diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000..997504b465 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.gitignore b/.gitignore index 755ad9fd95..30d93375e8 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,7 @@ __pycache__/ /Wrappers/Python/cil/lib/ *.vscode* *.egg* + +# Pixi environments +.pixi/* +!.pixi/config.toml diff --git a/.pixi/config.toml b/.pixi/config.toml new file mode 100644 index 0000000000..b487a83a43 --- /dev/null +++ b/.pixi/config.toml @@ -0,0 +1,3 @@ +# Can be removed when https://github.com/TomographicImaging/CIL/issues/1870#issuecomment-3792746939 is resolved +[repodata-config."https://tomography.stfc.ac.uk/"] +disable-sharded = true diff --git a/Wrappers/Python/cil/__init__.py b/Wrappers/Python/cil/__init__.py index 91bbd22021..e2b84e5702 100644 --- a/Wrappers/Python/cil/__init__.py +++ b/Wrappers/Python/cil/__init__.py @@ -15,5 +15,4 @@ # # Authors: # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt - -from .version import version as __version__ +from cil.version import version as __version__ \ No newline at end of file diff --git a/Wrappers/Python/test/utils.py b/Wrappers/Python/test/utils.py index 205cfdd8cb..c9491b5198 100644 --- a/Wrappers/Python/test/utils.py +++ b/Wrappers/Python/test/utils.py @@ -58,7 +58,7 @@ def initialise_tests(): has_nvidia = True except: if os.environ.get("TESTS_FORCE_GPU", ""): - raise ImportError + raise ImportError("nvidia-smi not found") has_nvidia = False system_state['has_nvidia']=has_nvidia @@ -66,7 +66,7 @@ def initialise_tests(): module_info = importlib.util.find_spec("astra") if module_info is None: if os.environ.get("TESTS_FORCE_GPU", ""): - raise ImportError + raise ImportError("module not found: astra") has_astra = False else: has_astra = True @@ -76,7 +76,7 @@ def initialise_tests(): module_info = importlib.util.find_spec("tigre") if module_info is None: if os.environ.get("TESTS_FORCE_GPU", ""): - raise ImportError + raise ImportError("module not found: tigre") has_tigre = False else: has_tigre = True diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000000..583595dbbe --- /dev/null +++ b/pixi.lock @@ -0,0 +1,8234 @@ +version: 6 +environments: + default: + channels: + - 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-[tool.setuptools] -package-dir = {"" = "Wrappers/Python"} - -[tool.setuptools.packages.find] -where = ["Wrappers/Python"] -include = ["cil", "cil.*"] -exclude = ["data", "test"] - -[project.urls] -#homepage = "https://ccpi.ac.uk/cil" -homepage = "https://tomographicimaging.github.io/CIL" -documentation = "https://tomographicimaging.github.io/CIL/nightly" -repository = "https://github.com/TomographicImaging/CIL" -changelog = "https://github.com/TomographicImaging/CIL/blob/master/CHANGELOG.md" - [project] name = "cil" dynamic = ["version"] description = "Core Imaging Library" -license = {text = "Apache-2.0"} -maintainers = [{name="CIL developers", email="tomography+cil@stfc.ac.uk"}] +license = { text = "Apache-2.0" } +maintainers = [{ name = "CIL developers", email = "tomography+cil@stfc.ac.uk" }] requires-python = ">=3.10" readme = "README.md" keywords = ["tomography", "optimisation"] dependencies = [ - #"cil-data>=22", # missing from PyPI "dxchange", "h5py", - #"ipp==2021.12.*", # PyPI conflicts with conda package + "ipp==2021.12.*", "numba", "numpy>=1.23, <2.0.0", "olefile>=0.46", @@ -54,39 +20,165 @@ dependencies = [ "tqdm", "packaging", ] + +[project.urls] +#homepage = "https://ccpi.ac.uk/cil" +homepage = "https://tomographicimaging.github.io/CIL/" +documentation = "https://tomographicimaging.github.io/CIL/nightly" +repository = "https://github.com/TomographicImaging/CIL" +changelog = "https://github.com/TomographicImaging/CIL/blob/master/CHANGELOG.md" + [project.optional-dependencies] plugins = [ "ipywidgets", #"tomophantom==2.0.0", # [linux] # missing from PyPI ] -gpu = [ - "astra-toolbox>=1.9.9.dev5,<=2.1", # [not osx] - #"tigre>=2.4,<=2.6", # missing from PyPI -] +# cuda = [ +# "astra-toolbox>=1.9.9.dev5,<=2.1", # [not osx] +# #"tigre>=2.4,<=2.6", # missing from PyPI +# ] [dependency-groups] + +data = [ + #"cil-data>=22", # missing from PyPI + "zenodo_get>=1.6", +] + test = [ #"ccpi-regulariser=24.0.1", # [not osx] # missing from PyPI "cvxpy", - "matplotlib-base>=3.3", + # "matplotlib-base>=3.3", "packaging", "scikit-image", "unittest-parametrize", "wget", "zenodo_get>=1.6", + "pytest", ] + docs = [ - "jinja2", - #"pydata-sphinx-theme", - "recommonmark", - "sphinx", - "sphinx_rtd_theme", - "sphinx-autobuild", - "sphinx-click", - "sphinx-copybutton", - "sphinx-panels", - "sphinxcontrib-bibtex", - "nbsphinx", - "sphinx-gallery", - "sphinx-copybutton", - "notebook", + "jinja2", + "pydata-sphinx-theme", + "recommonmark", + "sphinx<9", # Until https://github.com/sphinx-contrib/multiversion/issues/201 is resolved + "sphinx_rtd_theme", + "sphinx-autobuild", + "sphinx-click", + "sphinx-copybutton", + "sphinx-multiversion", + "sphinx-panels", + "sphinxcontrib-bibtex", + "nbsphinx", + "sphinx-gallery", + "notebook", + "ipywidgets", + "matplotlib", ] + +### PEP 517/518 build system configuration ### +[build-system] +requires = [ + "setuptools>=64", + "scikit-build-core>=0.10", + + "ipp-devel>=2021.10", + "ipp-static>=2021.10", + "intel-openmp", +] +build-backend = "scikit_build_core.build" + +[tool.scikit-build] +minimum-version = "build-system.requires" +cmake.version = ">=3.16" +metadata.version.provider = "scikit_build_core.metadata.setuptools_scm" +sdist.exclude = [ + "scripts", + "docs", + "Wrappers/Python/data", + "Wrappers/Python/test", + ".*", +] +[tool.scikit-build.wheel.packages] +cil = "Wrappers/Python/cil" + +[tool.setuptools] +package-dir = { "" = "Wrappers/Python" } + +[tool.setuptools.packages.find] +where = ["Wrappers/Python"] +include = ["cil", "cil.*"] +exclude = ["data", "test"] + +### Pixi Configuration ### +[tool.pixi.workspace] +channels = ["https://tomography.stfc.ac.uk/conda", "conda-forge"] +platforms = ["linux-64", "win-64"] +preview = ["pixi-build"] # Can be removed when pixi-build is stable. Last checked 2026-01-24 in pixi 0.63.2 + +[tool.pixi.workspace.build-variants] +# python = ["3.11.*", "3.12.*"] + +[tool.pixi.package.host-dependencies] +uv = "*" +cmake = { version = ">=3.16" } + +ipp-devel = { version = ">=2021.10" } +ipp-include = { version = ">=2021.10" } + +[tool.pixi.package.build] +backend = { name = "pixi-build-python", version = "*" } + +[tool.pixi.package.build.config] +ignore-pypi-mapping = false # Can be removed when this is default in pixi-build-python. Last checked 2026-01-24 in pixi 0.63.2 + +[tool.pixi.pypi-dependencies] +cil = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "default" } +gpu = { features = ["astra-gpu", "tigre"], solve-group = "cuda" } +dev = { features = ["data", "docs", "plugins", "test"], solve-group = "default" } +plugins = { features = ["plugins"], solve-group = "default" } +test = { features = ["test" ], solve-group = "default" } +test-gpu = { features = ["test", "astra-gpu", "tigre"], solve-group = "cuda" } +docs = { features = ["docs", "astra-gpu", "tigre", "plugin-tomophantom", "plugin-ccpi-regulariser"], solve-group = "cuda" } + +## Features ## +# Plugins # +[tool.pixi.feature.plugin-tomophantom.dependencies] +tomophantom = { version = "==2.0.0", channel = "https://tomography.stfc.ac.uk/conda" } + +[tool.pixi.feature.plugin-ccpi-regulariser.dependencies] +ccpi-regulariser = { version = "==24.0.1", channel = "https://tomography.stfc.ac.uk/conda" } + +[tool.pixi.feature.docs.tasks] +docs-build = { cmd = "sphinx-build -b html docs/source docs/build", default-environment = "docs" } +docs-serve = { cmd = "sphinx-autobuild docs/source docs/build --open-browser", default-environment = "docs" } + +[tool.pixi.feature.test.dependencies] +cil-data = { version = ">=22.0.0,<23", channel = "https://tomography.stfc.ac.uk/conda" } +tomophantom = { version = "==2.0.0", channel = "https://tomography.stfc.ac.uk/conda" } + +# To be handled when astra-toolbox-cpu is released +# See: https://github.com/astra-toolbox/astra-toolbox/issues/327#issuecomment-3799202745 +# See: https://discord.com/channels/1082332781146800168/1464650877750087732 +# [tool.pixi.feature.astra-cpu.dependencies] +# astra-toolbox = { version = "==2.1", build = "py*", channel = "conda-forge" } + +[tool.pixi.feature.astra-gpu.dependencies] +astra-toolbox = { version = "==2.1", build = "cuda*", channel = "conda-forge" } + +[tool.pixi.feature.tigre.dependencies] +tigre = { version = "==2.6", channel = "https://tomography.stfc.ac.uk/conda" } + +[tool.pixi.tasks] +test = { cmd = "python -m unittest discover -v ./Wrappers/Python/test", default-environment = "test"} +test-gpu = { cmd = "python -m unittest discover -v ./Wrappers/Python/test" , default-environment = "test-gpu", env = { TESTS_FORCE_GPU = "1" } } +jupyter = { cmd = "jupyter notebook" } + +[tool.pytest.ini_options] +testpaths = ["Wrappers/Python/test"] +python_files = ["test_*.py"] +python_classes = ["Test*"] +python_functions = ["test_*"] +addopts = "-v --tb=short" diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt index 11eff34554..daa08f3e9e 100644 --- a/src/Core/CMakeLists.txt +++ b/src/Core/CMakeLists.txt @@ -50,8 +50,30 @@ else() set (OpenMP_EXE_LINKER_FLAGS ${OpenMP_C_FLAGS}) endif() -list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") -find_package(IPP) +# Find Python to get the prefix path for PyPI-installed packages +find_package(Python COMPONENTS Interpreter QUIET) +if(Python_FOUND) + # Get the Python prefix (where PyPI .data packages install to) + execute_process( + COMMAND "${Python_EXECUTABLE}" -c "import sys; print(sys.prefix)" + OUTPUT_VARIABLE PYTHON_PREFIX + OUTPUT_STRIP_TRAILING_WHITESPACE + ERROR_QUIET + ) + if(PYTHON_PREFIX) + message(STATUS "Python prefix: ${PYTHON_PREFIX}") + # Add Python prefix to CMAKE_PREFIX_PATH for finding IPP from PyPI + list(APPEND CMAKE_PREFIX_PATH "${PYTHON_PREFIX}") + endif() +endif() + +# Try Intel's official IPPConfig.cmake first (for PyPI ipp-devel package) +# Fall back to our custom FindIPP.cmake for conda/system installs +find_package(IPP CONFIG QUIET) +if(NOT IPP_FOUND) + list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") + find_package(IPP) +endif() list(APPEND cilacc_SOURCES utilities.cpp axpby.cpp FiniteDifferenceLibrary.cpp) list(APPEND cilacc_INCLUDES ${CMAKE_CURRENT_SOURCE_DIR}/include)