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FUNPACK changelog
=================
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2.0.0 (Tuesday 7th April 2020)
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------------------------------
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Changed
^^^^^^^


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* The ``fmrib`` and ``fmrib_logs`` configuration profiles no longer define the
  variables/categories to be loaded - by default all variables in the input file
  will be loaded and processed.
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* The ``--non_numeric_file`` option has been replaced with ``--suppress_non_numerics``
  (which tells FUNPACK to only save numeric columns to the main output file),
  and the ``--write_non_numerics`` and ``--non_numerics_file`` options, which
  tell FUNPACK to save non-numeric columns to an auxillary output file.
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* The ``--tsv_var_format`` option has been renamed to ``--var_format``, and is
  applied to all export formats.
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* The default output file format is now inferred from the output file suffix -
  one of ``tsv``, ``csv``, or ``h5``.
* The format of the ``--unknown_vars_file`` has changed - the ``processed``
  column has been removed (as with the removal of the ``--import_all`` option,
  it is now equivalent to the ``exported`` column), and uncategorised columns
  now have a ``class`` of ``uncategorised`` instead of ``unprocessed``.


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Removed
^^^^^^^


* Removed several obscure, redundant, or deprecated options, including
  ``--import_all``, ``--remove_unknown``, ``--pass_through``,
  ``--output_id_column``, ``--column_pattern``, ``--column_name``,
  ``--low_memory``, and ``--work_dir``.


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1.9.1 (Sunday 29th March 2020)
------------------------------


Changed
^^^^^^^


* Updates to FMRIB categories.


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1.9.0 (Friday 28th February 2020)
---------------------------------
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Added
^^^^^


* New ``--write_log``, ``--write_unknown_vars``, ``--write_icd10_map``,
  ``--write_description``, and ``--write_summary`` options, which will save
  the respective auxillary output file using a default naming convention which
  is based on the name of the main output file. Exact names can still be
  specified via the ``--log_file``, ``--unknown_vars_file``,
  ``--icd10_map_file``, ``--description_file``, and ``--summary_file``
  options.


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Changed
^^^^^^^


* Refactored the ``fmrib`` configuration profile. ``fmrib`` now just applies
  cleaning/processing rules. ``fmrib_logs`` applies ``fmrib``, and also
  specifies logging/auxillary output files.


Removed
^^^^^^^


* Removed the built-in ``ukb`` configuration.


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Deprecated
^^^^^^^^^^

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* The ``--pass_through`` option is deprecated - the same behaviour can be
  achieved by running FUNPACK without specifying any cleaning or processing
  steps.


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1.8.2 (Monday 24th February 2020)
---------------------------------


Changed
^^^^^^^


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* The ``--config_file`` option can be used more than once, and can also be
  used from within a configuration file (i.e. one configuration file may
  "include" another).
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* Changed the way that the :func:`.removeIfRedundant`  process splits up
  the data set for parallel processing.


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1.8.1 (Wednesday 19th February 2020)
------------------------------------


Added
^^^^^


* New ``naval`` option to the :func:`.removeIfSparse` processing function.


Changed
^^^^^^^


* Changes to the ``fmrib`` configuration, to correctly apply sparsity check
  to variables 41202, 41203, 41270 and 41271.


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1.8.0 (Tuesday 18th February 2020)
----------------------------------
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Added
^^^^^


* New ``take`` option to the :func:`.binariseCategorical` processing function,
  which allows the generated columns to contain values from another column,
  instead of containing binary labels.
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* New ``fillval`` option to the :func:`.binariseCategorical` processing
  function, which can be used in conjunction with ``take``, to specify the
  fill value for missing rows.
* Argument **broadcasting** for processing functions - when a process is
  applied independently to more than one variable, the input arguments to the
  process may need to be different for each variable. This can be accomplished
  by using a _broadcast_ argument - simply prefix the argument name with
  ``'broadcast_'``, and then specify a list containing the argument.
* Processing functions can now be passed lists of values.
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Changed
^^^^^^^


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* Changes to the ``fmrib`` configuration - variables
  `41202 <http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=41202>`_,
  `41203 <http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=41203>`_,
  `41270 <http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=41270>`_, and
  `41271 <http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=41271>`_ are
  binarised, and the binarised values replaced with diagnosis dates from
  the corresponding date variables.
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* The processing function interface has been changed - processing functions
  which return metadata for newly added columns must now return a sequence of
  dicts containing arguments to the :class:`.Column` constructor, which can
  include metadata.


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Fixed
^^^^^


* Fixed a bug whereby only the first two conditions were being parsed in
  an expression comprising multiple identical chained boolean operations
  (e.g. `v10 == 1 || v20 == 2 || v30 == 3`).


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1.7.1 (Thursday 30th January 2020)
----------------------------------


Added
^^^^^


* New built-in ``ukb`` configuration, which applies NA insertion, categorical
  recoding, and child value replacement rules from the ``fmrib`` configuration.


Fixed
^^^^^

* Fixed a bug which arose from combining the ``--import_all`` and ``--column``
  options.


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1.7.0 (Friday 24th January 2020)
--------------------------------
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Added
^^^^^


* New ``--index_visits`` option, which re-arranges variables with separate
  columns per visit into single columns indexed by both subject ID and visit.


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Changed
^^^^^^^


* The ``--index`` option now supports specification of multiple index columns
  for each input file.
* The :func:`.fileinfo.has_header` function has been modified to be more
  lenient.
* The :mod:`.importing` module has been internally refactored to improve
  code cleanliness.
* Various minor internal API changes.
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* The :func:`.removeIfRedundant` processsing function will now drop columns
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  which are redundant with respect to other columns which have already been
  dropped.
* Update to the FMRIB configuration (handling variable `6150
  <https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=6150>`_).
* The ``'codingdesc'`` metaproc function takes into account possible
  categorical recodings when retrieving the description for a particular
  value.
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Fixed
^^^^^


* The :func:`.removeIfRedundant` processsing function was unnecessarily
  evaluating column pairs more than once, when run in parallel.
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1.6.0 (Wednesday 11th December 2019)
------------------------------------
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Added
^^^^^


* Non-numeric variables can now be used in conditional expressions, e.g.
  ``'v41202 == "A009"'`. Within such expressions, the value must be contained
  within single or double quotes.
* New ``contains`` operator, for use within conditional expressions to test
  presence of sub-strings.


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Changed
^^^^^^^


* Parallelisation is now disabled by default, and must be explicitly enabled
  via the ``--num_jobs`` option. This is done in the ``fmrib`` configuration.
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* Subject inclusion expressions are now evaluated during, rather than after,
  data import. They are now therefore performed in parallel on different
  chunks of the input file(s) (when parallelisaton is enabled).
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1.5.0 (Monday 9th December 2019)
--------------------------------
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Added
^^^^^


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* New :func:`.util.wc` function to count the rows (lines) of a file;
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  this is simply a wrapper around the UNIX ``wc`` tool.
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* New :func:`.util.cat` function to concatenate multiple files together;
  this is simply a wrapper around the UNIX ``cat`` tool.
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* New :func:`.util.inMainProcess` function so a process can determine whether
  it is the main process or a worker process.
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* New :meth:`.DataTable.subtable` and :meth:`.DataTable.merge` methods, to aid
  in passing data to/from worker processes.
* Processing functions can now be specified to run independently on a subset
  of variables by using ``'independent'`` in the variable list.
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* New ``any`` and ``all`` operations which can be used in conditional
  statements to control how the conditional results are combined across
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  multiple columns for one variable. These can be used with the ``--subject``
  option.
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Changed
^^^^^^^


* FUNPACK will now parallelise tasks by default; previously it would only
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  parallelise tasks if ``--low_memory`` mode were selected.
* The data import stage is parallelised by using multiple processes to read
  different chunks of the input file(s), and then concatenating the resulting
  ``pandas.DataFrame`` objects afterwards.
* Cleaning functions are executed on each variable in parallel.
* Each processing step is executed in parallel where possible
  (e.g. ``independent`` processes), but processing steps are still executed
  sequentially.  New columns created by processing functions are saved to
  disk, and re-loaded by the main process, rather than being passed back to
  the main process via inter-process communication.
* The ``removeIfRedundant`` process now compares pairs of columns in parallel.
* The data export stage is parallelised by writing chunks of rows to different
  files, and then concatenating them into a single output file afterwards.
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* The ``--variable``, ``--subject`` and ``--exclude`` options now accept
  comma-separated mixtures of IDs and MATLAB-style ranges.
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* Updates to FMRIB categories.
* Updates to FMRIB processing rules, to take advantage of parallelism.
* The ,:mod:`icd10` module must now be initialised via the
  :func:`.icd10.initialise` function, when it is to be used in a multiprocessing
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  context. This is not necessary when ``funpack`` is configured to not
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  parallelise tasks (e.g. with ``--num_jobs 1``).
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Deprecated
^^^^^^^^^^


* The ``--low_memory`` and ``--work_dir`` options have been deprecated, and no
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  longer have any effect. The :mod:`.storage` module is no longer used, but is
  still present for possible future usage.
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1.4.5 (Thursday 5th December 2019)
----------------------------------
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Changed
^^^^^^^


* The ``funpack_demo`` notebook is now executed from a temporary directory, so
  it does not require write-permissions to the FUNPACK installation directory.


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Fixed
^^^^^


* Fixed a bug where non-numeric variables (e.g. `41271
  <https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=41271>`_ ) were being
  interpreted by ``pandas`` as being numeric.


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1.4.4 (Friday 15th November 2019)
---------------------------------


Changed
^^^^^^^


* Updates to the FMRIB categories and configuration.


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1.4.3 (Monday 11th November 2019)
---------------------------------


Changed
^^^^^^^


* Updated internal variable and data coding tables to the latest available from
  the UK Biobank showcase.
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* Increased the file sample size used by :func:`.fileinfo.sniff`.
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1.4.2 (Tuesday 6th August 2019)
-------------------------------


Changed
^^^^^^^


* Minor changes to the FMRIB configuration.


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1.4.1 (Monday 8th July 2019)
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----------------------------
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Added
^^^^^


* New ``--trust_types`` command-line flag which tells FUNPACK to assume that
  the data in known-to-be-numeric columns is parseable (i.e. that there are no
  bad/unparseable values). This option improves import performance, but at the
  cost of causing FUNPACK to crash if the assumption is not true.


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1.4.0 (Sunday 7th July 2019
---------------------------


Added
^^^^^


* Added a new ``InternalType`` column to the variable table, which can be used
  to specify the type to use internally for a given variable
  (e.g. ``float64``).  This is so that the default type of ``float32`` can be
  overridden for specific variables for which this is problematic, such as
  variable :ref:`20003
  <https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=20003>`_. This column is
  initially populated from ``funpack/data/type.txt``.
* New :mod:`funpack.coding` module, for retrieving descriptive information
  about data codings. The information is stored in the
  ``funpack/data/coding/``directory.  Hierarchical data codings are still
  accessed via the :mod:`.hierarchy` module.
* New :func:`hierarchicalDescriptionFromCode`,
  :func:`hierarchicalDescriptionFromNumeric`, and
  :func:`codingDescriptionFromValue` metaprocessing functions.



Changed
^^^^^^^

* The hierarchical coding name no longer needs to be specified when using the
  :func:`.codeToNumeric` cleaning function - the coding is automatically looked
  up.
* Variable 4288 has been moved from ``cognitive phenotypes`` to
  ``miscellaneous`` in the FMRIB categories.
* Variable 20003 is now binarised in the FMRIB categories.
* Changed the meta-processing function signature - these functions are now
  passed the :class:`.DataTable` and variable ID, in addition the value.


Fixed
^^^^^


* Now using an internal type of ``float64`` for variable 20003, as it
  potentially has values which cannot be represented in ``float32``.


Deprecated
^^^^^^^^^^


* Deprecated the `xDescriptionFromCode` and `xDescriptionFromNumeric`
  metaprocessing functions.


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1.3.2 (Tuesday 4th June 2019)
-----------------------------


Changed
^^^^^^^


* Minor adjustments to the FMRIB categories.


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1.3.1 (Thursday 30th May 2019)
------------------------------


Changed
^^^^^^^


* Updates to documentation.


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1.3.0 (Wednesday 29th May 2019)
-------------------------------


Added
^^^^^


* New :func:`.codeToNumeric` cleaning function, for transforming hierarhical
  variable codes.
* New :func:`.hierarchy.codeToNumeric` and
  :func:`.hierarchy.numericToCode` functions.
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* New meta-process functions for generating descriptions for ICD9, OPCS3 and
  OPCS4 hierarchical variables.
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* Variable, data coding, processing, category and type files in the
  ``funpack/config`` directory can be specified on the command line and in
  configuration files as relative paths, and using a "dot" syntax, e.g.
  ``fmrib/categories.tsv``, or ``fmrib.categories``.
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Changed
^^^^^^^


* Built-in cleaning and processing rules are no longer applied by default -
  they are now a part of the built-in ``fmrib`` configuration, and can be
  applied via ``-cfg fmrib``.
* Updates to built-in ``fmrib`` processing.
* The ``flattenHierarchical`` processing function accepts a ``name`` argument,
  allowing the hierarchical data type name to be specified.  If not provided,
  the type is inferred from the variable ID if possible.


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Fixed
^^^^^


* Fixed a bug where a processing step attempted to add a new column with
  the same name as an existing one.


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Deprecated
^^^^^^^^^^


* The :func:`.convertICD10Codes` cleaning function has been replaced by
  the new :func:`.codeToNumeric` function, which can be used with any
  hierarchical variable.
* The :func:`.icd10.codeToNumeric` and :func:`.icd10.numericToCode` functions
  have been replaced by the :func:`.hierarchy.codeToNumeric` and
  :func:`.hierarchy.numericToCode` functions.
* The :func:`.loadDefaultTables` function is obsolete and has been deprecated.



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1.2.1 (Tuesday 28th May 2019)
-----------------------------


Changed
^^^^^^^


* Minor changes to built-in variable categories.


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1.2.0 (Saturday 25th May 2019)
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------------------------------


Added
^^^^^


* New ``--summary_file`` option, which exports a summary of the
  cleaning/processing steps that have been applied to each variable.


Changed
^^^^^^^


* Built-in recoding, NA insertion, and child value replacement rules have
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  been revised and updated.
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1.1.4 (Friday 17th May 2019)
----------------------------


Changed
^^^^^^^


* Changed default processing rules so a column with standard deviation less
  than ``1e-6`` is deemed sparse, and dropped.


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1.1.3 (Thursday 16th May 2019)
------------------------------


Changed
^^^^^^^

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* The :func:`.isSparse` function has been changed so that, when the ``mincat``
  or ``maxcat`` tests are specified as proportions, they are applied relative
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  to the number of *non-missing* data points, rather than the total number of
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  data points.


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1.1.2 (Thursday 16th May 2019)
------------------------------


Fixed
^^^^^


* Fixed a bug in :func:`.flattenHierarchical` with respect to handling missing
  values.


1.1.1 (Wednesday 15th May 2019)
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-------------------------------


Fixed
^^^^^


* Changed the :func:`.isSparse` function to avoid issues with non-numaric
  data.


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1.1.0 (Tuesday 14th May 2019)
-----------------------------


Changed
^^^^^^^


* The ``--visit``/``-vi`` command line option will no longer be applied to
  variables which do not have an `instancing
  <https://biobank.ctsu.ox.ac.uk/crystal/schema.cgi?id=9>`_ code 2.
  This is implemented in the :func:`.keepVisits` function.
* The :func:`.remove` and :func:`.keepVisits` function signatures have changed
  - they now require the variable table to be passed in as the first argument.


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1.0.2 (Tuesday 14th May 2019)
-----------------------------


Changed
^^^^^^^


* The :func:`.removeIfSparse` processing function accepts an ``ignoreType``
  parameter which forces all tests to be run, regardless of the variable type.


Fixed
^^^^^


* The :func:`.isSparse` function was skipping the ``mincat``/``maxcat`` tests
  for non-numeric categorical variables.

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1.0.1 (Friday 9th May 2019)
---------------------------


Changed
^^^^^^^


* Python package name changed from ``fmrib_unpack`` to ``fmrib-unpack``.


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1.0.0 (Friday 9th May 2019)
---------------------------


Changed
^^^^^^^


* ``ukbparse`` is now called ``FUNPACK`` - the *FMRIB UKBiobank Normalisation,
  Processing And Cleaning Kit*.
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Removed
^^^^^^^


* The ``ukbparse_htmlparse``, ``ukbparse_join``, and
  ``ukbparse_compare_tables`` scripts have been removed.
* The ``ukbparse.icd10.readICD10CodingFile`` function and
  ``ukbparse.icd10.ICD10Hierarchy`` class have been removed (their
  functionality was replaced by the :mod:`.hierarchy` module)
* The :func:`.processing_functions.removeIfSparse` and
  :func:`.processing_functions_core.removeIfSparse` functions no longer accept
  an ``absolute`` argument.



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0.21.1 (Thursday 8th May 2019)
------------------------------


Changed
^^^^^^^


* Addd categories 1, 2 and 99 to the ``fmrib`` configuration.



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0.21.0 (Thursday 8th May 2019)
------------------------------


Added
^^^^^


* :class:`.Column` objects now have a ``metadata`` attribute which may be used
  in the column description (if the ``--description_file`` option is used).
  Processing functions can set the metadata for newly added columns.
* New ``metaproc`` plugin type to manipulate column metadata.
* All processing functions accept a ``metaproc`` argument, allowing a
  ``metaproc`` function to be applied to any column metadata that is returned
  by the processing function..


Changed
^^^^^^^


* The :func:`.binariseCategorical` function sets the categorical value as
  column metadata on the new binarised columns.


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0.20.1 (Wednesday 8th May 2019)
-------------------------------


Fixed
^^^^^


* Fixed some typos in the ``README`` file.


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0.20.0 (Tuesday 7th May 2019)
-----------------------------


Added
^^^^^


* The :func:`.isSparse` and :func:`.removeIfSparse` functions accept
  a new option, ``mincat``, which allows a categorical to be deemed sparse
  if the size of its smallest category is below a given threshold.
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* New ``--description_file`` option which, for UK BioBank data, saves the
  description for each column to a text file.
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Changed
^^^^^^^


* The ``absolute`` parameter to the :func:`.isSparse` and
  :func:`.removeIfSparse` functions is deprecated. Instead, they now accept
  ``abspres`` and ``abscat`` arguments, allowing the
  absoluteness/proportionality of the ``minpres`` and ``mincat``/``maxcat``
  options to be specified separately.
* Changed default processing rules so that ICD10 variables undergo a slightly
  different sparsity test.
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Fixed
^^^^^


* Fixed a bug in the categorical recoding rules for Data Coding `100012
  <https://biobank.ctsu.ox.ac.uk/crystal/coding.cgi?id=100012>`_.



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0.19.2 (Friday 26th April 2019)
-------------------------------


Changed
^^^^^^^


* Changes to built-in categories and to ``fmrib`` configuration.


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0.19.1 (Thursday 25th April 2019)
---------------------------------


Changed
^^^^^^^


* Changed the default processing rules for ICD10 variables 40001, 40002,
  40006, 41202, and 41204.
* Added ICD10 variables 41201 and 41270 to the default cleaning/processing
  rules.


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0.19.0 (Wednesday 24th April 2019)
----------------------------------


Added
^^^^^


* The ``--column`` option now accepts a file which contains a list of column
  names to import.


Changed
^^^^^^^


* The :func:`.icd10.codeToNumeric` and :func:`.icd10.numericToCode` functions
  have been changed to use the integer node IDs in the ICD10 hierarchy
  file. The previous approach could not handle parent categories, nor a small
  number of ICD10 codes which do not have a ``<letter><number>`` structure.
* The :func:`.fileinfo.has_header` function has been made more lenient for
  files with a small number of columns.


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0.18.0 (Tuesday 23rd April 2019)
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--------------------------------


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Added
^^^^^


* New :func:`.icd10.numericToCode` function for converting from a numeric
  ICD10 code representation back to its alphanumeric representation.


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Changed
^^^^^^^


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* The default binarised ICD10 column name format has been changed from
  ``[variable_id][numeric_code]-[visit].0`` to
  ``[variable_id]-[visit].[numeric_code]``.
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* The ``--non_numeric_file`` will not be created if there are not any
  non-numeric columns.
* The built-in ``fmrib`` configuration now includes verbosity and logging
  settings.
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* The :func:`.isSparse` function now returns the reason and value for
  columns which fail the sparsity test.

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0.17.0 (Monday 22nd April 2019)
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-------------------------------


Added
^^^^^


* New ``--non_numeric_file`` option allows non-numeric columns to be saved to
  a separate file (TSV export only).
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* Built-in ``fmrib.cfg`` configuration file, which can be used via
  ``-cfg fmrib``.
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Changed
^^^^^^^


* The file generated by ``--unknown_vars_file`` now includes variables which
  are known, but are not in an existing category, and do not have any cleaning
  or processing rules specified for them.
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* Built-in categories have been updated.
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Fixed
^^^^^


* A bug in the column names generated for binarised ICD10 categorical codes
  has been fixed. This bug would potentially have resulted in collisions
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  between column names for different ICD10 codes.
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0.16.0 (Friday 22nd March 2019)
-------------------------------


Changed
^^^^^^^


* Full variable and datacoding table files no longer need to be provided -
  ``ukbparse`` uses ``ukbparse/data/field.txt`` and
  ``ukbparse/data/encoding.txt`` files, obtained from the UK Biobank showcase
  website, as the basis for recognising variables and data codings. The
  ``--variable_file``/``-vf`` and ``--datacoding_file``/``-df`` options now
  accept partial table definitions - these will be merged with the built-in
  rules (still stored in ``ukbparse/data/variables_*.tsv`` and
  ``ukbparse/data/datacodings_*.tsv``) when ``ukbparse`` is invoked.


Deprecated
^^^^^^^^^^


* The ``ukbparse_htmlparse``, ``ukbparse_join`` , and
  ``ukbparse_compare_tables`` commands.


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Removed
^^^^^^^


* The ``--icd10_file`` command-line option has been removed.

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0.15.1 (Thursday 21st March 2019)
---------------------------------


Fixed
^^^^^


* Fixed a bug which arose when using the ``--rename_column`` option.


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0.15.0 (Monday 18th March 2019)
-------------------------------
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Added
^^^^^


* New cleaning function, :func:`.flattenHierarchical`, for use with
  hierarchical variables (e.g. ICD10). The function can be used to replace
  leaf values with parent values.
* New :mod:`.hierarchy` module which contains helper functions and data
  structures for working with hierarchical variables.
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* Definitions for all hierarchical UK Biobank variables are located in the
  ``ukbparse/data/hierarchy/`` directory.
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Deprecated
^^^^^^^^^^


* The :func:`.readICD10ConfigFile` function has been replaced with the
  :func:`.loadHierarchyFile` function.
* The :class:`.ICD10Hierarchy` class has been replaced with the
  :class:`.Hierarchy` class .


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0.14.8 (Monday 18th March 2019)
-------------------------------


Fixed
^^^^^


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* Fixed an issue with the :func:`.binariseCategorical` processing function
  being applied to ICD10 codes.
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0.14.7 (Sunday 17th March 2019)
-------------------------------


Changed
^^^^^^^


* Changes to default cleaning rules - negative values for integer/categorical
  types are no longer discarded.


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0.14.6 (Saturday 16th March 2019)
---------------------------------
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Fixed
^^^^^


* Fixed a ``KeyError`` which was occurring during the child-value replacement
  stage for input files which did not have column names of the form
  ``[variable]-[visit].[instance]``.
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* Fixed some issues introduced by behavioural changes in the
  ``pandas.HDFStore`` class.
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0.14.5 (Thursday 17th January 2019)
-----------------------------------


Fixed
^^^^^


* Implemented a workaround for a `bug <https://bugs.python.org/issue9334>`_ in
  the Python ``argparse`` module.


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0.14.4 (Friday 11th January 2019)
---------------------------------


Changed