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-rw-r--r--CMakeLists.txt30
-rw-r--r--src/CMakeLists.txt14
-rw-r--r--src/Python/CMakeLists.txt108
-rw-r--r--src/Python/FindAnacondaEnvironment.cmake166
-rw-r--r--src/Python/compile.bat.in4
-rw-r--r--src/Python/compile.sh.in6
-rw-r--r--src/Python/conda-recipe/bld.bat14
-rw-r--r--src/Python/conda-recipe/build.sh14
-rw-r--r--src/Python/conda-recipe/meta.yaml30
9 files changed, 320 insertions, 66 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7eb7185..d05cdd9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,30 @@
+# Copyright 2017 Edoardo Pasca
#
-cmake_minimum_required(3.0.2 FATAL_ERROR)
+# 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
+#
+# 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.
+
+cmake_minimum_required (VERSION 3.0)
+
+project(FISTA)
+#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
+
+# The version number.
+set (FISTA_VERSION_MAJOR 1)
+set (FISTA_VERSION_MINOR 0)
+
+set (CIL_VERSION_MAJOR 0)
+set (CIL_VERSION_MINOR 9)
+set (CIL_VERSION_PATCH 1)
+
+set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}')
-project(FISTA) \ No newline at end of file
+add_subdirectory(src)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..cbe2fec
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,14 @@
+# Copyright 2017 Edoardo Pasca
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+add_subdirectory(Python) \ No newline at end of file
diff --git a/src/Python/CMakeLists.txt b/src/Python/CMakeLists.txt
index a75c062..3eb4158 100644
--- a/src/Python/CMakeLists.txt
+++ b/src/Python/CMakeLists.txt
@@ -1,20 +1,21 @@
-cmake_minimum_required (VERSION 3.0)
-
-project(FISTA)
-
-# The version number.
-set (FISTA_VERSION_MAJOR 1)
-set (FISTA_VERSION_MINOR 0)
-
-set (CIL_VERSION_MAJOR 0)
-set (CIL_VERSION_MINOR 9)
-set (CIL_VERSION_PATCH 1)
-
-set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}')
+# Copyright 2017 Edoardo Pasca
+#
+# 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
+#
+# 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.
message("CIL VERSION " ${CIL_VERSION})
-# variables we need to run the conda build
+# variables that are set by conda
+
#PREFIX=C:\Apps\Miniconda2\envs\cil\Library
#LIBRARY_INC=C:\\Apps\\Miniconda2\\envs\\cil\\Library\\include
@@ -22,58 +23,37 @@ set (NUMPY_VERSION 1.12)
#set (PYTHON_VERSION 3.5)
#https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/R9gWjl09UFs
-set (CONDA_ENVIRONMENT "C:\\Apps\\Miniconda2\\envs\\cil27" CACHE PATH "env dir")
-
-function (findPythonForAnacondaEnvironment env)
-
- file(TO_CMAKE_PATH ${env}/python.exe PYTHON_EXECUTABLE)
-
- message("Found " ${PYTHON_EXECUTABLE})
- execute_process(COMMAND ${PYTHON_EXECUTABLE} pythonversion.py major
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE major
- ERROR_QUIET)
- execute_process(COMMAND ${PYTHON_EXECUTABLE} pythonversion.py minor
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE minor
- ERROR_QUIET)
- execute_process(COMMAND ${PYTHON_EXECUTABLE} pythonversion.py patch
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE patch
- ERROR_QUIET)
- execute_process(COMMAND ${PYTHON_EXECUTABLE} pythonversion.py
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE version
- ERROR_QUIET)
+set (CONDA_ENVIRONMENT "cil")
+set (CONDA_ENVIRONMENT_PATH "C:\\Apps\\Miniconda2\\envs\\${CONDA_ENVIRONMENT}" CACHE PATH "env dir")
-
- set (PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE} PARENT_SCOPE)
- set (PYTHONINTERP_FOUND "ON" PARENT_SCOPE)
- set (PYTHON_VERSION_STRING ${version})
- message("My version found " ${PYTHON_VERSION_STRING})
-
-endfunction()
-
-findPythonForAnacondaEnvironment(${CONDA_ENVIRONMENT})
-
-set(Python_ADDITIONAL_VERSIONS 3)
+message("CIL VERSION " ${CIL_VERSION})
-find_package(PythonInterp)
-if (PYTHONINTERP_FOUND)
-
- message("Found interpret " ${PYTHON_EXECUTABLE})
-
- foreach(pv ${PYTHON_VERSION_STRING})
- message("Found interpret " ${pv})
- endforeach()
+# set the Python variables for the Conda environment
+include(FindAnacondaEnvironment.cmake)
+findPythonForAnacondaEnvironment(${CONDA_ENVIRONMENT_PATH})
+message("Python found " ${PYTHON_VERSION_STRING})
+findPythonPackagesPath()
+message("PYTHON_PACKAGES_FOUND " ${PYTHON_PACKAGES_PATH})
+
+# copy the Pyhon files of the package
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging/)
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi)
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging)
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/Regularizer.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging)
+
+
+# Copy and configure the relative conda build and recipes
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe)
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/meta.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe)
+
+if (WIN32)
+ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/)
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile.bat)
+elseif(UNIX)
+ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/)
+ # assumes we will use bash
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile.sh)
endif()
-find_package(PythonLibs)
-if (PYTHONLIB_FOUND)
- message("Found PythonLibs PYTHON_LIBRARIES " ${PYTHON_LIBRARIES})
- message("Found PythonLibs PYTHON_INCLUDE_PATH " ${PYTHON_INCLUDE_PATH})
- message("Found PythonLibs PYTHON_INCLUDE_DIRS " ${PYTHON_INCLUDE_DIRS})
- message("Found PythonLibs PYTHONLIBS_VERSION_STRING " ${PYTHONLIBS_VERSION_STRING} )
-
-endif()
diff --git a/src/Python/FindAnacondaEnvironment.cmake b/src/Python/FindAnacondaEnvironment.cmake
new file mode 100644
index 0000000..3abb5d1
--- /dev/null
+++ b/src/Python/FindAnacondaEnvironment.cmake
@@ -0,0 +1,166 @@
+# Copyright 2017 Edoardo Pasca
+#
+# 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
+#
+# 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.
+
+# #.rst:
+# FindAnacondaEnvironment
+# --------------
+#
+# Find Python executable and library for a specific Anaconda environment
+#
+# This module finds the Python interpreter for a specific Anaconda enviroment,
+# if installed and determines where the include files and libraries are.
+# This code sets the following variables:
+#
+# ::
+# PYTHONINTERP_FOUND - if the Python interpret has been found
+# PYTHON_EXECUTABLE - the Python interpret found
+# PYTHON_LIBRARY - path to the python library
+# PYTHON_INCLUDE_PATH - path to where Python.h is found (deprecated)
+# PYTHON_INCLUDE_DIRS - path to where Python.h is found
+# PYTHONLIBS_VERSION_STRING - version of the Python libs found (since CMake 2.8.8)
+# PYTHON_VERSION_MAJOR - major Python version
+# PYTHON_VERSION_MINOR - minor Python version
+# PYTHON_VERSION_PATCH - patch Python version
+
+
+
+function (findPythonForAnacondaEnvironment env)
+
+ file(TO_CMAKE_PATH ${env}/python.exe PYTHON_EXECUTABLE)
+
+ message("Found " ${PYTHON_EXECUTABLE})
+ ####### FROM FindPythonInterpr ########
+ # determine python version string
+ if(PYTHON_EXECUTABLE)
+ execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c
+ "import sys; sys.stdout.write(';'.join([str(x) for x in sys.version_info[:3]]))"
+ OUTPUT_VARIABLE _VERSION
+ RESULT_VARIABLE _PYTHON_VERSION_RESULT
+ ERROR_QUIET)
+ if(NOT _PYTHON_VERSION_RESULT)
+ string(REPLACE ";" "." _PYTHON_VERSION_STRING "${_VERSION}")
+ list(GET _VERSION 0 _PYTHON_VERSION_MAJOR)
+ list(GET _VERSION 1 _PYTHON_VERSION_MINOR)
+ list(GET _VERSION 2 _PYTHON_VERSION_PATCH)
+ if(PYTHON_VERSION_PATCH EQUAL 0)
+ # it's called "Python 2.7", not "2.7.0"
+ string(REGEX REPLACE "\\.0$" "" _PYTHON_VERSION_STRING "${PYTHON_VERSION_STRING}")
+ endif()
+ else()
+ # sys.version predates sys.version_info, so use that
+ execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c "import sys; sys.stdout.write(sys.version)"
+ OUTPUT_VARIABLE _VERSION
+ RESULT_VARIABLE _PYTHON_VERSION_RESULT
+ ERROR_QUIET)
+ if(NOT _PYTHON_VERSION_RESULT)
+ string(REGEX REPLACE " .*" "" _PYTHON_VERSION_STRING "${_VERSION}")
+ string(REGEX REPLACE "^([0-9]+)\\.[0-9]+.*" "\\1" _PYTHON_VERSION_MAJOR "${PYTHON_VERSION_STRING}")
+ string(REGEX REPLACE "^[0-9]+\\.([0-9])+.*" "\\1" _PYTHON_VERSION_MINOR "${PYTHON_VERSION_STRING}")
+ if(PYTHON_VERSION_STRING MATCHES "^[0-9]+\\.[0-9]+\\.([0-9]+)")
+ set(PYTHON_VERSION_PATCH "${CMAKE_MATCH_1}")
+ else()
+ set(PYTHON_VERSION_PATCH "0")
+ endif()
+ else()
+ # sys.version was first documented for Python 1.5, so assume
+ # this is older.
+ set(PYTHON_VERSION_STRING "1.4" PARENT_SCOPE)
+ set(PYTHON_VERSION_MAJOR "1" PARENT_SCOPE)
+ set(PYTHON_VERSION_MINOR "4" PARENT_SCOPE)
+ set(PYTHON_VERSION_PATCH "0" PARENT_SCOPE)
+ endif()
+ endif()
+ unset(_PYTHON_VERSION_RESULT)
+ unset(_VERSION)
+ endif()
+ ###############################################
+
+ set (PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE} PARENT_SCOPE)
+ set (PYTHONINTERP_FOUND "ON" PARENT_SCOPE)
+ set (PYTHON_VERSION_STRING ${_PYTHON_VERSION_STRING} PARENT_SCOPE)
+ set (PYTHON_VERSION_MAJOR ${_PYTHON_VERSION_MAJOR} PARENT_SCOPE)
+ set (PYTHON_VERSION_MINOR ${_PYTHON_VERSION_MINOR} PARENT_SCOPE)
+ set (PYTHON_VERSION_PATCH ${_PYTHON_VERSION_PATCH} PARENT_SCOPE)
+ message("My version found " ${PYTHON_VERSION_STRING})
+
+endfunction()
+
+
+
+set(Python_ADDITIONAL_VERSIONS 3.5)
+
+find_package(PythonInterp)
+if (PYTHONINTERP_FOUND)
+
+ message("Found interpret " ${PYTHON_EXECUTABLE})
+ message("Python Library " ${PYTHON_LIBRARY})
+ message("Python Include Dir " ${PYTHON_INCLUDE_DIR})
+ message("Python Include Path " ${PYTHON_INCLUDE_PATH})
+
+ foreach(pv ${PYTHON_VERSION_STRING})
+ message("Found interpret " ${pv})
+ endforeach()
+endif()
+
+
+
+find_package(PythonLibs)
+if (PYTHONLIB_FOUND)
+ message("Found PythonLibs PYTHON_LIBRARIES " ${PYTHON_LIBRARIES})
+ message("Found PythonLibs PYTHON_INCLUDE_PATH " ${PYTHON_INCLUDE_PATH})
+ message("Found PythonLibs PYTHON_INCLUDE_DIRS " ${PYTHON_INCLUDE_DIRS})
+ message("Found PythonLibs PYTHONLIBS_VERSION_STRING " ${PYTHONLIBS_VERSION_STRING} )
+else()
+ message("No PythonLibs Found")
+endif()
+
+
+
+
+function(findPythonPackagesPath)
+### https://openlab.ncl.ac.uk/gitlab/john.shearer/clappertracker/raw/549885e5decd37f7b23e9c1fd39e86f207156795/src/3rdparty/opencv/cmake/OpenCVDetectPython.cmake
+###
+if(CMAKE_HOST_UNIX)
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import *; print get_python_lib()"
+ RESULT_VARIABLE PYTHON_CVPY_PROCESS
+ OUTPUT_VARIABLE PYTHON_STD_PACKAGES_PATH
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ if("${PYTHON_STD_PACKAGES_PATH}" MATCHES "site-packages")
+ set(_PYTHON_PACKAGES_PATH "python${PYTHON_VERSION_MAJOR_MINOR}/site-packages")
+ else() #debian based assumed, install to the dist-packages.
+ set(_PYTHON_PACKAGES_PATH "python${PYTHON_VERSION_MAJOR_MINOR}/dist-packages")
+ endif()
+ if(EXISTS "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/${PYTHON_PACKAGES_PATH}")
+ set(_PYTHON_PACKAGES_PATH "lib${LIB_SUFFIX}/${_PYTHON_PACKAGES_PATH}")
+ else()
+ set(_PYTHON_PACKAGES_PATH "lib/${_PYTHON_PACKAGES_PATH}")
+ endif()
+ elseif(CMAKE_HOST_WIN32)
+ get_filename_component(PYTHON_PATH "${PYTHON_EXECUTABLE}" PATH)
+ file(TO_CMAKE_PATH "${PYTHON_PATH}" PYTHON_PATH)
+ if(NOT EXISTS "${PYTHON_PATH}/Lib/site-packages")
+ unset(PYTHON_PATH)
+ get_filename_component(PYTHON_PATH "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${PYTHON_VERSION_MAJOR_MINOR}\\InstallPath]" ABSOLUTE)
+ if(NOT PYTHON_PATH)
+ get_filename_component(PYTHON_PATH "[HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${PYTHON_VERSION_MAJOR_MINOR}\\InstallPath]" ABSOLUTE)
+ endif()
+ file(TO_CMAKE_PATH "${PYTHON_PATH}" PYTHON_PATH)
+ endif()
+ set(_PYTHON_PACKAGES_PATH "${PYTHON_PATH}/Lib/site-packages")
+ endif()
+ SET(PYTHON_PACKAGES_PATH "${_PYTHON_PACKAGES_PATH}" PARENT_SCOPE)
+
+endfunction()
+
+
diff --git a/src/Python/compile.bat.in b/src/Python/compile.bat.in
new file mode 100644
index 0000000..d4ddc92
--- /dev/null
+++ b/src/Python/compile.bat.in
@@ -0,0 +1,4 @@
+set CIL_VERSION=@CIL_VERSION@
+
+activate @CONDA_ENVIRONMENT@
+conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi \ No newline at end of file
diff --git a/src/Python/compile.sh.in b/src/Python/compile.sh.in
new file mode 100644
index 0000000..dd29973
--- /dev/null
+++ b/src/Python/compile.sh.in
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+export CIL_VERSION=@CIL_VERSION@
+module load python/anaconda
+source activate @CONDA_ENVIRONMENT@
+conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi \ No newline at end of file
diff --git a/src/Python/conda-recipe/bld.bat b/src/Python/conda-recipe/bld.bat
new file mode 100644
index 0000000..69491de
--- /dev/null
+++ b/src/Python/conda-recipe/bld.bat
@@ -0,0 +1,14 @@
+IF NOT DEFINED CIL_VERSION (
+ECHO CIL_VERSION Not Defined.
+exit 1
+)
+
+mkdir "%SRC_DIR%\ccpi"
+xcopy /e "%RECIPE_DIR%\..\.." "%SRC_DIR%\ccpi"
+
+cd %SRC_DIR%\ccpi\Python
+
+%PYTHON% setup.py build_ext
+if errorlevel 1 exit 1
+%PYTHON% setup.py install
+if errorlevel 1 exit 1
diff --git a/src/Python/conda-recipe/build.sh b/src/Python/conda-recipe/build.sh
new file mode 100644
index 0000000..855047f
--- /dev/null
+++ b/src/Python/conda-recipe/build.sh
@@ -0,0 +1,14 @@
+
+if [ -z "$CIL_VERSION" ]; then
+ echo "Need to set CIL_VERSION"
+ exit 1
+fi
+mkdir "$SRC_DIR/ccpi"
+cp -r "$RECIPE_DIR/../.." "$SRC_DIR/ccpi"
+
+cd $SRC_DIR/ccpi/Python
+
+$PYTHON setup.py build_ext
+$PYTHON setup.py install
+
+
diff --git a/src/Python/conda-recipe/meta.yaml b/src/Python/conda-recipe/meta.yaml
new file mode 100644
index 0000000..c5b7a89
--- /dev/null
+++ b/src/Python/conda-recipe/meta.yaml
@@ -0,0 +1,30 @@
+package:
+ name: ccpi-fista
+ version: {{ environ['CIL_VERSION'] }}
+
+
+build:
+ preserve_egg_dir: False
+ script_env:
+ - CIL_VERSION
+# number: 0
+
+requirements:
+ build:
+ - python
+ - numpy
+ - setuptools
+ - boost ==1.64
+ - boost-cpp ==1.64
+ - cython
+
+ run:
+ - python
+ - numpy
+ - boost ==1.64
+
+
+about:
+ home: http://www.ccpi.ac.uk
+ license: BSD license
+ summary: 'CCPi Core Imaging Library Quantification Toolbox'
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-07 19:27:00 +0000