DOC: ukbparse->funpack

CHANGELOG.rst

-``ukbparse`` changelog
-======================
+``funpack`` changelog
+=====================
+
+
+1.0.0 (Friday 9th May 2019)
+---------------------------
+
+
+Changed
+^^^^^^^
+
+
+* ``ukbparse`` is now called ``FUNPACK`` - the *FMRIB UKBiobank Normalisation,
+  Processing And Cleaning Kit*.
 
 
 0.21.1 (Thursday 8th May 2019)

LICENSE

-The ukbparse library
+The funpack library
 
-Copyright 2018 University of Oxford, Oxford, UK.
+Copyright 2018-2019 University of Oxford, Oxford, UK.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.rst

-``ukbparse`` - the FMRIB UK BioBank data parser
-===============================================
+``funpack`` - the FMRIB UKBioBank Normalisation, Processing And Cleaning Kit
+============================================================================
 
 
-.. image:: https://img.shields.io/pypi/v/ukbparse.svg
-   :target: https://pypi.python.org/pypi/ukbparse/
+.. image:: https://img.shields.io/pypi/v/fmrib_unpack.svg
+   :target: https://pypi.python.org/pypi/funpack/
+
+.. image:: https://anaconda.org/conda-forge/fmrib_unpack/badges/version.svg
+   :target: https://anaconda.org/conda-forge/fmrib_unpack
 
-.. image:: https://anaconda.org/conda-forge/ukbparse/badges/version.svg
-   :target: https://anaconda.org/conda-forge/ukbparse
 
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1997626.svg
    :target: https://doi.org/10.5281/zenodo.1997626
 
-.. image:: https://git.fmrib.ox.ac.uk/fsl/ukbparse/badges/master/coverage.svg
-   :target: https://git.fmrib.ox.ac.uk/fsl/ukbparse/commits/master/
+.. image:: https://git.fmrib.ox.ac.uk/fsl/funpack/badges/master/coverage.svg
+   :target: https://git.fmrib.ox.ac.uk/fsl/funpack/commits/master/
 
 
-``ukbparse`` is a Python library for pre-processing of UK BioBank data.
+``funpack`` is a Python library for pre-processing of UK BioBank data.
 
 
-    ``ukbparse`` is developed at the Wellcome Centre for Integrative
-    Neuroimaging (WIN@FMRIB), University of Oxford. ``ukbparse`` is in no way
+    ``funpack`` is developed at the Wellcome Centre for Integrative
+    Neuroimaging (WIN@FMRIB), University of Oxford. ``funpack`` is in no way
     endorsed, sanctioned, or validated by the `UK BioBank
     <https://www.ukbiobank.ac.uk/>`_.
 
-    ``ukbparse`` comes bundled with metadata about the variables present in UK
+    ``funpack`` comes bundled with metadata about the variables present in UK
     BioBank data sets. This metadata can be obtained from the `UK BioBank
     online data showcase <https://biobank.ctsu.ox.ac.uk/showcase/index.cgi>`_
 
@@ -32,30 +33,30 @@ Installation
 ------------
 
 
-Install ``ukbparse`` via pip::
+Install ``funpack`` via pip::
 
 
-    pip install ukbparse
+    pip install fmrib_unpack
 
 
 Or from ``conda-forge``::
 
-    conda install -c conda-forge ukbparse
+    conda install -c conda-forge fmrib_unpack
 
 
 Introductory notebook
 ---------------------
 
 
-The ``ukbparse_demo`` command will start a Jupyter Notebook which introduces
-the main features provided by ``ukbparse``. To run it, you need to install a
+The ``funpack_demo`` command will start a Jupyter Notebook which introduces
+the main features provided by ``funpack``. To run it, you need to install a
 few additional dependencies::
 
 
-    pip install ukbparse[demo]
+    pip install fmrib_unpack[demo]
 
 
-You can then start the demo by running ``ukbparse_demo``.
+You can then start the demo by running ``funpack_demo``.
 
 
 .. note:: The introductory notebook uses ``bash``, so is unlikely to work on
@@ -69,17 +70,17 @@ Usage
 General usage is as follows::
 
 
-    ukbparse [options] output.tsv input1.tsv input2.tsv
+    funpack [options] output.tsv input1.tsv input2.tsv
 
 
-You can get information on all of the options by typing ``ukbparse --help``.
+You can get information on all of the options by typing ``funpack --help``.
 
 
 Options can be specified on the command line, and/or stored in a configuration
 file. For example, the options in the following command line::
 
 
-    ukbparse \
+    funpack \
       --overwrite \
       --import_all \
       --log_file log.txt \
@@ -103,28 +104,28 @@ Could be stored in a configuration file ``config.txt``::
 And then executed as follows::
 
 
-    ukbparse -cfg config.txt output.tsv input1.tsv input2.tsv
+    funpack -cfg config.txt output.tsv input1.tsv input2.tsv
 
 
 Customising
 -----------
 
 
-``ukbparse`` contains a large number of built-in rules which have been
+``funpack`` contains a large number of built-in rules which have been
 specifically written to pre-process UK BioBank data variables. These rules are
 stored in the following files:
 
 
- * ``ukbparse/data/variables_*.tsv``: Cleaning rules for individual variables
- * ``ukbparse/data/datacodings_*.tsv``: Cleaning rules for data codings
- * ``ukbparse/data/types.tsv``: Cleaning rules for specific types
- * ``ukbparse/data/processing.tsv``: Processing steps
+ * ``funpack/data/variables_*.tsv``: Cleaning rules for individual variables
+ * ``funpack/data/datacodings_*.tsv``: Cleaning rules for data codings
+ * ``funpack/data/types.tsv``: Cleaning rules for specific types
+ * ``funpack/data/processing.tsv``: Processing steps
 
 
 You can customise or replace these files as you see fit. You can also pass
-your own versions of these files to ``ukbparse`` via the ``--variable_file``,
+your own versions of these files to ``funpack`` via the ``--variable_file``,
 ``--datacoding_file``, ``--type_file`` and ``--processing_file`` command-line
-options respectively. ``ukbparse`` will load all variable and datacoding files,
+options respectively. ``funpack`` will load all variable and datacoding files,
 and merge them into a single table which contains the cleaning rules for each
 variable.
 
@@ -136,7 +137,7 @@ Output
 ------
 
 
-The main output of ``ukbparse`` is a plain-text tab-delimited[*]_ file which
+The main output of ``funpack`` is a plain-text tab-delimited[*]_ file which
 contains the input data, after cleaning and processing, potentially with
 some columns removed, and new columns added.
 
@@ -148,7 +149,7 @@ file.
 
 You can use any tool of your choice to load this output file, such as Python,
 MATLAB, or Excel. It is also possible to pass the output back into
-``ukbparse``.
+``funpack``.
 
 
 .. [*] You can change the delimiter via the ``--tsv_sep`` / ``-ts`` option.
@@ -165,7 +166,7 @@ Loading output into MATLAB
 .. _table: https://uk.mathworks.com/help/matlab/ref/table.html
 
 
-If you are using MATLAB, you have several options for loading the ``ukbparse``
+If you are using MATLAB, you have several options for loading the ``funpack``
 output. The best option is |readtable|_, which will load column names, and
 will handle both non-numeric data and missing values.  Use ``readtable`` like
 so::
@@ -212,7 +213,7 @@ Tests
 To run the test suite, you need to install some additional dependencies::
 
 
-      pip install ukbparse[test]
+      pip install fmrib_unpack[test]
 
 
 Then you can run the test suite using ``pytest``::
@@ -224,5 +225,5 @@ Citing
 ------
 
 
-If you would like to cite ``ukbparse``, please refer to its `Zenodo page
+If you would like to cite ``funpack``, please refer to its `Zenodo page
 <https://doi.org/10.5281/zenodo.1997626>`_.