Merge pull request #99 from clEsperanto/test_new_backend_cuda_ocl

update backend

.github/workflows/build_and_test.yml

@@ -30,6 +30,7 @@ jobs:
       - name: Set up conda ${{ matrix.python-version }}
         uses: conda-incubator/[email protected]
         with:
+          miniconda-version: "latest"
           auto-update-conda: true
           activate-environment: test
           python-version: ${{ matrix.python-version }}
@@ -43,14 +44,18 @@ jobs:
         shell: bash -l {0}
         run: pip install scikit-build pytest pytest-cov pytest-benchmark
 
+      # - name: Install cuda
+      #   shell: bash -l {0}
+      #   run: conda install -y cudatoolkit 
+
       - name: Install pocl
         shell: bash -l {0}
-        run: conda install -y pocl
+        run: conda install -y pocl 
 
       - name: Compile
         shell: bash -l {0}
         run: |
-          pip install . -vvv
+          pip install . -vvv --config-settings=cmake.define.CMAKE_PREFIX_PATH=$CONDA_PREFIX
 
       - name: Tests
         shell: bash -l {0}

.github/workflows/pages.yml

@@ -42,7 +42,7 @@ jobs:
       - name: Setup Pages
         uses: actions/configure-pages@v3
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2x
         with:
           # Upload entire repository
           path: './docs/build/html'

.github/workflows/wheels.yml

@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.14.1
         env:
           CIBW_ARCHS_MACOS: x86_64 arm64
 
@@ -63,7 +63,7 @@ jobs:
           name: artifact
           path: dist
 
-      - uses: pypa/[email protected].6
+      - uses: pypa/[email protected].8
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip_existing: true

.gitignore

@@ -6,6 +6,9 @@ __pycache__/
 # C extensions
 *.so
 
+# Mac OS X
+.DS_Store
+
 # IDE 
 .vscode
 

CMakeLists.txt

@@ -3,10 +3,17 @@ cmake_minimum_required(VERSION 3.20)
 
 # Set project name and version
 # - package version is managed in file `version.py`
-project(pyClesperanto)
+project(
+  ${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
 
-# enforce release build type
+# enforce release build type if possible
 set(CMAKE_BUILD_TYPE Release)
+set(CMAKE_CXX_STANDARD 17)
+# if(WIN32)
+#   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /d2FH4-")
+# endif(WIN32)
 
 string(TOLOWER ${PROJECT_NAME} PY_PACKAGE_NAME)
 set(CY_PACKAGE_NAME _${PY_PACKAGE_NAME})
@@ -20,29 +27,23 @@ endif()
 # find python dev library
 # look for python in virtual env or conda first before checking the system.
 set(Python_FIND_VIRTUALENV "FIRST")
-find_package(Python3 COMPONENTS Interpreter Development.Embed Development.Module)
-if(Python3_Development.Module_FOUND)
-    message(STATUS "Python Developement Module found")
-endif()
-if(Python3_Development.Embed_FOUND)
-    message(STATUS "Python Developement Embed found")
-endif()
-
-if(NOT DEFINED OpenCL_LIBRARY)
-  find_package(OpenCL REQUIRED)
-endif()
-message(STATUS "OpenCL_LIBRARY: ${OpenCL_LIBRARY}")
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
 ## fetch CLIc using CMake FetchContent
 include(FetchContent)
 option(BUILD_TESTING  OFF)
 option(BUILD_BENCHMARK  OFF)
+option(BUILD_SHARED_LIBS OFF)
 FetchContent_Declare(
-  CLIc_lib 
+  CLIc 
   GIT_REPOSITORY https://github.com/clEsperanto/CLIc_prototype.git
-  GIT_TAG ${CLIC_VERSION}
+  GIT_TAG add-cuda-backend
 )
-FetchContent_MakeAvailable(CLIc_lib)
+FetchContent_MakeAvailable(CLIc)
+
+set(PACKAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${PY_PACKAGE_NAME})
+set(WRAPPER_DIR ${CMAKE_CURRENT_SOURCE_DIR}/wrapper)
+file(GLOB_RECURSE WRAPPER_SOURCES_FILES ${WRAPPER_DIR}/*.cpp)
 
 if(SKBUILD)
   # Scikit-Build does not add your site-packages to the search path
@@ -53,36 +54,30 @@ if(SKBUILD)
     OUTPUT_VARIABLE _tmp_dir
     OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND_ECHO STDOUT)
   list(APPEND CMAKE_PREFIX_PATH "${_tmp_dir}")
-endif()
 
-set(PACKAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${PY_PACKAGE_NAME})
-set(WRAPPER_DIR ${CMAKE_CURRENT_SOURCE_DIR}/wrapper)
-file(GLOB_RECURSE WRAPPER_SOURCES_FILES ${WRAPPER_DIR}/*.cpp)
-
-find_package(pybind11 CONFIG REQUIRED)
-pybind11_add_module(${CY_PACKAGE_NAME} MODULE ${WRAPPER_SOURCES_FILES})
+  find_package(pybind11 CONFIG REQUIRED)
+  python_add_library(${CY_PACKAGE_NAME} MODULE ${WRAPPER_SOURCES_FILES} WITH_SOABI)
 
-target_link_libraries(${CY_PACKAGE_NAME} PRIVATE CLIc::CLIc ${OpenCL_LIBRARY})
-add_dependencies(${CY_PACKAGE_NAME} CLIc)
-target_include_directories(${CY_PACKAGE_NAME} PUBLIC "$<BUILD_INTERFACE:${WRAPPER_DIR}>")
-target_compile_features(${CY_PACKAGE_NAME} PRIVATE cxx_std_17)
+  target_link_libraries(${CY_PACKAGE_NAME} PRIVATE CLIc::CLIc pybind11::headers)
+  add_dependencies(${CY_PACKAGE_NAME} CLIc)
+  target_include_directories(${CY_PACKAGE_NAME} PUBLIC "$<BUILD_INTERFACE:${WRAPPER_DIR}>")
+  target_compile_definitions(${CY_PACKAGE_NAME} PRIVATE VERSION_INFO=${PROJECT_VERSION})
 
-# Installing the extension module to the root of the package
-install(TARGETS ${CY_PACKAGE_NAME} DESTINATION .)
+  # Install the target to the appropriate location
+  install(TARGETS ${CY_PACKAGE_NAME} DESTINATION ${PY_PACKAGE_NAME})
 
-# if(APPLE)
-#     set_target_properties(
-#         ${CY_PACKAGE_NAME} PROPERTIES INSTALL_RPATH "@loader_path/${CMAKE_INSTALL_LIBDIR}")
-# else()
-#     set_target_properties(${CY_PACKAGE_NAME} PROPERTIES INSTALL_RPATH
-#         "$ORIGIN/${CMAKE_INSTALL_LIBDIR}")
-# endif()
+  # Configure the RPATH based on the platform
+  if(APPLE)
+      set(CY_PACKAGE_RPATH "@loader_path;@loader_path/${CMAKE_INSTALL_LIBDIR};@loader_path/${CMAKE_INSTALL_BINDIR}")
+  elseif(WIN32)
+      set(CY_PACKAGE_RPATH ".;@ORIGIN/${CMAKE_INSTALL_LIBDIR};@ORIGIN/${CMAKE_INSTALL_BINDIR}")
+  else()
+      set(CY_PACKAGE_RPATH "$ORIGIN;$ORIGIN/${CMAKE_INSTALL_LIBDIR};$ORIGIN/${CMAKE_INSTALL_BINDIR}")
+  endif()
 
-if(APPLE)
-    set_target_properties(
-        ${CY_PACKAGE_NAME} PROPERTIES INSTALL_RPATH "@loader_path/${CMAKE_INSTALL_LIBDIR};${CMAKE_PREFIX_PATH}/lib" INSTALL_RPATH_USE_LINK_PATH TRUE)
-else()
-    set_target_properties(${CY_PACKAGE_NAME} PROPERTIES INSTALL_RPATH
-        "$ORIGIN/${CMAKE_INSTALL_LIBDIR}:$ORIGIN/../lib:${CMAKE_PREFIX_PATH}/lib"
-        INSTALL_RPATH_USE_LINK_PATH TRUE)
-endif()
+  set_target_properties(${CY_PACKAGE_NAME} PROPERTIES
+      INSTALL_RPATH "${CY_PACKAGE_RPATH}"
+      BUILD_WITH_INSTALL_RPATH TRUE
+      INSTALL_RPATH_USE_LINK_PATH TRUE
+  )
+endif()

MANIFEST.in

@@ -0,0 +1,79 @@
+include .github/dependabot.yml
+include .github/workflows/build_and_test.yml
+include .github/workflows/pages.yml
+include .github/workflows/wheels.yml
+include .gitignore
+include CMakeLists.txt
+include LICENSE
+include MANIFEST.in
+include README.md
+include benchmarking/benchmark_basic_operations.ipynb
+include benchmarking/benchmark_gaussian.ipynb
+include benchmarking/benchmark_histogram.ipynb
+include benchmarking/benchmark_mini_pipeline.ipynb
+include benchmarking/benchmark_otsu.ipynb
+include benchmarking/benchmarking_tribolium_workflow.ipynb
+include demos/add_image_and_scalar.cl
+include demos/cell_segmentation.ipynb
+include demos/explore_API.ipynb
+include demos/find_local_maxima.ipynb
+include demos/image_API.ipynb
+include demos/image_filtering.ipynb
+include demos/images/cell_segmentation.png
+include demos/images/explore_API.png
+include demos/images/find_local_maxima.png
+include demos/images/image_filtering.png
+include demos/images/labeled_blobs.png
+include demos/images/multi-gpu.png
+include demos/images/tribolium3d_segmentation.png
+include demos/multi_gpu_demo.ipynb
+include demos/process_blobs.ipynb
+include demos/process_tribolium.ipynb
+include demos/run_custom_kernel.ipynb
+include developer_docs/API_demo.ipynb
+include docs/Makefile
+include docs/README.rst
+include docs/make.bat
+include docs/source/api.rst
+include docs/source/conf.py
+include docs/source/index.rst
+include docs/source/install.rst
+include docs/source/usage.rst
+include pyclesperanto/__init__.py
+include pyclesperanto/_array.py
+include pyclesperanto/_core.py
+include pyclesperanto/_decorators.py
+include pyclesperanto/_functionalities.py
+include pyclesperanto/_memory.py
+include pyclesperanto/_operators.py
+include pyclesperanto/_tier1.py
+include pyclesperanto/_tier2.py
+include pyclesperanto/_tier3.py
+include pyclesperanto/_tier4.py
+include pyclesperanto/_tier5.py
+include pyclesperanto/_version.py
+include pyproject.toml
+include scripts/build-opencl-linux.sh
+include scripts/build-opencl-macos.sh
+include scripts/build-opencl-windows.sh
+include scripts/pyclesperanto_autogen_tier_script.ipynb
+include setup.py
+include tests/test_core.py
+include tests/test_import.py
+include tests/test_tier1.py
+include tests/test_tier2.py
+include tests/test_tier3.py
+include tests/test_tier4.py
+include tests/test_tier5.py
+include tests/test_tier6.py
+include wrapper/array_.cpp
+include wrapper/core_.cpp
+include wrapper/pycle_wrapper.cpp
+include wrapper/pycle_wrapper.hpp
+include wrapper/tier1_.cpp
+include wrapper/tier2_.cpp
+include wrapper/tier3_.cpp
+include wrapper/tier4_.cpp
+include wrapper/tier5_.cpp
+include wrapper/types_.cpp
+exclude MANIFEST.in

README.md

@@ -1,8 +1,6 @@
 # py-clesperanto
 [![Build & Deploy](https://github.com/clEsperanto/pyclesperanto/actions/workflows/wheels.yml/badge.svg)](https://github.com/clEsperanto/pyclesperanto/actions/workflows/wheels.yml)
-[![Tests](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build_and_test.yml/badge.svg)](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build_and_test.yml)
-[![codecov](https://codecov.io/gh/clesperanto/pyclesperanto/branch/main/graph/badge.svg)](https://codecov.io/gh/clesperanto/pyclesperanto)
-[![License](https://img.shields.io/pypi/l/pyclesperanto.svg?color=green)](https://github.com/clEsperanto/pyclesperanto/raw/main/LICENSE)
+[![Tests](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build_and_test.yml/badge.svg)](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build_and_test.yml) <!-- [![codecov](https://codecov.io/gh/clesperanto/pyclesperanto/branch/main/graph/badge.svg)](https://codecov.io/gh/clesperanto/pyclesperanto) --> [![License](https://img.shields.io/pypi/l/pyclesperanto.svg?color=green)](https://github.com/clEsperanto/pyclesperanto/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/pyclesperanto.svg?color=green)](https://pypi.org/project/pyclesperanto)
 [![Python Version](https://img.shields.io/pypi/pyversions/pyclesperanto.svg?color=green)](https://python.org)
 [![Development Status](https://img.shields.io/pypi/status/pyclesperanto.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
@@ -26,7 +24,6 @@ conda activate my_env
 ```
 ~~Install pyclesperanto package using __conda__:~~ __(WIP, please use pip instead)__
 ```
-conda install -c conda-forge pyclesperanto
 ```
 OR using __pip__:
 ```
@@ -45,7 +42,7 @@ from skimage.io import imread, imsave
 device = cle.select_device()
 print("Used GPU: ", device)
 
-image = imread("https://imagej.nih.gov/ij/images/blobs.gif")
+image = imread("https://samples.fiji.sc/blobs.png")
 
 # push image to device memory
 input_image = cle.push(image)

demos/README.md

@@ -0,0 +1,25 @@
+# Demos
+
+This is a collection of notebooks and scripts that demonstrate how to use 'pyclesperanto' for image processing and analysis. They are here to show various use cases and to help you get started.
+
+These are note exaustives and we are happy to add more. Please get in touch if you have a demo that you would like to share.
+
+### pre-requisites
+
+To run these demos, you need to have 'pyclesperanto' installed. If you don't have it yet, please follow the instructions [here](../README.md) or read the documentation [here](https://clesperanto.github.io/pyclesperanto_prototype/).
+
+Most of the demos also require [scikit-image](https://scikit-image.org/) and [jupyter](https://jupyter.org/), which you can install via pip:
+
+```bash
+pip install scikit-image jupyterlab
+```
+
+or conda:
+
+```bash
+conda install scikit-image jupyterlab
+```
+
+# Warning
+
+These demos are not meant to be used for benchmarking. They are meant to be easy to understand and to get you started. Several costly operations are done on purpose to make the code easier to understand. If you want to use pyclesperanto in production, please read the documentation and don't hesitate to get in touch with us to get help with optimizing your code.