FIX: directory links, install instructions

7 files changed, 49 insertions, 33 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5d3bbbd..043f13c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -46,7 +46,7 @@ set(MATLAB_DEST "${CMAKE_INSTALL_PREFIX}/matlab")
 endif()
 message(STATUS "Matlab wrappers will be installed in " ${MATLAB_DEST})
 
-set(PYTHON_DEST_DIR "" CACHE PATH "Directory of the Matlab wrappers")
+set(PYTHON_DEST_DIR "" CACHE PATH "Directory of the Python wrappers")
 if (PYTHON_DEST_DIR)
  set(PYTHON_DEST "${PYTHON_DEST_DIR}")
 else() 
@@ -55,5 +55,5 @@ endif()
 message(STATUS "Python wrappers will be installed in " ${PYTHON_DEST})
 
 
-add_subdirectory(src/Core)
+#add_subdirectory(src/Core)
 add_subdirectory(src)
diff --git a/Readme.md b/Readme.md
index ebd4d20..a9433d2 100644
--- a/Readme.md
+++ b/Readme.md
@@ -50,13 +50,28 @@
 
 ## Installation:
 
-The package comes as a [CMake](https://cmake.org) project so you will need CMake (v.>=3) to configure it. Additionally you will need a C compiler, `make` (on linux) and CUDA SDK where available. The toolkit may be used directly from C/C++ as it is compiled as a shared library (check-out the include files in `Core` for this). We provide wrappers for Python and Matlab.
+The package comes as a [CMake](https://cmake.org) project
+and additional wrappers for Python and Matlab.
 
+To install precompiled binaries, you need `conda` and install from `ccpi` channel using :
+```
+conda install ccpi-regulariser -c ccpi -c conda-forge
+```
+
+In order to compile C/C++ sources and additional wrappers from source code, the recommended way is:
+```
+git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
+cd CCPi-Regularisation-Toolkit
+build/jenkins-build.sh
+```
+this will install `conda build` environment and compiles C/C++ and Python wrappers and performs basic tests.
+
+### CMake
+If you want to build directly using cmake, install CMake (v.>=3) to configure it. Additionally you will need a C compiler, `make` (on linux) and CUDA SDK where available. The toolkit may be used directly from C/C++ as it is compiled as a shared library (check-out the include files in `Core` for this) 
 1. Clone this repository to a directory, i.e. `CCPi-Regularisation-Toolkit`, 
 2. create a build directory. 
 3. Issue `cmake` to configure (or `cmake-gui`, or `ccmake`, or `cmake3`). Use additional flags to fine tune the configuration. 
 
-### CMake flags
 Flags used during configuration
 
 | CMake flag | type | meaning |
diff --git a/recipe/build.sh b/recipe/build.sh
index 1d54b6f..a156193 100644
--- a/recipe/build.sh
+++ b/recipe/build.sh
@@ -1,8 +1,8 @@
 
-mkdir "$SRC_DIR/ccpi"
-cp -rv "$RECIPE_DIR/../src/Matlab" "$SRC_DIR/ccpi"
-cp -rv "$RECIPE_DIR/../src/Python" "$SRC_DIR/ccpi"
-cp -rv "$RECIPE_DIR/../src/Core" "$SRC_DIR/Core"
+#mkdir "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/Matlab" "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/Python" "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/Core" "$SRC_DIR/Core"
 
 cd $SRC_DIR
 ##cuda=off
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
index 7435b2b..61d17bd 100644
--- a/recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -10,7 +10,7 @@ build:
   
 test:
   files:
-    - lena_gray_512.tif
+    - ../test/lena_gray_512.tif
   requires:
     - pillow=4.1.1
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index bdcb8f4..5fe1a57 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -11,6 +11,7 @@
 #   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.
+add_subdirectory(Core)
 if (BUILD_MATLAB_WRAPPER)
     add_subdirectory(Matlab)
 endif()
diff --git a/src/Python/CMakeLists.txt b/src/Python/CMakeLists.txt
index c2ef855..ab95ecc 100644
--- a/src/Python/CMakeLists.txt
+++ b/src/Python/CMakeLists.txt
@@ -7,7 +7,7 @@ project(regulariserPython)
 # The version number.
 
 #set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
-
+message("Creating Python Wrapper")
 # conda orchestrated build
 message("CIL_VERSION: ${CIL_VERSION}")
 #include (GenerateExportHeader)
@@ -19,7 +19,7 @@ endif()
 
 	
 ## Build the regularisers package as a library
-message("Creating Regularisers as shared library")
+#TODO message("Creating Regularisers as shared library")
 
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
 
@@ -87,7 +87,7 @@ if (PYTHONINTERP_FOUND)
     set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/setup-regularisers.py.in")
     set(SETUP_PY    "${CMAKE_CURRENT_BINARY_DIR}/setup-regularisers.py")
     #set(DEPS        "${CMAKE_CURRENT_SOURCE_DIR}/module/__init__.py")
-    set (DEPS       "${CMAKE_BINARY_DIR}/Core/")
+    set (DEPS       "${CMAKE_BINARY_DIR}/src/Core/")
     set(OUTPUT      "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp")
 
     configure_file(${SETUP_PY_IN} ${SETUP_PY})
@@ -99,9 +99,9 @@ if (PYTHONINTERP_FOUND)
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
                        COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
-                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} install
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
@@ -112,9 +112,9 @@ if (PYTHONINTERP_FOUND)
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
                        COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
-                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core/${CMAKE_BUILD_TYPE}
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core/${CMAKE_BUILD_TYPE}
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
@@ -123,9 +123,9 @@ if (PYTHONINTERP_FOUND)
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
                        COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
                        COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
-                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
-                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
diff --git a/src/Python/setup-regularisers.py.in b/src/Python/setup-regularisers.py.in
index 462edda..59be768 100644
--- a/src/Python/setup-regularisers.py.in
+++ b/src/Python/setup-regularisers.py.in
@@ -34,18 +34,18 @@ extra_libraries = ['cilreg']
 
 print ("extra_library_dirs " , extra_library_dirs)
 
-extra_include_dirs += [os.path.join(".." , ".." , "Core"),
-                       os.path.join(".." , ".." , "Core",  "regularisers_CPU"),
-                       os.path.join(".." , ".." , "Core",  "inpainters_CPU"),
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_FGP" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_ROF" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_SB" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TGV" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "LLTROF" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "NDF" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "dTV_FGP" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "DIFF4th" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "PatchSelect" ) ,
+extra_include_dirs += [os.path.join(".." , "Core"),
+                       os.path.join(".." , "Core",  "regularisers_CPU"),
+                       os.path.join(".." , "Core",  "inpainters_CPU"),
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_FGP" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_ROF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_SB" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TGV" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "LLTROF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "NDF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "dTV_FGP" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "DIFF4th" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "PatchSelect" ) ,
 						   "."]
 
 if platform.system() == 'Windows':