| 45760b0 | afniHQ | 25 May 2020, 15:52:43 UTC | version update | 25 May 2020, 15:52:43 UTC |
| d643ce4 | rick reynolds | 25 May 2020, 15:23:56 UTC | Merge branch 'master' of https://github.com/afni/AFNI | 25 May 2020, 15:23:56 UTC |
| 7c706dc | rick reynolds | 25 May 2020, 15:23:53 UTC | add libexpat to macos dist libs | 25 May 2020, 15:23:53 UTC |
| 06d986c | Paul Taylor | 24 May 2020, 19:54:49 UTC | quotize | 24 May 2020, 19:54:49 UTC |
| 58a054e | afni-discoraj | 24 May 2020, 06:52:35 UTC | ClustExp_StatParse.py error check for table and no clusters | 24 May 2020, 06:52:35 UTC |
| e2f472f | Gang Chen | 24 May 2020, 01:32:30 UTC | small fixes | 24 May 2020, 01:32:30 UTC |
| fcb3da2 | Gang Chen | 24 May 2020, 01:32:28 UTC | small fixes | 24 May 2020, 01:32:28 UTC |
| a09f670 | Gang Chen | 24 May 2020, 01:32:24 UTC | small fixes | 24 May 2020, 01:32:24 UTC |
| 23d6f34 | leej3 | 23 May 2020, 13:58:24 UTC | Fix incorporation of whats_my_exepath functionality | 23 May 2020, 17:10:45 UTC |
| bc9d4f1 | leej3 | 12 May 2020, 18:08:03 UTC | improve indentation consistency for whats_my_exepath.c | 23 May 2020, 17:10:45 UTC |
| 74837e7 | leej3 | 19 May 2020, 14:22:02 UTC | remove WHATS_MY_EXEPATH preprocessor wrapping | 23 May 2020, 17:10:45 UTC |
| d8e37f3 | leej3 | 19 May 2020, 14:21:36 UTC | print plugin search info | 23 May 2020, 17:10:45 UTC |
| b4d9173 | leej3 | 12 May 2020, 17:21:19 UTC | add scope some compilers will fail if definitions are after the if block. | 23 May 2020, 17:10:45 UTC |
| 5d3cae2 | rick reynolds | 11 May 2020, 21:37:28 UTC | minor mods | 23 May 2020, 17:10:45 UTC |
| c7724ad | leej3 | 11 May 2020, 15:56:35 UTC | add whats_my_exepath to make build | 23 May 2020, 17:10:45 UTC |
| c521ee5 | leej3 | 08 May 2020, 18:31:04 UTC | use whats_my_exepath for plugin search remove memory leak originally strdup was used to attempt to mitigate the potential pitfall that dirname may or may not allocate new memory. exe_path is instead immediately freed. | 23 May 2020, 17:10:45 UTC |
| 1cec90b | leej3 | 07 May 2020, 17:45:57 UTC | add whats_my_exepath | 23 May 2020, 17:10:45 UTC |
| 511cead | leej3 | 19 May 2020, 14:31:50 UTC | add tests for plugin search behavior | 23 May 2020, 17:10:45 UTC |
| cb55fcf | leej3 | 12 May 2020, 19:02:06 UTC | improve test utility run_x_prog the keyword argument run_kwargs is now expanded in to keyword arguments provided to the sp.run call allowing, among other things, the modification of the environment of the program call add fix for running multiple instances of xvfb-run | 23 May 2020, 17:10:45 UTC |
| 257b86b | leej3 | 06 May 2020, 20:05:34 UTC | set DYNAMIC_suffix in cmake build | 23 May 2020, 17:10:45 UTC |
| 1d6f818 | leej3 | 23 May 2020, 00:33:48 UTC | Use shared object build in Dockerfile | 23 May 2020, 15:53:54 UTC |
| 48481d0 | leej3 | 22 May 2020, 15:54:25 UTC | use afnipy except for 1d_tool | 23 May 2020, 15:53:54 UTC |
| 405293a | leej3 | 21 May 2020, 21:07:34 UTC | add some container setup checks to circleci | 23 May 2020, 15:53:54 UTC |
| 196be07 | leej3 | 21 May 2020, 18:56:50 UTC | improve testing of containers | 23 May 2020, 15:53:54 UTC |
| 6fe171f | leej3 | 18 May 2020, 20:57:42 UTC | adapt to new permissions management and improve dockerfiles Introduces some adaptations in the cmake docker file to work with the non-privileged user that was added. try to use pip for more python dependencies install pip to /opt: this avoids having to chown/chmod more than one directory Also, if the image is used with singularity, the home directory would likely override some of the files here The make build is not so readily adapted because of the difficulties of having an out of source build. add option for build dir removal in make image correctly raise error for failing pipe in cmake dockerfile | 23 May 2020, 15:53:54 UTC |
| 880733b | leej3 | 18 May 2020, 20:57:06 UTC | adapt jupyter-docker-stack permissions model For example of the gruesome details: https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html NB_UID and NB_GID have been replaced with CONTAINER_UID etc. The user jovyan has been changed to afni_user. | 23 May 2020, 15:53:54 UTC |
| 6d144a7 | leej3 | 14 May 2020, 20:37:39 UTC | rewrite configuration for circleci make the configuration more modular by abstracting motifs into jobs that run the make or cmake build base on an input parameter. These jobs are in turn downsized by abstracting code into "commands" that also take parameters. Add more comprehensive caching to circleci This caching can be reset for docker images and test data by bumping the appropriate cache number. It can be reset to zero upon a standard cache invalidation criteria: make and cmake build images invalidate each code revision (commit id) dev_base image invalidates on checksum of afni_dev_base.dockerfile test_data invalidates on commit id of afni_ci_test_data make cache fixes for circleci Paths for checksum function in caching can be absolute but should be wrapped in double quotes. Remember to use double braces for cache key templates Fix circleci cache versioning, and dev_base deployment rebuild dev_base image if no cache hit occurred fail if build image not found only write afni images to disk if it was not from a cache but built Dependency caching on macos: May be more work than it is worth. Not attempting this for now. extract test_data commit id without instantiating submodule: do not initialize datalad repo with git submodule. It generally leads to problems. git submodule stores a lot of the data in the parent repo rather than the submodule. In general very useful but we will not do that because datalad offers lots of conveniences and so sticking to datalad for initialization operations is better fix ownership and bump cache version It appears the remote docker engine runs as root user so perhaps use a different approach. Or just sudo chown post execution of the docker command as done here | 23 May 2020, 15:53:54 UTC |
| 24b490f | leej3 | 14 May 2020, 20:51:24 UTC | make fixes to test execution scripts | 23 May 2020, 15:53:54 UTC |
| 2c7a38a | leej3 | 13 May 2020, 16:43:30 UTC | drop python2 from dev images | 23 May 2020, 15:53:54 UTC |
| 1cb3ace | leej3 | 13 May 2020, 18:27:51 UTC | attempt to make datalad fetching a little more robust add fix for datalad repo upgrade: not sure why but version 8 keeps appearing. Wait before downloading datalad data: Using this in an attempt to prevent download failures. Will figure out a more elegant solution Install datalad repo before tests Sleep following datalad repo installation to minimize race conditions when running tests with multiple workers | 23 May 2020, 15:53:54 UTC |
| 2aa4258 | rick reynolds | 22 May 2020, 19:44:57 UTC | Merge branch 'master' of https://github.com/afni/AFNI | 22 May 2020, 19:44:57 UTC |
| 4c3e5e7 | rick reynolds | 22 May 2020, 19:44:39 UTC | and pass NN | 22 May 2020, 19:44:39 UTC |
| 0096276 | RWCox | 22 May 2020, 18:20:31 UTC | Merge branch 'master' of https://github.com/afni/afni | 22 May 2020, 18:20:31 UTC |
| c3ce619 | RWCox | 22 May 2020, 18:20:21 UTC | don't do realpath in NIFTI for symlinks | 22 May 2020, 18:20:21 UTC |
| 2fa7c7e | Paul Taylor | 22 May 2020, 18:17:30 UTC | @djunct_edgy_align_check: do all work in workdir (cleaner); no output changes | 22 May 2020, 18:17:30 UTC |
| aec32f7 | afni-gangc | 22 May 2020, 17:38:42 UTC | fixed small things in 3dLMEr | 22 May 2020, 17:38:42 UTC |
| 760fc3c | afniHQ | 21 May 2020, 22:10:13 UTC | version update | 21 May 2020, 22:10:13 UTC |
| 67928bd | rick reynolds | 21 May 2020, 21:57:51 UTC | Merge branch 'master' of https://github.com/afni/AFNI | 21 May 2020, 21:57:51 UTC |
| 40a1c4c | rick reynolds | 21 May 2020, 21:57:48 UTC | mask_tool -NN opts | 21 May 2020, 21:57:48 UTC |
| 0b6d9b0 | Paul Taylor | 21 May 2020, 21:47:06 UTC | afni_seeds_per_space.txt: change of macaque space name, stereoNMT -> NMT2 | 21 May 2020, 21:47:06 UTC |
| 45769bb | Paul Taylor | 21 May 2020, 21:42:31 UTC | @animal_warper, adjunct_aw_tableize_roi_info.py: include modal smooth value in report | 21 May 2020, 21:42:31 UTC |
| 08e7129 | Paul Taylor | 21 May 2020, 20:07:32 UTC | pt history fix | 21 May 2020, 20:07:32 UTC |
| 0ff58c9 | Paul Taylor | 21 May 2020, 19:37:46 UTC | @animal_warper: now makes reports/tables for atlas and seg dsets; adjunct_aw_tableize_roi_info.py added | 21 May 2020, 19:37:46 UTC |
| dc604e5 | RWCox | 21 May 2020, 18:58:07 UTC | Merge branch 'master' of https://github.com/afni/afni | 21 May 2020, 18:58:07 UTC |
| 24cf916 | RWCox | 21 May 2020, 18:45:53 UTC | use realpath() in thd_niftiread.c | 21 May 2020, 18:45:53 UTC |
| d2bf2f7 | afni-gangc | 21 May 2020, 17:19:45 UTC | fixed a bug about bounds | 21 May 2020, 17:19:45 UTC |
| 6e63fb4 | afni-gangc | 21 May 2020, 17:19:42 UTC | fixed a bug about bounds | 21 May 2020, 17:19:42 UTC |
| 94b7b0b | afni-gangc | 21 May 2020, 17:19:36 UTC | fixed a bug about bounds | 21 May 2020, 17:19:36 UTC |
| 1c95da8 | afni-gangc | 21 May 2020, 09:18:43 UTC | added outlier removal in 3dICC | 21 May 2020, 09:18:43 UTC |
| bc9e70f | rick reynolds | 20 May 2020, 21:08:03 UTC | hist | 20 May 2020, 21:08:03 UTC |
| 5d45061 | rick reynolds | 20 May 2020, 20:45:54 UTC | Merge branch 'master' of https://github.com/afni/AFNI | 20 May 2020, 20:45:54 UTC |
| 04dbc6b | rick reynolds | 20 May 2020, 16:30:37 UTC | apply updated THD_mask_dilate fix memory loss and lost dset history | 20 May 2020, 16:30:37 UTC |
| 679dbf5 | rick reynolds | 20 May 2020, 16:25:22 UTC | free copied name | 20 May 2020, 16:25:22 UTC |
| 4166ba4 | daniel glen | 19 May 2020, 21:32:49 UTC | Merge branch 'master' of https://github.com/afni/AFNI volume in 3dROIstats | 19 May 2020, 21:32:49 UTC |
| 50b14e4 | daniel glen | 19 May 2020, 21:32:29 UTC | ROI volumes | 19 May 2020, 21:32:29 UTC |
| 0d9293a | rick reynolds | 19 May 2020, 21:28:05 UTC | add NN param to THD_mask_erode_sym | 19 May 2020, 21:28:05 UTC |
| 62384b8 | Paul Taylor | 19 May 2020, 01:20:39 UTC | afni_seeds_per_space.txt : stereoNMT location update | 19 May 2020, 01:20:39 UTC |
| 1f508c0 | Paul Taylor | 19 May 2020, 01:13:26 UTC | @animal_warper: descriptor word fix | 19 May 2020, 01:13:26 UTC |
| 6d45bc0 | Paul Taylor | 18 May 2020, 04:34:32 UTC | @animal_warper: many changes; reorg under the hood, new opts; handle followers/abbrevs generally | 18 May 2020, 04:34:32 UTC |
| f201928 | afni-gangc | 18 May 2020, 00:55:39 UTC | added display of input range | 18 May 2020, 00:55:39 UTC |
| 26ec2be | afni-gangc | 18 May 2020, 00:55:36 UTC | added display of input range | 18 May 2020, 00:55:36 UTC |
| 3f98011 | afni-gangc | 18 May 2020, 00:55:30 UTC | added display of input range | 18 May 2020, 00:55:30 UTC |
| 79727ba | afni-gangc | 18 May 2020, 00:55:25 UTC | added display of input range | 18 May 2020, 00:55:25 UTC |
| d040a54 | afni-gangc | 18 May 2020, 00:55:20 UTC | added display of input range | 18 May 2020, 00:55:20 UTC |
| 01da17e | afni-gangc | 17 May 2020, 20:34:27 UTC | fixed a typo 3dLMEr | 17 May 2020, 20:34:27 UTC |
| d13c6cf | afni-gangc | 17 May 2020, 20:23:54 UTC | Fixed masking in 3dMVM | 17 May 2020, 20:23:54 UTC |
| 8165c66 | afni-gangc | 17 May 2020, 20:23:36 UTC | Fixed masking in 3dLME | 17 May 2020, 20:23:36 UTC |
| dae5f80 | afni-gangc | 17 May 2020, 20:23:13 UTC | Added an option for outlier removal and fixed masking in 3dLME | 17 May 2020, 20:23:13 UTC |
| 533cfb8 | afni-gangc | 17 May 2020, 20:22:55 UTC | Added an option for outlier removal and fixed masking in 3dISC | 17 May 2020, 20:22:55 UTC |
| ee7f66f | afni-gangc | 17 May 2020, 20:22:42 UTC | Added an option for outlier removal and fixed masking in 3dICC | 17 May 2020, 20:22:42 UTC |
| 9ef676f | afni-gangc | 17 May 2020, 11:27:53 UTC | Added option for outlier removal in 3dLMEr | 17 May 2020, 11:27:53 UTC |
| dcb1b20 | afni-gangc | 15 May 2020, 01:47:07 UTC | fixed two more typos | 15 May 2020, 01:47:07 UTC |
| ad0b8a1 | afni-gangc | 15 May 2020, 01:36:13 UTC | fixed a small typo in 3dMVM | 15 May 2020, 01:36:13 UTC |
| 101517a | daniel glen | 14 May 2020, 21:00:09 UTC | More minor commenting and editing of AFNI_atlas_spaces.niml | 14 May 2020, 21:00:09 UTC |
| 12121c4 | Paul Taylor | 14 May 2020, 20:05:38 UTC | @animal_warper: more readability changes; no output changes | 14 May 2020, 20:05:38 UTC |
| ddb364f | Paul Taylor | 14 May 2020, 19:52:31 UTC | @animal_warper: more readability changes; no output changes | 14 May 2020, 19:52:31 UTC |
| 7fbc3d7 | Paul Taylor | 14 May 2020, 19:41:50 UTC | @animal_warper: clarity-of-reading changes; no output effects | 14 May 2020, 19:41:50 UTC |
| d84b1c5 | daniel glen | 13 May 2020, 03:01:00 UTC | Merge branch 'master' of https://github.com/afni/AFNI comment and editing of AFNI_atlas_spaces.niml | 13 May 2020, 03:01:00 UTC |
| 35b1650 | daniel glen | 13 May 2020, 03:00:56 UTC | Minor commenting and editing of AFNI_atlas_spaces.niml | 13 May 2020, 03:00:56 UTC |
| fd4e1a6 | RWCox | 13 May 2020, 00:55:01 UTC | tweak 3dAllineate | 13 May 2020, 00:55:01 UTC |
| 206632e | RWCox | 12 May 2020, 20:35:05 UTC | tweak 3dAllineate more | 12 May 2020, 20:35:05 UTC |
| d2b9fb6 | leej3 | 12 May 2020, 14:02:05 UTC | rename custom slice order test | 12 May 2020, 17:19:21 UTC |
| be951b5 | leej3 | 12 May 2020, 13:40:13 UTC | update test data for retrots fix ci test_data again reverted original test data change and added the new data for the new tests (custom_slice_order) | 12 May 2020, 17:19:21 UTC |
| b62d47d | shotgunosine | 08 May 2020, 16:54:21 UTC | remove debug code | 12 May 2020, 17:19:21 UTC |
| d0e45a3 | shotgunosine | 08 May 2020, 16:52:27 UTC | Fix custom flag and add a test | 12 May 2020, 17:19:21 UTC |
| 53c09fd | RWCox | 12 May 2020, 15:02:06 UTC | add JPEG output to 3dAllineate if output is 2D and prefix ends in .jpg | 12 May 2020, 15:02:06 UTC |
| bddcfff | rick reynolds | 11 May 2020, 18:19:29 UTC | web links | 11 May 2020, 18:19:29 UTC |
| 7afe0a7 | rick reynolds | 11 May 2020, 17:42:35 UTC | p3 updates | 11 May 2020, 17:42:35 UTC |
| 1a9dd77 | rick reynolds | 11 May 2020, 16:53:26 UTC | p3 updates | 11 May 2020, 16:53:26 UTC |
| 734cdf0 | rick reynolds | 11 May 2020, 16:44:05 UTC | p3 updates | 11 May 2020, 16:44:05 UTC |
| 38b0aed | rick reynolds | 11 May 2020, 15:49:26 UTC | Merge branch 'master' of https://github.com/afni/AFNI | 11 May 2020, 15:49:26 UTC |
| 22a41dd | rick reynolds | 11 May 2020, 15:49:21 UTC | int | 11 May 2020, 15:49:21 UTC |
| 21ef50b | RWCox | 11 May 2020, 14:36:04 UTC | Merge branch 'master' of https://github.com/afni/afni | 11 May 2020, 14:36:04 UTC |
| 8ea7d11 | afni-gangc | 11 May 2020, 11:17:56 UTC | fixed a bug in writing output in MBA | 11 May 2020, 11:17:56 UTC |
| 1468b43 | leej3 | 08 May 2020, 18:02:15 UTC | increase timeout for circleci push to dockerhub | 08 May 2020, 18:02:15 UTC |
| d7ed0db | afni-gangc | 06 May 2020, 13:33:14 UTC | small fix | 06 May 2020, 13:33:14 UTC |
| d144060 | afni-gangc | 06 May 2020, 02:56:03 UTC | adopted changes from Andrew Davis in 3dMVM | 06 May 2020, 02:56:03 UTC |
| 8255ab3 | afni-gangc | 06 May 2020, 01:53:07 UTC | Fixed a bug about stat code for GLF in 3dLMEr | 06 May 2020, 01:53:07 UTC |
| 7cc953a | RWCox | 05 May 2020, 19:44:37 UTC | fix Lock menu bug | 05 May 2020, 19:44:37 UTC |
| f5f331e | RWCox | 05 May 2020, 14:07:04 UTC | tweak 1dmatcalc | 05 May 2020, 14:07:04 UTC |
