CHANGELOG.rst 11.3 KB
Newer Older
Paul McCarthy's avatar
Paul McCarthy committed
1
2
3
``ukbparse`` changelog
======================

Paul McCarthy's avatar
Paul McCarthy committed
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
22
23
24
25
26
27
28
29
0.15.0 (Under development)
--------------------------


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.


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
30
31
32
33
34
35
36
37
0.14.8 (Monday 18th March 2019)
-------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
38
39
* Fixed an issue with the :func:`.binariseCategorical` processing function
  being applied to ICD10 codes.
Paul McCarthy's avatar
Paul McCarthy committed
40

Paul McCarthy's avatar
Paul McCarthy committed
41
42
43
44
45
46
47
48
49
50
51
52
53

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
54
55
0.14.6 (Saturday 16th March 2019)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
56
57
58
59
60
61
62
63
64


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
65
66
* Fixed some issues introduced by behavioural changes in the
  ``pandas.HDFStore`` class.
Paul McCarthy's avatar
Paul McCarthy committed
67
68


Paul McCarthy's avatar
Paul McCarthy committed
69
70
71
72
73
74
75
76
77
78
79
80
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
81
82
83
84
85
86
87
88
89
0.14.4 (Friday 11th January 2019)
---------------------------------


Changed
^^^^^^^


* Updated the default processing rules for variable
Paul McCarthy's avatar
Paul McCarthy committed
90
  [1120-1150](https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=1120).
Paul McCarthy's avatar
Paul McCarthy committed
91
92


Paul McCarthy's avatar
Paul McCarthy committed
93
94
95
96
97
98
99
100
101
102
103
104
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
105
106
107
108
109
110
111
112
0.14.2 (Monday 7th January 2019)
--------------------------------


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
113
* Fixed a regression introduced in 0.14.1, where using the ``--variable`` and
Paul McCarthy's avatar
Paul McCarthy committed
114
115
  ``--visit`` options together could cause a crash.

Paul McCarthy's avatar
Paul McCarthy committed
116

Paul McCarthy's avatar
Paul McCarthy committed
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
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
133
134
0.14.0 (Tuesday 25th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
135
136
137
138
139
140


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
141
142
* New ``--column`` option, allowing columns to be selected by name/name
  pattern.
Paul McCarthy's avatar
Paul McCarthy committed
143
144
145
146
147
148
149
150
151
152
153
154
* ``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
155
156
157
158
159
160
161
162
163
164
165

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
166
167
168
169
170
171
172
173
174
175


Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
176
177
178
179
180
181
182
183
184
185
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
186
187
* 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
188
189


Paul McCarthy's avatar
Paul McCarthy committed
190
191
192
193
194
195
196
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
197
198
199
200
201
202
203
204
205
206
207
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
208
209
210
211
212
213
214
215
216
217
218
219
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
220
221
0.12.1 (Saturday 15th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240


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
241
* Added ``lxml`` as a dependency (required by ``beautifulsoup4``).
Paul McCarthy's avatar
Paul McCarthy committed
242
243


Paul McCarthy's avatar
Paul McCarthy committed
244
245
0.12.0 (Tuesday 11th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
246
247
248
249
250
251
252
253
254


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
255
256
257
* 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
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273


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
274
275
* Fixed mixed data type issues when merging the data coding and type tables into
  the variable table.
Paul McCarthy's avatar
Paul McCarthy committed
276

Paul McCarthy's avatar
Paul McCarthy committed
277
278
279
280
281
282
283
284
285
286
287
288
289
290

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
291
292
293
294
295
296
297
298
299
300
301
302
303
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
304
305
306
307
308
309
310
311
312
313
314
0.11.1 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
315
316
0.11.0 (Monday 10th December 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
317
318
319
320
321
322
323
324


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
325
326
327
* 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
328
329


Paul McCarthy's avatar
Paul McCarthy committed
330
331
332
333
334
335
336
337
338
339
340
341
342
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
343
344
345
346
347
348
349
350
351
352
353
0.10.4 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
354
355
356
357
358
359
360
361
362
363
364
365
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
366
367
368
369
370
371
372
373
374
375
376
0.10.2 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Removed relative imports from test modules.


Paul McCarthy's avatar
Paul McCarthy committed
377
378
379
380
381
382
383
384
385
386
387
388
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
389
390
391
392
393
394
395
396
397
398
399
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
400
401
* ``--dry_run`` mode now prints information about columns that would not be
  loaded.
Paul McCarthy's avatar
Paul McCarthy committed
402
403


Paul McCarthy's avatar
Paul McCarthy committed
404
405
406
407
408
409
Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
410

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
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
429
430
431
432
433
434
435
436
437
438
439
440
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
441
442
443
444
445
446
447
448
449
450
451
0.7.1
-----


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
452
453
454
455
456
457
458
459
460
461
462
463
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
464
465
466
467
468
469
470
471
472
473
474
0.6.3
-----


Changed
^^^^^^^


* Minor updates to avoid deprecation warnings.


Paul McCarthy's avatar
Paul McCarthy committed
475
476
477
478
479
480
481
482
483
484
485
486
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
487
488
489
490
491
492
493
494
495
496
497
498
0.6.1
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
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
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
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
549
550
551
552
553
554
555
556
557
558
559
0.4.1
-----


Changed
^^^^^^^


* Updates to variable table for UKBiobank spirometry variables.


Paul McCarthy's avatar
Paul McCarthy committed
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
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
581
582
583
584
585
586
587
588
589
590
591
0.3.3
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
592
593
594
595
596
597
598
599
600
601
602
603
604
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
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
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
625
626
627
628
629
630
631
632
633
634
635
636
637
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
638
639
* 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
640
641
642
643
644
645
646
647
648
649
* Keyword arguments can now be used when specifying processing.


Fixed
^^^^^


* Fixed handling of non-numeric categorical variables


Paul McCarthy's avatar
Paul McCarthy committed
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
0.2.0
-----


Added
^^^^^

* Added a changelog file


Changed
^^^^^^^


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