[med-svn] [Git][med-team/ismrmrd][master] 7 commits: New upstream version 1.15.0
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Feb 21 17:31:58 GMT 2026
Andreas Tille pushed to branch master at Debian Med / ismrmrd
Commits:
d60d47eb by Andreas Tille at 2026-02-21T18:12:08+01:00
New upstream version 1.15.0
- - - - -
08146842 by Andreas Tille at 2026-02-21T18:12:08+01:00
New upstream version
- - - - -
40bbd2a8 by Andreas Tille at 2026-02-21T18:12:09+01:00
Update upstream source from tag 'upstream/1.15.0'
Update to upstream version '1.15.0'
with Debian dir 4b88cf4547b3c681ebc4ef620b43d6dafe63c61c
- - - - -
0764f8ef by Andreas Tille at 2026-02-21T18:12:13+01:00
Drop use of autotools-dev debhelper.
Changes-By: lintian-brush
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated
See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html
- - - - -
e6749ee8 by Andreas Tille at 2026-02-21T18:16:46+01:00
Adapt patches to new upstream version. This also closes libboost1.90 issue thus the according patch can be dropped.
- - - - -
3eecf26d by Andreas Tille at 2026-02-21T18:24:49+01:00
Bump SONAME due to new upstream version
- - - - -
bedd993f by Andreas Tille at 2026-02-21T18:26:00+01:00
Upload to unstable
- - - - -
28 changed files:
- + .devcontainer/devcontainer.bashrc
- .devcontainer/devcontainer.json
- .github/workflows/ismrmrd_build.yml
- .github/workflows/ismrmrd_conda.yml
- − .github/workflows/ismrmrd_cpp98_smoketest.yml
- .github/workflows/ismrmrd_matlab.yml
- .github/workflows/ismrmrd_windows_build.yml
- .github/workflows/rpkg_build.yml
- .readthedocs.yaml
- CMakeLists.txt
- Dockerfile
- Dockerfile.build-static → Dockerfile.build-variants
- conda/build.sh
- conda/conda_build_config.yaml
- conda/meta.yaml
- + conda/setup-conda-build.sh
- debian/changelog
- debian/control
- debian/patches/Add-support-for-multiarch.patch
- debian/patches/add_static_lib.patch
- − debian/patches/libboost1.90.patch
- debian/patches/series
- debian/rules
- + docker/build-and-test-variant.sh
- docker/test-docker-images.sh → docker/test-images.sh
- environment.yml
- + justfile
- vcpkg.json
Changes:
=====================================
.devcontainer/devcontainer.bashrc
=====================================
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+# shellcheck source=/dev/null
+
+source /opt/conda/etc/profile.d/conda.sh
+conda activate ismrmrd
+
+source <(just --completions bash)
+
+if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then
+ # We don't want subshells to unnecessarily source this again.
+ unset BASH_ENV
+fi
=====================================
.devcontainer/devcontainer.json
=====================================
@@ -82,10 +82,7 @@
"common": {
"username": "automatic"
},
- "docker-from-docker": {
- "version": "20.10",
- "moby": false
- },
+ "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {},
"git": "os-provided"
}
}
=====================================
.github/workflows/ismrmrd_build.yml
=====================================
@@ -21,10 +21,9 @@ jobs:
runs-on: ubuntu-latest
permissions:
contents: read
- packages: write
steps:
- - uses: actions/checkout at v4
+ - uses: actions/checkout at v6
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
@@ -36,34 +35,38 @@ jobs:
- name: Configure CMake
working-directory: ${{github.workspace}}/build
- shell: bash
run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE
- name: Build
working-directory: ${{github.workspace}}/build
- shell: bash
run: |
cmake --build . --config $BUILD_TYPE
cmake --build . --target doc --config $BUILD_TYPE
+
- name: Test XML
working-directory: ${{github.workspace}}/schema
- shell: bash
run: for xml_file in *.xml; do xmllint --schema ismrmrd.xsd "$xml_file" --noout; done
- name: Test
working-directory: ${{github.workspace}}/build/tests
- shell: bash
run: ./test_ismrmrd
+ build-docker:
+ runs-on: ubuntu-latest
+ needs: build
+ permissions:
+ contents: read
+ packages: write
+ steps:
+ - uses: actions/checkout at v6
- name: Build and test docker images
working-directory: ${{github.workspace}}
- shell: bash
run: |
./docker/build-images.sh
- ./docker/test-docker-images.sh
+ ./docker/test-images.sh
- name: Log into registry ${{ env.REGISTRY }}
- uses: docker/login-action at 28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+ uses: docker/login-action at v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
@@ -72,31 +75,25 @@ jobs:
- name: Push images
if: ${{ github.event_name == 'release' }}
working-directory: ${{github.workspace}}
- shell: bash
run: |
./docker/build-images.sh --tag "${GITHUB_REF##*/}" --push
build-static:
runs-on: ubuntu-latest
+ needs: build
permissions:
contents: read
+ steps:
+ - uses: actions/checkout at v6
+ - name: Build and test static binaries
+ run: ./docker/build-and-test-variant.sh static
+ build-cpp98:
+ runs-on: ubuntu-latest
+ needs: build
+ permissions:
+ contents: read
steps:
- - uses: actions/checkout at v4
-
- - name: Build docker image
- run: |-
- docker build -f Dockerfile.build-static -t ismrmrd_static .
-
- - name: Test static binaries
- run: |-
- set -euo pipefail
- test_command="set -euo pipefail \
- && export PATH=$PATH:/opt/package/bin \
- && test -f /opt/package/lib/libismrmrd.a \
- && ! test -e /opt/package/lib/libismrmrd.so \
- && ismrmrd_generate_cartesian_shepp_logan -o testdata.h5 \
- && ismrmrd_hdf5_to_stream -i testdata.h5 --use-stdout \
- | ismrmrd_stream_recon_cartesian_2d --use-stdin --use-stdout \
- | ismrmrd_stream_to_hdf5 --use-stdin -o result.h5"
- docker run ismrmrd_static /bin/bash -c "$test_command"
+ - uses: actions/checkout at v6
+ - name: Build and test C++98 binaries
+ run: ./docker/build-and-test-variant.sh cpp98
=====================================
.github/workflows/ismrmrd_conda.yml
=====================================
@@ -12,29 +12,33 @@ jobs:
build-conda-packages:
strategy:
matrix:
- os: [ubuntu-latest, macos-13]
+ os: [ubuntu-latest]
runs-on: ${{ matrix.os }}
+ defaults:
+ run:
+ shell: bash -l {0}
+ working-directory: conda
+
steps:
- - uses: actions/checkout at v4
+ - uses: actions/checkout at v6
+
- uses: conda-incubator/setup-miniconda at v3
with:
miniforge-version: latest
- activate-environment: ismrmrd-build
- environment-file: conda/environment.yml
- python-version: 3.9
- auto-activate-base: false
+ auto-activate-base: true
+ activate-environment: ""
+ python-version: 3.13
+
- name: Build conda package
- shell: bash -l {0}
- working-directory: conda
run: |
+ bash -il ./setup-conda-build.sh
./package.sh
echo "Packages built: $(find build_pkg -name ismrmrd*.tar.bz2)"
- - name: Push conda package
- shell: bash -l {0}
+
+ - name: Publish conda package
if: ${{ github.event_name == 'release' }}
env:
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
- working-directory: conda
run: |
for p in $(find build_pkg -name ismrmrd*.tar.bz2)
do
=====================================
.github/workflows/ismrmrd_cpp98_smoketest.yml deleted
=====================================
@@ -1,42 +0,0 @@
-name: "C++98 Smoketest"
-
-on:
- push:
- branches: [master]
- tags: ["v*.*.*"]
- pull_request:
- branches: [master]
- workflow_dispatch:
-
-env:
- BUILD_TYPE: Release
-
-jobs:
- build:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout at v4
-
- - name: Create Build Environment
- run: cmake -E make_directory ${{github.workspace}}/build
-
- - name: Install dependencies
- run: |
- sudo apt-get update
- sudo apt-get -y install git-core libboost-all-dev libfftw3-dev libhdf5-serial-dev libxml2-utils libpugixml-dev socat
-
- - name: Configure CMake
- working-directory: ${{github.workspace}}/build
- shell: bash
- run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_CXX_STANDARD=98
-
- - name: Build
- working-directory: ${{github.workspace}}/build
- shell: bash
- run: |
- cmake --build . --config $BUILD_TYPE
-
- - name: Test
- working-directory: ${{github.workspace}}/build/tests
- shell: bash
- run: ./test_ismrmrd
=====================================
.github/workflows/ismrmrd_matlab.yml
=====================================
@@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v4
+ - uses: actions/checkout at v6
- name: Set up MATLAB
uses: matlab-actions/setup-matlab at v2
=====================================
.github/workflows/ismrmrd_windows_build.yml
=====================================
@@ -14,7 +14,7 @@ jobs:
runs-on: windows-latest
steps:
- - uses: actions/checkout at v4
+ - uses: actions/checkout at v6
- name: Create Build Environment
shell: pwsh
=====================================
.github/workflows/rpkg_build.yml
=====================================
@@ -18,7 +18,7 @@ jobs:
- name: Install dependencies
run: sudo dnf install rpkg git dnf-plugins-core -y
- - uses: actions/checkout at v4
+ - uses: actions/checkout at v6
with:
fetch-depth: 0
- name: Run RPKG
=====================================
.readthedocs.yaml
=====================================
@@ -6,9 +6,9 @@ version: 2
# Set the OS, Python version and other tools you might need
build:
- os: ubuntu-20.04
+ os: ubuntu-24.04
tools:
- python: "3.9"
+ python: "3.13"
# Build documentation in the "docs/" directory with Sphinx
sphinx:
=====================================
CMakeLists.txt
=====================================
@@ -40,7 +40,8 @@ endif()
# compiler flags
if(NOT "${CMAKE_CXX_STANDARD}")
- set(CMAKE_CXX_STANDARD 11)
+ set(CMAKE_CXX_STANDARD 17)
+ message(STATUS "CMAKE_CXX_STANDARD not set, defaulting to ${CMAKE_CXX_STANDARD}")
else()
message(STATUS "CMAKE_CXX_STANDARD set externally to ${CMAKE_CXX_STANDARD}")
endif()
@@ -74,8 +75,6 @@ elseif (build4GE)
set(Boost_USE_STATIC_LIBS "ON")
set(Boost_NO_SYSTEM_PATHS "TRUE")
set(HDF5_USE_STATIC_LIBRARIES "yes")
- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w -D_GLIBCXX_USE_CXX11_ABI=0")
else ()
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -Werror")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror")
@@ -92,8 +91,8 @@ endif ()
#in the utility libraries, that don't affect the data format itself.
# For more information see http://semver.org/
set(ISMRMRD_VERSION_MAJOR 1)
-set(ISMRMRD_VERSION_MINOR 14)
-set(ISMRMRD_VERSION_PATCH 3)
+set(ISMRMRD_VERSION_MINOR 15)
+set(ISMRMRD_VERSION_PATCH 0)
set(ISMRMRD_VERSION_STRING ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR}.${ISMRMRD_VERSION_PATCH})
set(ISMRMRD_SOVERSION ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR})
@@ -156,12 +155,14 @@ if (BUILD_STATIC)
set(Boost_USE_STATIC_LIBS On)
set(HDF5_USE_STATIC_LIBRARIES TRUE)
set(FFTW_USE_STATIC_LIBS TRUE)
+ message(STATUS "Building ISMRMRD as static library")
else()
add_definitions(-DBOOST_TEST_DYN_LINK)
+ message(STATUS "Building ISMRMRD as shared library")
endif()
# Find Boost for tests and utilities
-find_package(Boost COMPONENTS filesystem random program_options unit_test_framework)
+find_package(Boost CONFIG COMPONENTS filesystem random program_options unit_test_framework)
find_package(pugixml CONFIG REQUIRED)
find_package(FFTW COMPONENTS FLOAT_LIB)
=====================================
Dockerfile
=====================================
@@ -7,13 +7,9 @@
# subsequent stage and normalize the permissions.
#########################################################
-ARG USERNAME="vscode"
-ARG USER_UID=1000
-ARG USER_GID=$USER_UID
+FROM mcr.microsoft.com/oss/busybox/busybox:1.33.1 AS file-normalizer
-FROM mcr.microsoft.com/oss/busybox/busybox:1.33.1 as file-normalizer
-
-COPY environment.yml /data/
+COPY environment.yml .devcontainer/devcontainer.bashrc /data/
RUN chmod -R 555 /data/
RUN mkdir -p /entrypoints
@@ -23,13 +19,12 @@ COPY docker/entrypoint-stream.sh /entrypoints/
RUN sed -i 's/\r$//' /entrypoints/*.sh
RUN chmod +x /entrypoints/*.sh
-FROM mcr.microsoft.com/devcontainers/base:1.2.4-jammy AS basecontainer
+FROM mcr.microsoft.com/devcontainers/base:ubuntu-24.04 AS basecontainer
# Install needed packages and setup non-root user.
-ARG USERNAME
-ARG USER_UID
-ARG USER_GID
-
+ARG USERNAME="vscode"
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
ARG CONDA_GID=900
ARG CONDA_ENVIRONMENT_NAME=ismrmrd
@@ -37,7 +32,7 @@ RUN apt-get update && apt-get install -y \
libc6-dbg \
&& rm -rf /var/lib/apt/lists/*
-ARG MINIFORGE_VERSION=25.3.0-3
+ARG MINIFORGE_VERSION=25.11.0-1
# Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh \
@@ -61,25 +56,27 @@ ARG USER_GID
# Create a conda environment from the environment file in the repo root.
COPY --from=file-normalizer --chown=$USER_UID:conda /data/environment.yml /tmp/build/
RUN umask 0002 \
- && /opt/conda/bin/mamba env create -f /tmp/build/environment.yml \
- && /opt/conda/bin/mamba clean -fy \
+ && /opt/conda/bin/conda env create -f /tmp/build/environment.yml \
+ && /opt/conda/bin/conda clean -fy \
&& sudo chown -R :conda /opt/conda/envs
+# Add a file that is to be sourced from .bashrc and from the devops pipeline stages
+COPY --from=file-normalizer /data/devcontainer.bashrc /opt/devcontainer/
+
# Add a section to /etc/bash.bashrc that ensures that a section is present at the end of ~/.bashrc.
# We can't just write to .bashrc from here because it will be overwritten if the devcontainer user has
# opted to use their own dotfiles repo. The dotfiles repo is cloned after the postCreateCommand
# in the devcontainer.json file is executed.
RUN echo "\n\
-if ! grep -q \"^source /opt/conda/etc/profile.d/conda.sh\" /home/${USERNAME}/.bashrc; then\n\
- echo \"source /opt/conda/etc/profile.d/conda.sh\" >> /home/${USERNAME}/.bashrc\n\
- echo \"conda activate $(grep 'name:' /tmp/build/environment.yml | awk '{print $2}')\" >> /home/${USERNAME}/.bashrc\n\
+if ! grep -q \"^source /opt/devcontainer/devcontainer.bashrc\" \${HOME}/.bashrc; then\n\
+ echo \"source /opt/devcontainer/devcontainer.bashrc\" >> \${HOME}/.bashrc\n\
fi\n" >> /etc/bash.bashrc
ENV CMAKE_GENERATOR=Ninja
# Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
RUN mkdir -p /home/vscode/.local/share/CMakeTools \
- && echo '[{"name":"GCC-11","compilers":{"C":"/opt/conda/envs/ismrmrd/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/ismrmrd/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
+ && echo '[{"name":"GCC-15","compilers":{"C":"/opt/conda/envs/ismrmrd/bin/x86_64-conda-linux-gnu-gcc","CXX":"/opt/conda/envs/ismrmrd/bin/x86_64-conda-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
&& chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
FROM devcontainer AS ismrmrd-build
@@ -112,8 +109,8 @@ COPY --from=file-normalizer --chown=$USER_UID:conda /data/environment.yml /tmp/b
RUN grep -v "#.*\<dev\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml \
&& mv /tmp/build/filtered_environment.yml /tmp/build/environment.yml \
&& umask 0002 \
- && /opt/conda/bin/mamba env create -f /tmp/build/environment.yml \
- && /opt/conda/bin/mamba clean -fy \
+ && /opt/conda/bin/conda env create -f /tmp/build/environment.yml \
+ && /opt/conda/bin/conda clean -fy \
&& sudo chown -R :conda /opt/conda/envs
COPY --from=ismrmrd-build --chown=$USER_UID:conda /opt/package /opt/conda/envs/ismrmrd/
=====================================
Dockerfile.build-static → Dockerfile.build-variants
=====================================
@@ -1,4 +1,9 @@
-FROM ubuntu:noble AS ismrmrd_static
+ARG UBUNTU_VARIANT=noble
+
+FROM ubuntu:${UBUNTU_VARIANT} AS base
+
+ARG CXX_STANDARD=17
+ARG BUILD_STATIC=On
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install -y \
@@ -12,9 +17,9 @@ RUN apt-get update \
&& apt-get clean
RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US:en
-ENV LC_ALL en_US.UTF-8
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
RUN mkdir -p /opt/code/ismrmrd
COPY . /opt/code/ismrmrd/
@@ -25,9 +30,13 @@ RUN cd /opt/code/ismrmrd && \
cmake \
-G Ninja \
-D CMAKE_BUILD_TYPE=Release \
+ -D CMAKE_CXX_STANDARD=${CXX_STANDARD} \
+ -D BUILD_STATIC=${BUILD_STATIC} \
-D CMAKE_INSTALL_PREFIX=/opt/package \
- -D BUILD_STATIC=On \
../ && \
ninja && \
./tests/test_ismrmrd && \
ninja install
+
+ENV LD_LIBRARY_PATH=/opt/package/lib
+ENV PATH=$PATH:/opt/package/bin
=====================================
conda/build.sh
=====================================
@@ -2,10 +2,13 @@
set -euo pipefail
-mkdir -p build
-cd build
+mkdir -p build-conda
+cd build-conda
-cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+cmake -G Ninja \
+ -D CMAKE_BUILD_TYPE=Release \
+ -D CMAKE_CXX_STANDARD=17 \
+ -D CMAKE_INSTALL_PREFIX=${PREFIX} \
../
ninja
=====================================
conda/conda_build_config.yaml
=====================================
@@ -1,5 +1,5 @@
boost:
- - 1.76.0
- 1.80.0
+ - 1.84.0
pin_run_as_build:
boost: x.x
=====================================
conda/meta.yaml
=====================================
@@ -17,19 +17,19 @@ requirements:
- boost
- clang>=13.0.1 # [osx]
- clangxx>=13.0.1 # [osx]
- - cmake>=3.20.0
- - fftw=3.3.9
- - gcc_linux-64>=9.0.0 # [linux64]
- - gxx_linux-64>=9.0.0 # [linux64]
+ - cmake>=4.2.0
+ - fftw=3.3.*
+ - gcc_linux-64>=15.0.0 # [linux64]
+ - gxx_linux-64>=15.0.0 # [linux64]
- git
- - hdf5=1.10.6
- - ninja=1.10.*
- - pugixml=1.12.1
+ - hdf5=1.14.*
+ - ninja=1.13.*
+ - pugixml=1.15
run:
- boost {{ boost }}
- - hdf5=1.10.6
- - fftw=3.3.9
- - pugixml=1.12.1
+ - hdf5=1.14.*
+ - fftw=3.3.*
+ - pugixml=1.15
test:
requires:
=====================================
conda/setup-conda-build.sh
=====================================
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+set -e
+
+conda install -y -n base conda-build anaconda-client
+conda activate base
=====================================
debian/changelog
=====================================
@@ -1,13 +1,15 @@
-ismrmrd (1.14.3-4) UNRELEASED; urgency=medium
+ismrmrd (1.15.0-1) unstable; urgency=medium
* Team upload.
- * Port to boost 1.90
+ * New upstream version
Closes: #1128127
* Standards-Version: 4.7.3
* Build-Depends: architecture-is-64-bit
Closes: #863168
+ * Drop use of autotools-dev debhelper.
+ * Bump SONAME due to new upstream version
- -- Andreas Tille <tille at debian.org> Sat, 21 Feb 2026 18:03:31 +0100
+ -- Andreas Tille <tille at debian.org> Sat, 21 Feb 2026 18:24:53 +0100
ismrmrd (1.14.3-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -22,7 +22,7 @@ Vcs-Browser: https://salsa.debian.org/med-team/ismrmrd
Vcs-Git: https://salsa.debian.org/med-team/ismrmrd.git
Homepage: https://ismrmrd.github.io/
-Package: libismrmrd1.14
+Package: libismrmrd1.15
Architecture: any
Multi-Arch: same
Section: libs
@@ -54,7 +54,7 @@ Depends:
${misc:Depends},
libhdf5-dev,
libpugixml-dev,
- libismrmrd1.14 (= ${binary:Version}),
+ libismrmrd1.15 (= ${binary:Version}),
Suggests:
libismrmrd-doc,
Description: development files for ISMRMRD
=====================================
debian/patches/Add-support-for-multiarch.patch
=====================================
@@ -8,7 +8,7 @@ Subject: Add support for multiarch.
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -331,7 +331,7 @@ configure_file(cmake/ISMRMRDConfig.cmake
+@@ -332,7 +332,7 @@ configure_file(cmake/ISMRMRDConfig.cmake
set(CONFIG_ISMRMRD_SCHEMA_DIR ${CMAKE_INSTALL_PREFIX}/share/ismrmrd/schema)
set(CONFIG_ISMRMRD_TARGET_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/include)
=====================================
debian/patches/add_static_lib.patch
=====================================
@@ -4,16 +4,7 @@ Description: Add static library
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -161,7 +161,7 @@ else()
- endif()
-
- # Find Boost for tests and utilities
--find_package(Boost COMPONENTS filesystem random program_options unit_test_framework)
-+find_package(Boost REQUIRED COMPONENTS filesystem system random program_options unit_test_framework)
- find_package(pugixml CONFIG REQUIRED)
- find_package(FFTW COMPONENTS FLOAT_LIB)
-
-@@ -246,11 +246,13 @@ if (BUILD_STATIC)
+@@ -247,11 +247,13 @@ if (BUILD_STATIC)
else()
set(ISMRMRD_PUGIXML_LIBRARIES pugixml::shared)
add_library(ismrmrd SHARED ${ISMRMRD_TARGET_SOURCES})
@@ -27,7 +18,7 @@ Description: Add static library
if (USE_HDF5_DATASET_SUPPORT)
target_compile_options(ismrmrd PUBLIC ${HDF5_DEFINITIONS})
endif()
-@@ -271,7 +273,12 @@ set_target_properties(ismrmrd
+@@ -272,7 +274,12 @@ set_target_properties(ismrmrd
VERSION ${ISMRMRD_VERSION_STRING}
SOVERSION ${ISMRMRD_SOVERSION})
@@ -40,7 +31,7 @@ Description: Add static library
list(APPEND ISMRMRD_LIBRARIES ismrmrd) # Add to list of libraries to be found
list(APPEND ISMRMRD_LIBRARY_DIRS ${CMAKE_BINARY_DIR} ) # Add to list of directories to find libraries
-@@ -284,6 +291,7 @@ install(TARGETS ismrmrd EXPORT ISMRMRDTa
+@@ -285,6 +292,7 @@ install(TARGETS ismrmrd EXPORT ISMRMRDTa
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
COMPONENT Devel
)
=====================================
debian/patches/libboost1.90.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Description: Port to boost 1.90
-Author: Andreas Tille <tille at debian.org>
-Last-Update: 2026-02-21
-Bug-Debian: https://bugs.debian.org/1128127
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -161,7 +161,7 @@ else()
- endif()
-
- # Find Boost for tests and utilities
--find_package(Boost REQUIRED COMPONENTS filesystem system random program_options unit_test_framework)
-+find_package(Boost REQUIRED COMPONENTS filesystem random program_options unit_test_framework)
- find_package(pugixml CONFIG REQUIRED)
- find_package(FFTW COMPONENTS FLOAT_LIB)
-
=====================================
debian/patches/series
=====================================
@@ -4,4 +4,3 @@ remove-travis-build-status.patch
add_static_lib.patch
locale.patch
struct-padding.patch
-libboost1.90.patch
=====================================
debian/rules
=====================================
@@ -27,12 +27,12 @@ override_dh_install-arch:
find debian/tmp -name ismrmrd.xsd -delete
dh_install -a
d-shlibmove --commit \
- --multiarch \
- --devunversioned \
- --exclude-la \
- --movedev debian/tmp/usr/lib/*/cmake usr/lib/$(DEB_HOST_MULTIARCH) \
- --movedev debian/tmp/usr/include usr \
- debian/tmp/usr/lib/*/*.so
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ --movedev debian/tmp/usr/lib/*/cmake usr/lib/$(DEB_HOST_MULTIARCH) \
+ --movedev debian/tmp/usr/include usr \
+ debian/tmp/usr/lib/*/*.so
find debian -name "lib*.la" -delete
override_dh_auto_install-indep:
@@ -46,5 +46,5 @@ override_dh_compress:
dh_compress --exclude=examples
override_dh_missing-arch:
- find debian/tmp -type f \( -name '*.m' -o -name 'ismrmrd_c_example' \) -delete
+ find debian/tmp -type f \( -name '*.m' -o -name 'ismrmrd_c_example' \) -delete
dh_missing -a
=====================================
docker/build-and-test-variant.sh
=====================================
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# Parse command-line argument
+if [ $# -ne 1 ]; then
+ echo "Usage: $0 [static|cpp98]" >&2
+ echo " static - Build and test static variant" >&2
+ echo " cpp98 - Build and test C++98 variant" >&2
+ exit 1
+fi
+
+variant="$1"
+
+# Dockerfile is in the root director one level up from this script
+dockerfile="$(dirname "${BASH_SOURCE[0]}")/../Dockerfile.build-variants"
+context="$(dirname "${BASH_SOURCE[0]}")/.."
+
+case "$variant" in
+ "static")
+ echo "Building and testing static variant..."
+ docker build -f "$dockerfile" "$context" \
+ --build-arg UBUNTU_VARIANT=noble \
+ --build-arg CXX_STANDARD=17 \
+ --build-arg BUILD_STATIC=On \
+ -t ismrmrd-static
+
+ test_command="set -euo pipefail \
+ && export PATH=$PATH:/opt/package/bin \
+ && test -f /opt/package/lib/libismrmrd.a \
+ && ! test -e /opt/package/lib/libismrmrd.so \
+ && ismrmrd_generate_cartesian_shepp_logan -o testdata.h5 \
+ && ismrmrd_hdf5_to_stream -i testdata.h5 --use-stdout \
+ | ismrmrd_stream_recon_cartesian_2d --use-stdin --use-stdout \
+ | ismrmrd_stream_to_hdf5 --use-stdin -o result.h5"
+ docker run --rm ismrmrd-static /bin/bash -c "$test_command"
+ ;;
+
+ "cpp98")
+ echo "Building and testing C++98 variant..."
+ docker build -f "$dockerfile" "$context" \
+ --build-arg UBUNTU_VARIANT=jammy \
+ --build-arg CXX_STANDARD=98 \
+ --build-arg BUILD_STATIC=Off \
+ -t ismrmrd-cpp98
+
+ test_command="set -euo pipefail \
+ && export PATH=$PATH:/opt/package/bin \
+ && ismrmrd_generate_cartesian_shepp_logan -o testdata.h5 \
+ && ismrmrd_hdf5_to_stream -i testdata.h5 --use-stdout \
+ | ismrmrd_stream_recon_cartesian_2d --use-stdin --use-stdout \
+ | ismrmrd_stream_to_hdf5 --use-stdin -o result.h5"
+ docker run --rm ismrmrd-cpp98 /bin/bash -c "$test_command"
+ ;;
+
+ *)
+ echo "Error: Invalid argument '$variant'. Must be either 'static' or 'cpp98'." >&2
+ echo "Usage: $0 [static|cpp98]" >&2
+ exit 1
+ ;;
+esac
=====================================
docker/test-docker-images.sh → docker/test-images.sh
=====================================
=====================================
environment.yml
=====================================
@@ -1,21 +1,18 @@
name: ismrmrd
channels:
- conda-forge
- - defaults
dependencies:
- - boost=1.80.0
- - cmake=3.21.3 # dev
- - fftw=3.3.9
- - gcc_linux-64=11.2.0 # dev
- - gdb=11.1 # dev
- - gxx_linux-64=11.2.0 # dev
- - h5py=3.2.1 # dev
- - hdf5=1.10.6
- - matplotlib=3.4.3 # dev
- - ninja=1.10.2 # dev
- - numpy=1.22.1 # dev
- - pugixml=1.12.1
- - pyfftw=0.12.0 # dev
- - python=3.9 # dev
- - scipy=1.7.1 # dev
- - xsdata=22.2 # dev
+ - boost=1.84.0
+ - cmake=4.2.2 # dev
+ - doxygen=1.13.2 # dev
+ - fftw=3.3.10
+ - gcc_linux-64=15.2.0 # dev
+ - gdb=17.1 # dev
+ - gxx_linux-64=15.2.0 # dev
+ - h5py=3.15.1 # dev
+ - hdf5=1.14.6
+ - just=1.46.0 # dev
+ - ninja=1.13.2 # dev
+ - numpy=2.4.1 # dev
+ - pugixml=1.15
+ - python=3.13.7 # dev
=====================================
justfile
=====================================
@@ -0,0 +1,49 @@
+set shell := ['bash', '-ceuo', 'pipefail']
+
+cpp_version := "17"
+build_type := "RelWithDebInfo"
+
+ at default: test
+
+ at all: test build-docs build-docker build-static build-cpp98 build-conda
+
+ at configure:
+ mkdir -p build; \
+ cd build; \
+ cmake -GNinja \
+ -D CMAKE_BUILD_TYPE={{ build_type }} \
+ -D CMAKE_CXX_STANDARD={{ cpp_version }} \
+ -D CMAKE_INSTALL_PREFIX=$(conda info --json | jq -r .default_prefix) \
+ ..
+
+ at autoconfigure:
+ if [ ! -f "build/build.ninja" ]; then \
+ echo "Ninja file not found. Running cmake..."; \
+ just configure; \
+ fi
+
+ at build: autoconfigure
+ cd build && ninja
+
+ at test: build
+ cd build/tests && ./test_ismrmrd
+
+ at install: test
+ cd build && ninja install
+
+ at build-docker:
+ ./docker/build-images.sh; \
+ ./docker/test-images.sh
+
+ at build-static:
+ ./docker/build-and-test-variant.sh static
+
+ at build-cpp98:
+ ./docker/build-and-test-variant.sh cpp98
+
+ at build-docs: autoconfigure
+ cd build && ninja doc
+
+ at build-conda:
+ bash -il ./conda/setup-conda-build.sh; \
+ cd conda && ./package.sh
=====================================
vcpkg.json
=====================================
@@ -1,7 +1,7 @@
{
"$schema": "https://raw.githubusercontent.com/microsoft/vcpkg/master/scripts/vcpkg.schema.json",
"name": "ismrmrd",
- "version": "1.14.3",
+ "version": "1.15.0",
"dependencies": [
{
"name": "hdf5",
View it on GitLab: https://salsa.debian.org/med-team/ismrmrd/-/compare/c24406d85e9b6ab9c9c30ed689405cd758dea0c7...bedd993f42b99488da5fe818e0991b5649bbb7a7
--
View it on GitLab: https://salsa.debian.org/med-team/ismrmrd/-/compare/c24406d85e9b6ab9c9c30ed689405cd758dea0c7...bedd993f42b99488da5fe818e0991b5649bbb7a7
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