From 1c2bd461b8493a0d4f477fb0d0f8864003db2877 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 5 Apr 2018 15:46:47 +0000
Subject: [PATCH 01/59] first working conda recipe

---
 conda-recipe/build.sh  | 63 ++++++++++++++++++++++++++++++++++++++++++
 conda-recipe/meta.yaml | 56 +++++++++++++++++++++++++++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 conda-recipe/build.sh
 create mode 100644 conda-recipe/meta.yaml

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
new file mode 100644
index 00000000..d631cb80
--- /dev/null
+++ b/conda-recipe/build.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+#=========================================================================
+
+if [ -z "$SIRF_VERSION" ]; then
+    echo "Need to set SIRF_VERSION"
+    exit 1
+fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+cp -rv "$RECIPE_DIR/../" "$SRC_DIR/SIRF-SuperBuild"
+
+cd $SRC_DIR/build
+
+echo "$SRC_DIR/ccpi/Python"
+
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -USIRF_URL \
+    -USIRF_TAG \
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=Off \
+    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=On
+
+make  -j1
+cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
new file mode 100644
index 00000000..fbd25428
--- /dev/null
+++ b/conda-recipe/meta.yaml
@@ -0,0 +1,56 @@
+package:
+  name: sirf
+  version: {{ environ['SIRF_VERSION'] }}
+
+
+build:
+  preserve_egg_dir: False
+  script_env:
+    - SIRF_VERSION   
+#  number: 0
+    
+requirements:
+  build:
+#    - boost ==1.64.0	
+#    - boost-cpp ==1.64.0 
+    #- boost
+    #- boost-cpp
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - libxml2
+    - psutil
+    - nose
+    - coverage
+    - fftw
+    - swig >=3
+    - libxslt
+
+
+  run:
+    #- boost
+#    - libtiff
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - psutil
+    - fftw
+
+	
+about:
+  home: http://www.ccpi.ac.uk
+  license:  BSD license
+  summary: 'CCPi Toolbox'

From a283c0cbf1f776956e73d2a8f03d765b2cbbe9af Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 10 Apr 2018 09:34:06 +0000
Subject: [PATCH 02/59] use PYTHON_DEST to point to the site_packages

---
 conda-recipe/build.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index d631cb80..356708d5 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -40,6 +40,7 @@ echo "$SRC_DIR/ccpi/Python"
 
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST="${SP_DIR}/sirf" \
     -USIRF_URL \
     -USIRF_TAG \
     -USTIR_URL \

From 7dbd1c89b590e22d47276cfb38505da2c3ab00de Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 10 Apr 2018 14:30:49 +0000
Subject: [PATCH 03/59] do not overwrite the PYTHON_DEST?

---
 SuperBuild/External_SIRF.cmake | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/SuperBuild/External_SIRF.cmake b/SuperBuild/External_SIRF.cmake
index 98e699f2..b3cc9ae8 100644
--- a/SuperBuild/External_SIRF.cmake
+++ b/SuperBuild/External_SIRF.cmake
@@ -49,7 +49,11 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
   set (BUILD_PYTHON ${PYTHONLIBS_FOUND})
   if (BUILD_PYTHON)
-    set(PYTHON_DEST "${SIRF_Install_Dir}/python" CACHE PATH "Destination for python modules")
+    message("PYTHON_DEST ${PYTHON_DEST}")
+    if (NOT ${PYTHON_DEST})
+      set(PYTHON_DEST "${SIRF_Install_Dir}/python" CACHE PATH "Destination for python modules")
+    endif()
+    message("PYTHON_DEST ${PYTHON_DEST}")
   endif()
   set (BUILD_MATLAB ${Matlab_FOUND})
   if (BUILD_MATLAB)

From 1585c6d2e071531a93f758bb7d6222e70f128f00 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:39:57 +0000
Subject: [PATCH 04/59] removed messages

---
 SuperBuild/External_SIRF.cmake | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/SuperBuild/External_SIRF.cmake b/SuperBuild/External_SIRF.cmake
index b3cc9ae8..c5c82402 100644
--- a/SuperBuild/External_SIRF.cmake
+++ b/SuperBuild/External_SIRF.cmake
@@ -49,11 +49,10 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
   set (BUILD_PYTHON ${PYTHONLIBS_FOUND})
   if (BUILD_PYTHON)
-    message("PYTHON_DEST ${PYTHON_DEST}")
-    if (NOT ${PYTHON_DEST})
+    if (PYTHON_DEST)
+    else()
       set(PYTHON_DEST "${SIRF_Install_Dir}/python" CACHE PATH "Destination for python modules")
     endif()
-    message("PYTHON_DEST ${PYTHON_DEST}")
   endif()
   set (BUILD_MATLAB ${Matlab_FOUND})
   if (BUILD_MATLAB)

From d2e161578d593fcb731014e68b876e1c64b1c1c5 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:41:32 +0000
Subject: [PATCH 05/59] updated about, removed SIRF_VERSION env var

---
 conda-recipe/meta.yaml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index fbd25428..98e2fb6e 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -1,20 +1,19 @@
 package:
   name: sirf
-  version: {{ environ['SIRF_VERSION'] }}
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.0.0
 
 
 build:
   preserve_egg_dir: False
-  script_env:
-    - SIRF_VERSION   
 #  number: 0
     
 requirements:
   build:
 #    - boost ==1.64.0	
 #    - boost-cpp ==1.64.0 
-    #- boost
-    #- boost-cpp
+#    - boost
+#    - boost-cpp
     - python 3.6 # [py36]
     - python 2.7 # [py27]
     - cmake >=3.1
@@ -51,6 +50,6 @@ requirements:
 
 	
 about:
-  home: http://www.ccpi.ac.uk
-  license:  BSD license
-  summary: 'CCPi Toolbox'
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From cd54fe9f97c755e4d52e03ef3ac021e78c3e095d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:44:48 +0000
Subject: [PATCH 06/59] pulls the 1.0.0 tag

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

diff --git a/version_config.cmake b/version_config.cmake
index 3ac26e6f..2ba83a13 100644
--- a/version_config.cmake
+++ b/version_config.cmake
@@ -116,7 +116,7 @@ if (DEVEL_BUILD)
   set(DEFAULT_glog_TAG v035)
 
 else()
-  set(DEFAULT_SIRF_TAG v1.0.0-rc.3)
+  set(DEFAULT_SIRF_TAG v1.0.0)
 
   ## STIR
   set(DEFAULT_STIR_URL https://github.com/UCL/STIR )

From 234ab0e5398874996d67b1dc6baf70d0016e9b70 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:47:04 +0000
Subject: [PATCH 07/59] removed SIRF_VERSION env var

---
 conda-recipe/build.sh | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 356708d5..133b85e5 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -25,10 +25,10 @@
 #
 #=========================================================================
 
-if [ -z "$SIRF_VERSION" ]; then
-    echo "Need to set SIRF_VERSION"
-    exit 1
-fi  
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
 
 mkdir "$SRC_DIR/build"
 mkdir "$SRC_DIR/SIRF-SuperBuild"
@@ -40,15 +40,17 @@ echo "$SRC_DIR/ccpi/Python"
 
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST="${SP_DIR}/sirf" \
+    -DPYTHON_DEST=${SP_DIR}/sirf \
     -USIRF_URL \
     -USIRF_TAG \
+    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
     -DUSE_SYSTEM_Armadillo=Off \

From ed2c6a1d89b8b37f3426472edca3ccb18fe61e87 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 17 Apr 2018 02:30:58 +0100
Subject: [PATCH 08/59] initial setup.py

- depends on https://github.com/CCPPETMR/SIRF/pull/161
- fixes (partially) #107
- TODO: alias p(Gadgetron|STIR|Utilities) -> sirf.p*
- perhaps use `setup.py install` not `pip install`?
  - or drop `-e` argument in `pip install`?
---
 SuperBuild.cmake               | 31 +++++++++++++++++++++------
 SuperBuild/External_SIRF.cmake |  4 ++--
 SuperBuild/setup.py.in         | 39 ++++++++++++++++++++++++++++++++++
 3 files changed, 66 insertions(+), 8 deletions(-)
 create mode 100755 SuperBuild/setup.py.in

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index d5314acb..360ddf35 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -186,16 +186,14 @@ if(PYTHONINTERP_FOUND)
 
   set (ENV_PYTHON_CSH "\
     if $?PYTHONPATH then \n\
-      setenv PYTHONPATH ${PYTHON_DEST}:$PYTHONPATH \n\
+      #setenv PYTHONPATH ${PYTHON_DEST}:$PYTHONPATH \n\
     else \n\
-      setenv PYTHONPATH ${PYTHON_DEST} \n\
+      #setenv PYTHONPATH ${PYTHON_DEST} \n\
       setenv SIRF_PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE}")
 
   set (ENV_PYTHON_BASH "\
-     PYTHONPATH=${PYTHON_DEST}:$PYTHONPATH \n\
-     export PYTHONPATH \n\
-     SIRF_PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE} \n\
-     export SIRF_PYTHON_EXECUTABLE")
+     #export PYTHONPATH=${PYTHON_DEST}:$PYTHONPATH \n\
+     export SIRF_PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
 
 endif()
 
@@ -219,6 +217,27 @@ endif()
 configure_file(env_ccppetmr.sh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.sh)
 configure_file(env_ccppetmr.csh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.csh)
 
+if(PYTHONINTERP_FOUND)
+  set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/setup.py.in")
+  set(SETUP_PY "${PYTHON_DEST}/setup.py")
+  set(SETUP_PY_INIT "${PYTHON_DEST}/sirf/__init__.py")
+  message(STATUS "setup.py: ${SETUP_PY}")
+
+  configure_file("${SETUP_PY_IN}" "${SETUP_PY}")
+
+  add_custom_command(OUTPUT "${SETUP_PY_INIT}"
+    COMMAND "${CMAKE_COMMAND}" -E make_directory "${PYTHON_DEST}/sirf"
+    COMMAND "${CMAKE_COMMAND}" -E touch "${SETUP_PY_INIT}"
+    COMMAND "${PYTHON_EXECUTABLE}" setup.py build
+    DEPENDS "${SETUP_PY_IN}"
+    WORKING_DIRECTORY "${PYTHON_DEST}")
+
+  add_custom_target(pybuild_stir ALL DEPENDS ${SETUP_PY_INIT})
+
+  install(CODE "execute_process(COMMAND\n\
+    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${CCPPETMR_INSTALL}\")")
+endif(PYTHONINTERP_FOUND)
+
 
 # add tests
 enable_testing()
diff --git a/SuperBuild/External_SIRF.cmake b/SuperBuild/External_SIRF.cmake
index 98e699f2..fc9265f7 100644
--- a/SuperBuild/External_SIRF.cmake
+++ b/SuperBuild/External_SIRF.cmake
@@ -58,7 +58,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
   message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
   set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
-  
+
   ExternalProject_Add(${proj}
     ${${proj}_EP_ARGS}
     GIT_REPOSITORY ${${proj}_URL}
@@ -87,7 +87,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
         -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
         -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIRS}
         -DPYTHON_LIBRARY=${PYTHON_LIBRARIES}
-        -DPYTHON_DEST=${PYTHON_DEST}
+        -DPYTHON_DEST=${PYTHON_DEST}/sirf
 	INSTALL_DIR ${SIRF_Install_Dir}
     DEPENDS
         ${${proj}_DEPENDENCIES}
diff --git a/SuperBuild/setup.py.in b/SuperBuild/setup.py.in
new file mode 100755
index 00000000..71745844
--- /dev/null
+++ b/SuperBuild/setup.py.in
@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+__author__ = "Casper da Costa-Luis <imaging@caspersci.uk.to>"
+__version__ = "1.0.0"
+
+
+setup(
+    name='sirf',
+    version=__version__,
+    description='CCP PET-MR SIRF',
+    license='Apache 2.0',
+    author='CCP PET-MR',
+    author_email='ccppetmr@stfc.ac.uk',
+    url='https://github.com/CCPPETMR/SIRF',
+    platforms=['any'],
+    packages=['sirf'],
+    long_description='',
+    classifiers=[
+        # Trove classifiers
+        # (https://pypi.python.org/pypi?%3Aaction=list_classifiers)
+        'Development Status :: 5 - Production/Stable',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7'
+    ],
+    keywords='image reconstruction pet mr medical imaging',
+)

From f4ccbf62e5334d317c925770902c937568c79de6 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 17 Apr 2018 15:30:55 +0100
Subject: [PATCH 09/59] backward-compatible setup.py

- depends on https://github.com/CCPPETMR/SIRF/pull/160
- fixes #107
---
 SuperBuild.cmake          | 32 ++++++++++++++++++++++++++++----
 SuperBuild/__init__.py.in |  1 +
 SuperBuild/setup.py.in    |  2 +-
 3 files changed, 30 insertions(+), 5 deletions(-)
 create mode 100644 SuperBuild/__init__.py.in

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index 360ddf35..c6d08c74 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -1,6 +1,7 @@
 #========================================================================
 # Author: Benjamin A Thomas
 # Author: Edoardo Pasca
+# Author: Casper da Costa-Luis
 # Copyright 2017 University College London
 # Copyright 2017 Science Technology Facilities Council
 #
@@ -217,14 +218,36 @@ endif()
 configure_file(env_ccppetmr.sh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.sh)
 configure_file(env_ccppetmr.csh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.csh)
 
+# Install python packages via pip and setup.py
 if(PYTHONINTERP_FOUND)
+  set(PYTHON_SETUP_PKGS "sirf" CACHE INTERNAL "list of provided python packages")
+
+  # alias sirf.p* -> p* for backward-compatibility
+  function(python_pkg_alias PY_PKG_NEW PY_PKG_OLD)
+    list(APPEND PYTHON_SETUP_PKGS ${PY_PKG_NEW})
+    set(PYTHON_SETUP_PKGS "${PYTHON_SETUP_PKGS}" PARENT_SCOPE)
+    set(SETUP_PY_INIT_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/__init__.py.in")
+    set(SETUP_PY_INIT "${PYTHON_DEST}/${PY_PKG_NEW}/__init__.py")
+    configure_file("${SETUP_PY_INIT_IN}" "${SETUP_PY_INIT}")
+    # message(STATUS "setup.py:${SETUP_PY_INIT}")
+    message(STATUS "setup.py:${PY_PKG_NEW}<-${PY_PKG_OLD}")
+  endfunction(python_pkg_alias)
+  python_pkg_alias(pGadgetron "sirf.pGadgetron")
+  python_pkg_alias(pSTIR "sirf.pSTIR")
+  python_pkg_alias(pUtilities "sirf.pUtilities")
+  # convert to python CSV tuple for setup.py configure_file
+  string(REPLACE ";" "', '" PYTHON_SETUP_PKGS_CSV "${PYTHON_SETUP_PKGS}")
+  set(PYTHON_SETUP_PKGS_CSV "'${PYTHON_SETUP_PKGS_CSV}'")
+  # message(STATUS "setup.py:pacakges:${PYTHON_SETUP_PKGS_CSV}")
+
+  # Create setup.py
   set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/setup.py.in")
   set(SETUP_PY "${PYTHON_DEST}/setup.py")
   set(SETUP_PY_INIT "${PYTHON_DEST}/sirf/__init__.py")
-  message(STATUS "setup.py: ${SETUP_PY}")
-
+  message(STATUS "setup.py:${SETUP_PY}")
   configure_file("${SETUP_PY_IN}" "${SETUP_PY}")
 
+  # pip install -e
   add_custom_command(OUTPUT "${SETUP_PY_INIT}"
     COMMAND "${CMAKE_COMMAND}" -E make_directory "${PYTHON_DEST}/sirf"
     COMMAND "${CMAKE_COMMAND}" -E touch "${SETUP_PY_INIT}"
@@ -232,10 +255,11 @@ if(PYTHONINTERP_FOUND)
     DEPENDS "${SETUP_PY_IN}"
     WORKING_DIRECTORY "${PYTHON_DEST}")
 
-  add_custom_target(pybuild_stir ALL DEPENDS ${SETUP_PY_INIT})
+  add_custom_target(pybuild_sirf ALL DEPENDS ${SETUP_PY_INIT})
 
+  # N.B. `-e` picks up cythonised libraries without messing with LD_LIBRARY_PATH
   install(CODE "execute_process(COMMAND\n\
-    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${CCPPETMR_INSTALL}\")")
+    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${PYTHON_DEST}\")")
 endif(PYTHONINTERP_FOUND)
 
 
diff --git a/SuperBuild/__init__.py.in b/SuperBuild/__init__.py.in
new file mode 100644
index 00000000..fb3e25f7
--- /dev/null
+++ b/SuperBuild/__init__.py.in
@@ -0,0 +1 @@
+from ${PY_PKG_OLD} import *
diff --git a/SuperBuild/setup.py.in b/SuperBuild/setup.py.in
index 71745844..1e7ccee2 100755
--- a/SuperBuild/setup.py.in
+++ b/SuperBuild/setup.py.in
@@ -18,7 +18,7 @@ setup(
     author_email='ccppetmr@stfc.ac.uk',
     url='https://github.com/CCPPETMR/SIRF',
     platforms=['any'],
-    packages=['sirf'],
+    packages=[${PYTHON_SETUP_PKGS_CSV}],
     long_description='',
     classifiers=[
         # Trove classifiers

From 32b1332896da9ce1fdb89e623cc928172184c7a9 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 24 Apr 2018 13:28:51 +0000
Subject: [PATCH 10/59] missing packages

---
 SuperBuild.cmake | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index c6d08c74..cf22d813 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -235,6 +235,9 @@ if(PYTHONINTERP_FOUND)
   python_pkg_alias(pGadgetron "sirf.pGadgetron")
   python_pkg_alias(pSTIR "sirf.pSTIR")
   python_pkg_alias(pUtilities "sirf.pUtilities")
+  python_pkg_alias(pygadgetron "sirf.pygadgetron")
+  python_pkg_alias(pystir "sirf.pystir")
+  python_pkg_alias(pyiutilities "sirf.pyiutilities")
   # convert to python CSV tuple for setup.py configure_file
   string(REPLACE ";" "', '" PYTHON_SETUP_PKGS_CSV "${PYTHON_SETUP_PKGS}")
   set(PYTHON_SETUP_PKGS_CSV "'${PYTHON_SETUP_PKGS_CSV}'")

From 9adb67dc447bffb7cda700e85a39c65b30f78307 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 13:56:45 +0000
Subject: [PATCH 11/59] added missing package

---
 SuperBuild.cmake | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index c6d08c74..f9b6c6f5 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -235,6 +235,7 @@ if(PYTHONINTERP_FOUND)
   python_pkg_alias(pGadgetron "sirf.pGadgetron")
   python_pkg_alias(pSTIR "sirf.pSTIR")
   python_pkg_alias(pUtilities "sirf.pUtilities")
+  python_pkg_alias(pyiutilities "sirf.pyiutilities")
   # convert to python CSV tuple for setup.py configure_file
   string(REPLACE ";" "', '" PYTHON_SETUP_PKGS_CSV "${PYTHON_SETUP_PKGS}")
   set(PYTHON_SETUP_PKGS_CSV "'${PYTHON_SETUP_PKGS_CSV}'")
@@ -257,9 +258,11 @@ if(PYTHONINTERP_FOUND)
 
   add_custom_target(pybuild_sirf ALL DEPENDS ${SETUP_PY_INIT})
 
-  # N.B. `-e` picks up cythonised libraries without messing with LD_LIBRARY_PATH
-  install(CODE "execute_process(COMMAND\n\
-    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${PYTHON_DEST}\")")
+  if (NOT CONDA_BUILD)
+    # N.B. `-e` picks up cythonised libraries without messing with LD_LIBRARY_PATH
+    install(CODE "execute_process(COMMAND\n\
+      \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${PYTHON_DEST}\")")
+  endif()
 endif(PYTHONINTERP_FOUND)
 
 

From a1675836c8f28641a7e10a6a54dd754d7a788d04 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 13:57:22 +0000
Subject: [PATCH 12/59] bugfixes

---
 conda-recipe/build.sh  | 11 ++++++++---
 conda-recipe/meta.yaml |  5 +++--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 133b85e5..133b201d 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -38,9 +38,10 @@ cd $SRC_DIR/build
 
 echo "$SRC_DIR/ccpi/Python"
 
+#site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${SP_DIR}/sirf \
+    -DPYTHON_DEST=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
     -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
@@ -56,11 +57,15 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_Armadillo=Off \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
-    -DBUILD_siemens_to_ismrmrd=On
+    -DBUILD_siemens_to_ismrmrd=On \
+    -DCONDA_BUILD=On
 
-make  -j1
+make  -j3
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
+cd ${PREFIX}/python
+${PYTHON} setup.py develop
+
 # add to 
 #echo "${PREFIX}/python" > ${PREFIX}
 #${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 98e2fb6e..4c202218 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -10,8 +10,8 @@ build:
     
 requirements:
   build:
-#    - boost ==1.64.0	
-#    - boost-cpp ==1.64.0 
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
 #    - boost
 #    - boost-cpp
     - python 3.6 # [py36]
@@ -36,6 +36,7 @@ requirements:
   run:
     #- boost
 #    - libtiff
+    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From e84622facbaa1b5a52dc1d48ac4bf494718fef97 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 14:04:19 +0000
Subject: [PATCH 13/59] bugfixes

---
 conda-recipe/build.sh  | 2 +-
 conda-recipe/meta.yaml | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 133b201d..764a1d03 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -64,7 +64,7 @@ make  -j3
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
-${PYTHON} setup.py develop
+${PYTHON} setup.py install
 
 # add to 
 #echo "${PREFIX}/python" > ${PREFIX}
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 4c202218..0104ea21 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -48,6 +48,8 @@ requirements:
     - h5py
     - psutil
     - fftw
+    - libgcc-ng
+    - libstdcxx-ng
 
 	
 about:

From 74952079bfa95860eebd7cb8531d9c7d6e8afda7 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 16:59:58 +0000
Subject: [PATCH 14/59] copies the .so into the site-packages

---
 SuperBuild/setup.py.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SuperBuild/setup.py.in b/SuperBuild/setup.py.in
index 1e7ccee2..aec1a3e3 100755
--- a/SuperBuild/setup.py.in
+++ b/SuperBuild/setup.py.in
@@ -18,6 +18,7 @@ setup(
     author_email='ccppetmr@stfc.ac.uk',
     url='https://github.com/CCPPETMR/SIRF',
     platforms=['any'],
+    package_data={'sirf': ['*.so']},
     packages=[${PYTHON_SETUP_PKGS_CSV}],
     long_description='',
     classifiers=[

From 011cc36b583b9a27c4bd4be279951330b35b0020 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 16:59:58 +0000
Subject: [PATCH 15/59] copies the .so into the site-packages

---
 SuperBuild/setup.py.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SuperBuild/setup.py.in b/SuperBuild/setup.py.in
index 1e7ccee2..aec1a3e3 100755
--- a/SuperBuild/setup.py.in
+++ b/SuperBuild/setup.py.in
@@ -18,6 +18,7 @@ setup(
     author_email='ccppetmr@stfc.ac.uk',
     url='https://github.com/CCPPETMR/SIRF',
     platforms=['any'],
+    package_data={'sirf': ['*.so']},
     packages=[${PYTHON_SETUP_PKGS_CSV}],
     long_description='',
     classifiers=[

From 1f749171a22af242e942bfc0ace98d0c53af8fc4 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 24 Apr 2018 22:04:36 +0100
Subject: [PATCH 16/59] pip -> setup.py

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

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index cf22d813..a51d7320 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -250,7 +250,7 @@ if(PYTHONINTERP_FOUND)
   message(STATUS "setup.py:${SETUP_PY}")
   configure_file("${SETUP_PY_IN}" "${SETUP_PY}")
 
-  # pip install -e
+  # python setup.py build
   add_custom_command(OUTPUT "${SETUP_PY_INIT}"
     COMMAND "${CMAKE_COMMAND}" -E make_directory "${PYTHON_DEST}/sirf"
     COMMAND "${CMAKE_COMMAND}" -E touch "${SETUP_PY_INIT}"
@@ -260,9 +260,10 @@ if(PYTHONINTERP_FOUND)
 
   add_custom_target(pybuild_sirf ALL DEPENDS ${SETUP_PY_INIT})
 
-  # N.B. `-e` picks up cythonised libraries without messing with LD_LIBRARY_PATH
+  # python setup.py install
   install(CODE "execute_process(COMMAND\n\
-    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${PYTHON_DEST}\")")
+    \"${PYTHON_EXECUTABLE}\" setup.py install\n\
+    WORKING_DIRECTORY \"${PYTHON_DEST}\")")
 endif(PYTHONINTERP_FOUND)
 
 

From 08a97126e4c511d11a0d41b205bd7eabcd4501d3 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 24 Apr 2018 22:52:18 +0100
Subject: [PATCH 17/59] missing docker devel cache

---
 docker/docker-compose.devel.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docker/docker-compose.devel.yml b/docker/docker-compose.devel.yml
index 31b5d6a4..b4e98f29 100644
--- a/docker/docker-compose.devel.yml
+++ b/docker/docker-compose.devel.yml
@@ -5,3 +5,6 @@ services:
   build:
    args:
     EXTRA_BUILD_FLAGS: "-DDEVEL_BUILD=ON"
+   cache_from:
+    - ccppetmr/sirf:core
+    - ccppetmr/sirf:devel

From 9c326249e2db281bee504d801bcb3d4aa082446a Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 24 Apr 2018 15:11:47 +0100
Subject: [PATCH 18/59] pyvenv -> miniconda

---
 docker/user_python-ubuntu.sh | 39 +++++++++++++++++++++++++++++-------
 1 file changed, 32 insertions(+), 7 deletions(-)

diff --git a/docker/user_python-ubuntu.sh b/docker/user_python-ubuntu.sh
index e955b3c2..1536e006 100755
--- a/docker/user_python-ubuntu.sh
+++ b/docker/user_python-ubuntu.sh
@@ -1,16 +1,41 @@
 #!/usr/bin/env bash
 [ -f .bashrc ] && . .bashrc
 INSTALL_DIR="${1:-/opt/pyvenv}"
+PYTHON="${2:-miniconda}"
 
-# Python (virtualenv)
-curl https://bootstrap.pypa.io/get-pip.py > get-pip.py
-python2 get-pip.py
-rm get-pip.py
-python2 -m pip install -U pip virtualenv
-python2 -m virtualenv "$INSTALL_DIR"
-source "$INSTALL_DIR"/bin/activate
+# Python
+case "$PYTHON" in
+miniconda)
+  # miniconda
+  curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh > miniconda.sh
+  echo -e "\nyes\n${INSTALL_DIR}" | bash miniconda.sh
+  rm miniconda.sh
+  source "$INSTALL_DIR"/bin/activate
+  conda config --add channels conda-forge
+  conda update -c conda-forge -y conda
+  conda update -c conda-forge -y --all
+  ;;
+*python*)
+  # virtualenv
+  curl https://bootstrap.pypa.io/get-pip.py > get-pip.py
+  ${PYTHON} get-pip.py
+  rm get-pip.py
+  ${PYTHON} -m pip install -U pip virtualenv
+  ${PYTHON} -m virtualenv "$INSTALL_DIR"
+  source "$INSTALL_DIR"/bin/activate
+  ;;
+*)
+  >&2 echo "unknown '\$PYTHON' '$PYTHON'"
+  exit 1
+  ;;
+esac
 
 # Python (runtime)
 if [ -f requirements.txt ]; then
   pip install -U -r requirements.txt
 fi
+
+if [ "$PYTHON" = "miniconda" ]; then
+  conda update -c conda-forge -y --all
+  conda clean -y --all
+fi

From 64932433226e862b845c7e360d9b674b9c06e2da Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 25 Apr 2018 15:15:11 +0000
Subject: [PATCH 19/59] added dependency

---
 conda-recipe/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 0104ea21..3d47166f 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -50,6 +50,7 @@ requirements:
     - fftw
     - libgcc-ng
     - libstdcxx-ng
+    - openblas
 
 	
 about:

From 04f6d8f202afa84fc94c6ad35669086e273cb798 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 26 Apr 2018 11:01:08 +0000
Subject: [PATCH 20/59] removed boost dependency

currently the boost in conda-forge does not contain all the libs we need. So we need to build and install.
---
 conda-recipe/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3d47166f..3ead54cd 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -34,9 +34,6 @@ requirements:
 
 
   run:
-    #- boost
-#    - libtiff
-    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From 894ebb93cc8630c925981801d25abc6b9dea160a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 3 May 2018 11:34:12 +0000
Subject: [PATCH 21/59] Added dependency

---
 conda-recipe/build.sh  | 9 +++++----
 conda-recipe/meta.yaml | 5 ++++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 764a1d03..c8f34aa3 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -41,10 +41,10 @@ echo "$SRC_DIR/ccpi/Python"
 #site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${PREFIX}/python\
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
+    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -54,13 +54,14 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
-    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_Armadillo=On \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=On \
+    -DUSE_SYSTEM_GTEST=On\
     -DCONDA_BUILD=On
 
-make  -j3
+make  -j1
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3ead54cd..91deee26 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -31,6 +31,8 @@ requirements:
     - fftw
     - swig >=3
     - libxslt
+    - armadillo
+    - gtest
 
 
   run:
@@ -48,7 +50,8 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-
+    - armadillo
+    - gtest
 	
 about:
   home: http://www.ccppetmr.ac.uk

From fefe1f5551229413bb66cfd54de0626e568ba6f1 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 3 May 2018 14:51:31 +0000
Subject: [PATCH 22/59] build latest SIRF, use pre-built boost

---
 SuperBuild/External_SIRF.cmake | 2 +-
 conda-recipe/build.sh          | 8 ++++----
 conda-recipe/meta.yaml         | 2 ++
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/SuperBuild/External_SIRF.cmake b/SuperBuild/External_SIRF.cmake
index 5a43fce5..fca193b0 100644
--- a/SuperBuild/External_SIRF.cmake
+++ b/SuperBuild/External_SIRF.cmake
@@ -90,7 +90,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
         -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
         -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIRS}
         -DPYTHON_LIBRARY=${PYTHON_LIBRARIES}
-        -DPYTHON_DEST=${PYTHON_DEST}/sirf
+        -DPYTHON_DEST_DIR=${PYTHON_DEST}/sirf
 	INSTALL_DIR ${SIRF_Install_Dir}
     DEPENDS
         ${${proj}_DEPENDENCIES}
diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index c8f34aa3..3485f134 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -41,10 +41,10 @@ echo "$SRC_DIR/ccpi/Python"
 #site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST_DIR=${PREFIX}/python\
+    -DPYTHON_DEST=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=1237daebaab4aeccd4e6a14cb0eef0b55b49ef7c\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -53,7 +53,7 @@ cmake ../SIRF-SuperBuild \
     -UISMRMRD_TAG \
     -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
-    -DUSE_SYSTEM_Boost=Off \
+    -DUSE_SYSTEM_Boost=On \
     -DUSE_SYSTEM_Armadillo=On \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
@@ -61,7 +61,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_GTEST=On\
     -DCONDA_BUILD=On
 
-make  -j1
+make  -j2
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 91deee26..21e78ebe 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -14,6 +14,7 @@ requirements:
     #- boost-cpp ==1.64.0 
 #    - boost
 #    - boost-cpp
+    - boost-dev ==1.63
     - python 3.6 # [py36]
     - python 2.7 # [py27]
     - cmake >=3.1
@@ -36,6 +37,7 @@ requirements:
 
 
   run:
+    - boost-dev ==1.63
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From e3ebd134721725282f6a070760cd1736c57309a6 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 10 Apr 2018 09:34:06 +0000
Subject: [PATCH 23/59] use PYTHON_DEST to point to the site_packages

---
 conda-recipe/build.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index d631cb80..356708d5 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -40,6 +40,7 @@ echo "$SRC_DIR/ccpi/Python"
 
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST="${SP_DIR}/sirf" \
     -USIRF_URL \
     -USIRF_TAG \
     -USTIR_URL \

From a34049fd902ef7d944763e1cc445fb6f0ae6ed95 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 5 Apr 2018 15:46:47 +0000
Subject: [PATCH 24/59] first working conda recipe

---
 conda-recipe/build.sh  | 63 ++++++++++++++++++++++++++++++++++++++++++
 conda-recipe/meta.yaml | 56 +++++++++++++++++++++++++++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 conda-recipe/build.sh
 create mode 100644 conda-recipe/meta.yaml

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
new file mode 100644
index 00000000..d631cb80
--- /dev/null
+++ b/conda-recipe/build.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+#=========================================================================
+
+if [ -z "$SIRF_VERSION" ]; then
+    echo "Need to set SIRF_VERSION"
+    exit 1
+fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+cp -rv "$RECIPE_DIR/../" "$SRC_DIR/SIRF-SuperBuild"
+
+cd $SRC_DIR/build
+
+echo "$SRC_DIR/ccpi/Python"
+
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -USIRF_URL \
+    -USIRF_TAG \
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=Off \
+    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=On
+
+make  -j1
+cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
new file mode 100644
index 00000000..fbd25428
--- /dev/null
+++ b/conda-recipe/meta.yaml
@@ -0,0 +1,56 @@
+package:
+  name: sirf
+  version: {{ environ['SIRF_VERSION'] }}
+
+
+build:
+  preserve_egg_dir: False
+  script_env:
+    - SIRF_VERSION   
+#  number: 0
+    
+requirements:
+  build:
+#    - boost ==1.64.0	
+#    - boost-cpp ==1.64.0 
+    #- boost
+    #- boost-cpp
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - libxml2
+    - psutil
+    - nose
+    - coverage
+    - fftw
+    - swig >=3
+    - libxslt
+
+
+  run:
+    #- boost
+#    - libtiff
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - psutil
+    - fftw
+
+	
+about:
+  home: http://www.ccpi.ac.uk
+  license:  BSD license
+  summary: 'CCPi Toolbox'

From 3c31770f7ee7a8238a092303088283188e600d6e Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:41:32 +0000
Subject: [PATCH 25/59] updated about, removed SIRF_VERSION env var

---
 conda-recipe/meta.yaml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index fbd25428..98e2fb6e 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -1,20 +1,19 @@
 package:
   name: sirf
-  version: {{ environ['SIRF_VERSION'] }}
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.0.0
 
 
 build:
   preserve_egg_dir: False
-  script_env:
-    - SIRF_VERSION   
 #  number: 0
     
 requirements:
   build:
 #    - boost ==1.64.0	
 #    - boost-cpp ==1.64.0 
-    #- boost
-    #- boost-cpp
+#    - boost
+#    - boost-cpp
     - python 3.6 # [py36]
     - python 2.7 # [py27]
     - cmake >=3.1
@@ -51,6 +50,6 @@ requirements:
 
 	
 about:
-  home: http://www.ccpi.ac.uk
-  license:  BSD license
-  summary: 'CCPi Toolbox'
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From 8c8b5ceaa2d9468ae3da32663746fefcbb91a460 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:47:04 +0000
Subject: [PATCH 26/59] removed SIRF_VERSION env var

---
 conda-recipe/build.sh | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 356708d5..133b85e5 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -25,10 +25,10 @@
 #
 #=========================================================================
 
-if [ -z "$SIRF_VERSION" ]; then
-    echo "Need to set SIRF_VERSION"
-    exit 1
-fi  
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
 
 mkdir "$SRC_DIR/build"
 mkdir "$SRC_DIR/SIRF-SuperBuild"
@@ -40,15 +40,17 @@ echo "$SRC_DIR/ccpi/Python"
 
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST="${SP_DIR}/sirf" \
+    -DPYTHON_DEST=${SP_DIR}/sirf \
     -USIRF_URL \
     -USIRF_TAG \
+    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
     -DUSE_SYSTEM_Armadillo=Off \

From 0c96e87bb0cb7e2344c09a1d9ceff7919cc4c21b Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 13:57:22 +0000
Subject: [PATCH 27/59] bugfixes

---
 conda-recipe/build.sh  | 11 ++++++++---
 conda-recipe/meta.yaml |  5 +++--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 133b85e5..133b201d 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -38,9 +38,10 @@ cd $SRC_DIR/build
 
 echo "$SRC_DIR/ccpi/Python"
 
+#site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${SP_DIR}/sirf \
+    -DPYTHON_DEST=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
     -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
@@ -56,11 +57,15 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_Armadillo=Off \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
-    -DBUILD_siemens_to_ismrmrd=On
+    -DBUILD_siemens_to_ismrmrd=On \
+    -DCONDA_BUILD=On
 
-make  -j1
+make  -j3
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
+cd ${PREFIX}/python
+${PYTHON} setup.py develop
+
 # add to 
 #echo "${PREFIX}/python" > ${PREFIX}
 #${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 98e2fb6e..4c202218 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -10,8 +10,8 @@ build:
     
 requirements:
   build:
-#    - boost ==1.64.0	
-#    - boost-cpp ==1.64.0 
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
 #    - boost
 #    - boost-cpp
     - python 3.6 # [py36]
@@ -36,6 +36,7 @@ requirements:
   run:
     #- boost
 #    - libtiff
+    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From 947c2852cb4a6bcf30fc9080efff907e888e5d3b Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 14:04:19 +0000
Subject: [PATCH 28/59] bugfixes

---
 conda-recipe/build.sh  | 2 +-
 conda-recipe/meta.yaml | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 133b201d..764a1d03 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -64,7 +64,7 @@ make  -j3
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
-${PYTHON} setup.py develop
+${PYTHON} setup.py install
 
 # add to 
 #echo "${PREFIX}/python" > ${PREFIX}
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 4c202218..0104ea21 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -48,6 +48,8 @@ requirements:
     - h5py
     - psutil
     - fftw
+    - libgcc-ng
+    - libstdcxx-ng
 
 	
 about:

From 021fef78fd43b8894639e4c1d93e0dab8858d045 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 25 Apr 2018 15:15:11 +0000
Subject: [PATCH 29/59] added dependency

---
 conda-recipe/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 0104ea21..3d47166f 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -50,6 +50,7 @@ requirements:
     - fftw
     - libgcc-ng
     - libstdcxx-ng
+    - openblas
 
 	
 about:

From 28fc8c93decab56b5dc3d8e819e58c903a1181bf Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 26 Apr 2018 11:01:08 +0000
Subject: [PATCH 30/59] removed boost dependency

currently the boost in conda-forge does not contain all the libs we need. So we need to build and install.
---
 conda-recipe/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3d47166f..3ead54cd 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -34,9 +34,6 @@ requirements:
 
 
   run:
-    #- boost
-#    - libtiff
-    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From 5acdcf35184508edc7552dda2d17231303c20d1e Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 3 May 2018 11:34:12 +0000
Subject: [PATCH 31/59] Added dependency

---
 conda-recipe/build.sh  | 9 +++++----
 conda-recipe/meta.yaml | 5 ++++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 764a1d03..c8f34aa3 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -41,10 +41,10 @@ echo "$SRC_DIR/ccpi/Python"
 #site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${PREFIX}/python\
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
+    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -54,13 +54,14 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
-    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_Armadillo=On \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=On \
+    -DUSE_SYSTEM_GTEST=On\
     -DCONDA_BUILD=On
 
-make  -j3
+make  -j1
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3ead54cd..91deee26 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -31,6 +31,8 @@ requirements:
     - fftw
     - swig >=3
     - libxslt
+    - armadillo
+    - gtest
 
 
   run:
@@ -48,7 +50,8 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-
+    - armadillo
+    - gtest
 	
 about:
   home: http://www.ccppetmr.ac.uk

From f9e7507e4c7f528cfdb900e2bae1257aa246d600 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 11 Apr 2018 10:41:32 +0000
Subject: [PATCH 32/59] updated about, removed SIRF_VERSION env var

---
 conda-recipe/meta.yaml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index fbd25428..98e2fb6e 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -1,20 +1,19 @@
 package:
   name: sirf
-  version: {{ environ['SIRF_VERSION'] }}
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.0.0
 
 
 build:
   preserve_egg_dir: False
-  script_env:
-    - SIRF_VERSION   
 #  number: 0
     
 requirements:
   build:
 #    - boost ==1.64.0	
 #    - boost-cpp ==1.64.0 
-    #- boost
-    #- boost-cpp
+#    - boost
+#    - boost-cpp
     - python 3.6 # [py36]
     - python 2.7 # [py27]
     - cmake >=3.1
@@ -51,6 +50,6 @@ requirements:
 
 	
 about:
-  home: http://www.ccpi.ac.uk
-  license:  BSD license
-  summary: 'CCPi Toolbox'
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From cfe75733b98e69c33246cc092457020ed5f837ad Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 10 Apr 2018 09:34:06 +0000
Subject: [PATCH 33/59] removed SIRF_VERSION env var

---
 conda-recipe/build.sh | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index d631cb80..133b85e5 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -25,10 +25,10 @@
 #
 #=========================================================================
 
-if [ -z "$SIRF_VERSION" ]; then
-    echo "Need to set SIRF_VERSION"
-    exit 1
-fi  
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
 
 mkdir "$SRC_DIR/build"
 mkdir "$SRC_DIR/SIRF-SuperBuild"
@@ -40,14 +40,17 @@ echo "$SRC_DIR/ccpi/Python"
 
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST=${SP_DIR}/sirf \
     -USIRF_URL \
     -USIRF_TAG \
+    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
     -DUSE_SYSTEM_Armadillo=Off \

From f205edc433166fe1c925179a784e8b28c3b0c7b5 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 24 Apr 2018 13:57:22 +0000
Subject: [PATCH 34/59] bugfixes

---
 conda-recipe/build.sh  | 11 ++++++++---
 conda-recipe/meta.yaml |  7 +++++--
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 133b85e5..764a1d03 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -38,9 +38,10 @@ cd $SRC_DIR/build
 
 echo "$SRC_DIR/ccpi/Python"
 
+#site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${SP_DIR}/sirf \
+    -DPYTHON_DEST=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
     -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
@@ -56,11 +57,15 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_Armadillo=Off \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
-    -DBUILD_siemens_to_ismrmrd=On
+    -DBUILD_siemens_to_ismrmrd=On \
+    -DCONDA_BUILD=On
 
-make  -j1
+make  -j3
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
+cd ${PREFIX}/python
+${PYTHON} setup.py install
+
 # add to 
 #echo "${PREFIX}/python" > ${PREFIX}
 #${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 98e2fb6e..0104ea21 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -10,8 +10,8 @@ build:
     
 requirements:
   build:
-#    - boost ==1.64.0	
-#    - boost-cpp ==1.64.0 
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
 #    - boost
 #    - boost-cpp
     - python 3.6 # [py36]
@@ -36,6 +36,7 @@ requirements:
   run:
     #- boost
 #    - libtiff
+    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]
@@ -47,6 +48,8 @@ requirements:
     - h5py
     - psutil
     - fftw
+    - libgcc-ng
+    - libstdcxx-ng
 
 	
 about:

From 6469b60c905b85cf7bc8dea63bffd85822dd8f64 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 25 Apr 2018 15:15:11 +0000
Subject: [PATCH 35/59] added dependency

---
 conda-recipe/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 0104ea21..3d47166f 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -50,6 +50,7 @@ requirements:
     - fftw
     - libgcc-ng
     - libstdcxx-ng
+    - openblas
 
 	
 about:

From d5d3306fc4c6383f3c6e8bfe31bae3c03d8b2069 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 26 Apr 2018 11:01:08 +0000
Subject: [PATCH 36/59] removed boost dependency

currently the boost in conda-forge does not contain all the libs we need. So we need to build and install.
---
 conda-recipe/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3d47166f..3ead54cd 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -34,9 +34,6 @@ requirements:
 
 
   run:
-    #- boost
-#    - libtiff
-    #- boost ==1.64.0
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
     - python 3.6 # [py36]

From a06bd8513a9b5607cebe07412cbeb09bd3dd72dc Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 3 May 2018 11:34:12 +0000
Subject: [PATCH 37/59] Added dependency

---
 conda-recipe/build.sh  | 9 +++++----
 conda-recipe/meta.yaml | 5 ++++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index 764a1d03..c8f34aa3 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -41,10 +41,10 @@ echo "$SRC_DIR/ccpi/Python"
 #site-packages ${SP_DIR}/sirf
 cmake ../SIRF-SuperBuild \
     -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-    -DPYTHON_DEST=${PREFIX}/python\
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a4f7bd8676bb9c08dd6ba66a55e4ccbddce3bf5f\
+    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -54,13 +54,14 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_GADGETRON=On \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=Off \
-    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_Armadillo=On \
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=On \
+    -DUSE_SYSTEM_GTEST=On\
     -DCONDA_BUILD=On
 
-make  -j3
+make  -j1
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 3ead54cd..91deee26 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -31,6 +31,8 @@ requirements:
     - fftw
     - swig >=3
     - libxslt
+    - armadillo
+    - gtest
 
 
   run:
@@ -48,7 +50,8 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-
+    - armadillo
+    - gtest
 	
 about:
   home: http://www.ccppetmr.ac.uk

From b641d119cc2dab1e3f48aa7776e31530618937ed Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 3 May 2018 16:43:56 +0100
Subject: [PATCH 38/59] update SIRF tag to current master

---
 conda-recipe/build.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index c8f34aa3..b59a50b9 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -44,24 +44,24 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=1237daebaab4aeccd4e6a14cb0eef0b55b49ef7c \
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
-    -DBUILD_GADGETRON=On \
-    -DUSE_SYSTEM_SWIG=On \
-    -DUSE_SYSTEM_Boost=Off \
-    -DUSE_SYSTEM_Armadillo=On \
-    -DUSE_SYSTEM_FFTW3=On \
+    -DBUILD_GADGETRON=ON \
+    -DUSE_SYSTEM_SWIG=ON \
+    -DUSE_SYSTEM_Boost=OFF \
+    -DUSE_SYSTEM_Armadillo=ON \
+    -DUSE_SYSTEM_FFTW3=ON \
     -DUSE_SYSTEM_HDF5=ON \
-    -DBUILD_siemens_to_ismrmrd=On \
-    -DUSE_SYSTEM_GTEST=On\
-    -DCONDA_BUILD=On
+    -DBUILD_siemens_to_ismrmrd=ON \
+    -DUSE_SYSTEM_GTEST=ON \
+    -DCONDA_BUILD=ON
 
-make  -j1
+make -j
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python

From 8f91cc83292a1ff65c42ba80697c61ccf77791d4 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 4 May 2018 06:04:20 +0000
Subject: [PATCH 39/59] build Boost, remove dependency on Boost in meta.yaml

---
 conda-recipe/build.sh  | 11 ++++-------
 conda-recipe/meta.yaml |  6 ++----
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
index b59a50b9..b9c50f97 100644
--- a/conda-recipe/build.sh
+++ b/conda-recipe/build.sh
@@ -44,7 +44,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=1237daebaab4aeccd4e6a14cb0eef0b55b49ef7c \
+    -DSIRF_TAG=a27aee80e8db38767a4b42e8bbca34e9cc5d901d \
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -53,20 +53,17 @@ cmake ../SIRF-SuperBuild \
     -UISMRMRD_TAG \
     -DBUILD_GADGETRON=ON \
     -DUSE_SYSTEM_SWIG=ON \
-    -DUSE_SYSTEM_Boost=OFF \
+    -DUSE_SYSTEM_Boost=Off \
     -DUSE_SYSTEM_Armadillo=ON \
     -DUSE_SYSTEM_FFTW3=ON \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=ON \
-    -DUSE_SYSTEM_GTEST=ON \
+    -DUSE_SYSTEM_Gtest=ON \
     -DCONDA_BUILD=ON
 
-make -j
+make -j1
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 cd ${PREFIX}/python
 ${PYTHON} setup.py install
 
-# add to 
-#echo "${PREFIX}/python" > ${PREFIX}
-#${PREFIX}/python
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 91deee26..2320fac7 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -10,10 +10,7 @@ build:
     
 requirements:
   build:
-    #- boost ==1.64.0	
-    #- boost-cpp ==1.64.0 
-#    - boost
-#    - boost-cpp
+    #- boost-dev ==1.63
     - python 3.6 # [py36]
     - python 2.7 # [py27]
     - cmake >=3.1
@@ -40,6 +37,7 @@ requirements:
     - vc 9  # [win and py27]
     - python 3.6 # [py36]
     - python 2.7 # [py27]
+    #- boost-dev ==1.63
     - numpy
     - scipy
     - matplotlib

From 04212a50d7fe6b72ea92fb2921a930392639e31f Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 30 Jan 2019 15:23:14 +0000
Subject: [PATCH 40/59] first working compilation of SIRF with conda

---
 conda/gadgetron/build.sh  |  1 +
 conda/gadgetron/meta.yaml |  2 +
 conda/sirf/build.sh       | 78 +++++++++++++++++++++++++++++++++++++++
 conda/sirf/meta.yaml      | 63 +++++++++++++++++++++++++++++++
 4 files changed, 144 insertions(+)
 create mode 100644 conda/sirf/build.sh
 create mode 100644 conda/sirf/meta.yaml

diff --git a/conda/gadgetron/build.sh b/conda/gadgetron/build.sh
index 81acf028..34a2c35e 100644
--- a/conda/gadgetron/build.sh
+++ b/conda/gadgetron/build.sh
@@ -62,6 +62,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
+    -DUSE_SYSTEM_ACE=ON \
     -DCONDA_BUILD=On
 
 make  -j3 Gadgetron VERBOSE=0
diff --git a/conda/gadgetron/meta.yaml b/conda/gadgetron/meta.yaml
index ef4698e8..8cefadbe 100644
--- a/conda/gadgetron/meta.yaml
+++ b/conda/gadgetron/meta.yaml
@@ -34,6 +34,7 @@ requirements:
     - armadillo
     - gtest
     - ismrmrd
+    - ace
 
 
   run:
@@ -55,6 +56,7 @@ requirements:
     - armadillo
     - gtest
     - ismrmrd
+    - ace
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/sirf/build.sh b/conda/sirf/build.sh
new file mode 100644
index 00000000..b515576d
--- /dev/null
+++ b/conda/sirf/build.sh
@@ -0,0 +1,78 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+#=========================================================================
+
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+#cp -rv "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+rsync -rv --exclude=.git "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+
+
+cd $SRC_DIR/build
+
+
+#site-packages ${SP_DIR}/sirf
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST_DIR=${SP_DIR}\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=v1.1.1\
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=Off \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=On \
+    -DUSE_SYSTEM_Armadillo=On \
+    -DUSE_SYSTEM_ISMRMRD=ON\
+    -DUSE_SYSTEM_STIR=Off\
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=Off \
+    -DUSE_SYSTEM_GTest=On\
+    -DPYTHON_STRATEGY=SETUP_PY
+    #-DCONDA_BUILD=On
+
+make  -j3 STIR
+make  -j1 SIRF
+
+#cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+#cd ${PREFIX}/python
+#${PYTHON} setup.py install
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
new file mode 100644
index 00000000..0c4256f4
--- /dev/null
+++ b/conda/sirf/meta.yaml
@@ -0,0 +1,63 @@
+package:
+  name: sirf-stir
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.1.1
+
+
+build:
+  preserve_egg_dir: False
+  number: 0
+    
+requirements:
+  build:
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
+    - boost >=1.63
+#    - boost-cpp
+    - python {{ python }}
+#    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+    - numpy {{ numpy }}
+#    - scipy
+#    - matplotlib
+#    - docopt
+    - h5py
+#    - libxml2
+    - psutil
+    - nose
+    - coverage
+    - fftw
+    - swig >=3
+#    - libxslt
+#    - armadillo
+    - gtest
+#    - ismrmrd
+
+
+  run:
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+    - python {{ python }}
+    - numpy {{ numpy }}
+    - scipy
+    - matplotlib
+    - docopt
+#    - boost >=1.63
+#    - h5py
+#    - psutil
+#    - fftw
+#    - libgcc-ng
+#    - libstdcxx-ng
+#    - openblas
+#    - armadillo
+#    - gtest
+#    - ismrmrd
+    - gadgetron
+    - h5py
+	
+about:
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From a97725b729f9e12f197c1e92f2c2a5226575d07c Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 12 Jul 2019 10:10:47 -0400
Subject: [PATCH 41/59] fixed dependency

---
 conda/gtest/meta.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/conda/gtest/meta.yaml b/conda/gtest/meta.yaml
index cd34fa38..b4a6a744 100644
--- a/conda/gtest/meta.yaml
+++ b/conda/gtest/meta.yaml
@@ -13,6 +13,7 @@ requirements:
     #- boost ==1.64.0	
     #- boost-cpp ==1.64.0 
     - boost >=1.63
+    - boost-cpp >=1.63
 #    - boost-cpp
 #    - python 3.6 # [py36]
 #    - python 2.7 # [py27]
@@ -45,6 +46,7 @@ requirements:
 #    - matplotlib
 #    - docopt
     - boost >=1.63
+    - boost-cpp >=1.63
     - h5py
     - psutil
     - fftw

From 50a83b6b40580ce308480d78f23498cbfac9c599 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 12 Jul 2019 11:30:07 -0400
Subject: [PATCH 42/59] changed SIRF version; add ITK

---
 conda/armadillo/build.sh | 2 +-
 conda/boost/build.sh     | 2 +-
 conda/gadgetron/build.sh | 4 ++--
 conda/gtest/build.sh     | 6 +++---
 conda/ismrmrd/build.sh   | 2 +-
 conda/sirf/build.sh      | 8 +++++---
 conda/sirf/meta.yaml     | 4 +++-
 7 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/conda/armadillo/build.sh b/conda/armadillo/build.sh
index 6d8e2953..893572a3 100644
--- a/conda/armadillo/build.sh
+++ b/conda/armadillo/build.sh
@@ -43,7 +43,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
diff --git a/conda/boost/build.sh b/conda/boost/build.sh
index 5a3576a6..eb76d963 100644
--- a/conda/boost/build.sh
+++ b/conda/boost/build.sh
@@ -43,7 +43,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
diff --git a/conda/gadgetron/build.sh b/conda/gadgetron/build.sh
index 34a2c35e..81b7d2b7 100644
--- a/conda/gadgetron/build.sh
+++ b/conda/gadgetron/build.sh
@@ -45,7 +45,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -65,7 +65,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_ACE=ON \
     -DCONDA_BUILD=On
 
-make  -j3 Gadgetron VERBOSE=0
+make  -j1 Gadgetron VERBOSE=1
 
 cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/gtest/build.sh b/conda/gtest/build.sh
index 5b01d4db..744210d1 100644
--- a/conda/gtest/build.sh
+++ b/conda/gtest/build.sh
@@ -45,19 +45,19 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
-    -DBUILD_GADGETRON=On \
+    -DBUILD_GADGETRON=Off \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=On \
     -DUSE_SYSTEM_Armadillo=On \
     -DUSE_SYSTEM_ISMRMRD=ON\
-    -DUSE_SYSTEM_STIR=Off\
+    -DUSE_SYSTEM_STIR=On\
     -DUSE_SYSTEM_FFTW3=On \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=Off \
diff --git a/conda/ismrmrd/build.sh b/conda/ismrmrd/build.sh
index 83921539..71ea7b1e 100644
--- a/conda/ismrmrd/build.sh
+++ b/conda/ismrmrd/build.sh
@@ -43,7 +43,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
diff --git a/conda/sirf/build.sh b/conda/sirf/build.sh
index b515576d..8526084c 100644
--- a/conda/sirf/build.sh
+++ b/conda/sirf/build.sh
@@ -45,7 +45,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${SP_DIR}\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=v1.1.1\
+    -DSIRF_TAG=v2.0.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -62,8 +62,10 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
-    -DPYTHON_STRATEGY=SETUP_PY
-    #-DCONDA_BUILD=On
+    -DUSE_ITK=ON\
+    -DUSE_SYSTEM_ITK=ON\
+    #-DPYTHON_STRATEGY=SETUP_PY
+    -DCONDA_BUILD=On
 
 make  -j3 STIR
 make  -j1 SIRF
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index 0c4256f4..2c525926 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: sirf-stir
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: 1.1.1
+  version: 2.0.0
 
 
 build:
@@ -34,6 +34,7 @@ requirements:
 #    - armadillo
     - gtest
 #    - ismrmrd
+   -  itk
 
 
   run:
@@ -56,6 +57,7 @@ requirements:
 #    - ismrmrd
     - gadgetron
     - h5py
+    - itk
 	
 about:
   home: http://www.ccppetmr.ac.uk

From 8fc0f85170132f791c1d00edf5bc49b5139a7c32 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 06:15:16 -0400
Subject: [PATCH 43/59] allows build of Zlib if not present on system

---
 SuperBuild/External_NIFTYREG.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SuperBuild/External_NIFTYREG.cmake b/SuperBuild/External_NIFTYREG.cmake
index cffe0cdf..c51cda9c 100644
--- a/SuperBuild/External_NIFTYREG.cmake
+++ b/SuperBuild/External_NIFTYREG.cmake
@@ -66,6 +66,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       -DUSE_THROW_EXCEP=ON
       # fixes lib_reg_maths.a `GOMP_parallel' undefined reference linker errors
       -DUSE_OPENMP:BOOL=OFF
+      -DBUILD_ALL_DEP=ON
     INSTALL_DIR ${${proj}_Install_Dir}
     DEPENDS ${${proj}_DEPENDENCIES})
 

From ee5e5d884027d22e5ae7a96118bda566a46e9c4a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 06:16:36 -0400
Subject: [PATCH 44/59] updated gadgetron version

---
 conda/gadgetron/.build.sh.swp  | Bin 12288 -> 0 bytes
 conda/gadgetron/.meta.yaml.swp | Bin 12288 -> 0 bytes
 conda/gadgetron/meta.yaml      |   3 ++-
 3 files changed, 2 insertions(+), 1 deletion(-)
 delete mode 100644 conda/gadgetron/.build.sh.swp
 delete mode 100644 conda/gadgetron/.meta.yaml.swp

diff --git a/conda/gadgetron/.build.sh.swp b/conda/gadgetron/.build.sh.swp
deleted file mode 100644
index 51e6a251e3e324b765acbb758208241cb4723f9b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/conda/gadgetron/.meta.yaml.swp b/conda/gadgetron/.meta.yaml.swp
deleted file mode 100644
index 96b1c285ba1e9fd8eb604bb910b71230024a46a6..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/conda/gadgetron/meta.yaml b/conda/gadgetron/meta.yaml
index 8cefadbe..96aec093 100644
--- a/conda/gadgetron/meta.yaml
+++ b/conda/gadgetron/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: gadgetron
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: e7eb430673eb3272e8a821b51750c0a2a96dafed
+  version: b6191eaaa72ccca6c6a5fe4c0fa3319694f512ab
 
 
 build:
@@ -13,6 +13,7 @@ requirements:
     #- boost ==1.64.0	
     #- boost-cpp ==1.64.0 
     - boost >=1.63
+    - boost-cpp >=1.63
 #    - boost-cpp
 #    - python 3.6 # [py36]
 #    - python 2.7 # [py27]

From 3e7c6c5a55c30a9728ac060638be4cff4e827373 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 06:17:08 -0400
Subject: [PATCH 45/59] added build variants file

---
 conda/sirf/conda_build_config.yaml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 conda/sirf/conda_build_config.yaml

diff --git a/conda/sirf/conda_build_config.yaml b/conda/sirf/conda_build_config.yaml
new file mode 100644
index 00000000..ec2a5300
--- /dev/null
+++ b/conda/sirf/conda_build_config.yaml
@@ -0,0 +1,4 @@
+python:
+  - 2.7 
+numpy:
+  - 1.11

From d5421d38d3b3cf5c1429e2072127799c179d529b Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 07:31:06 -0400
Subject: [PATCH 46/59] added hdf5

---
 conda/hdf5/.build.sh.swp           | Bin 0 -> 12288 bytes
 conda/hdf5/.meta.yaml.swp          | Bin 0 -> 12288 bytes
 conda/hdf5/build.sh                |  79 +++++++++++++++++++++++++++++
 conda/hdf5/conda_build_config.yaml |   4 ++
 conda/hdf5/meta.yaml               |  50 ++++++++++++++++++
 5 files changed, 133 insertions(+)
 create mode 100644 conda/hdf5/.build.sh.swp
 create mode 100644 conda/hdf5/.meta.yaml.swp
 create mode 100644 conda/hdf5/build.sh
 create mode 100644 conda/hdf5/conda_build_config.yaml
 create mode 100644 conda/hdf5/meta.yaml

diff --git a/conda/hdf5/.build.sh.swp b/conda/hdf5/.build.sh.swp
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diff --git a/conda/hdf5/.meta.yaml.swp b/conda/hdf5/.meta.yaml.swp
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diff --git a/conda/hdf5/build.sh b/conda/hdf5/build.sh
new file mode 100644
index 00000000..f34bf955
--- /dev/null
+++ b/conda/hdf5/build.sh
@@ -0,0 +1,79 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+#=========================================================================
+
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+#cp -rv "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+rsync -rv --exclude=.git "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+
+
+cd $SRC_DIR/build
+
+
+#site-packages ${SP_DIR}/sirf
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST_DIR=${SP_DIR}\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=v2.0.0\
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=Off \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=On \
+    -DUSE_SYSTEM_Armadillo=On \
+    -DUSE_SYSTEM_ISMRMRD=Off\
+    -DUSE_SYSTEM_STIR=Off\
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=OFF \
+    -DBUILD_siemens_to_ismrmrd=Off \
+    -DUSE_SYSTEM_GTest=OFF\
+    -DUSE_ITK=ON\
+    -DUSE_SYSTEM_ITK=OFF\
+    -DUSE_SYSTEM_NIFTYREG=OFF\
+    -DCONDA_BUILD=On
+
+make -j2 HDF5
+
+#cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+#cd ${PREFIX}/python
+#${PYTHON} setup.py install
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python
diff --git a/conda/hdf5/conda_build_config.yaml b/conda/hdf5/conda_build_config.yaml
new file mode 100644
index 00000000..ec2a5300
--- /dev/null
+++ b/conda/hdf5/conda_build_config.yaml
@@ -0,0 +1,4 @@
+python:
+  - 2.7 
+numpy:
+  - 1.11
diff --git a/conda/hdf5/meta.yaml b/conda/hdf5/meta.yaml
new file mode 100644
index 00000000..e2d7dcf2
--- /dev/null
+++ b/conda/hdf5/meta.yaml
@@ -0,0 +1,50 @@
+package:
+  name: hdf5
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.10.1
+
+
+build:
+  preserve_egg_dir: False
+  number: 0
+    
+requirements:
+  build:
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
+    - boost >=1.63
+    - boost-cpp >=1.63
+    #- python 
+    #- {{ pin_compatible('numpy', max_pin='x.x') }}
+#    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+    #- numpy {{ numpy }}
+#    - scipy
+#    - matplotlib
+#    - docopt
+    #- h5py
+#    - libxml2
+    #- psutil
+    - nose
+    - coverage
+    - fftw
+    - swig >=3
+#    - libxslt
+#    - armadillo
+    #- gtest
+#    - ismrmrd
+
+
+  run:
+    - boost >=1.63
+    - boost-cpp >=1.63
+    - fftw
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+	
+about:
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From 63051ae380310cd933480445f59c08fc10ab88f5 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 07:35:06 -0400
Subject: [PATCH 47/59] additional fixes

---
 conda/armadillo/meta.yaml |   2 +-
 conda/hdf5/.build.sh.swp  | Bin 12288 -> 0 bytes
 conda/hdf5/.meta.yaml.swp | Bin 12288 -> 0 bytes
 conda/sirf/build.sh       |  10 ++++++----
 conda/sirf/meta.yaml      |  12 +++++-------
 5 files changed, 12 insertions(+), 12 deletions(-)
 delete mode 100644 conda/hdf5/.build.sh.swp
 delete mode 100644 conda/hdf5/.meta.yaml.swp

diff --git a/conda/armadillo/meta.yaml b/conda/armadillo/meta.yaml
index 56b1212b..adea62e9 100644
--- a/conda/armadillo/meta.yaml
+++ b/conda/armadillo/meta.yaml
@@ -10,7 +10,7 @@ build:
 requirements:
   build:
     #- boost ==1.64.0	
-    #- boost-cpp ==1.64.0 
+    - boost-cpp >=1.63.0 
     - boost >=1.63
 #    - boost-cpp
 #    - python 3.6 # [py36]
diff --git a/conda/hdf5/.build.sh.swp b/conda/hdf5/.build.sh.swp
deleted file mode 100644
index 51f0ae33da0c3f6cee076f07dfdeeb5764f14f72..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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zER8rFL%{VYrEb-<u8Y<zQ(aB?WxBzYnKnY2^sFg`TGgob+^eWQdUkD?QIus|&y~v}
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N(-@1iF=jYl|6d^BGqL~x

diff --git a/conda/hdf5/.meta.yaml.swp b/conda/hdf5/.meta.yaml.swp
deleted file mode 100644
index 7a0cf5c0318ba08dc8e4efd085cef19d40a9a38c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12288
zcmeI2O^6&t7=|l~NMfQvF~_9L2&3Ti{On(BST%~PEB?Ta=8`N!O?T}~v0Ytlb@j})
z>l)BwJPPW`lLtk;ix&?bgg`DH1dpCX@F)s;$lJ5s+1_M{CXhqmYk0P+>#O>z>Z$65
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zZ*P}{ot;_WHnc9T^RjE8#ilHl=XI+gliZDQ;(Oi_$4>3-5GH`36BQ2vqZ8rOFp^I+
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w>}t7I1pzXiC~M;L&Enho!MPXL`m1le-dx{Zag5&*cpvb6J;Up=iNoQus}T{JbpQYW

diff --git a/conda/sirf/build.sh b/conda/sirf/build.sh
index 8526084c..639cf020 100644
--- a/conda/sirf/build.sh
+++ b/conda/sirf/build.sh
@@ -63,12 +63,14 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
     -DUSE_ITK=ON\
-    -DUSE_SYSTEM_ITK=ON\
-    #-DPYTHON_STRATEGY=SETUP_PY
+    -DUSE_SYSTEM_ITK=OFF\
+    -DUSE_SYSTEM_NIFTYREG=OFF\
     -DCONDA_BUILD=On
 
-make  -j3 STIR
-make  -j1 SIRF
+make -j2 ITK
+make -j2 NIFTYREG
+make -j2 STIR
+make -j1 SIRF
 
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index 2c525926..29692f0a 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -1,5 +1,5 @@
 package:
-  name: sirf-stir
+  name: sirf
 #  version: {{ environ['SIRF_VERSION'] }}
   version: 2.0.0
 
@@ -14,12 +14,12 @@ requirements:
     #- boost-cpp ==1.64.0 
     - boost >=1.63
 #    - boost-cpp
-    - python {{ python }}
+    - python 
+    - {{ pin_compatible('numpy', max_pin='x.x') }}
 #    - python 2.7 # [py27]
     - cmake >=3.1
     - vc 14 # [win and py36] 
     - vc 9  # [win and py27]
-    - numpy {{ numpy }}
 #    - scipy
 #    - matplotlib
 #    - docopt
@@ -34,14 +34,13 @@ requirements:
 #    - armadillo
     - gtest
 #    - ismrmrd
-   -  itk
 
 
   run:
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
-    - python {{ python }}
-    - numpy {{ numpy }}
+    - python
+    - {{ pin_compatible('numpy', max_pin='x.x') }}
     - scipy
     - matplotlib
     - docopt
@@ -57,7 +56,6 @@ requirements:
 #    - ismrmrd
     - gadgetron
     - h5py
-    - itk
 	
 about:
   home: http://www.ccppetmr.ac.uk

From 9901082d47a2d6e50f60a197ed13877c98e2856f Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 15:28:13 +0100
Subject: [PATCH 48/59] updated recipe

---
 conda/sirf/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index 29692f0a..bc350bc6 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -24,6 +24,7 @@ requirements:
 #    - matplotlib
 #    - docopt
     - h5py
+    - hdf5 ==1.10.1
 #    - libxml2
     - psutil
     - nose

From 0ece523f390adaec355ba0e14e1a4cdd48a2a938 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Wed, 31 Jul 2019 11:27:41 -0400
Subject: [PATCH 49/59] added build variants for armadillo

---
 conda/armadillo/conda_build_config.yaml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 conda/armadillo/conda_build_config.yaml

diff --git a/conda/armadillo/conda_build_config.yaml b/conda/armadillo/conda_build_config.yaml
new file mode 100644
index 00000000..ec2a5300
--- /dev/null
+++ b/conda/armadillo/conda_build_config.yaml
@@ -0,0 +1,4 @@
+python:
+  - 2.7 
+numpy:
+  - 1.11

From eadc5f500603e5a929267027554308c37a1bad24 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 28 Nov 2019 10:28:22 +0000
Subject: [PATCH 50/59] require Boost 1.68

---
 conda/ismrmrd/build.sh  | 4 ++--
 conda/ismrmrd/meta.yaml | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/conda/ismrmrd/build.sh b/conda/ismrmrd/build.sh
index 71ea7b1e..7c602d8b 100644
--- a/conda/ismrmrd/build.sh
+++ b/conda/ismrmrd/build.sh
@@ -43,7 +43,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=v2.0.0\
+    -DSIRF_TAG=v2.1.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -60,7 +60,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_GTest=On\
     -DCONDA_BUILD=On
 
-make  -j1 ISMRMRD
+make  -j1 ISMRMRD VERBOSE=1
 
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/ismrmrd/meta.yaml b/conda/ismrmrd/meta.yaml
index aa81bfa4..09acfcdf 100644
--- a/conda/ismrmrd/meta.yaml
+++ b/conda/ismrmrd/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: ismrmrd
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: ba4773f9cf4bba5f3ccd19930e3548d8273fee01
+  version: v1.4.1
 
 
 build:
@@ -12,8 +12,8 @@ requirements:
   build:
     #- boost ==1.64.0	
     #- boost-cpp ==1.64.0 
-    - boost >=1.63
-#    - boost-cpp
+    - boost ==1.68
+      #- boost-cpp >=1.63
 #    - python 3.6 # [py36]
 #    - python 2.7 # [py27]
     - cmake >=3.1

From 64994453974060b37f32424dcd7e5ab62775fdb7 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 28 Nov 2019 10:30:02 +0000
Subject: [PATCH 51/59] install in CONDA build environment

---
 SuperBuild/External_ISMRMRD.cmake | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/SuperBuild/External_ISMRMRD.cmake b/SuperBuild/External_ISMRMRD.cmake
index 3eeec7f9..fa660307 100644
--- a/SuperBuild/External_ISMRMRD.cmake
+++ b/SuperBuild/External_ISMRMRD.cmake
@@ -41,7 +41,11 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   message(STATUS "${__indent}Adding project ${proj}")
 
   ### --- Project specific additions here
-  set(ISMRMRD_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+  if (CONDA_BUILD)
+    set(ISMRMRD_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+  else()
+    set(ISMRMRD_Install_Dir $ENV{PREFIX})
+  endif()
 
   if (NOT WIN32)
     if (USE_SYSTEM_Boost)
@@ -61,6 +65,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
     endif()
   endif ()
 
+
   ExternalProject_Add(${proj}
     ${${proj}_EP_ARGS}
     GIT_REPOSITORY ${${proj}_URL}

From d4b0c4bfd896c54486ac51463cde6775f4e288f5 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 28 Nov 2019 10:30:28 +0000
Subject: [PATCH 52/59] fix run boost requirement

---
 conda/ismrmrd/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda/ismrmrd/meta.yaml b/conda/ismrmrd/meta.yaml
index 09acfcdf..4a890611 100644
--- a/conda/ismrmrd/meta.yaml
+++ b/conda/ismrmrd/meta.yaml
@@ -44,7 +44,7 @@ requirements:
 #    - scipy
 #    - matplotlib
 #    - docopt
-    - boost >=1.63
+    - boost ==1.68
     - h5py
     - psutil
     - fftw

From c782334b179b7c95586c56885fcd6d2d86712c0d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 28 Nov 2019 16:25:22 +0000
Subject: [PATCH 53/59] updated version strings

---
 SuperBuild/External_Boost.cmake     |  2 +-
 SuperBuild/External_Gadgetron.cmake |  2 +-
 SuperBuild/External_ISMRMRD.cmake   |  6 +----
 conda/boost/build.sh                |  4 +--
 conda/gadgetron/meta.yaml           |  2 +-
 conda/ismrmrd/meta.yaml             |  4 +--
 conda/sirf/build.sh                 | 42 +++++++++++++++++++++++++----
 conda/sirf/meta.yaml                |  8 +++---
 conda/stir/build.sh                 |  6 +++--
 conda/stir/meta.yaml                | 16 +++++------
 10 files changed, 61 insertions(+), 31 deletions(-)

diff --git a/SuperBuild/External_Boost.cmake b/SuperBuild/External_Boost.cmake
index ec9de31b..c23a7e1b 100644
--- a/SuperBuild/External_Boost.cmake
+++ b/SuperBuild/External_Boost.cmake
@@ -47,7 +47,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   mark_as_superbuild(Boost_NO_SYSTEM_PATHS)
 
   ### --- Project specific additions here
-  set(Boost_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+  set(${proj}_Install_Dir ${SUPERBUILD_INSTALL_DIR})
   set(Boost_Configure_Script ${CMAKE_CURRENT_LIST_DIR}/External_Boost_configureboost.cmake)
   set(Boost_Build_Script ${CMAKE_CURRENT_LIST_DIR}/External_Boost_buildboost.cmake)
 
diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index 2e27634f..c21b4afe 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -43,7 +43,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   message(STATUS "${__indent}Adding project ${proj}")
 
   ### --- Project specific additions here
-  set(Gadgetron_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+  set(${proj}_Install_Dir ${SUPERBUILD_INSTALL_DIR})
 
   # Gadgetron only adds tests if (GTEST_FOUND AND ARMADILLO_FOUND)
   # but that's currently always the case.
diff --git a/SuperBuild/External_ISMRMRD.cmake b/SuperBuild/External_ISMRMRD.cmake
index fa660307..6c4759a8 100644
--- a/SuperBuild/External_ISMRMRD.cmake
+++ b/SuperBuild/External_ISMRMRD.cmake
@@ -41,11 +41,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   message(STATUS "${__indent}Adding project ${proj}")
 
   ### --- Project specific additions here
-  if (CONDA_BUILD)
-    set(ISMRMRD_Install_Dir ${SUPERBUILD_INSTALL_DIR})
-  else()
-    set(ISMRMRD_Install_Dir $ENV{PREFIX})
-  endif()
+  set(ISMRMRD_Install_Dir ${SUPERBUILD_INSTALL_DIR})
 
   if (NOT WIN32)
     if (USE_SYSTEM_Boost)
diff --git a/conda/boost/build.sh b/conda/boost/build.sh
index eb76d963..13f49e6d 100644
--- a/conda/boost/build.sh
+++ b/conda/boost/build.sh
@@ -43,7 +43,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=v2.0.0\
+    -DSIRF_TAG=v2.1.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -60,7 +60,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_GTEST=On\
     -DCONDA_BUILD=On
 
-make  -j1 Boost
+make  -j2 Boost
 
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/gadgetron/meta.yaml b/conda/gadgetron/meta.yaml
index 96aec093..078a20eb 100644
--- a/conda/gadgetron/meta.yaml
+++ b/conda/gadgetron/meta.yaml
@@ -39,7 +39,7 @@ requirements:
 
 
   run:
-    - vc 14 # [win and py35]
+    - vc 14 # [win and py36]
     - vc 9  # [win and py27]
 #    - python 3.6 # [py36]
 #    - python 2.7 # [py27]
diff --git a/conda/ismrmrd/meta.yaml b/conda/ismrmrd/meta.yaml
index 4a890611..e205c5bb 100644
--- a/conda/ismrmrd/meta.yaml
+++ b/conda/ismrmrd/meta.yaml
@@ -12,7 +12,7 @@ requirements:
   build:
     #- boost ==1.64.0	
     #- boost-cpp ==1.64.0 
-    - boost ==1.68
+    - boost >=1.63
       #- boost-cpp >=1.63
 #    - python 3.6 # [py36]
 #    - python 2.7 # [py27]
@@ -44,7 +44,7 @@ requirements:
 #    - scipy
 #    - matplotlib
 #    - docopt
-    - boost ==1.68
+    - boost >=1.63
     - h5py
     - psutil
     - fftw
diff --git a/conda/sirf/build.sh b/conda/sirf/build.sh
index 639cf020..8ddad63e 100644
--- a/conda/sirf/build.sh
+++ b/conda/sirf/build.sh
@@ -45,7 +45,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${SP_DIR}\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=v2.0.0\
+    -DSIRF_TAG=v2.1.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -63,15 +63,47 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
     -DUSE_ITK=ON\
-    -DUSE_SYSTEM_ITK=OFF\
-    -DUSE_SYSTEM_NIFTYREG=OFF\
+    -DUSE_SYSTEM_ITK=ON\
+    -DUSE_SYSTEM_NIFTYREG=ON\
     -DCONDA_BUILD=On
 
-make -j2 ITK
-make -j2 NIFTYREG
+#make -j2 NIFTYREG
 make -j2 STIR
 make -j1 SIRF
 
+# remove stuff installed by STIR
+rm ${PREFIX}/lib/libdata_buildblock.a
+rm ${PREFIX}/lib/libeval_buildblock.a
+rm ${PREFIX}/lib/libnumerics_buildblock.a
+rm ${PREFIX}/lib/libdisplay.a
+rm ${PREFIX}/lib/libmodelling_buildblock.a
+rm ${PREFIX}/lib/libanalytic_FBP2D.a
+rm ${PREFIX}/lib/libiterative_KOSMAPOSL.a
+rm ${PREFIX}/lib/libiterative_OSMAPOSL.a
+rm ${PREFIX}/lib/libanalytic_FBP3DRP.a
+rm ${PREFIX}/lib/libiterative_OSSPS.a
+rm ${PREFIX}/lib/libShape_buildblock.a
+rm ${PREFIX}/lib/libspatial_transformation_buildblock.a
+rm ${PREFIX}/lib/libscatter_buildblock.a
+rm ${PREFIX}/lib/liblistmode_buildblock.a
+rm ${PREFIX}/lib/libIO.a
+rm ${PREFIX}/lib/librecon_buildblock.a
+rm ${PREFIX}/lib/libbuildblock.a
+rm ${PREFIX}/lib/cmake/FindRDF.cmake
+rm ${PREFIX}/lib/cmake/FindAVW.cmake
+rm ${PREFIX}/lib/cmake/FindLLN.cmake
+rm ${PREFIX}/lib/cmake/FindNumpy.cmake
+rm ${PREFIX}/lib/cmake/STIRConfigVersion.cmake
+rm ${PREFIX}/lib/cmake/FindAllHeaderFiles.cmake
+rm ${PREFIX}/lib/cmake/FindCERN_ROOT.cmake
+rm ${PREFIX}/lib/cmake/STIRConfig.cmake
+rm ${PREFIX}/lib/cmake/STIRTargets.cmake
+rm ${PREFIX}/lib/cmake/STIRTargets-release.cmake
+rm -rf ${PREFIX}/include/stir
+rm -rf ${PREFIX}/share/stir
+rm -rf ${PREFIX}/include/stir_experimental
+
+
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
 #cd ${PREFIX}/python
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index bc350bc6..5777d589 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: sirf
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: 2.0.0
+  version: 2.1.0
 
 
 build:
@@ -45,6 +45,10 @@ requirements:
     - scipy
     - matplotlib
     - docopt
+    - gadgetron
+    - h5py
+    - stir
+    - niftyreg
 #    - boost >=1.63
 #    - h5py
 #    - psutil
@@ -55,8 +59,6 @@ requirements:
 #    - armadillo
 #    - gtest
 #    - ismrmrd
-    - gadgetron
-    - h5py
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/stir/build.sh b/conda/stir/build.sh
index 8a0dd1af..46a4dd23 100644
--- a/conda/stir/build.sh
+++ b/conda/stir/build.sh
@@ -45,7 +45,7 @@ cmake ../SIRF-SuperBuild \
     -DPYTHON_DEST_DIR=${PREFIX}/python\
     -USIRF_URL \
     -USIRF_TAG \
-    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -DSIRF_TAG=v2.1.0\
     -USTIR_URL \
     -USTIR_TAG \
     -UGadgetron_URL \
@@ -62,9 +62,11 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
+    -DUSE_ITK=ON\
+    -DUSE_SYSTEM_ITK=ON\
     -DCONDA_BUILD=On
 
-make  -j1 Gadgetron
+make -j2 STIR
 
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/stir/meta.yaml b/conda/stir/meta.yaml
index ef4698e8..02a7ca6d 100644
--- a/conda/stir/meta.yaml
+++ b/conda/stir/meta.yaml
@@ -1,7 +1,7 @@
 package:
-  name: gadgetron
+  name: stir
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: e7eb430673eb3272e8a821b51750c0a2a96dafed
+  version: 4.0.0_alpha
 
 
 build:
@@ -23,7 +23,7 @@ requirements:
 #    - scipy
 #    - matplotlib
 #    - docopt
-    - h5py
+#    - h5py
 #    - libxml2
     - psutil
     - nose
@@ -31,9 +31,10 @@ requirements:
     - fftw
     - swig >=3
 #    - libxslt
-    - armadillo
+#- armadillo
     - gtest
-    - ismrmrd
+      #- ismrmrd
+    - itk
 
 
   run:
@@ -46,15 +47,12 @@ requirements:
 #    - matplotlib
 #    - docopt
     - boost >=1.63
-    - h5py
     - psutil
     - fftw
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-    - armadillo
-    - gtest
-    - ismrmrd
+    - itk
 	
 about:
   home: http://www.ccppetmr.ac.uk

From 3770aaa5df77277bf7871ac24d84e3c15da06055 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 28 Nov 2019 16:27:09 +0000
Subject: [PATCH 54/59] added niftyreg

---
 conda/niftyreg/build.sh  | 78 ++++++++++++++++++++++++++++++++++++++++
 conda/niftyreg/meta.yaml | 60 +++++++++++++++++++++++++++++++
 2 files changed, 138 insertions(+)
 create mode 100644 conda/niftyreg/build.sh
 create mode 100644 conda/niftyreg/meta.yaml

diff --git a/conda/niftyreg/build.sh b/conda/niftyreg/build.sh
new file mode 100644
index 00000000..bdea0303
--- /dev/null
+++ b/conda/niftyreg/build.sh
@@ -0,0 +1,78 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+#=========================================================================
+
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+#cp -rv "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+rsync -rv --exclude=.git "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+
+
+cd $SRC_DIR/build
+
+
+#site-packages ${SP_DIR}/sirf
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=v2.1.0\
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=On \
+    -DUSE_SYSTEM_Armadillo=On \
+    -DUSE_SYSTEM_ISMRMRD=ON\
+    -DUSE_SYSTEM_STIR=Off\
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=Off \
+    -DUSE_SYSTEM_GTest=On\
+    -DUSE_ITK=ON\
+    -DUSE_SYSTEM_ITK=ON\
+    -DCONDA_BUILD=On
+
+make -j2 NIFTYREG
+
+#cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+#cd ${PREFIX}/python
+#${PYTHON} setup.py install
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python
diff --git a/conda/niftyreg/meta.yaml b/conda/niftyreg/meta.yaml
new file mode 100644
index 00000000..25b95b79
--- /dev/null
+++ b/conda/niftyreg/meta.yaml
@@ -0,0 +1,60 @@
+package:
+  name: niftyreg
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 99d584e2b8ea0bffe7e65e40c8dc818751782d92
+
+
+build:
+  preserve_egg_dir: False
+#  number: 0
+    
+requirements:
+  build:
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
+    - boost >=1.63
+#    - boost-cpp
+#    - python 3.6 # [py36]
+#    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+#    - numpy
+#    - scipy
+#    - matplotlib
+#    - docopt
+#    - h5py
+#    - libxml2
+    - psutil
+    - nose
+    - coverage
+#    - fftw
+#    - swig >=3
+#    - libxslt
+#- armadillo
+    - gtest
+      #- ismrmrd
+      #    - itk
+
+
+  run:
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+#    - python 3.6 # [py36]
+#    - python 2.7 # [py27]
+#    - numpy
+#    - scipy
+#    - matplotlib
+#    - docopt
+#    - boost >=1.63
+#    - psutil
+#    - fftw
+    - libgcc-ng
+    - libstdcxx-ng
+      #    - openblas
+      #    - itk
+	
+about:
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

From d0d3b745501086a804ede56a988bbd86b56a4c58 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 29 Nov 2019 14:20:28 +0000
Subject: [PATCH 55/59] updated meta

---
 conda/boost/meta.yaml | 2 +-
 conda/sirf/meta.yaml  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conda/boost/meta.yaml b/conda/boost/meta.yaml
index adcd6991..5e2ec0f4 100644
--- a/conda/boost/meta.yaml
+++ b/conda/boost/meta.yaml
@@ -1,7 +1,7 @@
 package:
   name: boost
 #  version: {{ environ['SIRF_VERSION'] }}
-  version: 1.63.0
+  version: 1.65.1
 
 
 build:
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index 5777d589..b5af5158 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -45,7 +45,7 @@ requirements:
     - scipy
     - matplotlib
     - docopt
-    - gadgetron
+    - gadgetron ==b6191eaaa72ccca6c6a5fe4c0fa3319694f512ab
     - h5py
     - stir
     - niftyreg

From 113fa93096ce3cd67bdea43fbe6e3eab76d7e97d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Mon, 15 Feb 2021 17:44:08 +0000
Subject: [PATCH 56/59] work in progress

---
 conda/boost/meta.yaml     | 26 ++++++++------------------
 conda/gadgetron/meta.yaml | 18 ++++++++++++++++--
 conda/hdf5/meta.yaml      | 30 ++++++++++--------------------
 conda/ismrmrd/build.sh    |  2 +-
 conda/ismrmrd/meta.yaml   |  9 +++++++++
 conda/niftyreg/build.sh   |  2 +-
 conda/niftyreg/meta.yaml  | 16 +++++++++++++---
 7 files changed, 58 insertions(+), 45 deletions(-)

diff --git a/conda/boost/meta.yaml b/conda/boost/meta.yaml
index 5e2ec0f4..7c0e2910 100644
--- a/conda/boost/meta.yaml
+++ b/conda/boost/meta.yaml
@@ -7,22 +7,20 @@ package:
 build:
   preserve_egg_dir: False
 #  number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
     
 requirements:
   build:
-    #- boost ==1.64.0	
-    #- boost-cpp ==1.64.0 
-#    - boost
-#    - boost-cpp
-#    - python 3.6 # [py36]
-#    - python 2.7 # [py27]
     - cmake >=3.1
     - vc 14 # [win and py36] 
     - vc 9  # [win and py27]
-#    - numpy
-#    - scipy
-#    - matplotlib
-#    - docopt
     - h5py
 #    - libxml2
     - psutil
@@ -38,20 +36,12 @@ requirements:
   run:
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
-#    - python 3.6 # [py36]
-#    - python 2.7 # [py27]
-#    - numpy
-#    - scipy
-#    - matplotlib
-#    - docopt
     - h5py
     - psutil
     - fftw
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-#    - armadillo
-#    - gtest
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/gadgetron/meta.yaml b/conda/gadgetron/meta.yaml
index 078a20eb..cf700c5e 100644
--- a/conda/gadgetron/meta.yaml
+++ b/conda/gadgetron/meta.yaml
@@ -7,6 +7,16 @@ package:
 build:
   preserve_egg_dir: False
 #  number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
+    - /lib64/ld-linux-x86-64.so.2
+    
     
 requirements:
   build:
@@ -24,9 +34,9 @@ requirements:
 #    - scipy
 #    - matplotlib
 #    - docopt
-    - h5py
+    # - h5py
 #    - libxml2
-    - psutil
+    # - psutil
     - nose
     - coverage
     - fftw
@@ -54,10 +64,14 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - openblas
+    - libopenblas
     - armadillo
     - gtest
     - ismrmrd
     - ace
+    - cudatoolkit =10.1
+    - _openmp_mutex # [linux]
+    - hdf5 
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/hdf5/meta.yaml b/conda/hdf5/meta.yaml
index e2d7dcf2..d9029aa4 100644
--- a/conda/hdf5/meta.yaml
+++ b/conda/hdf5/meta.yaml
@@ -7,42 +7,32 @@ package:
 build:
   preserve_egg_dir: False
   number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
     
 requirements:
   build:
-    #- boost ==1.64.0	
-    #- boost-cpp ==1.64.0 
     - boost >=1.63
     - boost-cpp >=1.63
-    #- python 
-    #- {{ pin_compatible('numpy', max_pin='x.x') }}
-#    - python 2.7 # [py27]
     - cmake >=3.1
     - vc 14 # [win and py36] 
     - vc 9  # [win and py27]
-    #- numpy {{ numpy }}
-#    - scipy
-#    - matplotlib
-#    - docopt
-    #- h5py
-#    - libxml2
-    #- psutil
     - nose
     - coverage
     - fftw
-    - swig >=3
-#    - libxslt
-#    - armadillo
-    #- gtest
-#    - ismrmrd
+      #    - swig >=3
 
 
   run:
-    - boost >=1.63
-    - boost-cpp >=1.63
-    - fftw
+          # - boost >=1.63
+          # - boost-cpp >=1.63
+          # - fftw
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
+    - libstdcxx-ng # [unix]
+    - libgcc-ng # [unix] 
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/ismrmrd/build.sh b/conda/ismrmrd/build.sh
index 7c602d8b..636096e4 100644
--- a/conda/ismrmrd/build.sh
+++ b/conda/ismrmrd/build.sh
@@ -60,7 +60,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_GTest=On\
     -DCONDA_BUILD=On
 
-make  -j1 ISMRMRD VERBOSE=1
+make -j1 ISMRMRD VERBOSE=1
 
 #cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
 
diff --git a/conda/ismrmrd/meta.yaml b/conda/ismrmrd/meta.yaml
index e205c5bb..d9c0e98f 100644
--- a/conda/ismrmrd/meta.yaml
+++ b/conda/ismrmrd/meta.yaml
@@ -7,6 +7,15 @@ package:
 build:
   preserve_egg_dir: False
 #  number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
+    
     
 requirements:
   build:
diff --git a/conda/niftyreg/build.sh b/conda/niftyreg/build.sh
index bdea0303..c39c779f 100644
--- a/conda/niftyreg/build.sh
+++ b/conda/niftyreg/build.sh
@@ -62,7 +62,7 @@ cmake ../SIRF-SuperBuild \
     -DUSE_SYSTEM_HDF5=ON \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
-    -DUSE_ITK=ON\
+    -DUSE_ITK=OFF\
     -DUSE_SYSTEM_ITK=ON\
     -DCONDA_BUILD=On
 
diff --git a/conda/niftyreg/meta.yaml b/conda/niftyreg/meta.yaml
index 25b95b79..d7e90be2 100644
--- a/conda/niftyreg/meta.yaml
+++ b/conda/niftyreg/meta.yaml
@@ -7,6 +7,15 @@ package:
 build:
   preserve_egg_dir: False
 #  number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
+    
     
 requirements:
   build:
@@ -33,8 +42,8 @@ requirements:
 #    - libxslt
 #- armadillo
     - gtest
-      #- ismrmrd
-      #    - itk
+    - ismrmrd
+    # - itk
 
 
   run:
@@ -51,8 +60,9 @@ requirements:
 #    - fftw
     - libgcc-ng
     - libstdcxx-ng
+    - ismrmrd
       #    - openblas
-      #    - itk
+    # - itk
 	
 about:
   home: http://www.ccppetmr.ac.uk

From 3e3ec95cbed372af7c57876100e5fb0d662994a9 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Mon, 15 Feb 2021 17:44:35 +0000
Subject: [PATCH 57/59] added missing_dso_whitelist

---
 conda/sirf/meta.yaml | 9 +++++++++
 conda/stir/meta.yaml | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index b5af5158..735e4bb8 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -7,6 +7,15 @@ package:
 build:
   preserve_egg_dir: False
   number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
+    
     
 requirements:
   build:
diff --git a/conda/stir/meta.yaml b/conda/stir/meta.yaml
index 02a7ca6d..9dd70711 100644
--- a/conda/stir/meta.yaml
+++ b/conda/stir/meta.yaml
@@ -7,6 +7,15 @@ package:
 build:
   preserve_egg_dir: False
 #  number: 0
+  missing_dso_whitelist:
+    - $RPATH/libc.so.6  # [linux]
+    - $RPATH/libm.so.6  # [linux]
+    - $RPATH/libdl.so.2 # [linux]
+    - $RPATH/libpthread.so.0 # [linux]
+    - $RPATH/librt.so.1 # [linux]
+    - $RPATH/libicuuc.so.60  #[linux]
+    - $RPATH/libicui18n.so.60 #[linux]
+    
     
 requirements:
   build:

From e62686355d8bbd5f6cf6d67d67072782b78c148a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Mon, 15 Feb 2021 17:49:53 +0000
Subject: [PATCH 58/59] add _openmp_mutex

---
 conda/niftyreg/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conda/niftyreg/meta.yaml b/conda/niftyreg/meta.yaml
index d7e90be2..ccd7c6dc 100644
--- a/conda/niftyreg/meta.yaml
+++ b/conda/niftyreg/meta.yaml
@@ -43,10 +43,11 @@ requirements:
 #- armadillo
     - gtest
     - ismrmrd
-    # - itk
+    - _openmp_mutex # [linux]
 
 
   run:
+    - _openmp_mutex # [linux]
     - vc 14 # [win and py35]
     - vc 9  # [win and py27]
 #    - python 3.6 # [py36]

From 6ead04e3e393ec823fd36e511405b455b3ab0bab Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 16 Feb 2021 22:12:20 +0000
Subject: [PATCH 59/59] updated recipes

---
 conda/niftyreg/meta.yaml |  1 +
 conda/sirf/build.sh      |  6 +++---
 conda/sirf/meta.yaml     | 11 ++++++++---
 conda/stir/build.sh      |  4 ++--
 conda/stir/meta.yaml     | 11 +++++++++--
 5 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/conda/niftyreg/meta.yaml b/conda/niftyreg/meta.yaml
index ccd7c6dc..1de42586 100644
--- a/conda/niftyreg/meta.yaml
+++ b/conda/niftyreg/meta.yaml
@@ -62,6 +62,7 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - ismrmrd
+    - _openmp_mutex # [linux]
       #    - openblas
     # - itk
 	
diff --git a/conda/sirf/build.sh b/conda/sirf/build.sh
index 8ddad63e..ef2d4645 100644
--- a/conda/sirf/build.sh
+++ b/conda/sirf/build.sh
@@ -63,11 +63,11 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
     -DUSE_ITK=ON\
-    -DUSE_SYSTEM_ITK=ON\
-    -DUSE_SYSTEM_NIFTYREG=ON\
+    -DUSE_SYSTEM_ITK=OFF\
+    -DUSE_SYSTEM_NIFTYREG=OFF\
     -DCONDA_BUILD=On
 
-#make -j2 NIFTYREG
+make -j2 NIFTYREG
 make -j2 STIR
 make -j1 SIRF
 
diff --git a/conda/sirf/meta.yaml b/conda/sirf/meta.yaml
index 735e4bb8..70cd2673 100644
--- a/conda/sirf/meta.yaml
+++ b/conda/sirf/meta.yaml
@@ -43,7 +43,7 @@ requirements:
 #    - libxslt
 #    - armadillo
     - gtest
-#    - ismrmrd
+    - ismrmrd
 
 
   run:
@@ -56,8 +56,8 @@ requirements:
     - docopt
     - gadgetron ==b6191eaaa72ccca6c6a5fe4c0fa3319694f512ab
     - h5py
-    - stir
-    - niftyreg
+    # - stir
+    # - niftyreg
 #    - boost >=1.63
 #    - h5py
 #    - psutil
@@ -68,6 +68,11 @@ requirements:
 #    - armadillo
 #    - gtest
 #    - ismrmrd
+    - libgcc-ng
+    - libstdcxx-ng
+    - ismrmrd
+    - _openmp_mutex # [linux]
+    - stir
 	
 about:
   home: http://www.ccppetmr.ac.uk
diff --git a/conda/stir/build.sh b/conda/stir/build.sh
index 46a4dd23..b4fd3438 100644
--- a/conda/stir/build.sh
+++ b/conda/stir/build.sh
@@ -52,7 +52,7 @@ cmake ../SIRF-SuperBuild \
     -UGadgetron_TAG \
     -UISMRMRD_URL \
     -UISMRMRD_TAG \
-    -DBUILD_GADGETRON=On \
+    -DBUILD_GADGETRON=OFF \
     -DUSE_SYSTEM_SWIG=On \
     -DUSE_SYSTEM_Boost=On \
     -DUSE_SYSTEM_Armadillo=On \
@@ -63,7 +63,7 @@ cmake ../SIRF-SuperBuild \
     -DBUILD_siemens_to_ismrmrd=Off \
     -DUSE_SYSTEM_GTest=On\
     -DUSE_ITK=ON\
-    -DUSE_SYSTEM_ITK=ON\
+    -DUSE_SYSTEM_ITK=OFF\
     -DCONDA_BUILD=On
 
 make -j2 STIR
diff --git a/conda/stir/meta.yaml b/conda/stir/meta.yaml
index 9dd70711..770cfce7 100644
--- a/conda/stir/meta.yaml
+++ b/conda/stir/meta.yaml
@@ -15,6 +15,7 @@ build:
     - $RPATH/librt.so.1 # [linux]
     - $RPATH/libicuuc.so.60  #[linux]
     - $RPATH/libicui18n.so.60 #[linux]
+    - /lib64/ld-linux-x86-64.so.2 # [linux]
     
     
 requirements:
@@ -41,9 +42,13 @@ requirements:
     - swig >=3
 #    - libxslt
 #- armadillo
+    - hdf5
     - gtest
       #- ismrmrd
-    - itk
+    # - itk ==4.13.1
+    - ismrmrd
+    - _openmp_mutex # [linux]
+    - cudatoolkit=10.1
 
 
   run:
@@ -61,7 +66,9 @@ requirements:
     - libgcc-ng
     - libstdcxx-ng
     - openblas
-    - itk
+    - ismrmrd
+    - _openmp_mutex # [linux]
+    - cudatoolkit=10.1
 	
 about:
   home: http://www.ccppetmr.ac.uk