From 7b5e56ffb9078d0c3ccbdbb5bdb89db3a2bf9307 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 15 Mar 2023 08:18:12 +0000
Subject: [PATCH 01/28] Update TomoPhantom and CCPi regularisation tags

closes #812
---
 version_config.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/version_config.cmake b/version_config.cmake
index 0c6dd3b5..a93e3a63 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -132,7 +132,7 @@ set(DEFAULT_astra-toolbox_TAG origin/master)
 
 ## TomoPhantom
 set(DEFAULT_TomoPhantom_URL https://github.com/dkazanc/TomoPhantom )
-set(DEFAULT_TomoPhantom_TAG v1.4)
+set(DEFAULT_TomoPhantom_TAG v2.0.0)
 
 ## NiftyPET
 set(DEFAULT_NiftyPET_URL https://github.com/pjmark/NIPET )
@@ -159,7 +159,7 @@ set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL.git)
 set(DEFAULT_CIL_TAG a6062410028c9872c5b355be40b96ed1497fed2a)
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git)
-set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v21.0.0")
+set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v22.0.0")
 
 # CERN ROOT
 set(DEFAULT_ROOT_URL https://github.com/root-project/root)

From dbca2368bc3c5dc6a42a5cc5fd3c7acb019596cd Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 20 Jul 2023 14:57:44 +0100
Subject: [PATCH 02/28] disable GPU tests

---
 SuperBuild/External_CCPi-Regularisation-Toolkit.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake b/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
index d3643c5b..2124a360 100644
--- a/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
+++ b/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
@@ -98,8 +98,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
     set(${proj}_ROOT        ${${proj}_SOURCE_DIR})
     set(${proj}_INCLUDE_DIR ${${proj}_SOURCE_DIR})
-    add_test(NAME CIL_REGULARISATION_TEST_1
-             COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -s test -p test_*.py
+    add_test(NAME CIL_REGULARISATION_TEST_CPU
+             COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -s test -p test_CPU_*.py
     WORKING_DIRECTORY ${${proj}_SOURCE_DIR})
 
   else()

From 21ce6de18f2c175f85644d2889f8cc67fed94f8b Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 21 Jun 2023 11:51:41 +0100
Subject: [PATCH 03/28] [docker] remove obsolete copying of gadgetron.xml

Fixes #815
---
 CHANGES.md        | 1 +
 docker/service.sh | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 6ffa497b..5827bc1a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -6,6 +6,7 @@
      most build files will be removed in the docker image.
    - introduce `RUN_CTESTS` variable. If set to 1 (which is the default),
      the CTests will be run while building the image.
+   - remove obsolete copying of gadgetron.xml
 - Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev, 
   libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev. 
 - Added SuperBuild project dependency: range-v3, RocksDB, Date, mrd-storage-server
diff --git a/docker/service.sh b/docker/service.sh
index 28560d60..a7917f9b 100755
--- a/docker/service.sh
+++ b/docker/service.sh
@@ -31,8 +31,6 @@ stop_service()
 pushd $SIRF_PATH/../..
 
 echo "start gadgetron"
-GCONFIG=./INSTALL/share/gadgetron/config/gadgetron.xml
-[ -f "$GCONFIG" ] || cp "$GCONFIG".example "$GCONFIG"
 [ -f ./INSTALL/bin/gadgetron ] \
   && ./INSTALL/bin/gadgetron >& ~/gadgetron.log&
 

From 7e285c303647b680db92555509b9f41c93338bb3 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 21 Jun 2023 17:51:35 +0100
Subject: [PATCH 04/28] [GHA] clean-up some disk space first

---
 .github/workflows/GHA_increase_disk_space.sh | 23 +++++++++++++++
 .github/workflows/c-cpp.yml                  | 13 ++++++++
 .github/workflows/docker_build.yml           | 31 ++++++++++++--------
 3 files changed, 54 insertions(+), 13 deletions(-)
 create mode 100755 .github/workflows/GHA_increase_disk_space.sh

diff --git a/.github/workflows/GHA_increase_disk_space.sh b/.github/workflows/GHA_increase_disk_space.sh
new file mode 100755
index 00000000..292a4cf4
--- /dev/null
+++ b/.github/workflows/GHA_increase_disk_space.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+df -h
+# locations from the internet, e.g. https://github.com/easimon/maximize-build-space
+# saves about 2GB
+if [ -d /usr/share/dotnet ]; then
+    echo removing dotnet
+    sudo rm -rf /usr/share/dotnet
+fi
+# saves about 10 GB
+if [ -d "$AGENT_TOOLSDIRECTORY" ]; then
+    echo removing agent_tools
+    sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+fi
+# saves about 10 GB
+if [ -d /usr/local/lib/android ]; then
+    echo removing android files
+    sudo rm -rf /usr/local/lib/android
+fi
+if [ -d /opt/ghc ]; then
+    echo removing android files
+    sudo rm -rf /opt/ghc
+fi
+df -h
diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 7d3bdb73..ffb2eee6 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -72,6 +72,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+
+    - name: disk space
+      shell: bash
+      run: |
+          case ${{matrix.os}} in
+            (ubuntu* | macOS*)
+              sudo .github/workflows/GHA_increase_disk_space.sh
+              ;;
+            (windows*)
+              # no idea what to do here
+              ;;
+           esac
+
     - name: install_dependencies
       run: 
           cd docker;
diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
index c604d524..46965f20 100644
--- a/.github/workflows/docker_build.yml
+++ b/.github/workflows/docker_build.yml
@@ -24,11 +24,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       
-      - name: Install docker and pre-reqs
+      - name: Install docker and pre-reqs and clean some disk-space
         shell: bash -l {0}
         run: |
-         # make the file runnable
-         sudo bash .github/workflows/install_docker.sh
+         sudo .github/workflows/install_docker.sh
+         sudo .github/workflows/GHA_increase_disk_space.sh
          
       - name: Build docker core image
         # Builds docker image from Docker file.
@@ -56,10 +56,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Install docker and pre-reqs
+      - name: Install docker and pre-reqs and clean some disk-space
         shell: bash -l {0}
         run: |
-         .github/workflows/install_docker.sh
+         sudo .github/workflows/install_docker.sh
+         sudo .github/workflows/GHA_increase_disk_space.sh
           
       - name: Build docker core-gpu image
         # Builds docker image from Docker file.
@@ -89,10 +90,11 @@ jobs:
         tag: ['latest', 'devel']
     steps:
       - uses: actions/checkout@v3
-      - name: Install docker and pre-reqs
+      - name: Install docker and pre-reqs and clean some disk-space
         shell: bash -l {0}
         run: |
-         .github/workflows/install_docker.sh
+         sudo .github/workflows/install_docker.sh
+         sudo .github/workflows/GHA_increase_disk_space.sh
           
       - name: Download artifact of core image
         uses: actions/download-artifact@v3
@@ -136,10 +138,11 @@ jobs:
       needs: build-core-gpu
       steps:
         - uses: actions/checkout@v3
-        - name: Install docker and pre-reqs
+        - name: Install docker and pre-reqs and clean some disk-space
           shell: bash -l {0}
           run: |
-           .github/workflows/install_docker.sh
+           sudo .github/workflows/install_docker.sh
+           sudo .github/workflows/GHA_increase_disk_space.sh
 
         - name: Download artifact of core image
           uses: actions/download-artifact@v3
@@ -189,10 +192,11 @@ jobs:
         tag: ['service', 'devel-service']
     steps:
       - uses: actions/checkout@v3
-      - name: Install docker and pre-reqs
+      - name: Install docker and pre-reqs and clean some disk-space
         shell: bash -l {0}
         run: |
-         .github/workflows/install_docker.sh
+         sudo .github/workflows/install_docker.sh
+         sudo .github/workflows/GHA_increase_disk_space.sh
          
       - name: setup variables
         shell: bash -l {0}
@@ -256,10 +260,11 @@ jobs:
   #       tag: ['core', 'latest', 'devel', 'service', 'devel-service', 'core-gpu', 'service-gpu']
   #   steps:
   #     - uses: actions/checkout@v3
-  #     - name: Install docker and pre-reqs
+  #     - name: Install docker and pre-reqs and clean some disk-space
   #       shell: bash -l {0}
   #       run: |
-  #        .github/workflows/install_docker.sh
+  #        sudo .github/workflows/install_docker.sh
+  #        sudo .github/workflows/GHA_increase_disk_space.sh
           
   #     - name: Download artifact of image
   #       uses: actions/download-artifact@v3

From a9e5d55c287ae0348cc33d22a99efa180a3d22bb Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Thu, 22 Jun 2023 08:16:56 +0100
Subject: [PATCH 05/28] [GHA] clear more docker images before saving

---
 .github/workflows/docker_build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
index 46965f20..dc525771 100644
--- a/.github/workflows/docker_build.yml
+++ b/.github/workflows/docker_build.yml
@@ -240,7 +240,8 @@ jobs:
         run: |
           # first we must delete image that is no longer needed, to save space:
           docker rmi synerbi/sirf:${{ env.prereq_image_name }}
-          yes | docker system prune
+          # get rid of everything over 2 days old
+          docker system prune -a --filter "until=2d"
           docker image ls
           docker save synerbi/sirf:service | gzip > ${{ matrix.tag }}.tar.gz 
           

From d46a29620fdd4fb294ff447c21e6da0dde9f74f1 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 11 Jul 2023 17:33:42 +0100
Subject: [PATCH 06/28] use environment.yml from SIRF-Exercise

Uses environment.yml from SIRF-Exercises if using conda, and it is found. Defaults to requirements.txt if not found or not using conda.
---
 docker/user_service-ubuntu.sh | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/docker/user_service-ubuntu.sh b/docker/user_service-ubuntu.sh
index c490c619..3f5f2952 100755
--- a/docker/user_service-ubuntu.sh
+++ b/docker/user_service-ubuntu.sh
@@ -28,17 +28,27 @@ fi
 
 #install SIRF-Exercises requirements
 cd $INSTALL_DIR/SIRF-Exercises
-if [ -f requirements.txt ]; then
-  cat requirements.txt
-  if [ "$PYTHON" = "miniconda" ]; then
-  # installing the requirements.txt with mamba requires some cleaning of the requirements.txt
-  # Also the requirements.txt contains some packages that are not found on conda-forge, i.e. brainweb
-  # Therefore, these need to be installed by pip. 
-  # This is handled by the install-sirf-exercises-dep.py script
-    python ~/install-sirf-exercises-dep.py requirements.txt
+if [ "$PYTHON" = "miniconda" ]; then
+  if [ -f environment.yml ]; then
+    mamba env update --file environment.yml
   else
-  # Otherwise, just install the requirements.txt with pip
+    if [ -f requirements.txt ]; then
+      cat requirements.txt
+      # installing the requirements.txt with mamba requires some cleaning of the requirements.txt
+      # Also the requirements.txt contains some packages that are not found on conda-forge, i.e. brainweb
+      # Therefore, these need to be installed by pip. 
+      # This is handled by the install-sirf-exercises-dep.py script
+      python ~/install-sirf-exercises-dep.py requirements.txt
+    else
+      echo "SIRF-Exercises requirements: did not find requirements.txt nor environment.yml. Skipping"
+    fi
+  fi
+else
+  if [ -f requirements.txt ]; then
+    # just install the requirements.txt with pip
     ${PYTHON} -m pip install -U -r requirements.txt
+  else
+    echo "SIRF-Exercises requirements: did not find requirements.txt. Skipping"
   fi
 fi
 

From 2e295c7fe881f3c354fcca05896e7ee096688ef7 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 12 Jul 2023 09:20:25 +0100
Subject: [PATCH 07/28] Update CHANGES.md

---
 CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.md b/CHANGES.md
index 5827bc1a..ef9c8d48 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -7,6 +7,7 @@
    - introduce `RUN_CTESTS` variable. If set to 1 (which is the default),
      the CTests will be run while building the image.
    - remove obsolete copying of gadgetron.xml
+   - Installing requirements for SIRF-Exercises uses its environment.yml or requirements.txt depending on settings.
 - Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev, 
   libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev. 
 - Added SuperBuild project dependency: range-v3, RocksDB, Date, mrd-storage-server

From 42e57717083b32f2f3a4e13ec779a272e09913fd Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Fri, 14 Jul 2023 23:14:13 +0100
Subject: [PATCH 08/28] Use value of BUILD_TESTING_Gadgetron

we forced BUILD_TESTING=ON for some reason. Now we use the value
of our own CMake variable

Fixes #824
---
 SuperBuild/External_Gadgetron.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index 816af779..8bb69a3f 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -47,7 +47,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
   # Gadgetron only adds tests if (GTEST_FOUND AND ARMADILLO_FOUND)
   # but that's currently always the case.
-  # Default to on, as we cannot disable it, and they're quite fast
+  # Default to on, as they're quite fast
   option(BUILD_TESTING_${proj} "Build tests for ${proj}" ON)
 
   #message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
@@ -135,7 +135,7 @@ endif()
       -DUSE_MKL:BOOL=${${proj}_USE_MKL}
       -DUSE_CUDA:BOOL=${${proj}_USE_CUDA}
       -DUSE_OPENMP:BOOL=${${proj}_ENABLE_OPENMP}
-      -DBUILD_TESTING:BOOL=ON
+      -DBUILD_TESTING:BOOL=${BUILD_TESTING_${proj}}
       )
 
 

From 523d2b6571b49a568f5ac7f496f53c93006f0a38 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Fri, 14 Jul 2023 23:15:21 +0100
Subject: [PATCH 09/28] remove python requirement for patching Gadgetron

we're no longer patching it
---
 SuperBuild/External_Gadgetron.cmake | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index 8bb69a3f..a9a49403 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -107,16 +107,6 @@ endif()
     set(${proj}_ENABLE_OPENMP OFF)
   endif()
 
-  # require to have access to Python for patching
-  if (NOT PYTHON_EXECUTABLE)
-    if (${CMAKE_VERSION} VERSION_LESS "3.12")
-      find_package(PythonInterp REQUIRED)
-    else()
-      find_package(Python COMPONENTS Interpreter REQUIRED)
-      set (PYTHON_EXECUTABLE ${Python_EXECUTABLE})
-    endif()
-  endif()
-
   # Sets ${proj}_URL_MODIFIED and ${proj}_TAG_MODIFIED
   SetGitTagAndRepo("${proj}")
   set (${proj}_CMAKE_ARGS 

From 053bdae2a2fff75d11c82d9bd0ea8f85d3697a57 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Fri, 14 Jul 2023 23:17:55 +0100
Subject: [PATCH 10/28] remove CMAKE_INCLUDE/LIBRARY_PATH in Gadgetron

should never have been here. The CMAKE_INCLUDE_PATH should
not point to CMAKE_INSTALL_PREFIX/include, as it should be
used for CMake files
---
 SuperBuild/External_Gadgetron.cmake | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index a9a49403..0f7ba7e4 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -50,10 +50,6 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   # Default to on, as they're quite fast
   option(BUILD_TESTING_${proj} "Build tests for ${proj}" ON)
 
-  #message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
-  set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
-  set(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} ${SUPERBUILD_INSTALL_DIR})
-
   # BLAS
   find_package(BLAS)
 
@@ -113,8 +109,6 @@ endif()
       -DBUILD_PYTHON_SUPPORT:BOOL=${${proj}_BUILD_PYTHON_SUPPORT}
       -DBUILD_MATLAB_SUPPORT:BOOL=${${proj}_BUILD_MATLAB_SUPPORT}
       -DCMAKE_PREFIX_PATH:PATH=${SUPERBUILD_INSTALL_DIR}
-      -DCMAKE_LIBRARY_PATH:PATH=${SUPERBUILD_INSTALL_DIR}/lib
-      -DCMAKE_INCLUDE_PATH:PATH=${SUPERBUILD_INSTALL_DIR}/include
       -DCMAKE_INSTALL_PREFIX:PATH=${${proj}_INSTALL_DIR}
       ${Boost_CMAKE_ARGS}
       ${PYTHONLIBS_CMAKE_ARGS}

From 59c9f4bbdc0a4edbac00aabd7b3cb602a3fb2ff7 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 9 Aug 2023 20:04:31 +0100
Subject: [PATCH 11/28] fix mamba install

- fixes #826
---
 docker/user_python-ubuntu.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docker/user_python-ubuntu.sh b/docker/user_python-ubuntu.sh
index 1fb8463d..248c5613 100755
--- a/docker/user_python-ubuntu.sh
+++ b/docker/user_python-ubuntu.sh
@@ -26,16 +26,16 @@ fi
 # Python
 case "$PYTHON" in
 miniconda)
-  # miniconda
-  curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh
+  #curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh
+  curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh > miniconda.sh
   echo -e "\nyes\n${INSTALL_DIR}\nno" | bash miniconda.sh
   rm miniconda.sh
   source "$INSTALL_DIR"/bin/activate
-  conda config --add channels conda-forge
+  #conda config --add channels conda-forge
   # https://github.com/conda/conda/issues/6030
   #conda update -c conda-forge -y conda
-  conda install -c conda-forge -y mamba
-  mamba update -c conda-forge -y setuptools pip
+  # https://github.com/SyneRBI/SIRF-SuperBuild/issues/826
+  #conda install -c conda-forge -c defaults -y mamba
   ;;
 *python*)
   # virtualenv

From 500448893e0c20d697921a57e8111517c5e5a831 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 9 Aug 2023 20:55:07 +0100
Subject: [PATCH 12/28] suppress pip warning

---
 docker/requirements.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/requirements.yml b/docker/requirements.yml
index 7ffa8204..141f8471 100644
--- a/docker/requirements.yml
+++ b/docker/requirements.yml
@@ -31,6 +31,7 @@ dependencies:
   - ipp-devel
   - ipp-include
   - tigre
+  - pip
   - pip:
     - git+https://github.com/data-exchange/dxchange.git  # CIL
     - git+https://github.com/ismrmrd/ismrmrd-python-tools.git@master#egg=ismrmrd-python-tools

From cfc92dd8fea2831402f3866faa633da118968601 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 20 Jul 2023 10:05:06 +0100
Subject: [PATCH 13/28] Update version_config.cmake

---
 version_config.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/version_config.cmake b/version_config.cmake
index 697a00b0..8a65f2d6 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -219,7 +219,7 @@ if (DEVEL_BUILD)
   
 
 else()
-  set(DEFAULT_SIRF_TAG v3.4.0)
+  set(DEFAULT_SIRF_TAG v3.5.0)
   
   ## STIR
   set(DEFAULT_STIR_URL https://github.com/UCL/STIR )

From 92e0da624122d49aaa5e62dec530b9c021e79e7c Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 20 Jul 2023 10:06:39 +0100
Subject: [PATCH 14/28] Update CHANGES.md

---
 CHANGES.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index ef9c8d48..c98229ab 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,6 +1,6 @@
 # ChangeLog
 
-## vx.x.x
+## v3.5.0
 - docker image updates
    - introduce `REMOVE_BUILD_FILES` variable. If set to 1 (which is the default),
      most build files will be removed in the docker image.
@@ -17,6 +17,7 @@
   - range-v3: 0.12.0
   - siemens_to_ismrmrd: 8bb8b08f53ce73c2de9ba5f47f1532f96292d92b
   - ISMRMRD: v1.13.2
+  - SIRF: v3.5.0
   
 ## v3.4.0
 - Removed CIL-ASTRA as it has been merged into CIL code base.

From 998e31be472da59fd8b206c9980d20f40d100349 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 20 Jul 2023 10:07:14 +0100
Subject: [PATCH 15/28] Update VM_version.txt

---
 VirtualBox/VM_version.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VirtualBox/VM_version.txt b/VirtualBox/VM_version.txt
index 18091983..1545d966 100644
--- a/VirtualBox/VM_version.txt
+++ b/VirtualBox/VM_version.txt
@@ -1 +1 @@
-3.4.0
+3.5.0

From fef68c6144043f3d599023c8400ce6012db27adf Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 20 Jul 2023 10:07:59 +0100
Subject: [PATCH 16/28] Update Vagrantfile

---
 VirtualBox/vagrant/Vagrantfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VirtualBox/vagrant/Vagrantfile b/VirtualBox/vagrant/Vagrantfile
index 7a3e4c6f..8d70ba52 100644
--- a/VirtualBox/vagrant/Vagrantfile
+++ b/VirtualBox/vagrant/Vagrantfile
@@ -74,7 +74,7 @@ Vagrant.configure("2") do |config|
        "--medium", "emptydrive"
        ]
 
-	vb.name = ENV["VB_NAME"] || "SIRF 3.4.0"
+	vb.name = ENV["VB_NAME"] || "SIRF 3.5.0"
     vb.customize ["modifyvm", :id, 
 	          "--clipboard", "bidirectional",
                   '--graphicscontroller', 'vmsvga',

From 84798be7e43db897935f6b44954ed4f23fda04f6 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 10 Aug 2023 08:46:27 +0100
Subject: [PATCH 17/28] disable CCPi regularisation unittests of CIL

---
 SuperBuild/External_CIL.cmake | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/SuperBuild/External_CIL.cmake b/SuperBuild/External_CIL.cmake
index 74fa0a8d..472e5dab 100644
--- a/SuperBuild/External_CIL.cmake
+++ b/SuperBuild/External_CIL.cmake
@@ -116,9 +116,10 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   add_test(NAME CIL_FRAMEWORK_TESTS_9
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_Operator.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
-  add_test(NAME CIL_FRAMEWORK_TESTS_10
-           COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_PluginsRegularisation.py
-           WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+  # temporarily disable regularisation toolkit tests due to #832
+  # add_test(NAME CIL_FRAMEWORK_TESTS_10
+  #         COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_PluginsRegularisation.py
+  #         WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
   add_test(NAME CIL_FRAMEWORK_TESTS_11
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_quality_measures.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)

From 2c1f7f8fe26588bf79e1e8040ff7bc57f189f41f Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 10 Aug 2023 08:47:41 +0100
Subject: [PATCH 18/28] disable build of CCPi Regularisation with CIL by
 default

---
 SuperBuild.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index 96a93a7e..981c9670 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -317,7 +317,7 @@ if ("${PYTHON_STRATEGY}" STREQUAL "CONDA")
   set (BUILD_CIL OFF)
 endif()
 if (BUILD_CIL)
-  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL CCPi-Regularisation-Toolkit TomoPhantom)
+  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL TomoPhantom)
 endif()
 if (BUILD_ASTRA)
   list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES astra-python-wrapper)

From cdce88184d522b13171b2aec26c4e34640ee4ad2 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 10 Aug 2023 08:50:30 +0100
Subject: [PATCH 19/28] [ci skip] Update CHANGES.md

---
 CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.md b/CHANGES.md
index c98229ab..f8fed16b 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,6 +1,7 @@
 # ChangeLog
 
 ## v3.5.0
+- Temporarily disable CCPi-Regularisation due to #832
 - docker image updates
    - introduce `REMOVE_BUILD_FILES` variable. If set to 1 (which is the default),
      most build files will be removed in the docker image.

From 893a6557cf4c50065c903f35b59242c71561236b Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 10 Aug 2023 09:40:17 +0100
Subject: [PATCH 20/28] remove comments

---
 SuperBuild/External_CIL.cmake | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/SuperBuild/External_CIL.cmake b/SuperBuild/External_CIL.cmake
index 472e5dab..0a9aaf2a 100644
--- a/SuperBuild/External_CIL.cmake
+++ b/SuperBuild/External_CIL.cmake
@@ -116,10 +116,6 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   add_test(NAME CIL_FRAMEWORK_TESTS_9
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_Operator.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
-  # temporarily disable regularisation toolkit tests due to #832
-  # add_test(NAME CIL_FRAMEWORK_TESTS_10
-  #         COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_PluginsRegularisation.py
-  #         WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
   add_test(NAME CIL_FRAMEWORK_TESTS_11
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_quality_measures.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)

From 3fc68fac8110ff1205c420abc0788fd9e1b8412a Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Fri, 21 Jul 2023 09:30:56 +0100
Subject: [PATCH 21/28] [CMAKE] default DISABLE_MATLAB to ON

SIRF Matlab support is out-of-date and could generate conflicts with Python shared libraries.
---
 CHANGES.md       | 5 ++++-
 SuperBuild.cmake | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index f8fed16b..21507512 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -2,6 +2,9 @@
 
 ## v3.5.0
 - Temporarily disable CCPi-Regularisation due to #832
+- CMake/building:
+  - default `DISABLE_MATLAB` to `ON` as SIRF Matlab support is out-of-date and enabling it could
+    generate conflicts with Python shared libraries.
 - docker image updates
    - introduce `REMOVE_BUILD_FILES` variable. If set to 1 (which is the default),
      most build files will be removed in the docker image.
@@ -11,7 +14,7 @@
    - Installing requirements for SIRF-Exercises uses its environment.yml or requirements.txt depending on settings.
 - Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev, 
   libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev. 
-- Added SuperBuild project dependency: range-v3, RocksDB, Date, mrd-storage-server
+- Added SuperBuild project dependencies for Gadgetron: range-v3, RocksDB, Date, mrd-storage-server
 - updated versions:
   - Gadgetron: 42f11bf14b77b16f1ca5bcfbfa435d5ee8cb22a6 (master)
   - RocksDB: 6.26.0
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index 981c9670..8354c71f 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -147,7 +147,7 @@ else()
 endif()
 
 #### MATLAB support
-option(DISABLE_Matlab "Disable building MATLAB support" OFF)
+option(DISABLE_Matlab "Disable building MATLAB support" ON)
 if (DISABLE_Matlab)
   message(STATUS "Matlab support disabled")
 else()

From 160a02ef0e6e0fbe3f533878a7bc5d8833ce843d Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Tue, 15 Aug 2023 14:38:54 +0100
Subject: [PATCH 22/28] remove obsolete version restriction for SciPy

---
 docker/requirements.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/requirements.yml b/docker/requirements.yml
index 141f8471..9f0d69c5 100644
--- a/docker/requirements.yml
+++ b/docker/requirements.yml
@@ -11,7 +11,7 @@ dependencies:
   - pytest
   - pytest-cov
   - numpy        # CIL
-  - scipy=1.7.3  # CIL prevents `GLIBCXX_3.4.30' not found
+  - scipy
   - docopt
   - matplotlib
   - Cython       # CIL

From cfa66b46b61b314d825d4fbcf9908c2bcc15e3fc Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 7 Sep 2023 10:38:23 +0100
Subject: [PATCH 23/28] Add SIRF/CIL integration tests

---
 SuperBuild/External_CIL.cmake | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/SuperBuild/External_CIL.cmake b/SuperBuild/External_CIL.cmake
index 0a9aaf2a..7fb5d092 100644
--- a/SuperBuild/External_CIL.cmake
+++ b/SuperBuild/External_CIL.cmake
@@ -95,9 +95,9 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   add_test(NAME CIL_FRAMEWORK_TESTS_3
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_run_*.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
-  # add_test(NAME CIL_SIRF_TESTS
-	#    COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_SIRF*.py
-  #          WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+  add_test(NAME CIL_SIRF_TESTS
+          COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_SIRF*.py
+          WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
   add_test(NAME CIL_FRAMEWORK_TESTS_4
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_Block_*.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)

From e04bd69bb8773deac13d860e7264c73813c594a2 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 7 Sep 2023 12:13:20 +0100
Subject: [PATCH 24/28] Update CIL version

---
 version_config.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/version_config.cmake b/version_config.cmake
index 8a65f2d6..0bcefb6d 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -148,7 +148,7 @@ set(DEFAULT_JSON_TAG v3.10.4)
 # CCPi CIL
 # minimum supported version of CIL supported is > 22.1.0 or from commit a6062410028c9872c5b355be40b96ed1497fed2a
 set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL.git)
-set(DEFAULT_CIL_TAG a6062410028c9872c5b355be40b96ed1497fed2a)
+set(DEFAULT_CIL_TAG e7e137b97d403576502ffc768e596ec1f66e038a)
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git)
 set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v22.0.0")

From 408a142023af4e0eb09e17e92c7a8758a3756383 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 7 Sep 2023 12:14:06 +0100
Subject: [PATCH 25/28] [ci skip] Update CHANGES.md

---
 CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.md b/CHANGES.md
index 21507512..fd92ffe1 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -22,6 +22,7 @@
   - siemens_to_ismrmrd: 8bb8b08f53ce73c2de9ba5f47f1532f96292d92b
   - ISMRMRD: v1.13.2
   - SIRF: v3.5.0
+  - CIL: e7e137b97d403576502ffc768e596ec1f66e038a
   
 ## v3.4.0
 - Removed CIL-ASTRA as it has been merged into CIL code base.

From 4090d0471dd6b1597947078cd35dab1e2e5bce7d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 7 Sep 2023 13:05:54 +0100
Subject: [PATCH 26/28] Update version_config.cmake

---
 version_config.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/version_config.cmake b/version_config.cmake
index 0bcefb6d..f44a270b 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -148,7 +148,7 @@ set(DEFAULT_JSON_TAG v3.10.4)
 # CCPi CIL
 # minimum supported version of CIL supported is > 22.1.0 or from commit a6062410028c9872c5b355be40b96ed1497fed2a
 set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL.git)
-set(DEFAULT_CIL_TAG e7e137b97d403576502ffc768e596ec1f66e038a)
+set(DEFAULT_CIL_TAG test_SIRF_fix)
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git)
 set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v22.0.0")

From 68f5cecff70fc6d2b3aa9008f29898c4a68ffd96 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 8 Sep 2023 08:19:38 +0100
Subject: [PATCH 27/28] use new CIL hash

---
 CHANGES.md           | 2 +-
 version_config.cmake | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index fd92ffe1..bb8829c9 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -22,7 +22,7 @@
   - siemens_to_ismrmrd: 8bb8b08f53ce73c2de9ba5f47f1532f96292d92b
   - ISMRMRD: v1.13.2
   - SIRF: v3.5.0
-  - CIL: e7e137b97d403576502ffc768e596ec1f66e038a
+  - CIL: 0ba2f8e2935db66ec3dfe8c88e407e8d0eb5609f
   
 ## v3.4.0
 - Removed CIL-ASTRA as it has been merged into CIL code base.
diff --git a/version_config.cmake b/version_config.cmake
index f44a270b..7c98925a 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -148,7 +148,7 @@ set(DEFAULT_JSON_TAG v3.10.4)
 # CCPi CIL
 # minimum supported version of CIL supported is > 22.1.0 or from commit a6062410028c9872c5b355be40b96ed1497fed2a
 set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL.git)
-set(DEFAULT_CIL_TAG test_SIRF_fix)
+set(DEFAULT_CIL_TAG 0ba2f8e2935db66ec3dfe8c88e407e8d0eb5609f)
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git)
 set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v22.0.0")

From d0ed5b6a2388392663cb1e51c5c387089d389d80 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 12 Sep 2023 09:22:20 +0100
Subject: [PATCH 28/28] update changelog [ci skip]

---
 CHANGES.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGES.md b/CHANGES.md
index bb8829c9..d7064056 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -23,6 +23,8 @@
   - ISMRMRD: v1.13.2
   - SIRF: v3.5.0
   - CIL: 0ba2f8e2935db66ec3dfe8c88e407e8d0eb5609f
+  - CCPi-Regularisation: v22.0.0
+  - TomoPhantom: v2.0.0
   
 ## v3.4.0
 - Removed CIL-ASTRA as it has been merged into CIL code base.