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Update connectome-workbench recipe #51770

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Update connectome-workbench recipe #51770

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e4d2ab8
Update connectome-workbench recipe
effigies Oct 29, 2024
25ad102
Remove connectome-workbench from blacklist
effigies Oct 29, 2024
ca812bb
The recipe name should be the same as its folder name
martin-g Dec 6, 2024
8aede91
Merge branch 'master' into connectome-workbench
martin-g Dec 6, 2024
ad2370e
Add run_exports
martin-g Dec 6, 2024
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3 changes: 0 additions & 3 deletions build-fail-blacklist
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Original file line number Diff line number Diff line change
Expand Up @@ -697,9 +697,6 @@ recipes/phylocsf
# Ruby build failes
recipes/protk

# Does not link include -lGL -lGLU when linking, might require libOSMesa.
recipes/connectome-workbench

# Build fails during boostrap of vendored Boost.
recipes/gvcftools
recipes/seer
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29 changes: 17 additions & 12 deletions recipes/connectome-workbench/build.sh
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@@ -1,15 +1,20 @@
#!/bin/bash

export PKG_CONFIG_PATH=${PREFIX}/lib/pkgconfig \
OPENMP_HEADER_DIR=${PREFIX}/include \
OPENMP_LIB_DIR=${PREFIX}/lib \
FREETYPE_DIR=${PREFIX}
#!/usr/bin/env bash

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DOPENSSL_ROOT_DIR=${PREFIX} \
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-DCMAKE_BUILD_TYPE=Release -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-L${PREFIX}/lib" \
-DWORKBENCH_USE_QT5=TRUE -DZLIB_ROOT=${PREFIX} -DWORKBENCH_MESA_DIR=${PREFIX} \
-DCMAKE_PREFIX_PATH=${PREFIX} -DPKG_CONFIG_USE_CMAKE_PREFIX_PATH=True ../src
make -j ${CPU_COUNT}
make install

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 .
170 changes: 126 additions & 44 deletions recipes/connectome-workbench/meta.yaml
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@@ -1,73 +1,155 @@
{% set name = "connectome-workbench" %}
{% set version = "1.3.2" %}
{% set sha256 = "5574da8fcba810f5de1a3f70691cd763f927413d73f3b107142041272bf4edc9" %}
{% set version = "2.0.1" %}

package:
name: {{ name }}
name: {{ name }}-split
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version: {{ version }}

source:
url: https://github.com/Washington-University/workbench/archive/v{{ version }}.tar.gz
sha256: {{ sha256 }}
url: https://github.com/Washington-University/workbench/archive/v{{ version }}.tar.gz
sha256: c80bb248d1d25b36dd92112b9d3fb4585474e117c0c49dc8a222d859624f0376
patches:
- patches/0001-Import-cstdint-into-libCZI.h.patch
- patches/0001-Fix-unsafe-narrowing.patch

build:
number: 1
skip: True # [osx]
number: 0
skip: true # [osx or win]

requirements:
build:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- cmake >=2.8
- {{ cdt('mesa-libgl-devel') }}
- {{ cdt('libselinux') }}
- {{ cdt('libxdamage') }}
- {{ cdt('libxxf86vm') }}
- {{ 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 >=5.7
- libpng
- zlib
- qt
- openssl
- openmp
- freetype
- mesa
- libglu
- xorg-libx11
- xorg-libxext
- xorg-libxfixes
- xorg-libxcb
- xorg-libxau
- xorg-libxdmcp

run:
- qt >=5.6
- libpng
- libzlib
- zlib
- openssl
- openmp
- freetype
- mesa
- libglu
- xorg-libx11
- xorg-libxext
- xorg-libxfixes
- xorg-libxcb
- xorg-libxau
- xorg-libxdmcp
- libglu # [linux]
- glew # [windows]

test:
commands:
- wb_command -help
- 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
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about:
home: https://www.humanconnectome.org/software/connectome-workbench
summary: "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"
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
license_family: GPL
license_file: LICENSE
license_file:
- LICENSE
- src/CZIlib/LICENSE
- src/QxtCore/LICENSE_qxt
- src/kloewe/cpuinfo/LICENSE
- src/kloewe/dot/LICENSE
doc_url: https://humanconnectome.org/software/workbench-command
dev_url: https://github.com/Washington-University/workbench

extra:
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34 changes: 34 additions & 0 deletions recipes/connectome-workbench/patches/0001-Fix-unsafe-narrowing.patch
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Original file line number Diff line number Diff line change
@@ -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

24 changes: 24 additions & 0 deletions recipes/connectome-workbench/patches/0001-Import-cstdint-into-libCZI.h.patch
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Original file line number Diff line number Diff line change
@@ -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

5 changes: 5 additions & 0 deletions recipes/connectome-workbench/yum_requirements.txt
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@@ -0,0 +1,5 @@
mesa-libGL
mesa-dri-drivers
libXdamage
libXxf86vm
libXext
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