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https://github.com/afni/afni
08 April 2024, 13:54:27 UTC
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Revision Author Date Message Commit Date
d7c2720 afniHQ 10 June 2020, 22:25:19 UTC version update 10 June 2020, 22:25:19 UTC
0f7aff0 mrneont 10 June 2020, 22:20:49 UTC convert_cdiflist_to_grads.py: update help (only use on axially-acquired DWIs) 10 June 2020, 22:20:49 UTC
ece617e mrneont 10 June 2020, 17:00:19 UTC convert_cdiflist_to_grads.py: boringly-named prog to convert GE DWI grad into into usable form 10 June 2020, 17:00:19 UTC
eeba184 daniel glen 10 June 2020, 15:51:30 UTC Merge branch 'master' of https://github.com/afni/AFNI environment variable description for longnames and short names in README.env.... 10 June 2020, 15:51:30 UTC
105d86a daniel glen 10 June 2020, 15:51:09 UTC atlas longname environment variable 10 June 2020, 15:51:09 UTC
4f5f78c mrneont 09 June 2020, 21:02:17 UTC lib_mat2d_plot.py: fix mat2d plotting with -xticks_off and -yticks_off 09 June 2020, 21:02:17 UTC
8f97847 mrneont 09 June 2020, 16:08:04 UTC fat_mat_tableize.py: merging CSV and tables; funcs and fixes in lib_mat2d_*py 09 June 2020, 16:08:04 UTC
b5e5b00 mrneont 09 June 2020, 16:03:54 UTC afni_util.py: fix some matrix initializions in funcs 09 June 2020, 16:03:54 UTC
01d64f2 mrneont 08 June 2020, 23:54:56 UTC lib_csv.py: more functionality for fat_mat* stuff 08 June 2020, 23:54:56 UTC
aa3d1b1 mrneont 08 June 2020, 23:51:36 UTC au (helper progs); fat_mat_tableize.py (start); lib_mat2d_tableize.py (start); lib_mat2d_base.py (row<->col) 08 June 2020, 23:51:36 UTC
6b66d48 mrneont 08 June 2020, 17:48:14 UTC afni_util.py: list_files_by_glob() 08 June 2020, 17:48:14 UTC
8b863d2 mrneont 08 June 2020, 15:56:02 UTC afni_util.py: update/generalize match_listA_str_in_listB_str, fix 08 June 2020, 15:56:02 UTC
a9bae79 mrneont 08 June 2020, 15:50:29 UTC afni_util.py: update/generalize match_listA_str_in_listB_str 08 June 2020, 15:50:29 UTC
2e23983 mrneont 08 June 2020, 13:24:51 UTC afni_util.py: match_listA_str_in_listB_str(A, B), for fatcat/mvm stuff 08 June 2020, 13:24:51 UTC
f15d0c6 mrneont 06 June 2020, 22:28:41 UTC test 06 June 2020, 22:28:41 UTC
6bf99f2 Paul Taylor 05 June 2020, 19:54:29 UTC afni_util.py: new funcs for lists of 2D list matrices 05 June 2020, 19:54:29 UTC
68f5768 Paul Taylor 05 June 2020, 13:48:35 UTC lib_csv.py: new; for reading in CSV for FAT-MVM and other stats 05 June 2020, 13:48:35 UTC
97e0dd0 rick reynolds 04 June 2020, 21:09:38 UTC Merge branch 'master' of https://github.com/afni/AFNI 04 June 2020, 21:09:38 UTC
b0edd6d rick reynolds 04 June 2020, 21:09:34 UTC f2c extern 04 June 2020, 21:09:34 UTC
bf6300e daniel glen 04 June 2020, 19:26:36 UTC Merge branch 'master' of https://github.com/afni/AFNI 04 June 2020, 19:26:36 UTC
015c3e3 daniel glen 04 June 2020, 19:25:48 UTC align_epi_anat.py epistrip_opts 04 June 2020, 19:25:48 UTC
8d02fc2 Paul Taylor 04 June 2020, 18:54:43 UTC lib_mat2d_base.py: new obj for mult netcc/grid files 04 June 2020, 18:54:43 UTC
eb2c31c Paul Taylor 04 June 2020, 16:53:22 UTC fat_mat2d_plot.py: remove old testing line; no change in output 04 June 2020, 16:53:22 UTC
c4eb05e Paul Taylor 04 June 2020, 16:51:04 UTC Merge branch 'master' of https://github.com/afni/afni 04 June 2020, 16:51:04 UTC
80aeda7 Paul Taylor 04 June 2020, 16:46:50 UTC lib_mat2d_{base,plot}.py: add functionality to add mats to existing file obj 04 June 2020, 16:46:50 UTC
214e7ea RWCox 04 June 2020, 16:35:21 UTC Merge branch 'master' of https://github.com/afni/afni 04 June 2020, 16:35:21 UTC
ca3223c RWCox 04 June 2020, 16:35:12 UTC tweak 3dGroupInCorr to get rid of compiler warning 04 June 2020, 16:35:12 UTC
0810717 Paul Taylor 04 June 2020, 11:49:44 UTC fat_mat2d_plot.py: reverse cbar 04 June 2020, 11:49:44 UTC
e606f22 Paul Taylor 04 June 2020, 11:47:30 UTC fat_mat2d_plot.py: improve help; change def cbar 04 June 2020, 11:47:30 UTC
ad104ec afniHQ 04 June 2020, 02:03:53 UTC version update 04 June 2020, 02:03:53 UTC
ff6d2b3 RWCox 03 June 2020, 19:38:37 UTC Merge branch 'master' of https://github.com/afni/afni 03 June 2020, 19:38:37 UTC
a4dd987 RWCox 03 June 2020, 19:38:26 UTC tweak graph smoothing 03 June 2020, 19:38:26 UTC
b4e1378 Paul Taylor 03 June 2020, 18:59:50 UTC lib_b0_corr.py: call ARG_missing_arg() correctly, when needed 03 June 2020, 18:59:50 UTC
a3c8b3a Paul Taylor 03 June 2020, 18:44:36 UTC fat_mat2d_plot.py: remove a few excess/old lines 03 June 2020, 18:44:36 UTC
ac9864e Paul Taylor 03 June 2020, 18:43:01 UTC fat_mat2d_plot.py: introduced, for plotting *.netcc/*.grid (3dNetCorr/3dTrackID) files 03 June 2020, 18:43:01 UTC
41c8c0c Paul Taylor 03 June 2020, 17:43:59 UTC epi_b0_correct.py, check_dset_for_fs.py: movin' on up to the scripts side 03 June 2020, 17:43:59 UTC
3e21f8a Paul Taylor 03 June 2020, 15:29:47 UTC afni_base.py : func to help parse help text for opt names 03 June 2020, 15:29:47 UTC
daa16f9 rick reynolds 03 June 2020, 14:25:54 UTC trap empty regs 03 June 2020, 14:25:54 UTC
78190dc rick reynolds 03 June 2020, 14:22:43 UTC forgot for p3 03 June 2020, 14:22:43 UTC
a882698 leej3 02 June 2020, 21:07:55 UTC act according to the cruel whim of the mistress circleci 02 June 2020, 23:06:33 UTC
ca5dde6 leej3 29 May 2020, 11:43:27 UTC Make more general cmake build improvements fix location of built binaries during tests fix path bug for testing f2c does not need nifticdf as public dependency Remove X11 include from libheaders on linux which does not require it only use TARGET_NAME_IF_EXISTS for optional target: TARGET_NAME_IF_EXISTS can be useful when target that is linked again does not necessarily exist. Examples are platform dependent opengl implementations or GLW which is linked against or, if the appropriate symbols have not been externed, added directly to the suma library from the local source tree. If an alternative strategy is not present the usage of TARGET_NAME_IF_EXISTS is just confusing and should not be used. make cmake test script executable 02 June 2020, 23:06:33 UTC
01916f6 AFNI CircleCI User 02 June 2020, 19:03:55 UTC make it hard to accidentally run as root in container the approach to users and permissions for the afni containers is quite similar to that used by the jupyter docker stack. See: https://jupyter-docker-stacks.readthedocs.io/en/latest/ With this change to the entrypoint, it becomes a lot harder to cause oneself trouble by running the container as root. Even when setting --user=root and executing bash, the start.sh script is run which switches to a non-privileged user. Permissions issues should be fixed by changing the container user id and by executing the chmod arguments available (-e CHMOD_HOME etc). The advantage of this approach is that the container will work with no issues when run as a singluarity container on a host where the user cannot get root but still wishes to use all of the afni software in the container. 02 June 2020, 23:06:33 UTC
01f7390 leej3 01 June 2020, 21:52:44 UTC only mount test data into container during tests 02 June 2020, 23:06:33 UTC
299aba3 leej3 01 June 2020, 15:08:56 UTC use xvfbwrapper instead of xvfb-run adapt afni gui test add xvfbwrapper to dev base dockerfile 02 June 2020, 23:06:33 UTC
c02885d leej3 01 May 2020, 17:41:08 UTC improve the cmake-build's management of AFNI's python code The logic for managing python code has been moved to the cmakelists file in the python_scripts directory Now by default: The python executable used for the build is hopefully a little more intuitive. OSX framework python is used as a last resort. Preference is given to python interpreters located in an environment (conda or virtualenv), indeed the build will fail if an environment is activate but no python interpeter is found in it. The default minimum version is 3.6 (this can be overridden to use any python 3 provided test execution or afnipy installation is not required). By default the AFNI python package is installed into the current python interpreter in development mode during the build, and installed into the interpreter's site-packages during installation. The build target "pytest" now checks that the python currently found and used for tests does not differ from the one that was used during the cmake configuration. If the interpreter does change by accident (due to an accidental change in PATH/environment, or because the first python found on the PATH does not satisfy the requirements) it can result in an irritating state where dependencies are installed into the "wrong" interpreter. For the brave or insistent this check can be removed by setting FORCE_CURRENT_PY_INTERP_FOR_TESTS to "ON" set 3.6 as a minimum supported python version for installing By default AFNI distributes python code in abin, a directory containing all binaries and scripts. This change does not effect that. It is simply to drop the burden of maintenance for the cmake build system and the circleci testing infrastructure (for example resolving testing dependencies pre python 3.6 starts to become very difficult). only find python interpreter if needed in cmake build change target name for removing python package refactor test data fetching code a little 02 June 2020, 23:06:33 UTC
c1924b5 leej3 04 May 2020, 18:55:06 UTC update nifti to version with header fix 02 June 2020, 23:06:33 UTC
5a49cd4 leej3 29 May 2020, 18:25:27 UTC Make improvements to cmake build temp fix for use_system_all rename installed_targets for var name conflicts fail if R not found add details on using system glw improve default settings for cmake build improve system dependency management improve install management move options inclusion for cmake 02 June 2020, 23:06:33 UTC
8e42a7e leej3 27 April 2020, 13:40:53 UTC use NIFTI-Imaging master for nifti and gifti 02 June 2020, 23:06:33 UTC
97d48c0 Paul Taylor 02 June 2020, 20:51:06 UTC Merge branch 'master' of https://github.com/afni/afni 02 June 2020, 20:51:06 UTC
3b78282 Paul Taylor 02 June 2020, 20:50:55 UTC afni_base.py: arg parse err func 02 June 2020, 20:50:55 UTC
e82a840 RWCox 02 June 2020, 19:37:22 UTC add PM (plus-minus) plotting to AFNI graph viewer 02 June 2020, 19:37:22 UTC
96e7f51 Paul Taylor 02 June 2020, 19:30:05 UTC lib_mat2d_plot.py: added cbar, size-guessing funcs 02 June 2020, 19:30:05 UTC
d322d26 leej3 02 June 2020, 15:38:06 UTC improve circleci image caching and WD management Pass the dev base image cache version as a parameter to setup_dev_base_image command so that now all images have the same cache version that is solely set in the workflow section. Tidy working directory behavior: Instead of setting working_directory instead rely on the fact that the default is always ~/afni. It prevents irritating bugs where the working_directory is not set correctly (although is unfortunately implicit rather than explicit). 02 June 2020, 19:08:17 UTC
3935241 Paul Taylor 02 June 2020, 18:04:56 UTC lib_mat2d_plot.py: plotting, with cbar 02 June 2020, 18:04:56 UTC
306b1bf Paul Taylor 02 June 2020, 17:13:05 UTC lib_mat2d_plot.py: basic plot working 02 June 2020, 17:13:05 UTC
9e94a53 Paul Taylor 02 June 2020, 15:31:09 UTC lib_mat2d_{plot,base}.py: adding in mat2d plotting capability, slooowly 02 June 2020, 15:31:09 UTC
9cc5313 Paul Taylor 02 June 2020, 13:45:13 UTC lib_mat2d_base: printing/writing 02 June 2020, 13:45:13 UTC
e50846b afniHQ 02 June 2020, 01:49:27 UTC version update 02 June 2020, 01:49:27 UTC
64a8196 Paul Taylor 02 June 2020, 01:48:04 UTC apqc_make_tcsh.py: vstat for seedbased corr (rest) thr -> 0.2 02 June 2020, 01:48:04 UTC
33daab6 Paul Taylor 02 June 2020, 01:21:32 UTC lib_mat2d_base.py: migrated from lib_mat2d.py; tweaks 02 June 2020, 01:21:32 UTC
3821ea1 Paul Taylor 01 June 2020, 23:31:02 UTC adjunct_aw_tableize_roi_info.py: update report format 01 June 2020, 23:31:02 UTC
1a3c55e Paul Taylor 01 June 2020, 22:06:09 UTC lib_mat2d.py: tweaks 01 June 2020, 22:06:09 UTC
c6a16bc Paul Taylor 01 June 2020, 21:54:04 UTC lib_mat2d.py: maybe paul is actually doing py2->3 conversions on fat_* progs??? 01 June 2020, 21:54:04 UTC
63f52b8 rick reynolds 01 June 2020, 20:04:08 UTC clear ntt 01 June 2020, 20:04:08 UTC
fabc6da rick reynolds 01 June 2020, 20:02:38 UTC avoid mastery confusion 01 June 2020, 20:02:38 UTC
93519e8 rick reynolds 01 June 2020, 17:32:52 UTC Merge branch 'master' of https://github.com/afni/AFNI 01 June 2020, 17:32:52 UTC
d9dd287 rick reynolds 01 June 2020, 17:32:50 UTC show allzero regs 01 June 2020, 17:32:50 UTC
a7c80f0 Paul Taylor 01 June 2020, 14:08:19 UTC afni_base.py: add in message print style funcs (info, err, warn) 01 June 2020, 14:08:19 UTC
73e7265 Paul Taylor 01 June 2020, 01:38:03 UTC apqc: grayscale range of EPI as ulay now 2-98perc 01 June 2020, 01:38:03 UTC
62970ae rick reynolds 31 May 2020, 20:44:09 UTC add -verb 31 May 2020, 20:44:09 UTC
19a0026 rick reynolds 31 May 2020, 20:30:17 UTC Merge branch 'master' of https://github.com/afni/AFNI 31 May 2020, 20:30:17 UTC
025e7a1 rick reynolds 31 May 2020, 20:30:10 UTC status 31 May 2020, 20:30:10 UTC
16a72b9 Paul Taylor 31 May 2020, 19:42:55 UTC @animal_warper: 2 bug fixes: setting src_prefix, passing atl|seg labels/atlases 31 May 2020, 19:42:55 UTC
857c865 rick reynolds 30 May 2020, 20:36:45 UTC rename 30 May 2020, 20:36:45 UTC
6703cc9 mrneont 30 May 2020, 20:13:57 UTC @animal_warper: apply input abbrev earlier on 30 May 2020, 20:13:57 UTC
a823b35 rick reynolds 30 May 2020, 20:04:22 UTC Merge branch 'master' of https://github.com/afni/AFNI 30 May 2020, 20:04:22 UTC
c60abe4 rick reynolds 30 May 2020, 20:03:54 UTC stat_mad 30 May 2020, 20:03:54 UTC
2f42e62 Paul Taylor 30 May 2020, 19:02:34 UTC @animal_warper: modal smoothing with replacement now default; opt to not replace. Also, More QC images 30 May 2020, 19:02:34 UTC
0c0a5ba Paul Taylor 30 May 2020, 16:42:02 UTC @djunct_modal_smoothing_with_rep: new prog for modal smoothing with replacement of smoothed-away ROIs 30 May 2020, 16:42:02 UTC
7aee496 leej3 29 May 2020, 21:26:56 UTC add a timeout for test data download may be related to https://github.com/datalad/datalad/issues/4499 Adding a timeout for the datalad process to prevent the stall 30 May 2020, 14:56:10 UTC
59a7097 leej3 28 May 2020, 20:17:26 UTC prevent race condition during multi process test execution 29 May 2020, 13:10:09 UTC
1f24eb0 leej3 29 May 2020, 11:20:01 UTC add missing checkout step to circleci deploy job 29 May 2020, 11:20:01 UTC
68a1132 RWCox 29 May 2020, 01:20:03 UTC add Smooth curves to AFNI graph viewer 29 May 2020, 01:20:03 UTC
6a160c2 RWCox 29 May 2020, 00:54:47 UTC Merge branch 'master' of https://github.com/afni/afni 29 May 2020, 00:54:47 UTC
1c1778d afniHQ 28 May 2020, 22:08:31 UTC version update 28 May 2020, 22:08:31 UTC
3e5edb3 Paul Taylor 28 May 2020, 20:08:28 UTC apqc_make_tcsh.py: report DF info in vstat 28 May 2020, 20:08:28 UTC
ed5eaa5 RWCox 28 May 2020, 17:53:42 UTC minor tweaks 28 May 2020, 17:53:42 UTC
5fbc1bc afni-gangc 28 May 2020, 02:39:12 UTC small fixes 28 May 2020, 02:39:12 UTC
89a33c1 afni-gangc 28 May 2020, 02:39:09 UTC small fixes 28 May 2020, 02:39:09 UTC
4974a3b afni-gangc 28 May 2020, 02:39:05 UTC small fixes 28 May 2020, 02:39:05 UTC
2b66d99 afni-gangc 28 May 2020, 02:39:02 UTC small fixes 28 May 2020, 02:39:02 UTC
ad1c2e4 afni-gangc 28 May 2020, 02:38:58 UTC small fixes 28 May 2020, 02:38:58 UTC
b792d84 leej3 26 May 2020, 17:02:22 UTC allow reaping when PID is not 1 27 May 2020, 00:14:32 UTC
4d4923a leej3 26 May 2020, 20:00:04 UTC add tests for singularity like container execution for more info see section "Tips for making Docker images compatible with Singularity" of https://quay.io/repository/singularity/docker2singularity 27 May 2020, 00:14:32 UTC
f7e2c85 leej3 26 May 2020, 19:59:36 UTC tidy container testing a little 27 May 2020, 00:14:32 UTC
c67a0a0 leej3 27 May 2020, 00:10:39 UTC fix deployment on circleci 27 May 2020, 00:10:39 UTC
1f36ff4 afniHQ 26 May 2020, 21:45:10 UTC version update 26 May 2020, 21:45:10 UTC
29f0116 leej3 26 May 2020, 19:47:36 UTC fix the circleci filters 26 May 2020, 19:47:36 UTC
8c651a4 leej3 26 May 2020, 18:14:55 UTC Revert "make another attempt at fixing circleci deployment" This reverts commit fd2710b51904fc20e9a119e8162fe04f00460456. 26 May 2020, 18:14:55 UTC
b2116fe Paul Taylor 26 May 2020, 16:55:01 UTC apqc_make_tcsh.py, @djunct_edgy_align_check: EPI as ulay for edgy images 26 May 2020, 16:55:01 UTC
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