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Tag 3.0_RC3 #1232

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merged 845 commits into from May 11, 2018

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Lestropie commented Jan 17, 2018

Creating the tag PR in order to produce the log of commits and code changes, which can then be used to write a changelog to post on the forum (to be drafted in the Staff section of the forum). Also created a milestone on GitHub.

@Lestropie Lestropie added this to the Milestone 3.0_RC3 milestone Jan 17, 2018

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maxpietsch commented Jan 31, 2018

Another fix to add is the Dicom Time class. I can not compile this branch using clang on macOS:

ERROR: (39/75) [CC] tmp/core/file/dicom/mapper.o

clang++ -c -std=c++11 -flto=thin -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.13 -DMRTRIX_WORD64 -DMRTRIX_TIFF_SUPPORT -isystem /usr/local/Cellar/libtiff/4.0.8_5/include -DEIGEN_FFTW_DEFAULT -isystem /usr/local/Cellar/fftw/3.3.6-pl2/include -Wall -O3 -DNDEBUG -Isrc -I./core -Icmd -isystem /usr/local/Cellar/eigen/3.3.4/include/eigen3 -DEIGEN_DONT_PARALLELIZE core/file/dicom/mapper.cpp -o tmp/core/file/dicom/mapper.o

failed with output

core/file/dicom/mapper.cpp:230:20: error: no matching function for call to 'isfinite'
        } else if (std::isfinite (frame.acquisition_time)) {
                   ^~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/math.h:397:5: note: candidate template ignored: disabled by 'enable_if' [with _A1 = MR::File::Dicom::Time]
    std::is_arithmetic<_A1>::value && std::numeric_limits<_A1>::has_infinity,
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/math.h:407:5: note: candidate template ignored: disabled by 'enable_if' [with _A1 = MR::File::Dicom::Time]
    std::is_arithmetic<_A1>::value && !std::numeric_limits<_A1>::has_infinity,
    ^
1 error generated.

Edit: done in e20d0b6

Lestropie and others added some commits Mar 21, 2018

Merge pull request #1267 from MRtrix3/config_fix_debug_windows
configure: Alter debug optimisation on Windows
Scripts: Fix erroneous error report
If a script is re-run using the -continue option, and the -nocleanup option is also used, then the file 'error.txt' resulting from the prior script failure will be detected and erroneously echoed to the command-line as an error. This is solved simply by erasing file 'error.txt' when the -continue option is used.
Connectome LUT: Better parsing
- Provide line numbers for lines that result in parsing failure
- Support comma-delimiting in addition to space-delimiting.
- Provide printout of detected column-wise data formatting when overall LUT format is unsupported.
Command-line usage: Warn on likely erroneous option usage
If one of the inputs to a command-line option starts with a dash character, it is likely that the contents of that command-line entry are intended as its own command-line option, and are not supposed to be an input argument to some other command-line option. If this occurs, the most likely scenario is that the user has not provided enough arguments to the first command-line option, and hence the second command-line option is being 'consumed' as one of the requisite inputs to the first option.
OpenGL: Prevent uninitialised variable memory warnings
GLenum MR::GUI::GL::Texture::tex_type was added in 3afcd2c, but not appropriately initialised on construction, leading to unwanted warnings when running mrview in valgrind.
Merge pull request #1284 from MRtrix3/opengl_texture_uninitialised_va…
…riable

OpenGL: Prevent uninitialised variable memory warnings
Merge pull request #1283 from MRtrix3/run_function_kwargs
run.function(): Support keyword arguments
Connectome LUT: Remove attempted support for comma delimiters
Initial attempt compiled and ran, but did not properly parse comma-delimited lookup table files. Support for such will require writing a function to split LUT lines based on quotation marks, commas and spaces as appropriate.
Merge pull request #1277 from MRtrix3/script_continue_fix
Scripts: Fix -continue option

jdtournier and others added some commits May 9, 2018

build: date now compiled alongside version
This should at the very least ensure that any changes to the git version
will trigger an update of the build date reported. Also ensure all dates
reported reference the same variable, rather than each reporting
potentially different __DATE__ macros.
mrhistmatch: Better handling of NaNs
- In scale and linear  modes, skip non-finite values at input.
In all modes, preserve non-finite values from input to output.
Merge pull request #1316 from MRtrix3/lightbox_outofbounds_fix
mrview: Fix memory error in Lightbox mode
TravisCI: Try using Clang version 6 on Linux
Attempted response to CI failures on #1327.
Merge pull request #1327 from MRtrix3/mrhistmatch_scale_linear
mrhistmatch: New matching modes
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Lestropie commented May 10, 2018

Pending a satisfactory solution to #1332, this is ready to go.

@jdtournier: Given the principal change is the SH precomputer fix, do you want to merge / tag / sign?

jdtournier and others added some commits May 10, 2018

build: add option -nopaginate
and make sure travis.sh uses it.
Tweaks to version string handling
- Rename MR::App::mrtrix_version to MR::App::library_version, and move file from core/version.cpp to core/library_version.cpp. Erase old file if it exists during build script.
- Rename MR::App::mrtrix_command_version to MR::App::command_version.
- Add brief comments to intentionally-empty files related to version string handling.
-
Tweak version string handling for external projects
When compiling an external project, make string MR::App::command_version equivalent to the external project version, rather than the version of the commands provided as part of the MRtrix3 package.
mrhistmatch: Use LU rather than normal equation
This provides greater precision with respect to ground truth when run on test data; tolerances on automated testing updated accordingly.
Merge pull request #1333 from MRtrix3/mrhistmatch_use_lu
mrhistmatch: Use LU rather than normal equation
version checking: revert previous changes and fix link errors
Also:

- change App::mrtrix_command_version to App::exec_uses_mrtrix_version

- record project build date
Merge pull request #1332 from MRtrix3/docs_use_git_pull_tags
changes to ensure consistent version and build date
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jdtournier commented May 11, 2018

OK, release is on!

@jdtournier jdtournier merged commit 57e351e into master May 11, 2018

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