From a8ba602415e9a044a30aa67e9cf81ac2f7c97113 Mon Sep 17 00:00:00 2001 From: Hui Xue Date: Mon, 5 Aug 2024 23:23:41 +0000 Subject: [PATCH 1/6] update for ismrmrd 1p14p1 --- CMakeLists.txt | 4 ++-- conda/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index f3c85f4..6219115 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -18,7 +18,7 @@ message(STATUS "Looking for packages in : ${CMAKE_PREFIX_PATH}") #VERSIONING set(SIEMENS_TO_ISMRMRD_VERSION_MAJOR 1) set(SIEMENS_TO_ISMRMRD_VERSION_MINOR 2) -set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 11) +set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 12) set(SIEMENS_TO_ISMRMRD_VERSION_STRING ${SIEMENS_TO_ISMRMRD_VERSION_MAJOR}.${SIEMENS_TO_ISMRMRD_VERSION_MINOR}.${SIEMENS_TO_ISMRMRD_VERSION_PATCH}) # Generate the converter_version.h header file @@ -67,7 +67,7 @@ set(Boost_USE_STATIC_RUNTIME OFF) find_package(Boost COMPONENTS system thread program_options filesystem timer REQUIRED) -find_package(ISMRMRD 1.8.0 REQUIRED) +find_package(ISMRMRD 1.14.1 REQUIRED) find_package(HDF5 REQUIRED COMPONENTS C) include_directories( ${ISMRMRD_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR} ) diff --git a/conda/meta.yaml b/conda/meta.yaml index 6875e20..dce1b77 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -17,13 +17,13 @@ requirements: - cmake>=3.20.0 - gcc_linux-64>=9.0.0 # [linux64] - gxx_linux-64>=9.0.0 # [linux64] - - ismrmrd=1.13.7 + - ismrmrd=1.14.1 - libxml2=2.9 - libxslt=1.1 - ninja=1.10.* run: - - ismrmrd=1.13.7 + - ismrmrd=1.14.1 - boost {{ boost }} - libxml2=2.9 - libxslt=1.1 From f6c0dc58e72252d3932b544639e1dbc337e9ca25 Mon Sep 17 00:00:00 2001 From: Hui Xue Date: Mon, 5 Aug 2024 23:31:36 +0000 Subject: [PATCH 2/6] upgrade depencies version --- Dockerfile | 2 +- conda/meta.yaml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 17f22bf..32a926e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,7 @@ RUN cd /usr/local/lib && tar -czvf libismrmrd.tar.gz libismrmrd* # ----- Start another clean build without all of the build dependencies of siemens_to_ismrmrd ----- FROM ubuntu:latest -RUN apt-get update && apt-get install -y --no-install-recommends libxslt1.1 libhdf5-103 && apt-get clean && rm -rf /var/lib/apt/lists/* +RUN apt-get update && apt-get install -y --no-install-recommends libxslt1.1 libhdf5 && apt-get clean && rm -rf /var/lib/apt/lists/* # Copy siemens_to_ismrmrd from last stage and re-add necessary dependencies COPY --from=ismrmrd_base /usr/local/bin/siemens_to_ismrmrd /usr/local/bin/siemens_to_ismrmrd diff --git a/conda/meta.yaml b/conda/meta.yaml index dce1b77..9fc4d8d 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -18,14 +18,14 @@ requirements: - gcc_linux-64>=9.0.0 # [linux64] - gxx_linux-64>=9.0.0 # [linux64] - ismrmrd=1.14.1 - - libxml2=2.9 + - libxml2=2.13.1 - libxslt=1.1 - - ninja=1.10.* + - ninja=1.12.* run: - ismrmrd=1.14.1 - boost {{ boost }} - - libxml2=2.9 + - libxml2=2.13.1 - libxslt=1.1 about: From 59d131b90f742841724be5a9825e156709974a5c Mon Sep 17 00:00:00 2001 From: Hui Xue Date: Mon, 5 Aug 2024 23:33:11 +0000 Subject: [PATCH 3/6] upgrade depencies version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 32a926e..62230a7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,7 @@ RUN cd /usr/local/lib && tar -czvf libismrmrd.tar.gz libismrmrd* # ----- Start another clean build without all of the build dependencies of siemens_to_ismrmrd ----- FROM ubuntu:latest -RUN apt-get update && apt-get install -y --no-install-recommends libxslt1.1 libhdf5 && apt-get clean && rm -rf /var/lib/apt/lists/* +RUN apt-get update && apt-get install -y --no-install-recommends libxslt1.1 libhdf5-dev && apt-get clean && rm -rf /var/lib/apt/lists/* # Copy siemens_to_ismrmrd from last stage and re-add necessary dependencies COPY --from=ismrmrd_base /usr/local/bin/siemens_to_ismrmrd /usr/local/bin/siemens_to_ismrmrd From 4210ca5633f8079b641237f75990901569483de2 Mon Sep 17 00:00:00 2001 From: Hui Xue Date: Mon, 5 Aug 2024 23:51:53 +0000 Subject: [PATCH 4/6] update ismrmrd --- Dockerfile | 2 +- dependencies/ismrmrd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 62230a7..e178a81 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ FROM ubuntu:latest as ismrmrd_base ARG DEBIAN_FRONTEND=noninteractive ENV TZ=America/Chicago -RUN apt-get update && apt-get install -y git cmake g++ libhdf5-dev libxml2-dev libxslt1-dev libboost-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-thread-dev libboost-timer-dev libboost-program-options-dev +RUN apt-get update && apt-get install -y git cmake g++ libhdf5-dev libxml2-dev libxslt1-dev libboost-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-thread-dev libboost-timer-dev libboost-program-options-dev libpugixml-dev RUN mkdir -p /opt/code diff --git a/dependencies/ismrmrd b/dependencies/ismrmrd index ea029d0..0546165 100644 --- a/dependencies/ismrmrd +++ b/dependencies/ismrmrd @@ -1 +1 @@ -f9e38ed8cda6428839005c060579d3dfdb043515 \ No newline at end of file +4037c41fcdcb8870234baaeb46ce4848aac1579a \ No newline at end of file From e0263edeb82c19a42f13aec681618a1a2b0dfd6b Mon Sep 17 00:00:00 2001 From: Joe Naegele Date: Tue, 6 Aug 2024 17:21:08 +0000 Subject: [PATCH 5/6] Fix Conda CI workflow --- .github/workflows/siemens_to_ismrmrd_conda.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/siemens_to_ismrmrd_conda.yml b/.github/workflows/siemens_to_ismrmrd_conda.yml index ff4f931..d5681df 100644 --- a/.github/workflows/siemens_to_ismrmrd_conda.yml +++ b/.github/workflows/siemens_to_ismrmrd_conda.yml @@ -5,16 +5,17 @@ on: release: types: - created + workflow_dispatch: jobs: build-conda-packages: strategy: matrix: - os: [ubuntu-latest, macos-latest] + os: [ubuntu-latest, macos-13] runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b - - uses: conda-incubator/setup-miniconda@e81abac10ce2c37423b54eae5af93aa3b4d3475c + - uses: actions/checkout@v4 + - uses: conda-incubator/setup-miniconda@v3 with: activate-environment: siemens-to-ismrmrd-build environment-file: conda/environment.yml From 5c52ee23ef4afa7434b559d6e107114d0b102b39 Mon Sep 17 00:00:00 2001 From: Hui Xue Date: Tue, 6 Aug 2024 20:11:35 +0000 Subject: [PATCH 6/6] loose libxml2 version --- conda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 9fc4d8d..995f99b 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -18,14 +18,14 @@ requirements: - gcc_linux-64>=9.0.0 # [linux64] - gxx_linux-64>=9.0.0 # [linux64] - ismrmrd=1.14.1 - - libxml2=2.13.1 + - libxml2>=2.9 - libxslt=1.1 - ninja=1.12.* run: - ismrmrd=1.14.1 - boost {{ boost }} - - libxml2=2.13.1 + - libxml2>=2.9 - libxslt=1.1 about: