forked from afni/afni
-
Notifications
You must be signed in to change notification settings - Fork 0
/
.deprecation.txt
355 lines (293 loc) · 10.5 KB
/
.deprecation.txt
1
2
3
4
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
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
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
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
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
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
This file serves as a log of removal of old functionality.
For each entry a commit id is provided to indicate the relevant commit in which
such a removal of code occurred. The command "git show <commit-id>" can be used
to inspect this commit. To inspect this commit and preceding commits (preceding
commits may include modifications to the build system etc) one can execute the
command "git log --patch <commit-id>.
# ===========================================================================
# overview of steps for deletion
# ---------------------------------------------------------------------------
0. update git, just to be sure we are current (no necessary, but preferable)
cd git/AFNI/afni
git checkout master
git pull
1. create and checkout new branch (that can be used for a pull request)
git checkout -b deletions_July_17
2. remove scripts, for example, or copy in updates from elsewhere
rm src/scripts_install/@make_stim_file
3. make afni_history updates (TYPE_REMOVE - per program/lib/functionality)
and, assuming those edits were made in the non-git tree ~/afni/src,
copy them into the local git tree (still on branch deletions_July_17):
cp ~/afni/src/afni_history_rickr.c src
4. commit changes
git commit -am 'script deletion'
5. add log of most current file changes to .deprecation.txt,
(see "making a 'git deprecate' alias", below)
(this makes new git commit, making this branch ready for a pull request)
git deprecate
6. push new branch
git push origin deletions_July_17
7. go to https://github.com/afni/afni and open a pull request
for that branch (deletions_July_17), and let the CI tests run
# 99. separate option: update git/afni_doc/educational/classified_progs.rst
# ----------------------------------------------------------------------
# making a 'git deprecate' alias
The purpose of the "deprecate" step is to add a list of files removed or
modified by the most recent commit. This alias *only* works for a single
commit (comparing HEAD~1 to HEAD, the previous to the current commits).
So it is preferable to run "git deprecate" after a single such change.
a. First create an alias that lists that log difference (of the "last commit"),
along with a header. Run "git lc" at any time to see the text.
git config --global alias.lc 'log --name-only --pretty=format:"%n%n%nDeprecation: %s%nTimestamp: %ai%nCommit: %h%nAuthor: %an%nFiles affected:" HEAD~1..HEAD'
git lc
b. Then create an alias that appends that log difference to .deprecation.txt,
and commits that extra change. Note that this alias should have an '!' in
it, which makes the way to create the alias shell-specific.
From bash:
git config --global alias.deprecate \
'!git lc >> .deprecation.txt;git add .deprecation.txt; git commit -m "Code removal"'
From tcsh (escape the initial '!' in the alias text):
git config --global alias.deprecate \
'\!git lc >> .deprecation.txt;git add .deprecation.txt; git commit -m "Code removal"'
These should both be visible from your ~/.gitconfig file.
# ----------------------------------------------------------------------
# using the new aliases
At this point, one can make deletions to the git tree:
rm -fr src/ptaylor
Commit those important deletions:
git commit -am 'getting rid of malware'
List the changes from that most recent commit
(this is only for text output, it does not affect the repository):
git lc
And make one more commit to append the list of removed files
to .deprecate.txt:
git deprecate
# ---------------------------------------------------------------------------
# end deletion overview
# ===========================================================================
Deprecation: Remove netcdf, volpack and associated c code
Timestamp: 2020-08-03 10:56:28 -0400
Commit: 7942d7255
Author: leej3
Files affected:
src/3dAFNItoMINC.c
src/3dMINCtoAFNI.c
src/3ddata.h
src/afni_plugin.c
src/afni_pplug_env.c
src/aren.c
src/aren.h
src/arentest.c
src/help_format.c
src/machdep.h
src/mri_render.c
src/mri_render.h
src/netcdf-3.5.0/src/COMPATIBILITY
src/netcdf-3.5.0/src/COPYRIGHT
src/netcdf-3.5.0/src/INSTALL.html
src/netcdf-3.5.0/src/MANIFEST
src/netcdf-3.5.0/src/Makefile
src/netcdf-3.5.0/src/README
src/netcdf-3.5.0/src/RELEASE_NOTES
src/netcdf-3.5.0/src/VERSION
src/netcdf-3.5.0/src/aclocal.m4
src/netcdf-3.5.0/src/configure
src/netcdf-3.5.0/src/configure.in
src/netcdf-3.5.0/src/cxx/Makefile
src/netcdf-3.5.0/src/cxx/README
src/netcdf-3.5.0/src/cxx/depend
src/netcdf-3.5.0/src/cxx/example.c
src/netcdf-3.5.0/src/cxx/expected
src/netcdf-3.5.0/src/f90/Makefile
src/netcdf-3.5.0/src/f90/NOTES
src/netcdf-3.5.0/src/f90/Readme
src/netcdf-3.5.0/src/f90/example_good.cdl
src/netcdf-3.5.0/src/f90/f90aux.m4
src/netcdf-3.5.0/src/f90/gen.m4
src/netcdf-3.5.0/src/f90/nvea.m4
src/netcdf-3.5.0/src/f90/nves.m4
src/netcdf-3.5.0/src/fortran/Makefile
src/netcdf-3.5.0/src/fortran/depend
src/netcdf-3.5.0/src/fortran/fills.nc
src/netcdf-3.5.0/src/fortran/netcdf.inc
src/netcdf-3.5.0/src/fortran/nfconfig.in
src/netcdf-3.5.0/src/fortran/nfconfig.inc
src/netcdf-3.5.0/src/libsrc/Makefile
src/netcdf-3.5.0/src/libsrc/attr.c
src/netcdf-3.5.0/src/libsrc/attr.m4
src/netcdf-3.5.0/src/libsrc/depend
src/netcdf-3.5.0/src/libsrc/dim.c
src/netcdf-3.5.0/src/libsrc/error.c
src/netcdf-3.5.0/src/libsrc/fbits.h
src/netcdf-3.5.0/src/libsrc/ffio.c
src/netcdf-3.5.0/src/libsrc/libvers.c
src/netcdf-3.5.0/src/libsrc/nc.c
src/netcdf-3.5.0/src/libsrc/nc.h
src/netcdf-3.5.0/src/libsrc/ncconfig.h
src/netcdf-3.5.0/src/libsrc/ncconfig.in
src/netcdf-3.5.0/src/libsrc/ncio.c
src/netcdf-3.5.0/src/libsrc/ncio.h
src/netcdf-3.5.0/src/libsrc/ncx.c
src/netcdf-3.5.0/src/libsrc/ncx.h
src/netcdf-3.5.0/src/libsrc/ncx.m4
src/netcdf-3.5.0/src/libsrc/ncx_cray.c
src/netcdf-3.5.0/src/libsrc/netcdf.3
src/netcdf-3.5.0/src/libsrc/netcdf.h
src/netcdf-3.5.0/src/libsrc/onstack.h
src/netcdf-3.5.0/src/libsrc/posixio.c
src/netcdf-3.5.0/src/libsrc/putget.m4
src/netcdf-3.5.0/src/libsrc/rnd.h
src/netcdf-3.5.0/src/libsrc/string.c
src/netcdf-3.5.0/src/libsrc/t_nc.c
src/netcdf-3.5.0/src/libsrc/t_ncio.c
src/netcdf-3.5.0/src/libsrc/t_ncx.c
src/netcdf-3.5.0/src/libsrc/t_ncxx.c
src/netcdf-3.5.0/src/libsrc/t_ncxx.m4
src/netcdf-3.5.0/src/libsrc/test_nc.sav
src/netcdf-3.5.0/src/libsrc/v1hpg.c
src/netcdf-3.5.0/src/libsrc/v2i.c
src/netcdf-3.5.0/src/libsrc/var.c
src/netcdf-3.5.0/src/macros.make.def
src/netcdf-3.5.0/src/macros.make.in
src/netcdf-3.5.0/src/man/Makefile
src/netcdf-3.5.0/src/man/netcdf.m4
src/netcdf-3.5.0/src/nc_test/Makefile
src/netcdf-3.5.0/src/nc_test/depend
src/netcdf-3.5.0/src/nc_test/error.h
src/netcdf-3.5.0/src/nc_test/test_get.m4
src/netcdf-3.5.0/src/nc_test/test_put.m4
src/netcdf-3.5.0/src/nc_test/tests.h
src/netcdf-3.5.0/src/ncdump/Makefile
src/netcdf-3.5.0/src/ncdump/depend
src/netcdf-3.5.0/src/ncdump/dumplib.c
src/netcdf-3.5.0/src/ncdump/dumplib.h
src/netcdf-3.5.0/src/ncdump/ncdump.1
src/netcdf-3.5.0/src/ncdump/ncdump.c
src/netcdf-3.5.0/src/ncdump/ncdump.h
src/netcdf-3.5.0/src/ncdump/test0.cdl
src/netcdf-3.5.0/src/ncdump/vardata.c
src/netcdf-3.5.0/src/ncdump/vardata.h
src/netcdf-3.5.0/src/ncgen/Makefile
src/netcdf-3.5.0/src/ncgen/c0.cdl
src/netcdf-3.5.0/src/ncgen/depend
src/netcdf-3.5.0/src/ncgen/ncgen.1
src/netcdf-3.5.0/src/ncgen/ncgen.l
src/netcdf-3.5.0/src/ncgen/ncgen.y
src/netcdf-3.5.0/src/nctest/Makefile
src/netcdf-3.5.0/src/nctest/README
src/netcdf-3.5.0/src/nctest/depend
src/netcdf-3.5.0/src/nctest/testfile_nc.sav
src/netcdf-3.5.0/src/nctest/timesum.awk
src/netcdf-3.5.0/src/nf_test/Makefile
src/netcdf-3.5.0/src/nf_test/depend
src/netcdf-3.5.0/src/nf_test/test_get.m4
src/netcdf-3.5.0/src/nf_test/test_put.m4
src/netcdf-3.5.0/src/nf_test/tests.inc
src/netcdf-3.5.0/src/rules.make
src/netcdf.h
src/plug_render.c
src/prog_opts.c
src/thd_initsess.c
src/thd_loaddblk.c
src/thd_mincread.c
src/thd_mincwrite.c
src/thd_opendset.c
src/volpack.h
src/volpack/CMakeLists.txt
src/volpack/Makefile
src/volpack/config.h
src/volpack/makeopts.c
src/volpack/patchlevel.h
src/volpack/volpack.h
src/volpack/vp_check.c
src/volpack/vp_compAC00G.c
src/volpack/vp_compAC11B.c
src/volpack/vp_compAC1NB.c
src/volpack/vp_compAC1NS.c
src/volpack/vp_compAC1PB.c
src/volpack/vp_compAC31B.c
src/volpack/vp_compAC32B.c
src/volpack/vp_compAC3NB.c
src/volpack/vp_compAC3NS.c
src/volpack/vp_compAC3PB.c
src/volpack/vp_compAR00G.c
src/volpack/vp_compAR11B.c
src/volpack/vp_compAR1NB.c
src/volpack/vp_compAR1NS.c
src/volpack/vp_compAR1PB.c
src/volpack/vp_compAR31B.c
src/volpack/vp_compAR32B.c
src/volpack/vp_compAR3NB.c
src/volpack/vp_compAR3NS.c
src/volpack/vp_compAR3PB.c
src/volpack/vp_context.c
src/volpack/vp_extract.c
src/volpack/vp_file.c
src/volpack/vp_global.h
src/volpack/vp_linalg.c
src/volpack/vp_octree.c
src/volpack/vp_opts.c
src/volpack/vp_renderA.c
src/volpack/vp_renderB.c
src/volpack/vp_renderC.c
src/volpack/vp_renderR.c
src/volpack/vp_resample.c
src/volpack/vp_rle.c
src/volpack/vp_shade.c
src/volpack/vp_transpose.c
src/volpack/vp_userguide.html
src/volpack/vp_util.c
src/volpack/vp_view.c
src/volpack/vp_warp.c
src/volpack/vp_warpA101N.c
src/volpack/vp_warpA110N.c
src/volpack/vp_warpA111N.c
src/volpack/vp_warpA301N.c
src/volpack/vp_warpA330N.c
src/volpack/vp_warpA330R.c
src/volpack/vp_warpA331N.c
src/volpack/vp_warpA331R.c
Deprecation: deletion of many scripts
Timestamp: 2020-08-25 14:15:50 -0400
Commit: a9b60b1f4
Author: rick reynolds
Files affected:
src/R_scripts/3dAOV.R
src/R_scripts/3dICC_REML.R
src/afni_history_rickr.c
src/python_scripts/afnipy/lib_fs.py
src/python_scripts/scripts/DoPerRoi.py
src/python_scripts/scripts/afni_restproc.py
src/python_scripts/scripts/check_dset_for_fs.py
src/python_scripts/scripts/lpc_align.py
src/scripts_install/@DTI_studio_reposition
src/scripts_install/@UpdateAfni
src/scripts_install/@auto_align
src/scripts_install/@make_stim_file
src/scripts_install/@snapshot_volreg3
Deprecation: distribution deletion of compiled programs
Timestamp: 2020-08-25 17:40:01 -0400
Commit: 1ac227bcc
Author: rick reynolds
Files affected:
src/Makefile.INCLUDE
src/afni_history_rickr.c
src/ptaylor/Makefile.ptaylor.INCLUDE
src/rickr/Makefile
src/scripts_install/3dMax
Deprecation: deletion/deprecation: fat_mvm_review.py, fat_proc_grad_plot
Timestamp: 2020-09-01 15:15:34 -0400
Commit: 509b759f3
Author: mrneont
Files affected:
src/afni_history_ptaylor.c
src/python_scripts/scripts/fat_mvm_review.py
src/scripts_install/fat_proc_grad_plot
Deprecation: delete/deprecate: fat_lat_csv.py
Timestamp: 2020-09-01 17:12:47 -0400
Commit: 6ae08226b
Author: mrneont
Files affected:
src/afni_history_ptaylor.c
src/python_scripts/afnipy/lib_fat_Rfactor.py
src/python_scripts/scripts/fat_lat_csv.py