,4 +1,6 @@
-.. Taken from xarray
+..
+    Taken from xarray
+
 {{ fullname }}
 {{ underline }}
 

docs/source/_templates/autosummary/accessor_callable.rst

@@ -1,4 +1,6 @@
-.. Taken from xarray
+..
+    Taken from xarray
+
 {{ fullname }}
 {{ underline }}
 

docs/source/_templates/autosummary/accessor_method.rst

@@ -1,4 +1,6 @@
-.. Taken from xarray
+..
+    Taken from xarray
+
 {{ fullname }}
 {{ underline }}
 

docs/source/_templates/autosummary/base.rst

@@ -1,2 +1,4 @@
-.. Taken from xarray
+..
+    Taken from xarray
+
 {% extends "!autosummary/base.rst" %}

docs/source/api_overview.rst

@@ -1,5 +1,5 @@
 IMASPy in the IMAS ecosystem
-=================
+============================
 
 .. image:: imaspy_ecosystem.png
 
@@ -9,8 +9,9 @@ read time, all files in the proper paths named IDSDef.zip are searched for data
 dictionary versions to support. Alternatively explicit paths to xml files can be
 used.
 
+
 IMASPy nested structure design
-=================
+==============================
 
 .. image:: imaspy_structure.png
 
@@ -33,7 +34,7 @@ https://numpy.org/doc/stable/reference/generated/numpy.lib.mixins.NDArrayOperato
 
 
 IMASPy usage
-=================
+============
 
 The IMASPy project defines a class :py:class:`IDSRoot` which can be instantiated
 with a DD version number or xml_path. It reads the XML file and recreates the
@@ -74,7 +75,8 @@ An example of instantiating this structure and opening an AL backend is:
 
 
 Loading multiple DD versions in the same environment
-=============
+====================================================
+
 The main change necessary to enable loading multiple DD versions into different
 :py:class:`IDSRoots` is to enable the finding of the relevant
 :py:class:`IDSDef.xml` files. In the ‘classical’ IMAS approach a single
@@ -96,8 +98,10 @@ is useful for development.
 Automated tests have been provided that check the loading of all of the DD
 versions tagged in the data-dictionary git repository.
 
+
 Extending the DD set
----------
+--------------------
+
 A new command has been defined python setup.py build_DD which fetches new tags
 from git and builds IDSDef.zip
 
@@ -112,7 +116,8 @@ All paths are searched in order.
 
 
 Conversion of IDSes between DD versions
-===============
+=======================================
+
 The conversion between DD versions hinges on the ability to read and write to a
 backend data store in a different version than the current DD. To enable this, IMASPy
 needs to read both the ‘main’ in-memory DD, as well as the ‘backend’ DD. This is
@@ -165,8 +170,10 @@ backend is opened, the DD version of the IDS is unknown. At the time of
 `get()` the DD version is found by `read_data_dictionary_version`, which
 reads :py:class:`IDS_properties/version_put/data_dictionary`
 
+
 Implicit conversions:
------------
+---------------------
+
 - Add field
   - No data can be converted
 - Delete field
@@ -176,12 +183,14 @@ Implicit conversions:
 - Move field
   - Handled by searching for change_nbc_previous_name on backend and current XML
   - This is complex, since we may have to search many elements to find the one
-     which was renamed. Changing depths makes this harder.
+    which was renamed. Changing depths makes this harder.
   - Currently implemented up to a single depth change, though multiple are
     possible within this design
 
+
 There are some limitations of the change_nbc paradigm:
-------------
+------------------------------------------------------
+
 - Forward only
 - May require reading an arbitrary number of intermediate versions
 - Does not cover more complex migrations
@@ -194,6 +203,7 @@ occurs the conversion can easily be done in multiple steps.
 
 Time slicing
 ============
+
 The lowlevel API provides `ual_write_slice_data` to write only a slice (in the
 last dimension, time) to the backend, as well as `ual_begin_slice_action`. After
 that normal `get()` can be used. We have implemented time slicing support, with
@@ -233,8 +243,10 @@ verifying as a global array Reading slice by slice (single slice only) The tests
 pass on the memory and MDSPlus backend (the ASCII backend does not support
 slicing).
 
+
 Resampling
-============
+==========
+
 For resampling of data we stick close to the numpy and scipy APIs. The relevant
 method signatures are reproduced here:
 
@@ -318,8 +330,9 @@ Or as such (explicit in-memory copy + interpolation, producing a new data leaf/c
 
 Implementation unit tests can be found in `test_latest_dd_resample.py`.
 
+
 Alternative resampling methods
--------
+------------------------------
 
 .. code-block:: python
 

docs/source/installing.rst

@@ -44,6 +44,7 @@ We are all developers, install imaspy in `pip editable <https://pip.pypa.io/en/s
 We should now be able to run the tests
 
 .. code-block:: bash
+
     pip install --user -r requirements_test.txt
     pytest imaspy/ --mini