CHANGELOG.rst 27.5 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
1.6.0 (Under development)
-------------------------


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
20
21
1.5.0 (Monday 9th December 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
22
23
24
25
26
27


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
28
* New :func:`.util.wc` function to count the rows (lines) of a file;
Paul McCarthy's avatar
Paul McCarthy committed
29
  this is simply a wrapper around the UNIX ``wc`` tool.
Paul McCarthy's avatar
Paul McCarthy committed
30
31
* 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
32
33
* 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
34
35
36
37
* 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
38
39
* 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
40
41
  multiple columns for one variable. These can be used with the ``--subject``
  option.
Paul McCarthy's avatar
Paul McCarthy committed
42
43
44
45
46
47
48


Changed
^^^^^^^


* FUNPACK will now parallelise tasks by default; previously it would only
Paul McCarthy's avatar
Paul McCarthy committed
49
50
51
52
53
54
55
56
57
58
59
60
61
  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
62
63
* The ``--variable``, ``--subject`` and ``--exclude`` options now accept
  comma-separated mixtures of IDs and MATLAB-style ranges.
Paul McCarthy's avatar
Paul McCarthy committed
64
65
66
67
* 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
68
  context. This is not necessary when ``funpack`` is configured to not
Paul McCarthy's avatar
Paul McCarthy committed
69
  parallelise tasks (e.g. with ``--num_jobs 1``).
Paul McCarthy's avatar
Paul McCarthy committed
70
71
72
73
74
75
76


Deprecated
^^^^^^^^^^


* The ``--low_memory`` and ``--work_dir`` options have been deprecated, and no
Paul McCarthy's avatar
Paul McCarthy committed
77
78
  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
79
80
81
82


1.4.5 (Thursday 5th December 2019)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
83
84


Paul McCarthy's avatar
Paul McCarthy committed
85
86
87
88
89
90
91
92
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
93
94
95
96
97
98
99
100
101
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
102
103
104
105
106
107
108
109
110
111
112
1.4.4 (Friday 15th November 2019)
---------------------------------


Changed
^^^^^^^


* Updates to the FMRIB categories and configuration.


Paul McCarthy's avatar
Paul McCarthy committed
113
114
115
116
117
118
119
120
121
122
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
123
* Increased the file sample size used by :func:`.fileinfo.sniff`.
Paul McCarthy's avatar
Paul McCarthy committed
124

Paul McCarthy's avatar
Paul McCarthy committed
125
126
127
128
129
130
131
132
133
134
135
136

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


Changed
^^^^^^^


* Minor changes to the FMRIB configuration.


Paul McCarthy's avatar
Paul McCarthy committed
137
1.4.1 (Monday 8th July 2019)
Paul McCarthy's avatar
Paul McCarthy committed
138
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
139
140
141
142
143
144
145
146
147
148
149
150


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
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
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
205
206
207
208
209
210
211
212
213
214
215
1.3.2 (Tuesday 4th June 2019)
-----------------------------


Changed
^^^^^^^


* Minor adjustments to the FMRIB categories.


Paul McCarthy's avatar
Paul McCarthy committed
216
217
218
219
220
221
222
223
224
225
226
1.3.1 (Thursday 30th May 2019)
------------------------------


Changed
^^^^^^^


* Updates to documentation.


Paul McCarthy's avatar
Paul McCarthy committed
227
228
229
230
231
232
233
234
235
236
237
238
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
239
240
* New meta-process functions for generating descriptions for ICD9, OPCS3 and
  OPCS4 hierarchical variables.
Paul McCarthy's avatar
Paul McCarthy committed
241
242
243
244
* 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
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259


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
260
261
262
263
264
265
266
267
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
268
269
270
271
272
273
274
275
276
277
278
279
280
281
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
282
283
284
285
286
287
288
289
290
291
292
1.2.1 (Tuesday 28th May 2019)
-----------------------------


Changed
^^^^^^^


* Minor changes to built-in variable categories.


Paul McCarthy's avatar
Paul McCarthy committed
293
1.2.0 (Saturday 25th May 2019)
Paul McCarthy's avatar
Paul McCarthy committed
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
------------------------------


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
310
  been revised and updated.
Paul McCarthy's avatar
Paul McCarthy committed
311
312


Paul McCarthy's avatar
Paul McCarthy committed
313
314
315
316
317
318
319
320
321
322
323
324
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
325
326
327
328
329
330
331
332

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


Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
333

Paul McCarthy's avatar
Paul McCarthy committed
334
335
* 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
336
  to the number of *non-missing* data points, rather than the total number of
Paul McCarthy's avatar
Paul McCarthy committed
337
338
339
  data points.


Paul McCarthy's avatar
Paul McCarthy committed
340
341
342
343
344
345
346
347
348
349
350
351
352
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
353
354
355
356
357
358
359
360
361
362
363
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
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
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
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
399
400
401
402
403
404
405
406
407
408
409
410

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
411
412
413
414
415
416
417
418
419
420
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
421

Paul McCarthy's avatar
Paul McCarthy committed
422

Paul McCarthy's avatar
Paul McCarthy committed
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
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
438
439
440
441
442
443
444
445
446
447
448
449
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
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
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
475
476
477
478
479
480
481
482
483
484
485
0.20.1 (Wednesday 8th May 2019)
-------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
486
487
488
489
490
491
492
493
494
495
496
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
497
498
* 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
499
500
501
502
503
504
505
506
507
508
509
510
511


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
512
513
514
515
516
517
518
519
520
521
522


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
523
524
525
526
527
528
529
530
531
532
533
0.19.2 (Friday 26th April 2019)
-------------------------------


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
534
535
536
537
538
539
540
541
542
543
544
545
546
547
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
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
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
572
0.18.0 (Tuesday 23rd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
573
574
575
--------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
576
577
578
579
580
581
582
583
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
584
585
586
587
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
588
589
590
* 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
591
592
593
594
* 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
595
596
597
* The :func:`.isSparse` function now returns the reason and value for
  columns which fail the sparsity test.

Paul McCarthy's avatar
Paul McCarthy committed
598
599


Paul McCarthy's avatar
Paul McCarthy committed
600
0.17.0 (Monday 22nd April 2019)
Paul McCarthy's avatar
Paul McCarthy committed
601
602
603
604
605
606
607
608
609
-------------------------------


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
610
611
* Built-in ``fmrib.cfg`` configuration file, which can be used via
  ``-cfg fmrib``.
Paul McCarthy's avatar
Paul McCarthy committed
612
613
614
615
616
617
618
619
620


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
621
* Built-in categories have been updated.
Paul McCarthy's avatar
Paul McCarthy committed
622
623
624
625
626
627
628
629


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
630
  between column names for different ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
631
632


Paul McCarthy's avatar
Paul McCarthy committed
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
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
659
660
661
662
663
664
Removed
^^^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
665

Paul McCarthy's avatar
Paul McCarthy committed
666
667
668
669
670
671
672
673
674
675
676
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
677
678
0.15.0 (Monday 18th March 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
679
680
681
682
683
684
685
686
687
688
689


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
690
691
* Definitions for all hierarchical UK Biobank variables are located in the
  ``ukbparse/data/hierarchy/`` directory.
Paul McCarthy's avatar
Paul McCarthy committed
692
693
694
695
696
697
698
699
700
701
702
703


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
704
705
706
707
708
709
710
711
0.14.8 (Monday 18th March 2019)
-------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
712
713
* Fixed an issue with the :func:`.binariseCategorical` processing function
  being applied to ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
714

Paul McCarthy's avatar
Paul McCarthy committed
715
716
717
718
719
720
721
722
723
724
725
726
727

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
728
729
0.14.6 (Saturday 16th March 2019)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
730
731
732
733
734
735
736
737
738


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
739
740
* Fixed some issues introduced by behavioural changes in the
  ``pandas.HDFStore`` class.
Paul McCarthy's avatar
Paul McCarthy committed
741
742


Paul McCarthy's avatar
Paul McCarthy committed
743
744
745
746
747
748
749
750
751
752
753
754
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
755
756
757
758
759
760
761
762
763
0.14.4 (Friday 11th January 2019)
---------------------------------


Changed
^^^^^^^


* Updated the default processing rules for variable
Paul McCarthy's avatar
Paul McCarthy committed
764
  [1120-1150](https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=1120).
Paul McCarthy's avatar
Paul McCarthy committed
765
766


Paul McCarthy's avatar
Paul McCarthy committed
767
768
769
770
771
772
773
774
775
776
777
778
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
779
780
781
782
783
784
785
786
0.14.2 (Monday 7th January 2019)
--------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
787
* Fixed a regression introduced in 0.14.1, where using the ``--variable`` and
Paul McCarthy's avatar
Paul McCarthy committed
788
789
  ``--visit`` options together could cause a crash.

Paul McCarthy's avatar
Paul McCarthy committed
790

Paul McCarthy's avatar
Paul McCarthy committed
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
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
807
808
0.14.0 (Tuesday 25th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
809
810
811
812
813
814


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
815
816
* New ``--column`` option, allowing columns to be selected by name/name
  pattern.
Paul McCarthy's avatar
Paul McCarthy committed
817
818
819
820
821
822
823
824
825
826
827
828
* ``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
829
830
831
832
833
834
835
836
837
838
839

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
840
841
842
843
844
845
846
847
848
849


Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
850
851
852
853
854
855
856
857
858
859
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
860
861
* 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
862
863


Paul McCarthy's avatar
Paul McCarthy committed
864
865
866
867
868
869
870
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
871
872
873
874
875
876
877
878
879
880
881
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
882
883
884
885
886
887
888
889
890
891
892
893
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
894
895
0.12.1 (Saturday 15th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914


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
915
* Added ``lxml`` as a dependency (required by ``beautifulsoup4``).
Paul McCarthy's avatar
Paul McCarthy committed
916
917


Paul McCarthy's avatar
Paul McCarthy committed
918
919
0.12.0 (Tuesday 11th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
920
921
922
923
924
925
926
927
928


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
929
930
931
* 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
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947


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
948
949
* Fixed mixed data type issues when merging the data coding and type tables into
  the variable table.
Paul McCarthy's avatar
Paul McCarthy committed
950

Paul McCarthy's avatar
Paul McCarthy committed
951
952
953
954
955
956
957
958
959
960
961
962
963
964

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
965
966
967
968
969
970
971
972
973
974
975
976
977
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
978
979
980
981
982
983
984
985
986
987
988
0.11.1 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
989
990
0.11.0 (Monday 10th December 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
991
992
993
994
995
996
997
998


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
999
1000
1001
* 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
1002
1003


Paul McCarthy's avatar
Paul McCarthy committed
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
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
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
0.10.4 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
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
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
0.10.2 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Removed relative imports from test modules.


Paul McCarthy's avatar
Paul McCarthy committed
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
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
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
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
1074
1075
* ``--dry_run`` mode now prints information about columns that would not be
  loaded.
Paul McCarthy's avatar
Paul McCarthy committed
1076
1077


Paul McCarthy's avatar
Paul McCarthy committed
1078
1079
1080
1081
1082
1083
Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
1084

Paul McCarthy's avatar
Paul McCarthy committed
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
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
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
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
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
0.7.1
-----


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
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
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
0.6.3
-----


Changed
^^^^^^^


* Minor updates to avoid deprecation warnings.


Paul McCarthy's avatar
Paul McCarthy committed
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
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
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
0.6.1
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
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
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
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
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
0.4.1
-----


Changed
^^^^^^^


* Updates to variable table for UKBiobank spirometry variables.


Paul McCarthy's avatar
Paul McCarthy committed
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
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
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
0.3.3
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
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
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
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
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
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
1312
1313
* 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
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
* Keyword arguments can now be used when specifying processing.


Fixed
^^^^^


* Fixed handling of non-numeric categorical variables


Paul McCarthy's avatar
Paul McCarthy committed
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
0.2.0
-----


Added
^^^^^

* Added a changelog file


Changed
^^^^^^^


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