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Merge remote-tracking branch 'origin/dev' into new_peaks_cmds
Conflicts: core/file/nifti_utils.h python/mrtrix3/commands/peakscheck
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@@ -119,3 +119,13 @@ cd8a6f1c2d0debcf3a6de185f8b92fc0be3e1401 | |
#Author: MRtrixBot <[email protected]> | ||
#Date: Fri, 5 Apr 2024 14:06:00 +0100 | ||
# Replace include guards with #pragma once | ||
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9b3de4d4defc3c7572bcd3ab9f214b72ce91abf3 | ||
#Author: MRtrixBot <[email protected]> | ||
#Date: Sun Jun 9 20:33:33 2024 +1000 | ||
# population_template: Split source code between files | ||
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10c49930a63e6a2b0ce7d25d3f6d8dde290b2719 | ||
#Author: MRtrixBot <[email protected]> | ||
#Date: Mon, 19 Aug 2024 16:18:12 +0100 | ||
# Remove core/file/json.h and core/half.hpp |
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@@ -25,7 +25,7 @@ jobs: | |
- name: install dependencies | ||
run: | | ||
sudo apt-get update | ||
sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy | ||
sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy | ||
- name: Run sccache-cache | ||
uses: mozilla-actions/[email protected] | ||
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@@ -86,7 +86,7 @@ jobs: | |
- name: install dependencies | ||
run: | | ||
sudo apt-get update | ||
sudo apt-get install g++-9 qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy | ||
sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy | ||
- name: Run sccache-cache | ||
uses: mozilla-actions/[email protected] | ||
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@@ -208,10 +208,8 @@ jobs: | |
${{env.MINGW_PACKAGE_PREFIX}}-bc | ||
${{env.MINGW_PACKAGE_PREFIX}}-cmake | ||
${{env.MINGW_PACKAGE_PREFIX}}-diffutils | ||
${{env.MINGW_PACKAGE_PREFIX}}-eigen3 | ||
${{env.MINGW_PACKAGE_PREFIX}}-fftw | ||
${{env.MINGW_PACKAGE_PREFIX}}-gcc | ||
${{env.MINGW_PACKAGE_PREFIX}}-libtiff | ||
${{env.MINGW_PACKAGE_PREFIX}}-ninja | ||
${{env.MINGW_PACKAGE_PREFIX}}-pkg-config | ||
${{env.MINGW_PACKAGE_PREFIX}}-qt6-base | ||
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@@ -268,7 +266,6 @@ jobs: | |
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- name: pylint | ||
run: | | ||
echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./python/lib/mrtrix3/_version.py | ||
./run_pylint || { cat pylint.log; false; } | ||
- name: check copyright headers | ||
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@@ -284,5 +281,4 @@ jobs: | |
extensions: 'h,cpp' | ||
clangFormatVersion: 16 | ||
# Ignore third party headers | ||
exclude: './core/file/json.h ./core/file/nifti1.h ./core/file/nifti2.h' | ||
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exclude: './thirdparty ./_deps' |
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@@ -17,7 +17,7 @@ jobs: | |
- uses: ZedThree/[email protected] | ||
id: review | ||
with: | ||
apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,libeigen3-dev,zlib1g-dev,libfftw3-dev,ninja-build | ||
apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,zlib1g-dev,libfftw3-dev,ninja-build | ||
config_file: .clang-tidy | ||
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- uses: ZedThree/clang-tidy-review/[email protected] | ||
|
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@@ -1,8 +0,0 @@ | ||
[submodule "testing/data"] | ||
path = testing/binaries/data | ||
url = https://github.com/MRtrix3/test_data | ||
ignore = dirty | ||
[submodule "testing/script_data"] | ||
path = testing/scripts/data | ||
url = https://github.com/MRtrix3/script_test_data.git | ||
ignore = dirty | ||
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@@ -1,4 +1,4 @@ | ||
#!/usr/env/python3 | ||
#!/usr/bin/env python3 | ||
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# Copyright (c) 2008-2024 the MRtrix3 contributors. | ||
# | ||
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@@ -0,0 +1,92 @@ | ||
include(FetchContent) | ||
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if(NOT ${MRTRIX_DEPENDENCIES_DIR} STREQUAL "") | ||
message(STATUS "Using local dependencies at ${MRTRIX_DEPENDENCIES_DIR}") | ||
set(MRTRIX_LOCAL_DEPENDENCIES ON) | ||
else() | ||
set(MRTRIX_LOCAL_DEPENDENCIES OFF) | ||
endif() | ||
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# Eigen | ||
# We avoid configuring the Eigen library via FetchContent_MakeAvaiable | ||
# to avoid the verbosity of Eigen's CMake configuration output. | ||
if(MRTRIX_LOCAL_DEPENDENCIES) | ||
set(eigen_url ${MRTRIX_DEPENDENCIES_DIR}/eigen-3.4.0.tar.gz) | ||
else() | ||
set(eigen_url "https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz") | ||
endif() | ||
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FetchContent_Declare( | ||
eigen3 | ||
DOWNLOAD_EXTRACT_TIMESTAMP ON | ||
URL ${eigen_url} | ||
) | ||
FetchContent_GetProperties(Eigen3) | ||
if(NOT eigen3_POPULATED) | ||
FetchContent_Populate(Eigen3) | ||
add_library(Eigen3 INTERFACE) | ||
add_library(Eigen3::Eigen ALIAS Eigen3) | ||
target_include_directories(Eigen3 INTERFACE "${eigen3_SOURCE_DIR}") | ||
endif() | ||
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# Json for Modern C++ | ||
if(MRTRIX_LOCAL_DEPENDENCIES) | ||
set(json_url ${MRTRIX_DEPENDENCIES_DIR}/json.tar.xz) | ||
else() | ||
set(json_url "https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz") | ||
endif() | ||
FetchContent_Declare( | ||
json | ||
DOWNLOAD_EXTRACT_TIMESTAMP ON | ||
URL ${json_url} | ||
) | ||
FetchContent_MakeAvailable(json) | ||
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# Half-precision floating-point library | ||
if(MRTRIX_LOCAL_DEPENDENCIES) | ||
set(half_url ${MRTRIX_DEPENDENCIES_DIR}/half-2.1.0.zip) | ||
else() | ||
set(half_url "https://sourceforge.net/projects/half/files/half/2.1.0/half-2.1.0.zip/download") | ||
endif() | ||
FetchContent_Declare( | ||
half | ||
DOWNLOAD_EXTRACT_TIMESTAMP ON | ||
URL ${half_url} | ||
) | ||
FetchContent_MakeAvailable(half) | ||
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add_library(half INTERFACE) | ||
add_library(half::half ALIAS half) | ||
target_include_directories(half INTERFACE "${half_SOURCE_DIR}/include") | ||
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# Nifti headers | ||
add_library(nifti INTERFACE) | ||
add_library(nifti::nifti ALIAS nifti) | ||
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if(MRTRIX_LOCAL_DEPENDENCIES) | ||
target_include_directories(nifti INTERFACE "${MRTRIX_DEPENDENCIES_DIR}/nifti") | ||
else() | ||
include(ExternalProject) | ||
ExternalProject_Add( | ||
nifti1 | ||
PREFIX nifti | ||
URL "https://raw.githubusercontent.com/NIFTI-Imaging/nifti_clib/master/nifti2/nifti1.h" | ||
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" | ||
DOWNLOAD_NO_EXTRACT ON | ||
DOWNLOAD_NO_PROGRESS ON | ||
LOG_DOWNLOAD ON | ||
) | ||
ExternalProject_Add( | ||
nifti2 | ||
PREFIX nifti | ||
URL "https://raw.githubusercontent.com/NIFTI-Imaging/nifti_clib/master/nifti2/nifti2.h" | ||
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" | ||
DOWNLOAD_NO_EXTRACT ON | ||
DOWNLOAD_NO_PROGRESS ON | ||
LOG_DOWNLOAD ON | ||
) | ||
target_include_directories(nifti INTERFACE "${CMAKE_CURRENT_BINARY_DIR}/nifti/src/") | ||
endif() | ||
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