From f16ccc9c9f61d785f339480a3570d958791197e8 Mon Sep 17 00:00:00 2001
From: Daniil Kazantsev <dkazanc@hotmail.com>
Date: Sun, 6 Jan 2019 23:16:57 +0000
Subject: adds CudaResetdevice to PatchSelect module

---
 Core/regularisers_GPU/PatchSelect_GPU_core.cu | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Core/regularisers_GPU/PatchSelect_GPU_core.cu b/Core/regularisers_GPU/PatchSelect_GPU_core.cu
index d173124..98c8488 100644
--- a/Core/regularisers_GPU/PatchSelect_GPU_core.cu
+++ b/Core/regularisers_GPU/PatchSelect_GPU_core.cu
@@ -449,10 +449,12 @@ extern "C" int PatchSelect_GPU_main(float *A, unsigned short *H_i, unsigned shor
     checkCudaErrors(cudaMemcpy(H_j, H_j_d, N*M*NumNeighb*sizeof(unsigned short),cudaMemcpyDeviceToHost) );  
     checkCudaErrors(cudaMemcpy(Weights, Weights_d, N*M*NumNeighb*sizeof(float),cudaMemcpyDeviceToHost) );   
     
+    
     cudaFree(Ad); 
     cudaFree(H_i_d); 
     cudaFree(H_j_d);    
-    cudaFree(Weights_d);    
+    cudaFree(Weights_d);
     cudaFree(Eucl_Vec_d);
+    cudaDeviceReset();
     return 0;
 }
-- 
cgit v1.2.3


From 3ee4173bf095696be9e2b5413518452b0512186f Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 7 Jan 2019 16:23:45 +0000
Subject: fixes #83

---
 Core/regularisers_CPU/TGV_core.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Core/regularisers_CPU/TGV_core.c b/Core/regularisers_CPU/TGV_core.c
index edd77b2..477e909 100644
--- a/Core/regularisers_CPU/TGV_core.c
+++ b/Core/regularisers_CPU/TGV_core.c
@@ -100,6 +100,9 @@ float TGV_main(float *U0, float *U, float lambda, float alpha1, float alpha0, in
             newU(V1, V1_old, (long)(dimX), (long)(dimY));
             newU(V2, V2_old, (long)(dimX), (long)(dimY));
         } /*end of iterations*/
+    /*freeing*/
+    free(P1);free(P2);free(Q1);free(Q2);free(Q3);free(U_old);
+    free(V1);free(V2);free(V1_old);free(V2_old);
 	return *U;
 }
 
-- 
cgit v1.2.3


From 865c3b390641a27ecc8a132ca7bad543756f871f Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Tue, 8 Jan 2019 14:30:20 +0000
Subject: ADD: variants, list of files in exported variable REG_FILES

---
 Wrappers/Python/conda-recipe/meta.yaml | 10 +++++-----
 build/jenkins-build.sh                 |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index 808493e..e3258ff 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -1,8 +1,7 @@
 package:
   name: ccpi-regulariser
-  version: 0.10.3
-
-
+  version: {{CIL_VERSION}}
+  
 build:
   preserve_egg_dir: False
   number: 0
@@ -16,7 +15,7 @@ test:
 requirements:
   build:
     - python
-    - numpy x.x
+    - numpy {{ numpy }}
     - setuptools
     - cython
     - vc 14 # [win and py36] 
@@ -25,8 +24,9 @@ requirements:
     - cmake 
 
   run:
+    - {{ pin_compatible('numpy', max_pin='x.x') }}
     - python
-    - numpy x.x
+    - numpy
     - vc 14 # [win and py36] 
     - vc 14 # [win and py35] 
     - vc 9  # [win and py27]
diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 0c397b1..1babeab 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -26,4 +26,4 @@ else
   echo Defining version: $CIL_VERSION
 fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
-conda build Wrappers/Python/conda-recipe
+export REG_FILES=`conda build Wrappers/Python/conda-recipe`
-- 
cgit v1.2.3


From b18a7376dc2a369da81edf0605a567bbfdc542a5 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Tue, 8 Jan 2019 15:09:52 +0000
Subject: update: disable load conda module

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 1babeab..3632baa 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Script to builds source code in Jenkins environment
-module try-load conda
+# module try-load conda
 
 # install miniconda if the module is not present
 if hash conda 2>/dev/null; then
-- 
cgit v1.2.3


From 34ac7f67f2a3c2bb3055be2c30357e354df76ac1 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Tue, 8 Jan 2019 15:24:33 +0000
Subject: UPDATE: output generated files

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 3632baa..874788a 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -26,4 +26,4 @@ else
   echo Defining version: $CIL_VERSION
 fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
-export REG_FILES=`conda build Wrappers/Python/conda-recipe`
+export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
-- 
cgit v1.2.3


From ca5c4e281d0b103ebc544a096b5ac90dd74eb215 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Tue, 8 Jan 2019 15:34:17 +0000
Subject: ADD: variants

---
 Wrappers/Python/conda-recipe/conda_build_config.yaml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 Wrappers/Python/conda-recipe/conda_build_config.yaml

diff --git a/Wrappers/Python/conda-recipe/conda_build_config.yaml b/Wrappers/Python/conda-recipe/conda_build_config.yaml
new file mode 100644
index 0000000..b7977f3
--- /dev/null
+++ b/Wrappers/Python/conda-recipe/conda_build_config.yaml
@@ -0,0 +1,7 @@
+python:
+  - 2.7 # [not win]
+  - 3.5
+  - 3.6
+numpy:
+  - 1.12
+  - 1.15
-- 
cgit v1.2.3


From 49163d7ebc31c2664d4bf0bb6ecb1fd61018b8b9 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Tue, 8 Jan 2019 16:08:41 +0000
Subject: UPDATE: build first, generate output files next

---
 build/jenkins-build.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 874788a..5614b8e 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -26,4 +26,8 @@ else
   echo Defining version: $CIL_VERSION
 fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
+# need to call first build
+conda build Wrappers/Python/conda-recipe
+# then need to call the same with --output 
+#- otherwise no build is done :-(, just fake file names are generated
 export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
-- 
cgit v1.2.3


From ddbc32fdcd4f0754b31786d00b2835223109a9d7 Mon Sep 17 00:00:00 2001
From: Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 9 Jan 2019 11:17:45 +0000
Subject: UPDATE: upload within jenkins build script, needs CCPI_CONDA_TOKEN

---
 build/jenkins-build.sh | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 5614b8e..3bd5016 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -14,7 +14,7 @@ else
   PATH=$PATH:./bin
 fi
 
-# presume that git clone is done before this script launch
+# presume that git clone is done before this script is launched, if not, uncomment
 # git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
 #export CIL_VERSION=0.10.2
@@ -31,3 +31,15 @@ conda build Wrappers/Python/conda-recipe
 # then need to call the same with --output 
 #- otherwise no build is done :-(, just fake file names are generated
 export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
+# REG_FILES variable should contain output files
+echo files created: $REG_FILES
+#upload to anaconda
+if [[ -n ${CCPI_CONDA_TOKEN}]]
+then
+  conda install anaconda-client
+  while read -r outfile; do
+    anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
+  done <<< "$REG_FILES"
+else
+  echo CCPI_CONDA_TOKEN not defined, will not upload to anaconda.
+fi
-- 
cgit v1.2.3


From 4cf1659f14e58001f715c9fb4ff1734d6ffd8661 Mon Sep 17 00:00:00 2001
From: Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 9 Jan 2019 12:02:41 +0000
Subject: Fix

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 3bd5016..4a18525 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -34,7 +34,7 @@ export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 # REG_FILES variable should contain output files
 echo files created: $REG_FILES
 #upload to anaconda
-if [[ -n ${CCPI_CONDA_TOKEN}]]
+if [[ -n ${CCPI_CONDA_TOKEN} ]]
 then
   conda install anaconda-client
   while read -r outfile; do
-- 
cgit v1.2.3


From 8d872f6d37c73dd1bc2e47f2bdf30058c78679f5 Mon Sep 17 00:00:00 2001
From: Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 9 Jan 2019 12:07:14 +0000
Subject: UPDATE version 0.10.4

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 4a18525..c660c02 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -22,7 +22,7 @@ if [[ -n ${CIL_VERSION} ]]
 then
   echo Using defined version: $CIL_VERSION
 else
-  export CIL_VERSION=0.10.3
+  export CIL_VERSION=0.10.4
   echo Defining version: $CIL_VERSION
 fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
-- 
cgit v1.2.3


From 73eab3d64f2bf5ad170bea35c4db1d3ae5758c06 Mon Sep 17 00:00:00 2001
From: Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 9 Jan 2019 12:45:42 +0000
Subject: version top in script

---
 build/jenkins-build.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index c660c02..4699e9b 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -1,4 +1,11 @@
 #!/usr/bin/env bash
+if [[ -n ${CIL_VERSION} ]]
+then
+  echo Using defined version: $CIL_VERSION
+else
+  export CIL_VERSION=0.10.4
+  echo Defining version: $CIL_VERSION
+fi
 # Script to builds source code in Jenkins environment
 # module try-load conda
 
@@ -18,13 +25,6 @@ fi
 # git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
 #export CIL_VERSION=0.10.2
-if [[ -n ${CIL_VERSION} ]]
-then
-  echo Using defined version: $CIL_VERSION
-else
-  export CIL_VERSION=0.10.4
-  echo Defining version: $CIL_VERSION
-fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
 # need to call first build
 conda build Wrappers/Python/conda-recipe
-- 
cgit v1.2.3


From da69e9f1074226e3d14faa89a270b4ef1593ee42 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Wed, 9 Jan 2019 14:11:05 +0000
Subject: fix

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 3bd5016..4a18525 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -34,7 +34,7 @@ export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 # REG_FILES variable should contain output files
 echo files created: $REG_FILES
 #upload to anaconda
-if [[ -n ${CCPI_CONDA_TOKEN}]]
+if [[ -n ${CCPI_CONDA_TOKEN} ]]
 then
   conda install anaconda-client
   while read -r outfile; do
-- 
cgit v1.2.3


From 3b114face28547468da9e1b491c67bd5ea53603b Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Wed, 9 Jan 2019 14:13:17 +0000
Subject: version in top 0.10.4

---
 build/jenkins-build.sh | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 4a18525..6da2c56 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -1,4 +1,11 @@
 #!/usr/bin/env bash
+if [[ -n ${CIL_VERSION} ]]
+then
+  echo Using defined version: $CIL_VERSION
+else
+  export CIL_VERSION=0.10.4
+  echo Defining version: $CIL_VERSION
+fi
 # Script to builds source code in Jenkins environment
 # module try-load conda
 
@@ -17,14 +24,6 @@ fi
 # presume that git clone is done before this script is launched, if not, uncomment
 # git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
-#export CIL_VERSION=0.10.2
-if [[ -n ${CIL_VERSION} ]]
-then
-  echo Using defined version: $CIL_VERSION
-else
-  export CIL_VERSION=0.10.3
-  echo Defining version: $CIL_VERSION
-fi
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
 # need to call first build
 conda build Wrappers/Python/conda-recipe
-- 
cgit v1.2.3


From 34d0b9f85c3bc73416f1dc2bb25ef669b9ff8076 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Tue, 15 Jan 2019 15:23:43 +0000
Subject: added jenkins build status

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

diff --git a/Readme.md b/Readme.md
index cdf823d..70c9e13 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,3 +1,4 @@
+[![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/)
 # CCPi-Regularisation Toolkit (CCPi-RGL)
 
 **Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.** 
-- 
cgit v1.2.3


From 3b309224fc4935a8dc627e8863479b3c29349ce8 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 15 Jan 2019 21:33:38 +0000
Subject: ADD: TODOs

---
 build/jenkins-build.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 4699e9b..afee0c9 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -1,8 +1,10 @@
 #!/usr/bin/env bash
+# TODO put git tag recognition
 if [[ -n ${CIL_VERSION} ]]
 then
   echo Using defined version: $CIL_VERSION
 else
+# TODO put git tag recognition, or default
   export CIL_VERSION=0.10.4
   echo Defining version: $CIL_VERSION
 fi
@@ -38,6 +40,8 @@ if [[ -n ${CCPI_CONDA_TOKEN} ]]
 then
   conda install anaconda-client
   while read -r outfile; do
+    #TODO if git tag is defined than call anaconda without --label dev
+    #TODO if pull request??? do not upload 
     anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
   done <<< "$REG_FILES"
 else
-- 
cgit v1.2.3


From 400894771a9ff54c3f88e84ecc79d97a3e08235f Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 14:18:00 +0000
Subject: UPDATE: detect git version

---
 build/jenkins-build.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index afee0c9..d1a3427 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -5,8 +5,11 @@ then
   echo Using defined version: $CIL_VERSION
 else
 # TODO put git tag recognition, or default
-  export CIL_VERSION=0.10.4
-  echo Defining version: $CIL_VERSION
+  #export CIL_VERSION=0.10.4
+  #get tag, remove first char ('v') and leave rest
+  export CIL_VERSION_RAW=`git describe --tags | tail -c +2`
+
+  echo Defining version from last git tag and commit: $CIL_VERSION
 fi
 # Script to builds source code in Jenkins environment
 # module try-load conda
-- 
cgit v1.2.3


From be48430f8de0ccb8e64abba4f00c771228ff0df0 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:05:59 +0000
Subject: UPDATE: CIL_VERSION from git tag, dash in version is assumed as dev
 version

---
 build/jenkins-build.sh | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index d1a3427..44fd59d 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -7,9 +7,15 @@ else
 # TODO put git tag recognition, or default
   #export CIL_VERSION=0.10.4
   #get tag, remove first char ('v') and leave rest
-  export CIL_VERSION_RAW=`git describe --tags | tail -c +2`
-
-  echo Defining version from last git tag and commit: $CIL_VERSION
+  export CIL_VERSION=`git describe --tags | tail -c +2`  
+  if [[ $CIL_VERSION == *"-"*]]; then
+    # detected dash means that it is dev version
+    # version is then string-string and all after second dash is ignored (usually commit sha)
+    export CIL_VERSION=`echo $C1 | cut -d "-" -f -2`
+    echo Building dev version
+  else
+    echo Defining version from last git tag and commit: $CIL_VERSION
+  fi 
 fi
 # Script to builds source code in Jenkins environment
 # module try-load conda
@@ -27,7 +33,7 @@ else
 fi
 
 # presume that git clone is done before this script is launched, if not, uncomment
-# git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
+#git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
 #export CIL_VERSION=0.10.2
 #cd CCPi-Regularisation-Toolkit # already there by jenkins
@@ -45,7 +51,12 @@ then
   while read -r outfile; do
     #TODO if git tag is defined than call anaconda without --label dev
     #TODO if pull request??? do not upload 
-    anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
+    if [[ $CIL_VERSION == *"-"*]]; then
+      # upload with dev label
+      anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
+    else 
+      anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force
+    fi
   done <<< "$REG_FILES"
 else
   echo CCPI_CONDA_TOKEN not defined, will not upload to anaconda.
-- 
cgit v1.2.3


From 53695bd509b06de9f0564ceec43b4e5b669fa135 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:11:34 +0000
Subject: typo

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 44fd59d..beb26f7 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -8,7 +8,7 @@ else
   #export CIL_VERSION=0.10.4
   #get tag, remove first char ('v') and leave rest
   export CIL_VERSION=`git describe --tags | tail -c +2`  
-  if [[ $CIL_VERSION == *"-"*]]; then
+  if [[ $CIL_VERSION == *"-"* ]]; then
     # detected dash means that it is dev version
     # version is then string-string and all after second dash is ignored (usually commit sha)
     export CIL_VERSION=`echo $C1 | cut -d "-" -f -2`
-- 
cgit v1.2.3


From 94d1e4b289d9e9ffbf69826337ea05e2a3bb0101 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:13:44 +0000
Subject: echo version

---
 build/jenkins-build.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index beb26f7..d0e9c96 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -8,11 +8,11 @@ else
   #export CIL_VERSION=0.10.4
   #get tag, remove first char ('v') and leave rest
   export CIL_VERSION=`git describe --tags | tail -c +2`  
-  if [[ $CIL_VERSION == *"-"* ]]; then
+  if [[ ${CIL_VERSION} == *"-"* ]]; then
     # detected dash means that it is dev version
     # version is then string-string and all after second dash is ignored (usually commit sha)
-    export CIL_VERSION=`echo $C1 | cut -d "-" -f -2`
-    echo Building dev version
+    export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
+    echo Building dev version ${CIL_VERSION}
   else
     echo Defining version from last git tag and commit: $CIL_VERSION
   fi 
-- 
cgit v1.2.3


From cf9689e81bb69b7732a168463b17a47de1ef59a5 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:28:12 +0000
Subject: UPDATE: conda build don't like dash in version

---
 build/jenkins-build.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index d0e9c96..b64631f 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -12,6 +12,8 @@ else
     # detected dash means that it is dev version
     # version is then string-string and all after second dash is ignored (usually commit sha)
     export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
+    # but dash is prohibited for conda build
+    export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
     echo Building dev version ${CIL_VERSION}
   else
     echo Defining version from last git tag and commit: $CIL_VERSION
@@ -51,7 +53,7 @@ then
   while read -r outfile; do
     #TODO if git tag is defined than call anaconda without --label dev
     #TODO if pull request??? do not upload 
-    if [[ $CIL_VERSION == *"-"*]]; then
+    if [[ $CIL_VERSION == *"_"*]]; then
       # upload with dev label
       anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
     else 
-- 
cgit v1.2.3


From e4683c6c7be92ba65b13ef5ea4306948bcbded74 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:43:08 +0000
Subject: UPDATE: version from env

---
 CMakeLists.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 550b896..e3e59e9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,9 @@ set (CIL_VERSION_MAJOR 0)
 set (CIL_VERSION_MINOR 10)
 set (CIL_VERSION_PATCH 2)
 
-set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# get CIL_VERSION from environment variable
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
 
 # set the Python variables for the Conda environment
 #include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
-- 
cgit v1.2.3


From 204dc742ee5a8fda3f168b3e84632f5cdb75ce2e Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 15:43:41 +0000
Subject: typo

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index b64631f..6965180 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -53,7 +53,7 @@ then
   while read -r outfile; do
     #TODO if git tag is defined than call anaconda without --label dev
     #TODO if pull request??? do not upload 
-    if [[ $CIL_VERSION == *"_"*]]; then
+    if [[ $CIL_VERSION == *"_"* ]]; then
       # upload with dev label
       anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
     else 
-- 
cgit v1.2.3


From 5e436eab5cea50569df9c85159be69d8e88688f0 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 16:41:10 +0000
Subject: UPDATE: propagate CIL_VERSION

---
 CMakeLists.txt                         | 3 ++-
 Core/CMakeLists.txt                    | 2 +-
 Wrappers/Python/CMakeLists.txt         | 2 +-
 Wrappers/Python/conda-recipe/build.sh  | 1 +
 Wrappers/Python/conda-recipe/meta.yaml | 2 ++
 recipes/regularisers/bld.bat           | 2 +-
 recipes/regularisers/build.sh          | 4 ++--
 7 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e3e59e9..b95107a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,8 +26,9 @@ set (CIL_VERSION_MINOR 10)
 set (CIL_VERSION_PATCH 2)
 
 # set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
-# get CIL_VERSION from environment variable
+# get CIL_VERSION from environment variable and set it in cmake
 set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+message(STATUS "CIL_VERSION set to " ${CIL_VERSION})
 
 # set the Python variables for the Conda environment
 #include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index d92db82..b3c0dfb 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -6,7 +6,7 @@ project(RGL_core)
 
 # The version number.
 
-#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
 
 # conda orchestrated build
 message("CIL_VERSION ${CIL_VERSION}")
diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
index d86d0ea..c2ef855 100644
--- a/Wrappers/Python/CMakeLists.txt
+++ b/Wrappers/Python/CMakeLists.txt
@@ -9,7 +9,7 @@ project(regulariserPython)
 #set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
 
 # conda orchestrated build
-message("CIL_VERSION ${CIL_VERSION}")
+message("CIL_VERSION: ${CIL_VERSION}")
 #include (GenerateExportHeader)
 
 find_package(PythonInterp REQUIRED)
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
index eec7c2f..39c0f2c 100644
--- a/Wrappers/Python/conda-recipe/build.sh
+++ b/Wrappers/Python/conda-recipe/build.sh
@@ -5,6 +5,7 @@ cp -rv "$RECIPE_DIR/../../../Core" "$SRC_DIR/Core"
 
 cd $SRC_DIR
 ##cuda=off
+
 cmake -G "Unix Makefiles" $RECIPE_DIR/../../../ -DBUILD_PYTHON_WRAPPER=ON -DCONDA_BUILD=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE="Release" -DLIBRARY_LIB=$CONDA_PREFIX/lib -DLIBRARY_INC=$CONDA_PREFIX -DCMAKE_INSTALL_PREFIX=$PREFIX
 
 
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index e3258ff..9fe813d 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -5,6 +5,8 @@ package:
 build:
   preserve_egg_dir: False
   number: 0
+  script_env:
+    - CIL_VERSION
   
 test:
   files:
diff --git a/recipes/regularisers/bld.bat b/recipes/regularisers/bld.bat
index 43a5286..63e7681 100644
--- a/recipes/regularisers/bld.bat
+++ b/recipes/regularisers/bld.bat
@@ -10,7 +10,7 @@ cd "%SRC_DIR%\build"
 
 echo "we should be in %SRC_DIR%\build"
 
-cmake -G "NMake Makefiles" "%RECIPE_DIR%\..\..\" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" -DCONDA_BUILD=ON -DBUILD_WRAPPERS=OFF
+cmake -G "NMake Makefiles" "%RECIPE_DIR%\..\..\" -DCIL_VERSION="%CIL_VERSION%" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" -DCONDA_BUILD=ON -DBUILD_WRAPPERS=OFF
 
 ::-DBOOST_LIBRARYDIR="%CONDA_PREFIX%\Library\lib" -DBOOST_INCLUDEDIR="%CONDA_PREFIX%\Library\include" -DBOOST_ROOT="%CONDA_PREFIX%\Library\lib"
 
diff --git a/recipes/regularisers/build.sh b/recipes/regularisers/build.sh
index 0b8bce2..aede303 100644
--- a/recipes/regularisers/build.sh
+++ b/recipes/regularisers/build.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-echo $CIL_VERSION
+echo build.sh CIL_VERSION: $CIL_VERSION
 #if [ -z "$CIL_VERSION" ]; then
 #    echo "Need to set CIL_VERSION"
 #    exit 1
@@ -13,7 +13,7 @@ mkdir ${SRC_DIR}/build
 cp -rv ${RECIPE_DIR}/../../Core/ ${SRC_DIR}/build
 mkdir ${SRC_DIR}/build/build
 cd ${SRC_DIR}/build/build
-cmake -G "Unix Makefiles" -DLIBRARY_LIB="${CONDA_PREFIX}/lib" -DLIBRARY_INC="${CONDA_PREFIX}" -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../Core
+cmake -G "Unix Makefiles" -DCIL_VERSION="${CIL_VERSION}" -DLIBRARY_LIB="${CONDA_PREFIX}/lib" -DLIBRARY_INC="${CONDA_PREFIX}" -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../Core
 
 make -j2 VERBOSE=1
 make install
-- 
cgit v1.2.3


From d0052abf619d327e18791aeefd1b0a0a513c546b Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 16:41:25 +0000
Subject: UPDATE: build

---
 recipes/regularisers/bld.bat  | 2 +-
 recipes/regularisers/build.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/regularisers/bld.bat b/recipes/regularisers/bld.bat
index 63e7681..43a5286 100644
--- a/recipes/regularisers/bld.bat
+++ b/recipes/regularisers/bld.bat
@@ -10,7 +10,7 @@ cd "%SRC_DIR%\build"
 
 echo "we should be in %SRC_DIR%\build"
 
-cmake -G "NMake Makefiles" "%RECIPE_DIR%\..\..\" -DCIL_VERSION="%CIL_VERSION%" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" -DCONDA_BUILD=ON -DBUILD_WRAPPERS=OFF
+cmake -G "NMake Makefiles" "%RECIPE_DIR%\..\..\" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" -DCONDA_BUILD=ON -DBUILD_WRAPPERS=OFF
 
 ::-DBOOST_LIBRARYDIR="%CONDA_PREFIX%\Library\lib" -DBOOST_INCLUDEDIR="%CONDA_PREFIX%\Library\include" -DBOOST_ROOT="%CONDA_PREFIX%\Library\lib"
 
diff --git a/recipes/regularisers/build.sh b/recipes/regularisers/build.sh
index aede303..eaa778e 100644
--- a/recipes/regularisers/build.sh
+++ b/recipes/regularisers/build.sh
@@ -13,7 +13,7 @@ mkdir ${SRC_DIR}/build
 cp -rv ${RECIPE_DIR}/../../Core/ ${SRC_DIR}/build
 mkdir ${SRC_DIR}/build/build
 cd ${SRC_DIR}/build/build
-cmake -G "Unix Makefiles" -DCIL_VERSION="${CIL_VERSION}" -DLIBRARY_LIB="${CONDA_PREFIX}/lib" -DLIBRARY_INC="${CONDA_PREFIX}" -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../Core
+cmake -G "Unix Makefiles" -DLIBRARY_LIB="${CONDA_PREFIX}/lib" -DLIBRARY_INC="${CONDA_PREFIX}" -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../Core
 
 make -j2 VERBOSE=1
 make install
-- 
cgit v1.2.3


From b9ee6fad5b3119e738f6999eb4dd78bafb98a7cd Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 17:07:25 +0000
Subject: test

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

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 6965180..8c10484 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -46,6 +46,7 @@ conda build Wrappers/Python/conda-recipe
 export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 # REG_FILES variable should contain output files
 echo files created: $REG_FILES
+
 #upload to anaconda
 if [[ -n ${CCPI_CONDA_TOKEN} ]]
 then
-- 
cgit v1.2.3


From 774ed3351991266b0c9289b2b9ba1afe328c3e70 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@localhost.localdomain>
Date: Mon, 21 Jan 2019 17:09:05 +0000
Subject: pr-test

---
 build/jenkins-build.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 6965180..20c97f3 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -33,7 +33,6 @@ else
   ./Miniconda3-latest-Linux-x86_64.sh -u -b -p .
   PATH=$PATH:./bin
 fi
-
 # presume that git clone is done before this script is launched, if not, uncomment
 #git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
-- 
cgit v1.2.3


From 6c497653590f6c916496f1eb2f464d97d63b1ae9 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 11:57:50 +0000
Subject: Update jenkins-build.sh

---
 build/jenkins-build.sh | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index ca5b57a..de22368 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -5,19 +5,19 @@ then
   echo Using defined version: $CIL_VERSION
 else
 
-  #get tag, remove first char ('v') and leave rest
-  export CIL_VERSION=`git describe --tags | tail -c +2`  
-  if [[ ${CIL_VERSION} == *"-"* ]]; then
-    # detected dash means that it is dev version
-    # version is then string-string and all after second dash is ignored (usually commit sha)
-    export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
-    # but dash is prohibited for conda build
-    export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
-    echo Building dev version ${CIL_VERSION}
-  else
-    echo Defining version from last git tag and commit: $CIL_VERSION
-  fi 
-fi
+#get tag, remove first char ('v') and leave rest
+export CIL_VERSION=`git describe --tags | tail -c +2`  
+if [[ ${CIL_VERSION} == *"-"* ]]; then
+  # detected dash means that it is dev version
+  # version is then string-string and all after second dash is ignored (usually commit sha)
+  export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
+  # but dash is prohibited for conda build, replace with underscore
+  export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
+  echo Building dev version ${CIL_VERSION}
+else
+  echo Defining version from last git tag and commit: $CIL_VERSION
+fi 
+
 # Script to builds source code in Jenkins environment
 # module try-load conda
 
-- 
cgit v1.2.3


From ec5d74d59a26192288f1430581e2a27567f91b86 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 12:05:16 +0000
Subject: Update jenkins-build.sh

---
 build/jenkins-build.sh | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index de22368..e440717 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -4,19 +4,20 @@ if [[ -n ${CIL_VERSION} ]]
 then
   echo Using defined version: $CIL_VERSION
 else
-
-#get tag, remove first char ('v') and leave rest
-export CIL_VERSION=`git describe --tags | tail -c +2`  
-if [[ ${CIL_VERSION} == *"-"* ]]; then
-  # detected dash means that it is dev version
-  # version is then string-string and all after second dash is ignored (usually commit sha)
-  export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
-  # but dash is prohibited for conda build, replace with underscore
-  export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
-  echo Building dev version ${CIL_VERSION}
-else
-  echo Defining version from last git tag and commit: $CIL_VERSION
-fi 
+  # define CIL_VERSION from last git tag, remove first char ('v') and leave rest
+  export CIL_VERSION=`git describe --tags | tail -c +2`  
+  # dash means that it's some commit after tag release -thus will be treated as dev
+  if [[ ${CIL_VERSION} == *"-"* ]]; then
+    # detected dash means that it is dev version
+    # version is then string-string and all after second dash is ignored (usually commit sha)
+    export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
+    # but dash is prohibited for conda build, replace with underscore
+    export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
+    echo Building dev version ${CIL_VERSION}
+  else
+    echo Defining version from last git tag and commit: $CIL_VERSION
+  fi
+fi
 
 # Script to builds source code in Jenkins environment
 # module try-load conda
@@ -49,7 +50,7 @@ then
   conda install anaconda-client
   while read -r outfile; do
     #if 0 commit after tag then call anaconda without --label dev
-    #TODO if pull request??? do not upload 
+    #TODO pull request not to upload 
     if [[ $CIL_VERSION == *"_"* ]]; then
       # upload with dev label
       anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
-- 
cgit v1.2.3


From 19fce0003d558b4eb9dadfb6aef7c79deef13489 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 12:13:01 +0000
Subject: Update jenkins-build.sh

---
 build/jenkins-build.sh | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index e440717..6c863c0 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -8,14 +8,13 @@ else
   export CIL_VERSION=`git describe --tags | tail -c +2`  
   # dash means that it's some commit after tag release -thus will be treated as dev
   if [[ ${CIL_VERSION} == *"-"* ]]; then
-    # detected dash means that it is dev version
-    # version is then string-string and all after second dash is ignored (usually commit sha)
-    export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2`
-    # but dash is prohibited for conda build, replace with underscore
-    export CIL_VERSION=`echo ${CIL_VERSION} | tr - _`
-    echo Building dev version ${CIL_VERSION}
+    # detected dash means that it is dev version, 
+    # get first and second part between first dash and ignore all after other dash (usually sha)
+    # and as dash is prohibited for conda build, replace with underscore
+    export CIL_VERSION=`echo ${CIL_VERSION} | cut -d "-" -f -2 | tr - _`    
+    echo Building dev version: ${CIL_VERSION}
   else
-    echo Defining version from last git tag and commit: $CIL_VERSION
+    echo Building release version: $CIL_VERSION
   fi
 fi
 
-- 
cgit v1.2.3


From 84811ac4418fb7f72dfcb7cb8329cf05ed0fb538 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 12:52:34 +0000
Subject: Update jenkins-build.sh

---
 build/jenkins-build.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 6c863c0..a808699 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -43,13 +43,15 @@ conda build Wrappers/Python/conda-recipe
 export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 # REG_FILES variable should contain output files
 echo files created: $REG_FILES
-#upload to anaconda
+
+# upload to anaconda only if token is defined
+# and TODO pull request not to upload 
 if [[ -n ${CCPI_CONDA_TOKEN} ]]
 then
   conda install anaconda-client
   while read -r outfile; do
     #if 0 commit after tag then call anaconda without --label dev
-    #TODO pull request not to upload 
+    
     if [[ $CIL_VERSION == *"_"* ]]; then
       # upload with dev label
       anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
-- 
cgit v1.2.3


From 440693750ee94044f4f0bcd7c5e737487bfb6e64 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 13:20:04 +0000
Subject: Update jenkins-build.sh

---
 build/jenkins-build.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index e4a0535..7ac4539 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -23,7 +23,7 @@ fi
 
 # install miniconda if the module is not present
 if hash conda 2>/dev/null; then
-  echo using conda
+  echo using installed conda
 else
   if [ ! -f Miniconda3-latest-Linux-x86_64.sh ]; then
     wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
@@ -44,7 +44,6 @@ export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 # REG_FILES variable should contain output files
 echo files created: $REG_FILES
 
-
 # upload to anaconda only if token is defined
 # and TODO pull request not to upload 
 
-- 
cgit v1.2.3


From 74bfad3cfa5462856d03872c02229423f9a36b9f Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 14:14:33 +0000
Subject: UPDATE: check git branch, upload master build

---
 build/jenkins-build.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 7ac4539..840afac 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -32,6 +32,7 @@ else
   ./Miniconda3-latest-Linux-x86_64.sh -u -b -p .
   PATH=$PATH:./bin
 fi
+
 # presume that git clone is done before this script is launched, if not, uncomment
 #git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
@@ -46,8 +47,10 @@ echo files created: $REG_FILES
 
 # upload to anaconda only if token is defined
 # and TODO pull request not to upload 
+GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+echo on branch ${GIT_BRANCH}
 
-if [[ -n ${CCPI_CONDA_TOKEN} ]]
+if [[ -n ${CCPI_CONDA_TOKEN} && ${GIT_BRANCH}=="master" ]]
 then
   conda install anaconda-client
   while read -r outfile; do
@@ -61,5 +64,5 @@ then
     fi
   done <<< "$REG_FILES"
 else
-  echo CCPI_CONDA_TOKEN not defined, will not upload to anaconda.
+  echo CCPI_CONDA_TOKEN not defined or git branch is not master, will not upload to anaconda.
 fi
-- 
cgit v1.2.3


From e7f26cab5e6522d521c6b0e42f1991c3e7c0ac7d Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 14:43:14 +0000
Subject: UPDATE 2: check git branch, upload master build

---
 build/jenkins-build.sh | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 840afac..03de4e6 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -50,19 +50,21 @@ echo files created: $REG_FILES
 GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
 echo on branch ${GIT_BRANCH}
 
-if [[ -n ${CCPI_CONDA_TOKEN} && ${GIT_BRANCH}=="master" ]]
-then
-  conda install anaconda-client
-  while read -r outfile; do
-    #if 0 commit after tag then call anaconda without --label dev
-    
-    if [[ $CIL_VERSION == *"_"* ]]; then
-      # upload with dev label
-      anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
-    else 
-      anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force
-    fi
-  done <<< "$REG_FILES"
+if [[ -n ${CCPI_CONDA_TOKEN} ]]; then
+  if [[ ${GIT_BRANCH}=="master" ]]; then
+    conda install anaconda-client
+    while read -r outfile; do
+      #if >0 commit (some _ in version) then marking as dev build
+      if [[ $CIL_VERSION == *"_"* ]]; then
+        # upload with dev label
+        anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force --label dev
+      else
+        anaconda -v -t ${CCPI_CONDA_TOKEN}  upload $outfile --force
+      fi
+    done <<< "$REG_FILES"
+  else
+    echo git branch is not master, will not upload to anaconda.
+  fi
 else
-  echo CCPI_CONDA_TOKEN not defined or git branch is not master, will not upload to anaconda.
+  echo CCPI_CONDA_TOKEN not defined, will not upload to anaconda.
 fi
-- 
cgit v1.2.3


From b63188fc01a6c0a2bf9637ed1660d0dbdd48e6fe Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 15:03:38 +0000
Subject: UPDATE 2: check git branch, upload master build

---
 build/jenkins-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 03de4e6..b8b2aef 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -47,7 +47,7 @@ echo files created: $REG_FILES
 
 # upload to anaconda only if token is defined
 # and TODO pull request not to upload 
-GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+GIT_BRANCH=`git symbolic-ref --short HEAD`
 echo on branch ${GIT_BRANCH}
 
 if [[ -n ${CCPI_CONDA_TOKEN} ]]; then
-- 
cgit v1.2.3


From 93224f30e5072ec0b19958f053e2f58d07bf1f4b Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 15:29:16 +0000
Subject: UPDATE 3: check git branch

---
 build/jenkins-build.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index b8b2aef..4f96194 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -33,6 +33,9 @@ else
   PATH=$PATH:./bin
 fi
 
+GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
+echo on branch ${GIT_BRANCH}
+
 # presume that git clone is done before this script is launched, if not, uncomment
 #git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
 conda install -y conda-build
@@ -46,9 +49,7 @@ export REG_FILES=`conda build Wrappers/Python/conda-recipe --output`
 echo files created: $REG_FILES
 
 # upload to anaconda only if token is defined
-# and TODO pull request not to upload 
-GIT_BRANCH=`git symbolic-ref --short HEAD`
-echo on branch ${GIT_BRANCH}
+# and TODO pull request not to upload
 
 if [[ -n ${CCPI_CONDA_TOKEN} ]]; then
   if [[ ${GIT_BRANCH}=="master" ]]; then
-- 
cgit v1.2.3


From 53cbfdca7373b86fcf2f1a2ae8618265a628bc05 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 16:03:22 +0000
Subject: UPDATE 4: check git branch

---
 build/jenkins-build.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 4f96194..87ca54f 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -35,6 +35,7 @@ fi
 
 GIT_BRANCH=`git rev-parse --abbrev-ref HEAD`
 echo on branch ${GIT_BRANCH}
+cat .git/HEAD
 
 # presume that git clone is done before this script is launched, if not, uncomment
 #git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
@@ -52,7 +53,7 @@ echo files created: $REG_FILES
 # and TODO pull request not to upload
 
 if [[ -n ${CCPI_CONDA_TOKEN} ]]; then
-  if [[ ${GIT_BRANCH}=="master" ]]; then
+  if [[ ${GIT_BRANCH} == "master" ]]; then
     conda install anaconda-client
     while read -r outfile; do
       #if >0 commit (some _ in version) then marking as dev build
-- 
cgit v1.2.3


From 450ee88cb6a7dd48cd0911937a8a0ed309b5392d Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 16:24:46 +0000
Subject: UPDATE 5: minor

---
 build/jenkins-build.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 87ca54f..2936fed 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -20,7 +20,6 @@ fi
 
 # Script to builds source code in Jenkins environment
 # module try-load conda
-
 # install miniconda if the module is not present
 if hash conda 2>/dev/null; then
   echo using installed conda
-- 
cgit v1.2.3


From 952e9f45b04a42d5b8ef6ce3fbc50046c00e61b9 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Tue, 22 Jan 2019 16:27:06 +0000
Subject: UPDATE 6: minor

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

diff --git a/build/jenkins-build.sh b/build/jenkins-build.sh
index 2936fed..87ca54f 100755
--- a/build/jenkins-build.sh
+++ b/build/jenkins-build.sh
@@ -20,6 +20,7 @@ fi
 
 # Script to builds source code in Jenkins environment
 # module try-load conda
+
 # install miniconda if the module is not present
 if hash conda 2>/dev/null; then
   echo using installed conda
-- 
cgit v1.2.3


From 00bcc569758d9429ecb3234e64c7ac05b3f8e3c1 Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 23 Jan 2019 10:08:11 +0000
Subject: Update Readme.md

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

diff --git a/Readme.md b/Readme.md
index 70c9e13..f155c16 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,4 +1,5 @@
-[![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/)
+Master: [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/)
+Development status (PR, non-master branch): [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/badge/icon)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/)
 # CCPi-Regularisation Toolkit (CCPi-RGL)
 
 **Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.** 
-- 
cgit v1.2.3


From b9b1254ea345330326db3883aafd8a8a66c6c67a Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 23 Jan 2019 10:09:32 +0000
Subject: Update Readme.md

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

diff --git a/Readme.md b/Readme.md
index f155c16..e7cc1f0 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,5 +1,5 @@
 Master: [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/)
-Development status (PR, non-master branch): [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/badge/icon)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/)
+Development status (PR, non-master branch): [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit-dev)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/)
 # CCPi-Regularisation Toolkit (CCPi-RGL)
 
 **Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.** 
-- 
cgit v1.2.3


From 06771c554d4c1ecd1e4a38a600e530222b86b28d Mon Sep 17 00:00:00 2001
From: Tomas Kulhanek <tomas.kulhanek@stfc.ac.uk>
Date: Wed, 23 Jan 2019 10:24:48 +0000
Subject: Update Readme.md

---
 Readme.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Readme.md b/Readme.md
index e7cc1f0..1745b9e 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,5 +1,6 @@
-Master: [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/)
-Development status (PR, non-master branch): [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit-dev)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/)
+| Master | Development |
+|--------|-------------|
+| [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/) | [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit-dev)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/) |
 # CCPi-Regularisation Toolkit (CCPi-RGL)
 
 **Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.** 
-- 
cgit v1.2.3


From 2694ad1b18d14fcfd7d57ded7290ebd1bf845fda Mon Sep 17 00:00:00 2001
From: Kazantsev <daniil.kazantsev@diamond.ac.uk>
Date: Wed, 23 Jan 2019 11:52:40 +0000
Subject: fixes gpu build on windows

---
 Core/regularisers_GPU/TV_FGP_GPU_core.h  |  9 ++++-----
 Core/regularisers_GPU/TV_SB_GPU_core.h   | 10 +++++-----
 Core/regularisers_GPU/dTV_FGP_GPU_core.h |  9 ++++-----
 Wrappers/Python/conda-recipe/meta.yaml   |  2 +-
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/Core/regularisers_GPU/TV_FGP_GPU_core.h b/Core/regularisers_GPU/TV_FGP_GPU_core.h
index b28cdf3..bf13508 100755
--- a/Core/regularisers_GPU/TV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/TV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _TV_FGP_GPU_
 #define _TV_FGP_GPU_
 
-extern "C" int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Core/regularisers_GPU/TV_SB_GPU_core.h b/Core/regularisers_GPU/TV_SB_GPU_core.h
index d44ab77..901b90f 100755
--- a/Core/regularisers_GPU/TV_SB_GPU_core.h
+++ b/Core/regularisers_GPU/TV_SB_GPU_core.h
@@ -1,10 +1,10 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _SB_TV_GPU_
 #define _SB_TV_GPU_
 
-extern "C" int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+
+extern "C" CCPI_EXPORT int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Core/regularisers_GPU/dTV_FGP_GPU_core.h b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
index 9020b1a..f9281e8 100644
--- a/Core/regularisers_GPU/dTV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _dTV_FGP_GPU_
 #define _dTV_FGP_GPU_
 
-extern "C" int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index 9fe813d..9dd5544 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -12,7 +12,7 @@ test:
   files:
     - lena_gray_512.tif
   requires:
-    - pillow
+    - pillow=4.1.1
 
 requirements:
   build:
-- 
cgit v1.2.3