Add stub documentation for sample and assay plans

Author: djcomlab

docs/index.rst

@@ -20,6 +20,7 @@ flexible way to build and use ISA content, as well as provide utility functions
 #. :doc:`Validating ISA-Tab and ISA JSON </validation>`
 #. :doc:`Importing data in ISA formats </importdata>`
 #. :doc:`Exporting data in ISA formats </exportdata>`
+#. :doc:`Creating ISA content with a Sample and Assay plan </sampleassayplan>`
 #. :doc:`Known Issues </knownissues>`
 
 License
@@ -45,4 +46,5 @@ This code is licensed under the `CPAL License <https://raw.githubusercontent.com
    Validating ISA-Tab and ISA JSON <validation>
    Importing data in ISA formats <importdata>
    Exporting data from ISA formats <exportdata>
+   Creating ISA content with a Sample and Assay plan </sampleassayplan>
    Known Issues <knownissues>

docs/knownissues.rst

@@ -4,11 +4,11 @@ Known issues
 
 isatools v0.9 package
 ---------------------
-- Various API packages have been refactored and moved. ``isatools.model.v1`` is now in ``isatools.model``. Packages ``isatools.validate``, ``isatools.config``, ``isatools.schemas`` have been removed. Some items from ``isatools.convert`` and ``isatools.io`` have been split into the ``isatools.io`` or ``isatools.net`` packages, where the latter has been created to distinguish parts of the ISA API that require network access.
-- Issues #153 is still outstanding since version 0.4, as per below; new issue #235 where missing `Protocol REF`s are sometimes incorrectly inserted on loading ISA-Tab
-- New ISA creation functionality from planning objects in ``isatools.create.models`` currently only support a limited number of technology types (DNA microarray, DNA sequencing, mass spectrometry, and NMR).
+- Various API packages have been refactored and moved. ``isatools.model.v1`` is now in ``isatools.model``. Packages ``isatools.validate``, ``isatools.config``, ``isatools.schemas`` have been removed. Some items from ``isatools.convert`` and ``isatools.io`` have been split into the ``isatools.io`` or ``isatools.net`` packages, where the latter has been created to distinguish parts of the ISA API that require network access
+- Issue #153 is still outstanding since version 0.4, as per below; new issue #235 where missing `Protocol REF`s are sometimes incorrectly inserted on loading ISA-Tab
+- New ISA creation functionality from planning objects in ``isatools.create.models`` currently only support a limited number of technology types (DNA microarray, DNA sequencing, mass spectrometry, and NMR)
 - SRA/ENA importer and Biocrates importer relies on XSLT2 processing only available with SAXON and requires .jar file to run
-- It has been decided to stop work retrofitting support for Python 2.7 and focus on keeping up to date with the current and future Python versions
+- It has been decided to stop work on retrofitting support for Python 2.7 and focus on keeping up to date with the current and future Python versions
 
 isatools v0.8 package
 ---------------------

docs/sampleassayplan.rst

@@ -0,0 +1,8 @@
+#################################################
+Creating ISA content with a Sample and Assay plan
+#################################################
+
+The ISA API provides a set of classes that you can use to plan a study, in terms of sample collection and assay run patterns. Objects of these classes can then be used to dump ISA-Tab or ISA-JSON templates corresponding to your study design. They are found in the ``isatools.create.models`` module.
+
+Take a look at the `isatools-notebooks <https://github.com/ISA-tools/isatools-notebooks>`_ GitHub repository for Jupyter Notebook examples of using the planning objects.
+