Add connectome-workbench packages

recipes/connectome-workbench/build.bat

@@ -0,0 +1,25 @@
+mkdir build_cli
+if errorlevel 1 exit 1
+cd build_cli
+if errorlevel 1 exit 1
+
+if  %vc% LEQ 9 set MSVC_VER=1500
+if  %vc% GTR 9 set MSVC_VER=1900
+
+if  %vc% LEQ 9 set MSVC_TS_VER=90
+if  %vc% GTR 9 set MSVC_TS_VER=140
+
+cmake -G "Ninja" ^
+      "%CMAKE_ARGS%" ^
+      -DMSVC_VERSION="%MSVC_VER%" ^
+      -DMSVC_TOOLSET_VERSION="%MSVC_TS_VER%" ^
+      -DCMAKE_BUILD_TYPE=Release ^
+      -DCMAKE_PREFIX_PATH:PATH="%LIBRARY_PREFIX%" ^
+      -DCMAKE_INSTALL_PREFIX:PATH="%LIBRARY_PREFIX%" ^
+      -DBUILD_SHARED_LIBS=ON ^
+      "%SRC_DIR%"
+
+if errorlevel 1 exit /b 1
+
+cmake --build . -j %CPU_COUNT% --verbose --config Release
+if errorlevel 1 exit /b 1

recipes/connectome-workbench/build.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+mkdir build
+cd build
+
+if [[ "$target_platform" == linux-* ]]; then
+    export CXX_FLAGS="$CXX_FLAGS -lGL -lGLU"
+fi
+
+cmake $CMAKE_ARGS -GNinja \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DCMAKE_INSTALL_PREFIX:STRING=$PREFIX \
+    -DCMAKE_CXX_FLAGS="$CXX_FLAGS" \
+    ../src
+
+cmake --build .
+
+ctest --extra-verbose --output-on-failure .
+
+cmake --install .

recipes/connectome-workbench/meta.yaml

@@ -0,0 +1,166 @@
+# Note: there are many handy hints in comments in this example -- remove them when you've finalized your recipe
+# If your package is python based, we recommend using Grayskull to generate it instead:
+# https://github.com/conda-incubator/grayskull
+
+# Jinja variables help maintain the recipe as you'll update the version only here.
+# Using the name variable with the URL in line 16 is convenient
+# when copying and pasting from another recipe, but not really needed.
+{% set name = "connectome-workbench" %}
+{% set version = "2.0.0" %}
+
+package:
+  name: {{ name }}-split
+  version: {{ version }}
+
+source:
+  url: https://github.com/Washington-University/workbench/archive/v{{ version }}.tar.gz
+  sha256: 2d5a2603a1acb4fabc2b66fab3a8257f05ccd1705cf7f39681be5ff86169dfcf
+  patches:
+    - patches/0001-Import-cstdint-into-libCZI.h.patch
+    - patches/0001-Fix-unsafe-narrowing.patch
+
+build:
+  number: 0
+  skip: true  # [osx or win]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - {{ stdlib('c') }}
+    - cmake >=3.0
+    - ninja
+    - qwt
+    # OpenMP
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+    # libGL
+    - {{ cdt('mesa-libgl-devel') }}  # [linux]
+    - {{ cdt('mesa-dri-drivers') }}  # [linux]
+    - {{ cdt('libxdamage') }}        # [linux]
+    - {{ cdt('libxxf86vm') }}        # [linux]
+    - {{ cdt('libxext') }}           # [linux]
+  host:
+    - qt
+    - openssl
+    - libzlib
+    - zlib
+    - freetype
+    - libglu                         # [linux]
+    - glew                           # [windows]
+
+test:
+  commands:
+    - wb_view -help
+    - wb_command -version
+    - wb_shortcuts -help
+
+outputs:
+  - name: {{ name }}-gui
+    # build/host requirements should exactly match the root requirements
+    requirements:
+      build:
+        - {{ compiler('cxx') }}
+        - {{ stdlib('c') }}
+        - cmake >=3.0
+        - ninja
+        - qwt
+        # OpenMP
+        - llvm-openmp  # [osx]
+        - libgomp      # [linux]
+        # libGL
+        - {{ cdt('mesa-libgl-devel') }}  # [linux]
+        - {{ cdt('mesa-dri-drivers') }}  # [linux]
+        - {{ cdt('libxdamage') }}        # [linux]
+        - {{ cdt('libxxf86vm') }}        # [linux]
+        - {{ cdt('libxext') }}           # [linux]
+      host:
+        - qt
+        - openssl
+        - libzlib
+        - zlib
+        - freetype
+        - libglu                         # [linux]
+        - glew                           # [windows]
+      run:
+        - qt-main
+        - libgl                             # [linux]
+        - libglu                            # [linux]
+    files:
+      include:
+        - bin/wb_view
+    test:
+      commands:
+        - wb_view -help
+  - name: {{ name }}-cli
+    # build/host requirements should exactly match the root requirements
+    requirements:
+      build:
+        - {{ compiler('cxx') }}
+        - {{ stdlib('c') }}
+        - cmake >=3.0
+        - ninja
+        - qwt
+        # OpenMP
+        - llvm-openmp  # [osx]
+        - libgomp      # [linux]
+        # libGL
+        - {{ cdt('mesa-libgl-devel') }}  # [linux]
+        - {{ cdt('mesa-dri-drivers') }}  # [linux]
+        - {{ cdt('libxdamage') }}        # [linux]
+        - {{ cdt('libxxf86vm') }}        # [linux]
+        - {{ cdt('libxext') }}           # [linux]
+      host:
+        - qt
+        - openssl
+        - libzlib
+        - zlib
+        - freetype
+        - libglu                         # [linux]
+        - glew                           # [windows]
+      run:
+        - qt-main
+        - libgl                             # [linux]
+        - libglu                            # [linux]
+    files:
+      include:
+        - bin/wb_command
+        - bin/wb_shortcuts
+        - share/bash-completion/completions/*
+    test:
+      commands:
+        - wb_command -version
+        - wb_shortcuts -help
+  - name: {{ name }}
+    requirements:
+      run:
+        - {{ pin_subpackage('connectome-workbench-cli', exact=True) }}
+        - {{ pin_subpackage('connectome-workbench-gui', exact=True) }}
+    test:
+      commands:
+        - wb_view -help
+        - wb_command -version
+        - wb_shortcuts -help
+
+about:
+  home: https://www.humanconnectome.org/software/connectome-workbench
+  summary: 'Neuroimaging utility for the Human Connectome Project'
+  description: |
+    Connectome Workbench is an open source, freely available visualization and discovery
+    tool used to map neuroimaging data, especially data generated by the Human
+    Connectome Project.
+  license: GPL-2.0-only
+  # Please also note that some projects have multiple license files which all need to be added using a valid yaml list.
+  # See https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#license-file
+  license_file:
+    - LICENSE
+    - src/CZIlib/LICENSE
+    - src/QxtCore/LICENSE_qxt
+    - src/kloewe/cpuinfo/LICENSE
+    - src/kloewe/dot/LICENSE
+  # The doc_url and dev_url are optional.
+  doc_url: https://humanconnectome.org/software/workbench-command
+  dev_url: https://github.com/Washington-University/workbench
+
+extra:
+  recipe-maintainers:
+    - effigies

recipes/connectome-workbench/patches/0001-Fix-unsafe-narrowing.patch

@@ -0,0 +1,34 @@
+From cc3d4d74235978b136f637620032595cb388933b Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <[email protected]>
+Date: Mon, 14 Oct 2024 13:49:05 -0400
+Subject: [PATCH] Fix unsafe narrowing
+
+---
+ src/Algorithms/AlgorithmCiftiSeparate.cxx | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/Algorithms/AlgorithmCiftiSeparate.cxx b/src/Algorithms/AlgorithmCiftiSeparate.cxx
+index 9a64a262e..f49c04e73 100644
+--- a/src/Algorithms/AlgorithmCiftiSeparate.cxx
++++ b/src/Algorithms/AlgorithmCiftiSeparate.cxx
+@@ -654,7 +654,7 @@ void AlgorithmCiftiSeparate::getCroppedVolSpace(const CiftiFile* ciftiIn, const
+     int64_t numVoxels = (int64_t)myMap.size();
+     if (numVoxels > 0)
+     {//make a voxel bounding box to minimize memory usage
+-        int extrema[6] = { myMap[0].m_ijk[0],
++        int64_t extrema[6] = { myMap[0].m_ijk[0],
+             myMap[0].m_ijk[0],
+             myMap[0].m_ijk[1],
+             myMap[0].m_ijk[1],
+@@ -699,7 +699,7 @@ void AlgorithmCiftiSeparate::getCroppedVolSpaceAll(const CiftiFile* ciftiIn, con
+     int64_t numVoxels = (int64_t)myMap.size();
+     if (numVoxels > 0)
+     {//make a voxel bounding box to minimize memory usage
+-        int extrema[6] = { myMap[0].m_ijk[0],
++        int64_t extrema[6] = { myMap[0].m_ijk[0],
+             myMap[0].m_ijk[0],
+             myMap[0].m_ijk[1],
+             myMap[0].m_ijk[1],
+-- 
+2.45.2
+

recipes/connectome-workbench/patches/0001-Import-cstdint-into-libCZI.h.patch

@@ -0,0 +1,24 @@
+From 28d007d44f4683ce430e8b29d184977ff488007c Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <[email protected]>
+Date: Sun, 13 Oct 2024 11:29:03 -0400
+Subject: [PATCH] Import cstdint into libCZI.h
+
+---
+ src/CZIlib/CZI/libCZI.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/CZIlib/CZI/libCZI.h b/src/CZIlib/CZI/libCZI.h
+index 7799f1aec..6a5c3e047 100644
+--- a/src/CZIlib/CZI/libCZI.h
++++ b/src/CZIlib/CZI/libCZI.h
+@@ -22,6 +22,7 @@
+
+ #pragma once
+
++#include <cstdint>
+ #include "ImportExport.h"
+
+ #include "priv_guiddef.h"
+-- 
+2.45.2
+

recipes/connectome-workbench/yum_requirements.txt

@@ -0,0 +1,5 @@
+mesa-libGL
+mesa-dri-drivers
+libXdamage
+libXxf86vm
+libXext