CHANGELOG.rst 30.7 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
1.8.0 (Tuesday 18th February 2020)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
7
8
9
10
11
12
13
14
15


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
16
17
18
19
20
21
22
23
24
* 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
25
26


Paul McCarthy's avatar
Paul McCarthy committed
27
28
29
30
31
32
33
34
35
36
Changed
^^^^^^^


* 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
37
38
39
40
41
42
43
44
45
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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
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
65
66
1.7.0 (Friday 24th January 2020)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
67
68
69
70
71
72
73
74
75
76


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
77
78
79
80
81
82
83
84
85
86
87
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
88
* The :func:`.removeIfRedundant` processsing function will now drop columns
Paul McCarthy's avatar
Paul McCarthy committed
89
90
91
92
93
94
95
  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
96
97
98
99
100
101
102
103


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
104
105


Paul McCarthy's avatar
Paul McCarthy committed
106
107
1.6.0 (Wednesday 11th December 2019)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
108
109
110
111
112
113
114
115
116
117
118
119
120


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
121
122
123
124
125
126
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
127
128
129
* 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
130
131


Paul McCarthy's avatar
Paul McCarthy committed
132
133
1.5.0 (Monday 9th December 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
134
135
136
137
138
139


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
140
* New :func:`.util.wc` function to count the rows (lines) of a file;
Paul McCarthy's avatar
Paul McCarthy committed
141
  this is simply a wrapper around the UNIX ``wc`` tool.
Paul McCarthy's avatar
Paul McCarthy committed
142
143
* 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
144
145
* 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
146
147
148
149
* 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
150
151
* 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
152
153
  multiple columns for one variable. These can be used with the ``--subject``
  option.
Paul McCarthy's avatar
Paul McCarthy committed
154
155
156
157
158
159
160


Changed
^^^^^^^


* FUNPACK will now parallelise tasks by default; previously it would only
Paul McCarthy's avatar
Paul McCarthy committed
161
162
163
164
165
166
167
168
169
170
171
172
173
  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
174
175
* The ``--variable``, ``--subject`` and ``--exclude`` options now accept
  comma-separated mixtures of IDs and MATLAB-style ranges.
Paul McCarthy's avatar
Paul McCarthy committed
176
177
178
179
* 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
180
  context. This is not necessary when ``funpack`` is configured to not
Paul McCarthy's avatar
Paul McCarthy committed
181
  parallelise tasks (e.g. with ``--num_jobs 1``).
Paul McCarthy's avatar
Paul McCarthy committed
182
183
184
185
186
187
188


Deprecated
^^^^^^^^^^


* The ``--low_memory`` and ``--work_dir`` options have been deprecated, and no
Paul McCarthy's avatar
Paul McCarthy committed
189
190
  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
191
192
193
194


1.4.5 (Thursday 5th December 2019)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
195
196


Paul McCarthy's avatar
Paul McCarthy committed
197
198
199
200
201
202
203
204
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
205
206
207
208
209
210
211
212
213
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
214
215
216
217
218
219
220
221
222
223
224
1.4.4 (Friday 15th November 2019)
---------------------------------


Changed
^^^^^^^


* Updates to the FMRIB categories and configuration.


Paul McCarthy's avatar
Paul McCarthy committed
225
226
227
228
229
230
231
232
233
234
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
235
* Increased the file sample size used by :func:`.fileinfo.sniff`.
Paul McCarthy's avatar
Paul McCarthy committed
236

Paul McCarthy's avatar
Paul McCarthy committed
237
238
239
240
241
242
243
244
245
246
247
248

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


Changed
^^^^^^^


* Minor changes to the FMRIB configuration.


Paul McCarthy's avatar
Paul McCarthy committed
249
1.4.1 (Monday 8th July 2019)
Paul McCarthy's avatar
Paul McCarthy committed
250
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
251
252
253
254
255
256
257
258
259
260
261
262


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
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
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
317
318
319
320
321
322
323
324
325
326
327
1.3.2 (Tuesday 4th June 2019)
-----------------------------


Changed
^^^^^^^


* Minor adjustments to the FMRIB categories.


Paul McCarthy's avatar
Paul McCarthy committed
328
329
330
331
332
333
334
335
336
337
338
1.3.1 (Thursday 30th May 2019)
------------------------------


Changed
^^^^^^^


* Updates to documentation.


Paul McCarthy's avatar
Paul McCarthy committed
339
340
341
342
343
344
345
346
347
348
349
350
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
351
352
* New meta-process functions for generating descriptions for ICD9, OPCS3 and
  OPCS4 hierarchical variables.
Paul McCarthy's avatar
Paul McCarthy committed
353
354
355
356
* 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
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371


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
372
373
374
375
376
377
378
379
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
380
381
382
383
384
385
386
387
388
389
390
391
392
393
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
394
395
396
397
398
399
400
401
402
403
404
1.2.1 (Tuesday 28th May 2019)
-----------------------------


Changed
^^^^^^^


* Minor changes to built-in variable categories.


Paul McCarthy's avatar
Paul McCarthy committed
405
1.2.0 (Saturday 25th May 2019)
Paul McCarthy's avatar
Paul McCarthy committed
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
------------------------------


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
422
  been revised and updated.
Paul McCarthy's avatar
Paul McCarthy committed
423
424


Paul McCarthy's avatar
Paul McCarthy committed
425
426
427
428
429
430
431
432
433
434
435
436
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
437
438
439
440
441
442
443
444

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


Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
445

Paul McCarthy's avatar
Paul McCarthy committed
446
447
* 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
448
  to the number of *non-missing* data points, rather than the total number of
Paul McCarthy's avatar
Paul McCarthy committed
449
450
451
  data points.


Paul McCarthy's avatar
Paul McCarthy committed
452
453
454
455
456
457
458
459
460
461
462
463
464
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
465
466
467
468
469
470
471
472
473
474
475
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
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
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
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
511
512
513
514
515
516
517
518
519
520
521
522

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
523
524
525
526
527
528
529
530
531
532
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
533

Paul McCarthy's avatar
Paul McCarthy committed
534

Paul McCarthy's avatar
Paul McCarthy committed
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
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
550
551
552
553
554
555
556
557
558
559
560
561
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
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
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
587
588
589
590
591
592
593
594
595
596
597
0.20.1 (Wednesday 8th May 2019)
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
598
599
600
601
602
603
604
605
606
607
608
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
609
610
* 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
611
612
613
614
615
616
617
618
619
620
621
622
623


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
624
625
626
627
628
629
630
631
632
633
634


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
635
636
637
638
639
640
641
642
643
644
645
0.19.2 (Friday 26th April 2019)
-------------------------------


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
646
647
648
649
650
651
652
653
654
655
656
657
658
659
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
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
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
684
0.18.0 (Tuesday 23rd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
685
686
687
--------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
688
689
690
691
692
693
694
695
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
696
697
698
699
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
700
701
702
* 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
703
704
705
706
* 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
707
708
709
* The :func:`.isSparse` function now returns the reason and value for
  columns which fail the sparsity test.

Paul McCarthy's avatar
Paul McCarthy committed
710
711


Paul McCarthy's avatar
Paul McCarthy committed
712
0.17.0 (Monday 22nd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
713
714
715
716
717
718
719
720
721
-------------------------------


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
722
723
* Built-in ``fmrib.cfg`` configuration file, which can be used via
  ``-cfg fmrib``.
Paul McCarthy's avatar
Paul McCarthy committed
724
725
726
727
728
729
730
731
732


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
733
* Built-in categories have been updated.
Paul McCarthy's avatar
Paul McCarthy committed
734
735
736
737
738
739
740
741


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
742
  between column names for different ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
743
744


Paul McCarthy's avatar
Paul McCarthy committed
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
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
771
772
773
774
775
776
Removed
^^^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
777

Paul McCarthy's avatar
Paul McCarthy committed
778
779
780
781
782
783
784
785
786
787
788
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
789
790
0.15.0 (Monday 18th March 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
791
792
793
794
795
796
797
798
799
800
801


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
802
803
* Definitions for all hierarchical UK Biobank variables are located in the
  ``ukbparse/data/hierarchy/`` directory.
Paul McCarthy's avatar
Paul McCarthy committed
804
805
806
807
808
809
810
811
812
813
814
815


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
816
817
818
819
820
821
822
823
0.14.8 (Monday 18th March 2019)
-------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
824
825
* Fixed an issue with the :func:`.binariseCategorical` processing function
  being applied to ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
826

Paul McCarthy's avatar
Paul McCarthy committed
827
828
829
830
831
832
833
834
835
836
837
838
839

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
840
841
0.14.6 (Saturday 16th March 2019)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
842
843
844
845
846
847
848
849
850


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
851
852
* Fixed some issues introduced by behavioural changes in the
  ``pandas.HDFStore`` class.
Paul McCarthy's avatar
Paul McCarthy committed
853
854


Paul McCarthy's avatar
Paul McCarthy committed
855
856
857
858
859
860
861
862
863
864
865
866
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
867
868
869
870
871
872
873
874
875
0.14.4 (Friday 11th January 2019)
---------------------------------


Changed
^^^^^^^


* Updated the default processing rules for variable
Paul McCarthy's avatar
Paul McCarthy committed
876
  [1120-1150](https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=1120).
Paul McCarthy's avatar
Paul McCarthy committed
877
878


Paul McCarthy's avatar
Paul McCarthy committed
879
880
881
882
883
884
885
886
887
888
889
890
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
891
892
893
894
895
896
897
898
0.14.2 (Monday 7th January 2019)
--------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
899
* Fixed a regression introduced in 0.14.1, where using the ``--variable`` and
Paul McCarthy's avatar
Paul McCarthy committed
900
901
  ``--visit`` options together could cause a crash.

Paul McCarthy's avatar
Paul McCarthy committed
902

Paul McCarthy's avatar
Paul McCarthy committed
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
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
919
920
0.14.0 (Tuesday 25th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
921
922
923
924
925
926


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
927
928
* New ``--column`` option, allowing columns to be selected by name/name
  pattern.
Paul McCarthy's avatar
Paul McCarthy committed
929
930
931
932
933
934
935
936
937
938
939
940
* ``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
941
942
943
944
945
946
947
948
949
950
951

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
952
953
954
955
956
957
958
959
960
961


Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
962
963
964
965
966
967
968
969
970
971
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
972
973
* 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
974
975


Paul McCarthy's avatar
Paul McCarthy committed
976
977
978
979
980
981
982
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
983
984
985
986
987
988
989
990
991
992
993
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
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
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
1006
1007
0.12.1 (Saturday 15th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026


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
1027
* Added ``lxml`` as a dependency (required by ``beautifulsoup4``).
Paul McCarthy's avatar
Paul McCarthy committed
1028
1029


Paul McCarthy's avatar
Paul McCarthy committed
1030
1031
0.12.0 (Tuesday 11th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1032
1033
1034
1035
1036
1037
1038
1039
1040


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
1041
1042
1043
* 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
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059


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
1060
1061
* Fixed mixed data type issues when merging the data coding and type tables into
  the variable table.
Paul McCarthy's avatar
Paul McCarthy committed
1062

Paul McCarthy's avatar
Paul McCarthy committed
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076

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
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
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
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
0.11.1 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1101
1102
0.11.0 (Monday 10th December 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1103
1104
1105
1106
1107
1108
1109
1110


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
1111
1112
1113
* 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
1114
1115


Paul McCarthy's avatar
Paul McCarthy committed
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
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
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
0.10.4 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
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
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
0.10.2 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Removed relative imports from test modules.


Paul McCarthy's avatar
Paul McCarthy committed
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
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
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
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
1186
1187
* ``--dry_run`` mode now prints information about columns that would not be
  loaded.
Paul McCarthy's avatar
Paul McCarthy committed
1188
1189


Paul McCarthy's avatar
Paul McCarthy committed
1190
1191
1192
1193
1194
1195
Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
1196

Paul McCarthy's avatar
Paul McCarthy committed
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
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
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
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
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
0.7.1
-----


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
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
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
0.6.3
-----


Changed
^^^^^^^


* Minor updates to avoid deprecation warnings.


Paul McCarthy's avatar
Paul McCarthy committed
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
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
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
0.6.1
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
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
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
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
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
0.4.1
-----


Changed
^^^^^^^


* Updates to variable table for UKBiobank spirometry variables.


Paul McCarthy's avatar
Paul McCarthy committed
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
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
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
0.3.3
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
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
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
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
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
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
1424
1425
* 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
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
* Keyword arguments can now be used when specifying processing.


Fixed
^^^^^


* Fixed handling of non-numeric categorical variables


Paul McCarthy's avatar
Paul McCarthy committed
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
0.2.0
-----


Added
^^^^^

* Added a changelog file


Changed
^^^^^^^


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