From 687a1de426b4a3980a30ab378433e49d0ead0f5a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Mon, 13 May 2024 17:33:26 +0000
Subject: [PATCH 01/22] update CIL and CCPi-Regularisation version and
 reinstate tests

---
 SuperBuild.cmake              | 2 +-
 SuperBuild/External_CIL.cmake | 4 ++++
 version_config.cmake          | 6 +++---
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index cee9de0d..f87acce4 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -325,7 +325,7 @@ if ("${PYTHON_STRATEGY}" STREQUAL "CONDA")
   set (BUILD_CIL OFF)
 endif()
 if (BUILD_CIL)
-  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL TomoPhantom)
+  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL CCPi-Regularisation-Toolkit TomoPhantom)
 endif()
 if (BUILD_ASTRA)
   list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES astra-python-wrapper)
diff --git a/SuperBuild/External_CIL.cmake b/SuperBuild/External_CIL.cmake
index f985aae7..a113c000 100644
--- a/SuperBuild/External_CIL.cmake
+++ b/SuperBuild/External_CIL.cmake
@@ -115,6 +115,9 @@ if(NOT ( DEFINED "USE_SYSTEM_${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)
   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)
@@ -130,6 +133,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   add_test(NAME CIL_FRAMEWORK_TESTS_15
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_TranslateFunction.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+
   # add_test(NAME CIL_FRAMEWORK_TESTS_ALL
   #          COMMAND ${PYTHON_EXECUTABLE} -m unittest discover
   #          WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
diff --git a/version_config.cmake b/version_config.cmake
index f0291ac6..afbe736a 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -161,10 +161,10 @@ set(DEFAULT_JSON_TAG v3.11.3)
 # 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)
-set(DEFAULT_CIL_TAG db5a2a6cd3bddfbbf53e65f0549ac206096e5b44) # 13 Feb 2024
+set(DEFAULT_CIL_TAG b066d588dc6de0188fd33dafd8e5e669b7434b7e) # 13 May 2024
 
-set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/vais-ral/CCPi-Regularisation-Toolkit)
-set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "71f8d304d804b54d378f0ed05539f01aaaf13758")
+set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
+set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "fix_3D_regularisers") # fix_
 
 # CERN ROOT
 set(DEFAULT_ROOT_URL https://github.com/root-project/root)

From e311b869a9b00557dd6415d9089eafde57a10868 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Mon, 13 May 2024 20:06:41 +0000
Subject: [PATCH 02/22] update build command

---
 SuperBuild/External_CCPi-Regularisation-Toolkit.cmake | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake b/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
index 2124a360..ecbb27fd 100644
--- a/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
+++ b/SuperBuild/External_CCPi-Regularisation-Toolkit.cmake
@@ -72,7 +72,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
         -DPYTHON_DEST_DIR:PATH=${PYTHON_DEST}
 
       BUILD_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG} ${CMAKE_COMMAND} --build .
-      INSTALL_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG} ${CMAKE_COMMAND} --build . --target install
+      INSTALL_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG} ${CMAKE_COMMAND} --build . --target install && 
+       ${PYTHON_EXECUTABLE} -m pip install ${${proj}_SOURCE_DIR}/src/Python
       #TEST_COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -s ${${proj}_SOURCE_DIR}/test/ -p test*.py
       DEPENDS
         ${${proj}_DEPENDENCIES}

From f13ab947685073f76bfc42c875e360cd67768883 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Mon, 13 May 2024 20:36:40 +0000
Subject: [PATCH 03/22] update SIRF tags

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

diff --git a/version_config.cmake b/version_config.cmake
index afbe736a..6680a321 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -141,7 +141,7 @@ set(DEFAULT_STIR_TAG rel_6.0.0)
 
 ## SIRF
 set(DEFAULT_SIRF_URL https://github.com/SyneRBI/SIRF)
-set(DEFAULT_SIRF_TAG v3.6.0)
+set(DEFAULT_SIRF_TAG d54c4550d1533132c6a281b6cf2159c8fd22f45c) # #1254
 
 ## pet-rd-tools
 set(DEFAULT_pet_rd_tools_URL https://github.com/UCL/pet-rd-tools)

From 01232568e7f99ca279242a757cfea50fff96bd17 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Mon, 13 May 2024 21:53:51 +0000
Subject: [PATCH 04/22] test if ROOT errors are due to GCC 11

removed added GCC 11 builds

From e3d4115bd0c05047cfbbde43029f0c30fec691e8 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 14 May 2024 10:41:33 +0000
Subject: [PATCH 05/22] update Changelog

---
 CHANGES.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 47e74393..8929a32d 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,9 +1,13 @@
 # ChangeLog
 
 ## vx.x.x
-
+- Adds CCPi-Regularisation-Toolkit as prerequisite for CIL and reinstate unit tests
 - CMake:
   - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
+- Updated Versions:
+  - SIRF (master): d54c4550d1533132c6a281b6cf2159c8fd22f45c
+  - CIL: b066d588dc6de0188fd33dafd8e5e669b7434b7e # 13 May 2024
+  - CCPi-Regularisation-Toolkit: fix_3D_regularisers branch
 
 ## v3.6.0
 - build the STIR native Python interface by default (STIR_BUILD_SWIG_PYTHON=ON). You can still switch this off.

From 4b19647af9fef458ca081f85809e85bb09e01734 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 15 May 2024 08:00:48 +0000
Subject: [PATCH 06/22] install cil from source if BUILD_CIL=ON and not from
 conda

---
 docker/user_demos.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index 3527b887..a1c6edb2 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -22,7 +22,13 @@ if [ "$PYTHON" = "miniconda" ]; then
       # delete GPU deps
       sed -r -e '/^\s*- (astra-toolbox|tigre).*/d' -e '/^\s*- \S+.*#.*GPU/d' environment.yml > environment-sirf.yml
     fi
-    conda env update --file environment-sirf.yml
+    # do not install CIL from conda if BUILD_CIL is set
+    if test "${BUILD_CIL:-0}" != 0; then
+      # delete CIL package from the environment file
+      sed -r -e '/^\s*- (cil).*/d' environment-sirf.yml > tmp
+      mv tmp environment-sirf.yml
+    fi
+    conda env update --file environment-sirf.yml -v
   else
     if [ -f requirements.txt ]; then
       cat requirements.txt

From 711ce31c086e22e2bcc468c65f6147f71593e50d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 15 May 2024 14:39:35 +0000
Subject: [PATCH 07/22] install CIL via conda if BUILD_CIL=OFF

---
 Dockerfile           | 2 +-
 docker/user_demos.sh | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 0ddea696..c9e35b0e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -111,7 +111,7 @@ COPY --from=build --link --chown=${NB_USER} /opt/SIRF-SuperBuild/INSTALL/ /opt/S
 
 # install {SIRF-Exercises,CIL-Demos}
 COPY docker/user_demos.sh /opt/scripts/
-RUN bash /opt/scripts/user_demos.sh \
+RUN BUILD_CIL="${BUILD_CIL}" bash /opt/scripts/user_demos.sh \
  && fix-permissions /opt/SIRF-Exercises /opt/CIL-Demos "${CONDA_DIR}" /home/${NB_USER}
 
 # docker-stacks notebook
diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index a1c6edb2..79186563 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -25,8 +25,7 @@ if [ "$PYTHON" = "miniconda" ]; then
     # do not install CIL from conda if BUILD_CIL is set
     if test "${BUILD_CIL:-0}" != 0; then
       # delete CIL package from the environment file
-      sed -r -e '/^\s*- (cil).*/d' environment-sirf.yml > tmp
-      mv tmp environment-sirf.yml
+      sed -r -i -e '/^\s*- (cil).*/d' environment-sirf.yml
     fi
     conda env update --file environment-sirf.yml -v
   else

From 1b886428cca733571bbf20ebe26c03b5e1fa739d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 15 May 2024 16:39:17 +0000
Subject: [PATCH 08/22] this works

---
 docker/user_demos.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index 79186563..d6454049 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -25,7 +25,11 @@ if [ "$PYTHON" = "miniconda" ]; then
     # do not install CIL from conda if BUILD_CIL is set
     if test "${BUILD_CIL:-0}" != 0; then
       # delete CIL package from the environment file
+      echo "Deleting CIL from the environment file BUILD_CIL is set to >${BUILD_CIL}<"
       sed -r -i -e '/^\s*- (cil).*/d' environment-sirf.yml
+      cat environment-sirf.yml
+    else
+      echo "Not deleting CIL from the environment file BUILD_CIL is set to >${BUILD_CIL}<"
     fi
     conda env update --file environment-sirf.yml -v
   else

From 65e2d7027cc7c064118e5518d21850bf5808443a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 15 May 2024 21:57:26 +0000
Subject: [PATCH 09/22] remove CIL if BUILD_CIL=ON

---
 CHANGES.md | 2 ++
 Dockerfile | 8 +++++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 8929a32d..ecb2a956 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -2,6 +2,8 @@
 
 ## vx.x.x
 - Adds CCPi-Regularisation-Toolkit as prerequisite for CIL and reinstate unit tests
+- Docker:
+  - Handle BUILD_CIL correctly and not install CIL from conda if BUILD_CIL=ON
 - CMake:
   - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
 - Updated Versions:
diff --git a/Dockerfile b/Dockerfile
index c9e35b0e..d715491c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,12 +21,16 @@ RUN bash /opt/scripts/build_system-ubuntu.sh
 
 # SIRF python deps
 ARG BUILD_GPU=0
+ARG BUILD_CIL="OFF"
 COPY docker/requirements.yml /opt/scripts/
 # https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html#conda-environments
 # https://github.com/TomographicImaging/CIL/blob/master/Dockerfile
 RUN if test "$BUILD_GPU" != 0; then \
   sed -ri 's/^(\s*)#\s*(- \S+.*#.*GPU.*)$/\1\2/' /opt/scripts/requirements.yml; \
  fi \
+ && if test "$BUILD_CIL" != 0; then \
+  sed -r -i -e '/^\s*- (cil).*/d' /opt/scripts/requirements.yml; \
+ fi \
  && conda config --env --set channel_priority strict \
  && for ch in defaults ccpi intel conda-forge; do conda config --env --add channels $ch; done \
  && mamba env update -n base -f /opt/scripts/requirements.yml \
@@ -66,7 +70,8 @@ ARG USE_NiftyPET="OFF"
 ARG BUILD_siemens_to_ismrmrd="ON"
 ARG BUILD_pet_rd_tools="ON"
 ARG Gadgetron_USE_CUDA="ON"
-ARG BUILD_CIL="OFF"
+# BUILD_CIL is defined in the previous stage
+ARG BUILD_CIL
 ARG EXTRA_BUILD_FLAGS=""
 
 # build, install in /opt/SIRF-SuperBuild/{INSTALL,sources/SIRF}, test (if RUN_CTEST)
@@ -110,6 +115,7 @@ COPY --from=build --link --chown=${NB_USER} /opt/SIRF-SuperBuild/INSTALL/ /opt/S
 #COPY --from=build --link /opt/conda/ /opt/conda/
 
 # install {SIRF-Exercises,CIL-Demos}
+ARG BUILD_CIL
 COPY docker/user_demos.sh /opt/scripts/
 RUN BUILD_CIL="${BUILD_CIL}" bash /opt/scripts/user_demos.sh \
  && fix-permissions /opt/SIRF-Exercises /opt/CIL-Demos "${CONDA_DIR}" /home/${NB_USER}

From 146641069a5bc1f6c5f921b15f9ee611ae16360c Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Wed, 15 May 2024 22:02:42 +0000
Subject: [PATCH 10/22] removed partial comment

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

diff --git a/version_config.cmake b/version_config.cmake
index 6680a321..351089cb 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -164,7 +164,7 @@ set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL)
 set(DEFAULT_CIL_TAG b066d588dc6de0188fd33dafd8e5e669b7434b7e) # 13 May 2024
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
-set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "fix_3D_regularisers") # fix_
+set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "fix_3D_regularisers")
 
 # CERN ROOT
 set(DEFAULT_ROOT_URL https://github.com/root-project/root)

From 6a0bf4b7c397da6cad18d76e36e6a6ea44d1fbfa Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 16 May 2024 11:40:04 +0100
Subject: [PATCH 11/22] fix BUILD_CIL value handling

---
 Dockerfile           | 2 +-
 docker/user_demos.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d715491c..dfa780cf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,7 +28,7 @@ COPY docker/requirements.yml /opt/scripts/
 RUN if test "$BUILD_GPU" != 0; then \
   sed -ri 's/^(\s*)#\s*(- \S+.*#.*GPU.*)$/\1\2/' /opt/scripts/requirements.yml; \
  fi \
- && if test "$BUILD_CIL" != 0; then \
+ && if test "$BUILD_CIL" != "OFF"; then \
   sed -r -i -e '/^\s*- (cil).*/d' /opt/scripts/requirements.yml; \
  fi \
  && conda config --env --set channel_priority strict \
diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index d6454049..5d757ee7 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -23,7 +23,7 @@ if [ "$PYTHON" = "miniconda" ]; then
       sed -r -e '/^\s*- (astra-toolbox|tigre).*/d' -e '/^\s*- \S+.*#.*GPU/d' environment.yml > environment-sirf.yml
     fi
     # do not install CIL from conda if BUILD_CIL is set
-    if test "${BUILD_CIL:-0}" != 0; then
+    if test "${BUILD_CIL:-OFF}" != "OFF"; then
       # delete CIL package from the environment file
       echo "Deleting CIL from the environment file BUILD_CIL is set to >${BUILD_CIL}<"
       sed -r -i -e '/^\s*- (cil).*/d' environment-sirf.yml

From a0e88711c0ea0d40c061815145001cb297886065 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 16 May 2024 12:27:59 +0000
Subject: [PATCH 12/22] update test to look for OFF

---
 Dockerfile           | 2 +-
 docker/user_demos.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d715491c..dfa780cf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,7 +28,7 @@ COPY docker/requirements.yml /opt/scripts/
 RUN if test "$BUILD_GPU" != 0; then \
   sed -ri 's/^(\s*)#\s*(- \S+.*#.*GPU.*)$/\1\2/' /opt/scripts/requirements.yml; \
  fi \
- && if test "$BUILD_CIL" != 0; then \
+ && if test "$BUILD_CIL" != "OFF"; then \
   sed -r -i -e '/^\s*- (cil).*/d' /opt/scripts/requirements.yml; \
  fi \
  && conda config --env --set channel_priority strict \
diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index d6454049..47906f69 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -23,7 +23,7 @@ if [ "$PYTHON" = "miniconda" ]; then
       sed -r -e '/^\s*- (astra-toolbox|tigre).*/d' -e '/^\s*- \S+.*#.*GPU/d' environment.yml > environment-sirf.yml
     fi
     # do not install CIL from conda if BUILD_CIL is set
-    if test "${BUILD_CIL:-0}" != 0; then
+    if test "${BUILD_CIL:-"OFF"}" != "OFF"; then
       # delete CIL package from the environment file
       echo "Deleting CIL from the environment file BUILD_CIL is set to >${BUILD_CIL}<"
       sed -r -i -e '/^\s*- (cil).*/d' environment-sirf.yml

From 0caafd351bb4851b1f726aa43d98a9d30bfc75ee Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 16 May 2024 17:39:19 +0000
Subject: [PATCH 13/22] updated SIRF and CIL tags

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

diff --git a/version_config.cmake b/version_config.cmake
index 351089cb..1e385122 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -141,7 +141,7 @@ set(DEFAULT_STIR_TAG rel_6.0.0)
 
 ## SIRF
 set(DEFAULT_SIRF_URL https://github.com/SyneRBI/SIRF)
-set(DEFAULT_SIRF_TAG d54c4550d1533132c6a281b6cf2159c8fd22f45c) # #1254
+set(DEFAULT_SIRF_TAG origin/master)
 
 ## pet-rd-tools
 set(DEFAULT_pet_rd_tools_URL https://github.com/UCL/pet-rd-tools)
@@ -161,7 +161,7 @@ set(DEFAULT_JSON_TAG v3.11.3)
 # 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)
-set(DEFAULT_CIL_TAG b066d588dc6de0188fd33dafd8e5e669b7434b7e) # 13 May 2024
+set(DEFAULT_CIL_TAG 501726d8f09c16faef19ceb69b85c212db2eeca6) # 16 May 2024
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
 set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "fix_3D_regularisers")

From f7424c0c217ae3800e07ae4b9ed2d5cd8e420915 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 16 May 2024 21:54:59 +0000
Subject: [PATCH 14/22] update Changelog

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

diff --git a/CHANGES.md b/CHANGES.md
index 2dbe6cf9..6894eda6 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -8,7 +8,7 @@
   - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
 - Updated Versions:
   - SIRF (master): d54c4550d1533132c6a281b6cf2159c8fd22f45c
-  - CIL: b066d588dc6de0188fd33dafd8e5e669b7434b7e # 13 May 2024
+  - CIL: 501726d8f09c16faef19ceb69b85c212db2eeca6 # 16 May 2024
   - CCPi-Regularisation-Toolkit: fix_3D_regularisers branch
   - STIR: v6.1.0
 

From 6699a8a3713219edc806cf0995447b153c1122f9 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Sun, 19 May 2024 14:05:37 +0000
Subject: [PATCH 15/22] workaround for jupyterhub blasting our .bashrc

---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index dfa780cf..6575e2a3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -104,7 +104,7 @@ RUN apt update -qq && apt install -yq --no-install-recommends \
   && mkdir -p /usr/share/X11/xkb \
   && test -e /usr/bin/X || ln -s /usr/bin/Xorg /usr/bin/X
 
-RUN echo 'test -z "$OMP_NUM_THREADS" && export OMP_NUM_THREADS=$(python -c "import multiprocessing as mc; print(mc.cpu_count() // 2)")' > /usr/local/bin/before-notebook.d/omp_num_threads.sh
+RUN echo 'test -z "$OMP_NUM_THREADS" && export OMP_NUM_THREADS=$(python -c "import multiprocessing as mc; print(mc.cpu_count() - 2)")' > /usr/local/bin/before-notebook.d/omp_num_threads.sh
 
 COPY --chown=${NB_USER} --chmod=644 --link docker/.bashrc /home/${NB_USER}/
 # RUN sed -i s:PYTHON_INSTALL_DIR:${CONDA_DIR}:g /home/${NB_USER}/.bashrc
@@ -132,4 +132,6 @@ ENV GADGETRON_RELAY_HOST="0.0.0.0"
 
 # run gadgetron in the background before start-notebook.py
 COPY --link --chown=${NB_USER} docker/start-gadgetron-notebook.sh /opt/scripts/
+# COPY --from=build --link --chown=${NB_USER} /opt/SIRF-SuperBuild/INSTALL/lib /opt/conda/lib
+COPY --from=build --link --chown=${NB_USER} /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh /opt/conda/etc/conda/activate.d
 CMD ["/opt/scripts/start-gadgetron-notebook.sh"]

From da65e19d5daf2452e1af0238ac98dfe3dd41a0bd Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 31 May 2024 11:48:56 +0100
Subject: [PATCH 16/22] bash: source once

---
 env_sirf.sh.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/env_sirf.sh.in b/env_sirf.sh.in
index 6726b1ef..7243b0b0 100755
--- a/env_sirf.sh.in
+++ b/env_sirf.sh.in
@@ -2,6 +2,7 @@
 # Use it like this		
 #    source /path/to/whereever/env_ccppetmr.sh		
 # Preferably add this line to your .basrhc, .profile or whatever file is appropriate for your shell		
+test -n "$SIRF_ENV_SOURCED" && return; SIRF_ENV_SOURCED=1 # pragma once
   		  
 SIRF_PATH=@SIRF_SOURCE_DIR@
 export SIRF_PATH

From 4f88a989b872cc074810282771f770d9da366442 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 3 Jun 2024 15:49:48 +0100
Subject: [PATCH 17/22] revert one line

---
 env_sirf.sh.in | 1 -
 1 file changed, 1 deletion(-)

diff --git a/env_sirf.sh.in b/env_sirf.sh.in
index 7243b0b0..6726b1ef 100755
--- a/env_sirf.sh.in
+++ b/env_sirf.sh.in
@@ -2,7 +2,6 @@
 # Use it like this		
 #    source /path/to/whereever/env_ccppetmr.sh		
 # Preferably add this line to your .basrhc, .profile or whatever file is appropriate for your shell		
-test -n "$SIRF_ENV_SOURCED" && return; SIRF_ENV_SOURCED=1 # pragma once
   		  
 SIRF_PATH=@SIRF_SOURCE_DIR@
 export SIRF_PATH

From 7a0ac56d637db14fe1b6fd13a59946969f5282fa Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 6 Jun 2024 11:24:24 +0100
Subject: [PATCH 18/22] update to newest CCPi code versions

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org>
---
 docker/user_demos.sh | 2 +-
 version_config.cmake | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docker/user_demos.sh b/docker/user_demos.sh
index c54a02e4..7bdef143 100755
--- a/docker/user_demos.sh
+++ b/docker/user_demos.sh
@@ -31,7 +31,7 @@ if test "${BUILD_CIL:-OFF}" != "OFF"; then
     else
       echo "Not deleting CIL from the environment file BUILD_CIL is set to >${BUILD_CIL}<"
     fi
-    conda env update --file environment-sirf.yml -v
+    conda env update --file environment-sirf.yml
   else
     if [ -f requirements.txt ]; then
       cat requirements.txt
diff --git a/version_config.cmake b/version_config.cmake
index 1bf34878..b806fb94 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -161,10 +161,10 @@ set(DEFAULT_JSON_TAG v3.11.3)
 # 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)
-set(DEFAULT_CIL_TAG 501726d8f09c16faef19ceb69b85c212db2eeca6) # 16 May 2024
+set(DEFAULT_CIL_TAG ccf17f393ba911d13b74f2327779dde030098fe6) # 28 May 2024
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
-set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "fix_3D_regularisers")
+set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v24.0.1")
 
 # CERN ROOT
 set(DEFAULT_ROOT_URL https://github.com/root-project/root)

From 1cb17ad7b106670aef3637f36eae92e6166915fa Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 6 Jun 2024 12:40:20 +0000
Subject: [PATCH 19/22] add cil requirements as we delete cil if BUILD_CIL=ON

---
 Dockerfile              |  2 +-
 docker/requirements.yml | 14 +++++++++++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6575e2a3..8376b35c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -29,7 +29,7 @@ RUN if test "$BUILD_GPU" != 0; then \
   sed -ri 's/^(\s*)#\s*(- \S+.*#.*GPU.*)$/\1\2/' /opt/scripts/requirements.yml; \
  fi \
  && if test "$BUILD_CIL" != "OFF"; then \
-  sed -r -i -e '/^\s*- (cil).*/d' /opt/scripts/requirements.yml; \
+  sed -r -i -e '/^\s*- (cil|ccpi-regulariser).*/d' /opt/scripts/requirements.yml; \
  fi \
  && conda config --env --set channel_priority strict \
  && for ch in defaults ccpi intel conda-forge; do conda config --env --add channels $ch; done \
diff --git a/docker/requirements.yml b/docker/requirements.yml
index f359d32c..dd1ddada 100644
--- a/docker/requirements.yml
+++ b/docker/requirements.yml
@@ -18,9 +18,17 @@ dependencies:
   - deprecation
   - nose
   - pip
-  - cil              # cil
-  - ccpi-regulariser # cil
-  - dxchange         # cil
+  - cil               # cil
+  - ccpi-regulariser  # cil
+  - dxchange          # cil
+  - h5py              # cil
+  - pillow            # cil
+  - olefile >=0.46    # cil
+  - pywavelets        # cil
+  - cil-data >=21.3.0 # cil
+  - ipp >=2021.10     # cil
+  - tqdm              # cil
+  - numba             # cil 
   # - tigre          # cil (GPU)
   # - astra-toolbox  # cil (GPU)
   - pip:

From a73251d54709c133da563cc48f14a7a8bb58230a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Thu, 6 Jun 2024 22:54:12 +0100
Subject: [PATCH 20/22] update changelog

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org>
---
 CHANGES.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index fbd33668..b5df2e3c 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -9,7 +9,7 @@
 - Updated Versions:
   - SIRF: v3.7.0
   - CIL: 501726d8f09c16faef19ceb69b85c212db2eeca6 # 16 May 2024
-  - CCPi-Regularisation-Toolkit: fix_3D_regularisers branch
+  - CCPi-Regularisation-Toolkit: v24.0.1
   - STIR: v6.1.0
 
 ## v3.6.0

From bd0f0905b1726c7912c762b9d79939a1708642bc Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 7 Jun 2024 14:30:08 +0100
Subject: [PATCH 21/22] min 1 thread

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 8376b35c..40fa6012 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -104,7 +104,7 @@ RUN apt update -qq && apt install -yq --no-install-recommends \
   && mkdir -p /usr/share/X11/xkb \
   && test -e /usr/bin/X || ln -s /usr/bin/Xorg /usr/bin/X
 
-RUN echo 'test -z "$OMP_NUM_THREADS" && export OMP_NUM_THREADS=$(python -c "import multiprocessing as mc; print(mc.cpu_count() - 2)")' > /usr/local/bin/before-notebook.d/omp_num_threads.sh
+RUN echo 'test -z "$OMP_NUM_THREADS" && export OMP_NUM_THREADS=$(python -c "import multiprocessing as mc; print(max(1, mc.cpu_count() - 2))")' > /usr/local/bin/before-notebook.d/omp_num_threads.sh
 
 COPY --chown=${NB_USER} --chmod=644 --link docker/.bashrc /home/${NB_USER}/
 # RUN sed -i s:PYTHON_INSTALL_DIR:${CONDA_DIR}:g /home/${NB_USER}/.bashrc

From e89966685a1324ed71714b2aa64f9775ed561cf5 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 10 Jun 2024 11:06:45 +0100
Subject: [PATCH 22/22] Update CHANGES.md

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

diff --git a/CHANGES.md b/CHANGES.md
index b5df2e3c..4804a120 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -8,7 +8,7 @@
   - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler) https://github.com/SyneRBI/SIRF-SuperBuild/pull/879
 - Updated Versions:
   - SIRF: v3.7.0
-  - CIL: 501726d8f09c16faef19ceb69b85c212db2eeca6 # 16 May 2024
+  - CIL: ccf17f393ba911d13b74f2327779dde030098fe6 # 28 May 2024
   - CCPi-Regularisation-Toolkit: v24.0.1
   - STIR: v6.1.0