CHANGELOG.rst 8.61 KB
Newer Older
Paul McCarthy's avatar
Paul McCarthy committed
1
2
3
4
``ukbparse`` changelog
======================


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
0.14.0 (Under development)
--------------------------


Added
^^^^^


* ``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
25
26
27
28
29
30
31
32
33
34
35
36


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
37
38
39
40
41
42
43
44
45
46


Added
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
47
48
49
50
51
52
53
54
55
56
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
57
58
* 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
59
60


Paul McCarthy's avatar
Paul McCarthy committed
61
62
63
64
65
66
67
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
68
69
70
71
72
73
74
75
76
77
78
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
79
80
81
82
83
84
85
86
87
88
89
90
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
91
92
0.12.1 (Saturday 15th December 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111


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
112
* Added ``lxml`` as a dependency (required by ``beautifulsoup4``).
Paul McCarthy's avatar
Paul McCarthy committed
113
114


Paul McCarthy's avatar
Paul McCarthy committed
115
116
0.12.0 (Tuesday 11th December 2018)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
117
118
119
120
121
122
123
124
125


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
126
127
128
* 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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144


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
145
146
* Fixed mixed data type issues when merging the data coding and type tables into
  the variable table.
Paul McCarthy's avatar
Paul McCarthy committed
147

Paul McCarthy's avatar
Paul McCarthy committed
148
149
150
151
152
153
154
155
156
157
158
159
160
161

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
162
163
164
165
166
167
168
169
170
171
172
173
174
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
175
176
177
178
179
180
181
182
183
184
185
0.11.1 (Monday 10th December 2018)
----------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
186
187
0.11.0 (Monday 10th December 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
188
189
190
191
192
193
194
195


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
196
197
198
* 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
199
200


Paul McCarthy's avatar
Paul McCarthy committed
201
202
203
204
205
206
207
208
209
210
211
212
213
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
214
215
216
217
218
219
220
221
222
223
224
0.10.4 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
225
226
227
228
229
230
231
232
233
234
235
236
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
237
238
239
240
241
242
243
244
245
246
247
0.10.2 (Friday 7th December 2018)
---------------------------------


Fixed
^^^^^


* Removed relative imports from test modules.


Paul McCarthy's avatar
Paul McCarthy committed
248
249
250
251
252
253
254
255
256
257
258
259
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
260
261
262
263
264
265
266
267
268
269
270
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
271
272
* ``--dry_run`` mode now prints information about columns that would not be
  loaded.
Paul McCarthy's avatar
Paul McCarthy committed
273
274


Paul McCarthy's avatar
Paul McCarthy committed
275
276
277
278
279
280
Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
281

Paul McCarthy's avatar
Paul McCarthy committed
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
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
300
301
302
303
304
305
306
307
308
309
310
311
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
312
313
314
315
316
317
318
319
320
321
322
0.7.1
-----


Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
323
324
325
326
327
328
329
330
331
332
333
334
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
335
336
337
338
339
340
341
342
343
344
345
0.6.3
-----


Changed
^^^^^^^


* Minor updates to avoid deprecation warnings.


Paul McCarthy's avatar
Paul McCarthy committed
346
347
348
349
350
351
352
353
354
355
356
357
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
358
359
360
361
362
363
364
365
366
367
368
369
0.6.1
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
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
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
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
420
421
422
423
424
425
426
427
428
429
430
0.4.1
-----


Changed
^^^^^^^


* Updates to variable table for UKBiobank spirometry variables.


Paul McCarthy's avatar
Paul McCarthy committed
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
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
452
453
454
455
456
457
458
459
460
461
462
0.3.3
-----


Changed
^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
463
464
465
466
467
468
469
470
471
472
473
474
475
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
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
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
496
497
498
499
500
501
502
503
504
505
506
507
508
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
509
510
* 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
511
512
513
514
515
516
517
518
519
520
* Keyword arguments can now be used when specifying processing.


Fixed
^^^^^


* Fixed handling of non-numeric categorical variables


Paul McCarthy's avatar
Paul McCarthy committed
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
0.2.0
-----


Added
^^^^^

* Added a changelog file


Changed
^^^^^^^


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