diff options
| -rw-r--r-- | CMakeLists.txt | 30 | ||||
| -rw-r--r-- | src/CMakeLists.txt | 14 | ||||
| -rw-r--r-- | src/Python/CMakeLists.txt | 58 | ||||
| -rw-r--r-- | src/Python/FindAnacondaEnvironment.cmake | 166 | ||||
| -rw-r--r-- | src/Python/compile.bat.in | 4 | ||||
| -rw-r--r-- | src/Python/compile.sh.in | 6 | ||||
| -rw-r--r-- | src/Python/conda-recipe/bld.bat | 14 | ||||
| -rw-r--r-- | src/Python/conda-recipe/build.sh | 14 | ||||
| -rw-r--r-- | src/Python/conda-recipe/meta.yaml | 30 |
9 files changed, 336 insertions, 0 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..c9e8cb7 --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,30 @@ +# 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. + +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}') + +add_subdirectory(src)
\ No newline at end of file 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 new file mode 100644 index 0000000..fd377cc --- /dev/null +++ b/src/Python/CMakeLists.txt @@ -0,0 +1,58 @@ +# 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 " ${CIL_VERSION}) + +# variables that are set by conda +#PREFIX=C:\Apps\Miniconda2\envs\cil\Library +#LIBRARY_INC=C:\\Apps\\Miniconda2\\envs\\cil\\Library\\include + +set (NUMPY_VERSION 1.12) +#set (PYTHON_VERSION 3.5) + +#https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/R9gWjl09UFs +set (CONDA_ENVIRONMENT "cil") +set (CONDA_ENVIRONMENT_PATH "C:\\Apps\\Miniconda2\\envs\\${CONDA_ENVIRONMENT}" CACHE PATH "env dir") + +message("CIL VERSION " ${CIL_VERSION}) + +# set the Python variables for the Conda environment +include(FindAnacondaEnvironment.cmake) +findPythonForAnacondaEnvironment(${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() + + 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' |