CHANGELOG.rst 39.9 KB
Newer Older
Paul McCarthy's avatar
Paul McCarthy committed
1
2
FUNPACK changelog
=================
Paul McCarthy's avatar
Paul McCarthy committed
3
4


Paul McCarthy's avatar
Paul McCarthy committed
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
2.6.0 (Monday 29th March 2021)
------------------------------


Changed
^^^^^^^


* The way that "uncategorised" variables are identified has been changed.
  Previously, a variable which was not in a category *and* which had no
  cleaning/processing rules specified was classified as uncategorised. This
  has been simplified so that a variable which not in a category is classified
  as uncategorised. This has been done to avoid the possibility of missing
  newly added variables which use an existing data coding, and therefore may
  implicitly have cleaning rules specified for them.


Paul McCarthy's avatar
Paul McCarthy committed
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
2.5.2 (Monday 15th March 2021)
------------------------------


Changed
^^^^^^^


* A warning message is now emitted if a processing step is requested for a
  variable that is not present in the input data.


Fixed
^^^^^


* Fixed an issue with the ``binariseCatgegorical`` processing function where,
  when it was applied to multiple variables, each with a separate ``take``
  variable (as is the case in the ``fmrib`` configuration), would cause an
  error if any of the ``take`` variables were not present.


44
45
2.5.1 (Wednesday 3rd March 2021)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
46
47


Paul McCarthy's avatar
Paul McCarthy committed
48
49
50
51
52
53
54
55
Added
^^^^^


* New ``--escape_newlines`` option, which causes non-numeric values containing
  escape characters (e.g. ``\n``, ``\t``, etc) to be output literally.


Paul McCarthy's avatar
Paul McCarthy committed
56
57
58
59
60
61
Fixed
^^^^^


* Fixed a bug where subject inclusion expressions were causing zero rows to be
  imported if the variable was not present in the input file.
Paul McCarthy's avatar
Paul McCarthy committed
62
* Fixed some compatibility issues with Pandas 1.2.
Paul McCarthy's avatar
Paul McCarthy committed
63
64


Paul McCarthy's avatar
Paul McCarthy committed
65
66
67
68
69
70
71
72
73
74
2.5.0 (Wednesday 9th December 2020)
-----------------------------------


Added
^^^^^


* New ``--rename_duplicates`` option, which can be used to give duplicate
  columns unique names.
Paul McCarthy's avatar
Paul McCarthy committed
75
76
77
78
79
80


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
81
82
* Conditional expressions used with the ``--subject`` option can now be used
  on date/time variables.
Paul McCarthy's avatar
Paul McCarthy committed
83
84
85
* Internal re-organisation of the ``funpack.fileinfo`` module, and minor
  changes to function interfaces in the ``funpack.importing`` and
  ``funpack.loadtables`` modules.
Paul McCarthy's avatar
Paul McCarthy committed
86
87


Paul McCarthy's avatar
Paul McCarthy committed
88
89
90
91
92
93
94
95
96
97
98
2.4.0 (Thursday 26th November 2020)
___________________________________


Added
^^^^^


* New ``--ids_only`` option which causes only the subject IDs to be saved,
  suitable for use with the ``--subject`` option in subsequent calls to
  ``funpack``.
Paul McCarthy's avatar
Paul McCarthy committed
99
100
101
102
103
104
105


Changed
^^^^^^^

* Changed how binary subject selection expressions are evaluated when the
  different variables have different numbers of columns.
Paul McCarthy's avatar
Paul McCarthy committed
106
107
108
109
110
* All internal UKB showcase data tables have been updated to their
  latest versions.
* The node name for `Chapter V - Supplementary classification ...` in the ICD9
  data table has been changed from `Chapter V` to `Chapter V sup` to avoid
  collisions with the `Chapter V` node.
Paul McCarthy's avatar
Paul McCarthy committed
111
112


Paul McCarthy's avatar
Paul McCarthy committed
113
114
115
116
117
118
119
120
121
122
123
2.3.3 (Wednesday 5th October 2020)
----------------------------------


Changed
^^^^^^^


* Improved performance when appying the ``--column`` command-line argument.


Paul McCarthy's avatar
Paul McCarthy committed
124
125
126
127
128
129
130
131
132
133
134
135
2.3.2 (Wednesday 10th June 2020)
--------------------------------


Fixed
^^^^^


* Fixed an issue which was preventing FUNPACK from being used on Windows
  platforms (!65).


Paul McCarthy's avatar
Paul McCarthy committed
136
137
2.3.1 (Sunday 17th May 2020)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
138
139


Paul McCarthy's avatar
Paul McCarthy committed
140
141
142
143
144
145
Changed
^^^^^^^


* The :func:`.removeIfSparse` processing function can now parallelise the
  check across columns, rather than relying on the :mod:`.processing` module
Paul McCarthy's avatar
Paul McCarthy committed
146
  to parallelise calls across variables (!64).
Paul McCarthy's avatar
Paul McCarthy committed
147
148


Paul McCarthy's avatar
Paul McCarthy committed
149
150
151
152
153
Fixed
^^^^^


* The improved :mod:`.fmrib` date/time normalisation routines were not
Paul McCarthy's avatar
Paul McCarthy committed
154
155
156
  converting ``NaTs`` (Not-a-Time) correctly (!62).
* Fixed a problem in the FMRIB configuration - diagnosis timestamps were not
  being injected into binarised ICD variables (!63).
Paul McCarthy's avatar
Paul McCarthy committed
157
158


Paul McCarthy's avatar
Paul McCarthy committed
159
160
2.3.0 (Tuesday 12th May 2020)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
161
162
163
164
165
166
167
168


Changed
^^^^^^^


* Modified the :func:`.binariseCategorical` function so that it parallelises
  tasks internally, instead of being called in parallel for different
Paul McCarthy's avatar
Paul McCarthy committed
169
  variables. This should give superior performance (!60).
Paul McCarthy's avatar
Paul McCarthy committed
170
* Revisited the :meth:`.DataTable.merge` to optimise performance in all
Paul McCarthy's avatar
Paul McCarthy committed
171
  scenarios (!60).
Paul McCarthy's avatar
Paul McCarthy committed
172
173
174
175
* Improved performance of the :mod:`.fmrib` date/time normalisation routines,
  and changed their usage so they are now applied as "cleaning" functions
  after data import, rather than just before export. This means that date/
  time columns can be subjected to the redundancy check (as they will have
Paul McCarthy's avatar
Paul McCarthy committed
176
  a numeric type), and will improve data export performance (!60, !61).
Paul McCarthy's avatar
Paul McCarthy committed
177
178


Paul McCarthy's avatar
Paul McCarthy committed
179
180
181
182
183
184
185
186
187
188
189
190
2.2.1 (Monday 4th May 2020)
---------------------------


Fixed
^^^^^


* Reverted some changes to :meth:`.DataTable.merge` which caused performance
  degradations.


Paul McCarthy's avatar
Paul McCarthy committed
191
192
2.2.0 (Friday 1st May 2020)
---------------------------
Paul McCarthy's avatar
Paul McCarthy committed
193
194
195
196
197
198


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
199
200
201
* Substantial performance improvements to the :func:`.codeToNumeric` cleaning
  function, and to :func:`.removeIfRedundant`, :func:`.binariseCategorical`,
  and other processing functions.
Paul McCarthy's avatar
Paul McCarthy committed
202
203
204
205
206
207
* The default implementation of :func:`.removeIfRedundant` now uses matrix
  algebra rather thsn pairwise comparisons. This requires more memory, but
  is much faster.
* Added [`threadpoolctl`](https://github.com/joblib/threadpoolctl/) as a
  dependency, for setting the number of threads to use when parallelising
  ``numpy`` operations.
Paul McCarthy's avatar
Paul McCarthy committed
208
209
210
211
212
213
214
215


Fixed
^^^^^


* The :func:`.removeIfRedundant` processing function was not testing columns
  with no missing values when a NA correlation threshold was being used.
Paul McCarthy's avatar
Paul McCarthy committed
216
217
* :func:`.removeIfRedundant` was also potentially producing inconsistent
  results for columns with no present values, or with a constant value.
Paul McCarthy's avatar
Paul McCarthy committed
218
219


Paul McCarthy's avatar
Paul McCarthy committed
220
221
222
223
224
225
226
227
228
229
2.1.0 (Tuesday 21st April 2020)
-------------------------------


Added
^^^^^


* New ``--drop_na_rows`` option, which tells ``funpack`` to drop rows which do
  not contain a value for any column.
Paul McCarthy's avatar
Paul McCarthy committed
230
231
232
233
234
235
236
237
238


Changed
^^^^^^^


* Internal changes to improve performance.


Paul McCarthy's avatar
Paul McCarthy committed
239
2.0.0 (Tuesday 7th April 2020)
Paul McCarthy's avatar
Paul McCarthy committed
240
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
241
242


Paul McCarthy's avatar
Paul McCarthy committed
243
244
245
246
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
247
248
249
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
250
251
252
253
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
254
255
* The ``--tsv_var_format`` option has been renamed to ``--var_format``, and is
  applied to all export formats.
Paul McCarthy's avatar
Paul McCarthy committed
256
257
258
259
260
261
262
263
* 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``.


Paul McCarthy's avatar
Paul McCarthy committed
264
265
266
267
268
269
270
271
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``.
Paul McCarthy's avatar
Paul McCarthy committed
272
273
* Removed the unused :mod:`funpack.storage` module.
* Removed the unused :meth:`.DataTable.order` method.
Paul McCarthy's avatar
Paul McCarthy committed
274
275


Paul McCarthy's avatar
Paul McCarthy committed
276
277
278
279
280
281
282
283
284
285
286
1.9.1 (Sunday 29th March 2020)
------------------------------


Changed
^^^^^^^


* Updates to FMRIB categories.


Paul McCarthy's avatar
Paul McCarthy committed
287
288
1.9.0 (Friday 28th February 2020)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303


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.


Paul McCarthy's avatar
Paul McCarthy committed
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
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.


Paul McCarthy's avatar
Paul McCarthy committed
320
321
322
Deprecated
^^^^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
323

Paul McCarthy's avatar
Paul McCarthy committed
324
325
326
327
328
* The ``--pass_through`` option is deprecated - the same behaviour can be
  achieved by running FUNPACK without specifying any cleaning or processing
  steps.


Paul McCarthy's avatar
Paul McCarthy committed
329
330
331
332
333
334
335
336
1.8.2 (Monday 24th February 2020)
---------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
337
338
339
* 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).
Paul McCarthy's avatar
Paul McCarthy committed
340
341
342
343
* Changed the way that the :func:`.removeIfRedundant`  process splits up
  the data set for parallel processing.


Paul McCarthy's avatar
Paul McCarthy committed
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
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.


Paul McCarthy's avatar
Paul McCarthy committed
363
364
1.8.0 (Tuesday 18th February 2020)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
365
366
367
368
369
370
371
372
373


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.
Paul McCarthy's avatar
Paul McCarthy committed
374
375
376
377
378
379
380
381
382
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
383
384


Paul McCarthy's avatar
Paul McCarthy committed
385
386
387
388
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
389
390
391
392
393
394
395
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
396
397
398
399
400
401
* 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.


Paul McCarthy's avatar
Paul McCarthy committed
402
403
404
405
406
407
408
409
410
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`).


Paul McCarthy's avatar
Paul McCarthy committed
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
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.


Paul McCarthy's avatar
Paul McCarthy committed
430
431
1.7.0 (Friday 24th January 2020)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
432
433
434
435
436
437
438
439
440
441


Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
442
443
444
445
446
447
448
449
450
451
452
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.
Paul McCarthy's avatar
Paul McCarthy committed
453
* The :func:`.removeIfRedundant` processsing function will now drop columns
Paul McCarthy's avatar
Paul McCarthy committed
454
455
456
457
458
459
460
  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.
Paul McCarthy's avatar
Paul McCarthy committed
461
462
463
464
465
466
467
468


Fixed
^^^^^


* The :func:`.removeIfRedundant` processsing function was unnecessarily
  evaluating column pairs more than once, when run in parallel.
Paul McCarthy's avatar
Paul McCarthy committed
469
470


Paul McCarthy's avatar
Paul McCarthy committed
471
472
1.6.0 (Wednesday 11th December 2019)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
473
474
475
476
477
478
479
480
481
482
483
484
485


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.


Paul McCarthy's avatar
Paul McCarthy committed
486
487
488
489
490
491
Changed
^^^^^^^


* Parallelisation is now disabled by default, and must be explicitly enabled
  via the ``--num_jobs`` option. This is done in the ``fmrib`` configuration.
Paul McCarthy's avatar
Paul McCarthy committed
492
493
494
* 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).
Paul McCarthy's avatar
Paul McCarthy committed
495
496


Paul McCarthy's avatar
Paul McCarthy committed
497
498
1.5.0 (Monday 9th December 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
499
500
501
502
503
504


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
505
* New :func:`.util.wc` function to count the rows (lines) of a file;
Paul McCarthy's avatar
Paul McCarthy committed
506
  this is simply a wrapper around the UNIX ``wc`` tool.
Paul McCarthy's avatar
Paul McCarthy committed
507
508
* New :func:`.util.cat` function to concatenate multiple files together;
  this is simply a wrapper around the UNIX ``cat`` tool.
Paul McCarthy's avatar
Paul McCarthy committed
509
510
* New :func:`.util.inMainProcess` function so a process can determine whether
  it is the main process or a worker process.
Paul McCarthy's avatar
Paul McCarthy committed
511
512
513
514
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
515
516
* New ``any`` and ``all`` operations which can be used in conditional
  statements to control how the conditional results are combined across
Paul McCarthy's avatar
Paul McCarthy committed
517
518
  multiple columns for one variable. These can be used with the ``--subject``
  option.
Paul McCarthy's avatar
Paul McCarthy committed
519
520
521
522
523
524
525


Changed
^^^^^^^


* FUNPACK will now parallelise tasks by default; previously it would only
Paul McCarthy's avatar
Paul McCarthy committed
526
527
528
529
530
531
532
533
534
535
536
537
538
  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.
Paul McCarthy's avatar
Paul McCarthy committed
539
540
* The ``--variable``, ``--subject`` and ``--exclude`` options now accept
  comma-separated mixtures of IDs and MATLAB-style ranges.
Paul McCarthy's avatar
Paul McCarthy committed
541
542
543
544
* 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
Paul McCarthy's avatar
Paul McCarthy committed
545
  context. This is not necessary when ``funpack`` is configured to not
Paul McCarthy's avatar
Paul McCarthy committed
546
  parallelise tasks (e.g. with ``--num_jobs 1``).
Paul McCarthy's avatar
Paul McCarthy committed
547
548
549
550
551
552
553


Deprecated
^^^^^^^^^^


* The ``--low_memory`` and ``--work_dir`` options have been deprecated, and no
Paul McCarthy's avatar
Paul McCarthy committed
554
555
  longer have any effect. The :mod:`.storage` module is no longer used, but is
  still present for possible future usage.
Paul McCarthy's avatar
Paul McCarthy committed
556
557
558
559


1.4.5 (Thursday 5th December 2019)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
560
561


Paul McCarthy's avatar
Paul McCarthy committed
562
563
564
565
566
567
568
569
Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
570
571
572
573
574
575
576
577
578
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.


Paul McCarthy's avatar
Paul McCarthy committed
579
580
581
582
583
584
585
586
587
588
589
1.4.4 (Friday 15th November 2019)
---------------------------------


Changed
^^^^^^^


* Updates to the FMRIB categories and configuration.


Paul McCarthy's avatar
Paul McCarthy committed
590
591
592
593
594
595
596
597
598
599
1.4.3 (Monday 11th November 2019)
---------------------------------


Changed
^^^^^^^


* Updated internal variable and data coding tables to the latest available from
  the UK Biobank showcase.
Paul McCarthy's avatar
Paul McCarthy committed
600
* Increased the file sample size used by :func:`.fileinfo.sniff`.
Paul McCarthy's avatar
Paul McCarthy committed
601

Paul McCarthy's avatar
Paul McCarthy committed
602
603
604
605
606
607
608
609
610
611
612
613

1.4.2 (Tuesday 6th August 2019)
-------------------------------


Changed
^^^^^^^


* Minor changes to the FMRIB configuration.


Paul McCarthy's avatar
Paul McCarthy committed
614
1.4.1 (Monday 8th July 2019)
Paul McCarthy's avatar
Paul McCarthy committed
615
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
616
617
618
619
620
621
622
623
624
625
626
627


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.


Paul McCarthy's avatar
Paul McCarthy committed
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
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.


Paul McCarthy's avatar
Paul McCarthy committed
682
683
684
685
686
687
688
689
690
691
692
1.3.2 (Tuesday 4th June 2019)
-----------------------------


Changed
^^^^^^^


* Minor adjustments to the FMRIB categories.


Paul McCarthy's avatar
Paul McCarthy committed
693
694
695
696
697
698
699
700
701
702
703
1.3.1 (Thursday 30th May 2019)
------------------------------


Changed
^^^^^^^


* Updates to documentation.


Paul McCarthy's avatar
Paul McCarthy committed
704
705
706
707
708
709
710
711
712
713
714
715
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.
Paul McCarthy's avatar
Paul McCarthy committed
716
717
* New meta-process functions for generating descriptions for ICD9, OPCS3 and
  OPCS4 hierarchical variables.
Paul McCarthy's avatar
Paul McCarthy committed
718
719
720
721
* 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``.
Paul McCarthy's avatar
Paul McCarthy committed
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736


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.


Paul McCarthy's avatar
Paul McCarthy committed
737
738
739
740
741
742
743
744
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
745
746
747
748
749
750
751
752
753
754
755
756
757
758
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.



Paul McCarthy's avatar
Paul McCarthy committed
759
760
761
762
763
764
765
766
767
768
769
1.2.1 (Tuesday 28th May 2019)
-----------------------------


Changed
^^^^^^^


* Minor changes to built-in variable categories.


Paul McCarthy's avatar
Paul McCarthy committed
770
1.2.0 (Saturday 25th May 2019)
Paul McCarthy's avatar
Paul McCarthy committed
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
------------------------------


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
Paul McCarthy's avatar
Paul McCarthy committed
787
  been revised and updated.
Paul McCarthy's avatar
Paul McCarthy committed
788
789


Paul McCarthy's avatar
Paul McCarthy committed
790
791
792
793
794
795
796
797
798
799
800
801
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.


Paul McCarthy's avatar
Paul McCarthy committed
802
803
804
805
806
807
808
809

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


Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
810

Paul McCarthy's avatar
Paul McCarthy committed
811
812
* The :func:`.isSparse` function has been changed so that, when the ``mincat``
  or ``maxcat`` tests are specified as proportions, they are applied relative
Paul McCarthy's avatar
Paul McCarthy committed
813
  to the number of *non-missing* data points, rather than the total number of
Paul McCarthy's avatar
Paul McCarthy committed
814
815
816
  data points.


Paul McCarthy's avatar
Paul McCarthy committed
817
818
819
820
821
822
823
824
825
826
827
828
829
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)
Paul McCarthy's avatar
Paul McCarthy committed
830
831
832
833
834
835
836
837
838
839
840
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
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.


Paul McCarthy's avatar
Paul McCarthy committed
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
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.

Paul McCarthy's avatar
Paul McCarthy committed
876
877
878
879
880
881
882
883
884
885
886
887

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


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
888
889
890
891
892
893
894
895
896
897
1.0.0 (Friday 9th May 2019)
---------------------------


Changed
^^^^^^^


* ``ukbparse`` is now called ``FUNPACK`` - the *FMRIB UKBiobank Normalisation,
  Processing And Cleaning Kit*.
Paul McCarthy's avatar
Paul McCarthy committed
898

Paul McCarthy's avatar
Paul McCarthy committed
899

Paul McCarthy's avatar
Paul McCarthy committed
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
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.



Paul McCarthy's avatar
Paul McCarthy committed
915
916
917
918
919
920
921
922
923
924
925
926
0.21.1 (Thursday 8th May 2019)
------------------------------


Changed
^^^^^^^


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



Paul McCarthy's avatar
Paul McCarthy committed
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
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.


Paul McCarthy's avatar
Paul McCarthy committed
952
953
954
955
956
957
958
959
960
961
962
0.20.1 (Wednesday 8th May 2019)
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
963
964
965
966
967
968
969
970
971
972
973
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.
Paul McCarthy's avatar
Paul McCarthy committed
974
975
* New ``--description_file`` option which, for UK BioBank data, saves the
  description for each column to a text file.
Paul McCarthy's avatar
Paul McCarthy committed
976
977
978
979
980
981
982
983
984
985
986
987
988


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.
Paul McCarthy's avatar
Paul McCarthy committed
989
990
991
992
993
994
995
996
997
998
999


Fixed
^^^^^


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



Paul McCarthy's avatar
Paul McCarthy committed
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
0.19.2 (Friday 26th April 2019)
-------------------------------


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
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.


Paul McCarthy's avatar
Paul McCarthy committed
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
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.


Paul McCarthy's avatar
Paul McCarthy committed
1049
0.18.0 (Tuesday 23rd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
1050
1051
1052
--------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
1053
1054
1055
1056
1057
1058
1059
1060
Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1061
1062
1063
1064
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1065
1066
1067
* The default binarised ICD10 column name format has been changed from
  ``[variable_id][numeric_code]-[visit].0`` to
  ``[variable_id]-[visit].[numeric_code]``.
Paul McCarthy's avatar
Paul McCarthy committed
1068
1069
1070
1071
* 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.
Paul McCarthy's avatar
Paul McCarthy committed
1072
1073
1074
* The :func:`.isSparse` function now returns the reason and value for
  columns which fail the sparsity test.

Paul McCarthy's avatar
Paul McCarthy committed
1075
1076


Paul McCarthy's avatar
Paul McCarthy committed
1077
0.17.0 (Monday 22nd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
1078
1079
1080
1081
1082
1083
1084
1085
1086
-------------------------------


Added
^^^^^


* New ``--non_numeric_file`` option allows non-numeric columns to be saved to
  a separate file (TSV export only).
Paul McCarthy's avatar
Paul McCarthy committed
1087
1088
* Built-in ``fmrib.cfg`` configuration file, which can be used via
  ``-cfg fmrib``.
Paul McCarthy's avatar
Paul McCarthy committed
1089
1090
1091
1092
1093
1094
1095
1096
1097


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.
Paul McCarthy's avatar
Paul McCarthy committed
1098
* Built-in categories have been updated.
Paul McCarthy's avatar
Paul McCarthy committed
1099
1100
1101
1102
1103
1104
1105
1106


Fixed
^^^^^


* A bug in the column names generated for binarised ICD10 categorical codes
  has been fixed. This bug would potentially have resulted in collisions
Paul McCarthy's avatar
Paul McCarthy committed
1107
  between column names for different ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
1108
1109


Paul McCarthy's avatar
Paul McCarthy committed
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
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.


Paul McCarthy's avatar
Paul McCarthy committed
1136
1137
1138
1139
1140
1141
Removed
^^^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
1142

Paul McCarthy's avatar
Paul McCarthy committed
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
0.15.1 (Thursday 21st March 2019)
---------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1154
1155
0.15.0 (Monday 18th March 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166


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.
Paul McCarthy's avatar
Paul McCarthy committed
1167
1168
* Definitions for all hierarchical UK Biobank variables are located in the
  ``ukbparse/data/hierarchy/`` directory.
Paul McCarthy's avatar
Paul McCarthy committed
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180


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 .


Paul McCarthy's avatar
Paul McCarthy committed
1181
1182
1183
1184
1185
1186
1187
1188
0.14.8 (Monday 18th March 2019)
-------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1189
1190
* Fixed an issue with the :func:`.binariseCategorical` processing function
  being applied to ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
1191

Paul McCarthy's avatar
Paul McCarthy committed
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204

0.14.7 (Sunday 17th March 2019)
-------------------------------


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1205
1206
0.14.6 (Saturday 16th March 2019)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1207
1208
1209
1210
1211
1212
1213
1214
1215


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]``.
Paul McCarthy's avatar
Paul McCarthy committed
1216
1217
* Fixed some issues introduced by behavioural changes in the
  ``pandas.HDFStore`` class.
Paul McCarthy's avatar
Paul McCarthy committed
1218
1219


Paul McCarthy's avatar
Paul McCarthy committed
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
0.14.5 (Thursday 17th January 2019)
-----------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1232
1233
1234
1235
1236
1237
1238
1239
1240
0.14.4 (Friday 11th January 2019)
---------------------------------


Changed
^^^^^^^


* Updated the default processing rules for variable
Paul McCarthy's avatar
Paul McCarthy committed
1241
  [1120-1150](https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=1120).
Paul McCarthy's avatar
Paul McCarthy committed
1242
1243


Paul McCarthy's avatar
Paul McCarthy committed
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
0.14.3 (Tuesday 8th January 2019)
---------------------------------


Fixed
^^^^^


* Fixed a regression introduced in 0.14.2, where column loading restrictions
  (e.g. ``--variable``) were not being honoured


Paul McCarthy's avatar
Paul McCarthy committed
1256
1257
1258
1259
1260
1261
1262
1263
0.14.2 (Monday 7th January 2019)
--------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1264
* Fixed a regression introduced in 0.14.1, where using the ``--variable`` and
Paul McCarthy's avatar
Paul McCarthy committed
1265
1266
  ``--visit`` options together could cause a crash.

Paul McCarthy's avatar
Paul McCarthy committed
1267

Paul McCarthy's avatar
Paul McCarthy committed
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
0.14.1 (Monday 7th January 2019)
--------------------------------


Fixed
^^^^^


* If the index columns for each input file have different names, the output
  index column was unnamed.  It is now given the name of the index column in
  the first input file.
* When the ``--column`` and ``--variable`` options were used together, only
  columns which passed both tests were being loaded. Now, columns which pass
  either test are loaded.


Paul McCarthy's avatar
Paul McCarthy committed
1284
1285
0.14.0 (Tuesday 25th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1286
1287
1288
1289
1290
1291


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1292
1293
* New ``--column`` option, allowing columns to be selected by name/name
  pattern.
Paul McCarthy's avatar
Paul McCarthy committed
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
* ``ukbparse`` can now be installed from `conda-forge
  <https://anaconda.org/conda-forge/ukbparse>`_.


Changed
^^^^^^^


* The index column in the output file no longer defaults to being named
  ``'eid'``. It defaults to the name of the index in the input file, but
  can still be overridden by the ``--output_id_column`` option.

Paul McCarthy's avatar
Paul McCarthy committed
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316

Fixed
^^^^^


* Blank lines are now allowed in configuration files (#2)
* Fix to derived column names for ICD10 variables in default processing rules.


0.13.1 (Thursday 20th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326


Added
^^^^^


* Unit test to make sure that ``ukbparse`` crashes if given bad input
  arguments.


Paul McCarthy's avatar
Paul McCarthy committed
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
0.13.0 (Thursday 20th Deember 2018)
-----------------------------------


Added
^^^^^


* New ``--index`` option, allowing the position of the index column in input
  files to be specified.
Paul McCarthy's avatar
Paul McCarthy committed
1337
1338
* The ``--variable``, ``--subject``, and ``--exclude`` options now accept
  comma-separated lists, in addition to IDs, ID ranges, and text files.
Paul McCarthy's avatar
Paul McCarthy committed
1339
1340


Paul McCarthy's avatar
Paul McCarthy committed
1341
1342
1343
1344
1345
1346
1347
Fixed
^^^^^


* Memory usage estimates in log messages were wrong under Linux.


Paul McCarthy's avatar
Paul McCarthy committed
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
0.12.3 (Tuesday 18th December 2018
----------------------------------


Changed
^^^^^^^


* Changes to new :func:`.fileinfo.has_header` function to improve robustness.


Paul McCarthy's avatar
Paul McCarthy committed
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
0.12.2 (Monday 17th December 2018)
----------------------------------


Changed
^^^^^^^


* Now using a custom implementation of ``csv.Sniffer.has_header``, as the
  standard library version does not handle some scenarios.


Paul McCarthy's avatar
Paul McCarthy committed
1371
1372
0.12.1 (Saturday 15th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391


Added
^^^^^


* Added some instructions for generating your own variable and data coding
  tables to the README.


Changed
^^^^^^^


* The ``ukbparse_demo`` script ensures that the Jupyter ``bash_kernel`` is
  installed.
* The ``ukbparse_compare_tables``, ``ukbparse_htmlparse`` and
  ``ukbparse_join`` scripts print some help documentation when called without
  any arguments.
Paul McCarthy's avatar
Paul McCarthy committed
1392
* Added ``lxml`` as a dependency (required by ``beautifulsoup4``).
Paul McCarthy's avatar
Paul McCarthy committed
1393
1394


Paul McCarthy's avatar
Paul McCarthy committed
1395
1396
0.12.0 (Tuesday 11th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1397
1398
1399
1400
1401
1402
1403
1404
1405


Added
^^^^^


* The ``join``, ``compare_tables``, and ``htmlparse`` scripts are now
  installed as entry points called ``ukbparse_join``,
  ``ukbparse_compare_tables``, and ``ukbparse_htmlparse``.
Paul McCarthy's avatar
Paul McCarthy committed
1406
1407
1408
* Jupyter notebook, demonstrating most of the features in ``ukbparse``, at
  ``ukbparse/demo/ukbparse_demonstration.ipynb``. You can run the demo via the
  ``ukbparse_demo`` entry point.
Paul McCarthy's avatar
Paul McCarthy committed
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424


Changed
^^^^^^^


* Moved the ``scripts/`` directory into the ``ukbparse/`` directory.
* Improved string representation of process functions.


Fixed
^^^^^


* Fix to configuration file parsing code - ``shlex.split`` is now used instead
  of ``str.split``.
Paul McCarthy's avatar
Paul McCarthy committed
1425
1426
* Fixed mixed data type issues when merging the data coding and type tables into
  the variable table.
Paul McCarthy's avatar
Paul McCarthy committed
1427

Paul McCarthy's avatar
Paul McCarthy committed
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441

0.11.3 (Monday 10th December 2018)
----------------------------------


Changed
^^^^^^^


* Made the ``vid``, ``visit``, and ``instance`` parameters to the
  :class:`.Column` class optional, to make life easier for custom sniffer
  functions.


Paul McCarthy's avatar
Paul McCarthy committed
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
0.11.2 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


* Fixed a bug in the handling of new variable IDs returned by processing
  functions.



Paul McCarthy's avatar
Paul McCarthy committed
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
0.11.1 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


* Fixed a bug in the :func:`.removeIfSparse` processing function.


Paul McCarthy's avatar
Paul McCarthy committed
1466
1467
0.11.0 (Monday 10th December 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1468
1469
1470
1471
1472
1473
1474
1475


Added
^^^^^


* New ``--no_builtins`` option, which causes the built-in variable, data
  coding, type, and category table files to be bypassed.
Paul McCarthy's avatar
Paul McCarthy committed
1476
1477
1478
* New :meth:`.PluginRegistry.get` function for getting a reference to a plugin
  function.
* Cleaning/processing functions are listed in command-line help.
Paul McCarthy's avatar
Paul McCarthy committed
1479
1480


Paul McCarthy's avatar
Paul McCarthy committed
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
0.10.5 (Saturday 8th December 2018)
-----------------------------------


Changed
^^^^^^^


* The ``minpres`` option to the :func:`.removeIfSparse` processing function
  is ignored if it is specified as an absolute value, and the data set length
  is less than it.


Paul McCarthy's avatar
Paul McCarthy committed
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
0.10.4 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Fixed an issue with the `--subject` command line option.


Paul McCarthy's avatar
Paul McCarthy committed
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
0.10.3 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Made use of the standard library ``resource`` module conditional, as it is
  not present on Windows.


Paul McCarthy's avatar
Paul McCarthy committed
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
0.10.2 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Removed relative imports from test modules.


Paul McCarthy's avatar
Paul McCarthy committed
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
0.10.1 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* The :mod:`ukbparse.plugins` package was missing an ``__init__.py``, and was
  not being included in PyPI packages.


Paul McCarthy's avatar
Paul McCarthy committed
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
0.10.0 (Thursday 6th December 2018)
-----------------------------------


Added
^^^^^


* New ``--na_values``, ``--recoding``, and ``--child_values`` command-line
  options for specifying/overriding NA insertion, categorical recodings,
  and child variable value replacement.
Paul McCarthy's avatar
Paul McCarthy committed
1551
1552
* ``--dry_run`` mode now prints information about columns that would not be
  loaded.
Paul McCarthy's avatar
Paul McCarthy committed
1553
1554


Paul McCarthy's avatar
Paul McCarthy committed
1555
1556
1557
1558
1559
1560
Fixed
^^^^^


* Fixed a bug in the :func:`.calculateExpressionEvaluationOrder` function.

Paul McCarthy's avatar
Paul McCarthy committed
1561

Paul McCarthy's avatar
Paul McCarthy committed
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
0.9.0 (Thursday 6th December 2018)
----------------------------------


Added
^^^^^


* Infrastructure for automatic deployment to PyPI and Zenodo.


Changed
^^^^^^^


* Improved ``--dry_run`` output formatting.


Paul McCarthy's avatar
Paul McCarthy committed
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
0.8.0
-----


Added
^^^^^


* New ``--dry_run`` command-line option, which prints a summary of the cleaning
  and processing that would take place.


Paul McCarthy's avatar
Paul McCarthy committed
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
0.7.1
-----


Fixed
^^^^^


* Fixed a bug in the :func:`.icd10.saveCodes` function.


Paul McCarthy's avatar
Paul McCarthy committed
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
0.7.0
-----


Changed
^^^^^^^


* Small refactorings in :mod:`ukbparse.config` so that command line arguments
  can be logged easily.


Paul McCarthy's avatar
Paul McCarthy committed
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
0.6.3
-----


Changed
^^^^^^^


* Minor updates to avoid deprecation warnings.


Paul McCarthy's avatar
Paul McCarthy committed
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
0.6.2
-----


Fixed
^^^^^


* Fixed a bug with the ``--import_all`` option, where an error would be thrown
  if a specifically requested variable was removed during processing.


Paul McCarthy's avatar
Paul McCarthy committed
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
0.6.1
-----


Changed
^^^^^^^


* Changed default processing for variables 41202/41204 so they are binarised
  *within* visit.


Paul McCarthy's avatar
Paul McCarthy committed
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
0.6.0
-----


Added
^^^^^


* New ``--import_all`` and ``--unknown_vars_file`` options for outputting
  information about previously unknown variables/columns.


Changed
^^^^^^^


* Changed processing function return value interface - see the
  :mod:`.processing_functions` module for details.


Paul McCarthy's avatar
Paul McCarthy committed
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
0.5.0
-----


Added
^^^^^


* Ability to export a mapping file containing the numeric values that ICD10
  codes have been converted into - see the ``--icd10_map_file`` argument.


Changed
^^^^^^^


* Changes to default processing - all ICD10 variables are binarised by default.
  Sparsity/redundancy tests happen at the end, so that columns generated by
  previous steps are tested.


Fixed
^^^^^


* :meth:`.HDFStoreCollection.loc` method returns a ``pandas.DataFrame`` when
  a list of columns are indexed, and a ``pandas.Series`` when a single column
  is indexed.


Paul McCarthy's avatar
Paul McCarthy committed
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
0.4.1
-----


Changed
^^^^^^^


* Updates to variable table for UKBiobank spirometry variables.


Paul McCarthy's avatar
Paul McCarthy committed
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
0.4.0
-----


Added
^^^^^


* New :func:`.parseSpirometryData` function for parsing spirometry data
  (i.e. `UKBiobank variable 3066
  <https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=3066>`_


Removed
^^^^^^^


* Removed the ``--disable_rename`` command line option, because having the
  columns renamed is really annoying.


Paul McCarthy's avatar
Paul McCarthy committed
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
0.3.3
-----


Changed
^^^^^^^


* Reverted the behaviour of :func:`.isSparse`.


Paul McCarthy's avatar
Paul McCarthy committed
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
0.3.2
-----


Changed
^^^^^^^


* Changed the behaviour of :func:`.isSparse` so that series which are *greater
  than* the ``minpres`` threshold pass, rather than *greater than or equal
  to*.


Paul McCarthy's avatar
Paul McCarthy committed
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
0.3.1
-----


Changed
^^^^^^^


* The :func:`.isSparse` function ignores the ``minpres`` argument if it
  is larger than the number of samples in the data set.


Fixed
^^^^^


* The :func:`.binariseCategorical` function now works on data with missing
  values.


Paul McCarthy's avatar
Paul McCarthy committed
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
0.3.0
-----


Added
^^^^^


* New :meth:`.DataTable.addColumns` method, so processing functions can
  now add new columns.
* New :func:`.binariseCategorical` processing function, which expands a
  categorical column into multiple binary columns, one for each unique
  value in the data.
Paul McCarthy's avatar
Paul McCarthy committed
1789
1790
* New :func:`.expandCompound` processing function, which expands a
  compound column into columns, one for each value in the compound data.
Paul McCarthy's avatar
Paul McCarthy committed
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
* Keyword arguments can now be used when specifying processing.


Fixed
^^^^^


* Fixed handling of non-numeric categorical variables


Paul McCarthy's avatar
Paul McCarthy committed
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
0.2.0
-----


Added
^^^^^

* Added a changelog file


Changed
^^^^^^^


* Updated variable/datacoding files to bring them in line with the latest
  Biobank data release.