PartSegCore-compiled-backend 0.15.7__tar.gz → 0.15.9__tar.gz

{partsegcore_compiled_backend-0.15.7 → partsegcore_compiled_backend-0.15.9}/.gitignore

@@ -1,3 +1,4 @@
+cmake
 *.cpp
 src/PartSegCore_compiled_backend/version.py
 src/**.html

partsegcore_compiled_backend-0.15.9/.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+default_language_version:
+    python: python3.9
+
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.8.6
+    hooks:
+      # Run the linter.
+      - id: ruff
+      # Run the formatter.
+      - id: ruff-format
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    - id: check-json
+    - id: check-yaml
+    - id: check-merge-conflict
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      exclude: .*\.md
+    - id: debug-statements
+    - id: mixed-line-ending
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+    -   id: rst-backticks
+-   repo: https://github.com/markdownlint/markdownlint
+    rev: v0.12.0  # Use the ref you want to point at
+    hooks:
+    - id: markdownlint
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+      - tomli
+-   repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v19.1.6  # Use the sha / tag you want to point at
+    hooks:
+    - id: clang-format
+      args: ["-style=Google"]
+      exclude: ^notebooks/

partsegcore_compiled_backend-0.15.9/CMakeLists.txt

@@ -0,0 +1,131 @@
+cmake_minimum_required(VERSION 3.21)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_FLAGS_DEBUG_INIT "-DDEBUG -g")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -DDEBUG")
+
+
+# Define compiler directive
+add_definitions(-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
+
+if(DEFINED ENV{CUSTOM_MODULE_PATH})
+    list(APPEND CMAKE_MODULE_PATH $ENV{CUSTOM_MODULE_PATH})
+    message("Custom module path: ${CMAKE_MODULE_PATH}")
+endif()
+
+
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(Cython MODULE REQUIRED VERSION 3.0)
+include(UseCython)
+
+if(DEFINED ENV{OMP})
+    list(APPEND CMAKE_PREFIX_PATH $ENV{OMP})
+endif()
+
+# find OpenMP
+find_package(OpenMP REQUIRED)
+
+
+execute_process(
+        COMMAND "${Python_EXECUTABLE}"
+        -c "import numpy; print(numpy.get_include())"
+        OUTPUT_VARIABLE NUMPY_INCLUDE_DIR
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+
+cython_transpile(src/PartSegCore_compiled_backend/sprawl_utils/euclidean_cython.pyx LANGUAGE CXX OUTPUT_VARIABLE euclidean_cython_cxx)
+python_add_library(euclidean_cython MODULE
+        "${euclidean_cython_cxx}"
+        src/PartSegCore_compiled_backend/sprawl_utils/my_queue.h
+        src/PartSegCore_compiled_backend/sprawl_utils/global_consts.h
+        WITH_SOABI)
+target_include_directories(euclidean_cython PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_include_directories(euclidean_cython PRIVATE src/PartSegCore_compiled_backend/sprawl_utils/)
+
+cython_transpile(src/PartSegCore_compiled_backend/sprawl_utils/path_sprawl_cython.pyx LANGUAGE CXX OUTPUT_VARIABLE path_sprawl_cython_cxx)
+python_add_library(path_sprawl_cython MODULE
+        "${path_sprawl_cython_cxx}"
+        src/PartSegCore_compiled_backend/sprawl_utils/my_queue.h
+        src/PartSegCore_compiled_backend/sprawl_utils/global_consts.h
+        WITH_SOABI)
+target_include_directories(path_sprawl_cython PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_include_directories(path_sprawl_cython PRIVATE src/PartSegCore_compiled_backend/sprawl_utils/)
+
+cython_transpile(src/PartSegCore_compiled_backend/sprawl_utils/sprawl_utils.pyx LANGUAGE CXX OUTPUT_VARIABLE sprawl_utils_cython_cxx)
+python_add_library(sprawl_utils MODULE
+        "${sprawl_utils_cython_cxx}"
+        src/PartSegCore_compiled_backend/sprawl_utils/my_queue.h
+        src/PartSegCore_compiled_backend/sprawl_utils/global_consts.h
+        WITH_SOABI)
+target_include_directories(sprawl_utils PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_include_directories(sprawl_utils PRIVATE src/PartSegCore_compiled_backend/sprawl_utils/)
+
+
+cython_transpile(src/PartSegCore_compiled_backend/sprawl_utils/fuzzy_distance.pyx LANGUAGE CXX OUTPUT_VARIABLE fuzzy_distance_cython_cxx)
+python_add_library(fuzzy_distance MODULE
+        "${fuzzy_distance_cython_cxx}"
+        src/PartSegCore_compiled_backend/sprawl_utils/my_queue.h
+        src/PartSegCore_compiled_backend/sprawl_utils/global_consts.h
+        WITH_SOABI)
+target_include_directories(fuzzy_distance PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_include_directories(fuzzy_distance PRIVATE src/PartSegCore_compiled_backend/sprawl_utils/)
+
+
+cython_transpile(src/PartSegCore_compiled_backend/color_image_cython.pyx LANGUAGE CXX OUTPUT_VARIABLE color_image_cython_cxx)
+python_add_library(color_image_cython MODULE "${color_image_cython_cxx}" WITH_SOABI)
+target_include_directories(color_image_cython PRIVATE "${NUMPY_INCLUDE_DIR}")
+
+
+cython_transpile(src/PartSegCore_compiled_backend/calc_bounds.pyx LANGUAGE CXX OUTPUT_VARIABLE calc_bounds_cython_cxx)
+python_add_library(calc_bounds MODULE "${calc_bounds_cython_cxx}" WITH_SOABI)
+target_include_directories(calc_bounds PRIVATE "${NUMPY_INCLUDE_DIR}")
+
+
+cython_transpile(src/PartSegCore_compiled_backend/multiscale_opening/mso_bind.pyx LANGUAGE CXX OUTPUT_VARIABLE mso_bind_cython_cxx)
+python_add_library(
+    mso_bind MODULE
+    "${mso_bind_cython_cxx}"
+    # src/PartSegCore_compiled_backend/multiscale_opening/mso.cpp
+    src/PartSegCore_compiled_backend/multiscale_opening/mso.h
+    src/PartSegCore_compiled_backend/multiscale_opening/my_queue.h
+    WITH_SOABI)
+target_include_directories(mso_bind PRIVATE src/PartSegCore_compiled_backend/multiscale_opening/)
+target_include_directories(mso_bind PRIVATE "${NUMPY_INCLUDE_DIR}")
+
+
+cython_transpile(src/PartSegCore_compiled_backend/_fast_unique.pyx LANGUAGE CXX OUTPUT_VARIABLE fast_unique_cython_cxx)
+python_add_library(_fast_unique MODULE "${fast_unique_cython_cxx}" WITH_SOABI)
+target_include_directories(_fast_unique PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_link_libraries(_fast_unique PRIVATE OpenMP::OpenMP_CXX)
+
+
+cython_transpile(src/PartSegCore_compiled_backend/_napari_mapping.pyx LANGUAGE CXX OUTPUT_VARIABLE napari_mapping_cython_cxx)
+python_add_library(_napari_mapping MODULE "${napari_mapping_cython_cxx}" WITH_SOABI)
+target_include_directories(_napari_mapping PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_link_libraries(_napari_mapping PRIVATE OpenMP::OpenMP_CXX)
+
+cython_transpile(src/PartSegCore_compiled_backend/triangulate.pyx LANGUAGE CXX OUTPUT_VARIABLE triangulate_cython_cxx)
+python_add_library(
+        triangulate MODULE
+        "${triangulate_cython_cxx}"
+        src/PartSegCore_compiled_backend/triangulation/triangulate.hpp
+        src/PartSegCore_compiled_backend/triangulation/intersection.hpp
+        src/PartSegCore_compiled_backend/triangulation/point.hpp
+        src/PartSegCore_compiled_backend/triangulation/debug_util.hpp
+        WITH_SOABI)
+target_include_directories(triangulate PRIVATE "${NUMPY_INCLUDE_DIR}")
+target_include_directories(triangulate PRIVATE src/PartSegCore_compiled_backend/)
+
+
+install(TARGETS euclidean_cython DESTINATION PartSegCore_compiled_backend/sprawl_utils)
+install(TARGETS path_sprawl_cython DESTINATION PartSegCore_compiled_backend/sprawl_utils)
+install(TARGETS sprawl_utils DESTINATION PartSegCore_compiled_backend/sprawl_utils)
+install(TARGETS fuzzy_distance DESTINATION PartSegCore_compiled_backend/sprawl_utils)
+install(TARGETS color_image_cython DESTINATION PartSegCore_compiled_backend)
+install(TARGETS calc_bounds DESTINATION PartSegCore_compiled_backend)
+install(TARGETS mso_bind DESTINATION PartSegCore_compiled_backend/multiscale_opening)
+install(TARGETS _fast_unique DESTINATION PartSegCore_compiled_backend)
+install(TARGETS _napari_mapping DESTINATION PartSegCore_compiled_backend)
+install(TARGETS triangulate DESTINATION PartSegCore_compiled_backend)

{partsegcore_compiled_backend-0.15.7 → partsegcore_compiled_backend-0.15.9}/PKG-INFO

@@ -1,16 +1,10 @@
 Metadata-Version: 2.1
 Name: PartSegCore_compiled_backend
-Version: 0.15.7
+Version: 0.15.9
 Summary: PartSegCore compiled backend,
-Author-email: Grzegorz Bokota <g.bokota@cent.uw.edu.pl>
-License: BSD-3-Clause
-Project-URL: Homepage, https://4dnucleome.cent.uw.edu.pl/PartSeg/
-Project-URL: Documentation, https://partsegcore-compiled-backend.readthedocs.io/en/stable/
-Project-URL: Source Code, https://github.com/4DNucleome/PartSegCore-compiled-backend
 Keywords: bioimaging
-Platform: Linux
-Platform: Windows
-Platform: MacOs
+Author-Email: Grzegorz Bokota <g.bokota@cent.uw.edu.pl>
+License: BSD-3-Clause
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
@@ -22,14 +16,16 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Project-URL: Homepage, https://4dnucleome.cent.uw.edu.pl/PartSeg/
+Project-URL: Documentation, https://partsegcore-compiled-backend.readthedocs.io/en/stable/
+Project-URL: Source code, https://github.com/4DNucleome/PartSegCore-compiled-backend
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: License.txt
-Requires-Dist: numpy>=1.25.0
-Provides-Extra: test
+Requires-Dist: numpy>=1.23.5
 Requires-Dist: pytest>=7.0.0; extra == "test"
-Provides-Extra: docs
 Requires-Dist: sphinx>=5.0.0; extra == "docs"
+Provides-Extra: test
+Provides-Extra: docs
+Description-Content-Type: text/markdown
 
 # PartSegCore_compiled_backend
 

{partsegcore_compiled_backend-0.15.7 → partsegcore_compiled_backend-0.15.9}/pyproject.toml

@@ -1,7 +1,16 @@
 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ["setuptools>=70.0.0", "Cython", "numpy>=2", "setuptools_scm[toml]>=8.1"]  # PEP 508 specifications.
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core", "Cython", "cython-cmake", "numpy>=2", "setuptools_scm[toml]>=8.1"]  # PEP 508 specifications.
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["src/PartSegCore_compiled_backend/version.py"]
+cmake.version = ">=3.21"
+sdist.exclude = [".github", "tox.ini", "build_utils", "notebooks", ".readthedocs.yaml"]
+wheel.exclude = ["**.pyx"]
+#cmake.build-type = "Debug"
+
 
 [project]
 name = "PartSegCore_compiled_backend"
@@ -27,7 +36,7 @@ keywords = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "numpy>=1.25.0",
+    "numpy>=1.23.5",
 ]
 dynamic = [
     "version",
@@ -112,7 +121,7 @@ ignore = ["src/PartSegCore_compiled_backend/changelog.py", "src/PartSegCore_comp
 [tool.cibuildwheel]
 test-command = "pytest {project}/src/tests"
 test-extras = ["test"]
-skip = "pp*macos* pp31*"
+skip = "pp*macos* pp31* pp39-manylinux*"
 build = "*64"
 
 [tool.cibuildwheel.macos]
@@ -124,10 +133,72 @@ before-all = [
 
 [tool.ruff]
 line-length = 120
+fix=true
 
 [tool.ruff.format]
 quote-style = "single"
 indent-style = "space"
 docstring-code-format = true
 line-ending = "lf"
-skip-magic-trailing-comma = true
+skip-magic-trailing-comma = false
+
+
+[tool.ruff.lint]
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "YTT", #flake8-2020
+    "TCH", # flake8-type-checing
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "COM", # flake8-commas
+    "SIM", # flake8-simplify
+    "INP", # flake8-no-pep420
+    "PYI", # flake8-pyi
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "TID",  # flake8-tidy-imports # replace absolutify import
+    "TRY", # tryceratops
+    "ICN", # flake8-import-conventions
+    "RUF", # ruff specyfic rules
+    "NPY201", # checks compatibility with numpy version 2.0
+    "ASYNC", # flake8-async
+    "EXE", # flake8-executable
+    "FA", # flake8-future-annotations
+    "LOG", # flake8-logging
+    "SLOT", # flake8-slots
+    "PT", # flake8-pytest-style
+    "T20", # flake8-print
+]
+ignore = [
+    "E501", # line lenngth is handled by formatter
+    "COM812", # flake8-commas - we don't like adding comma on single line of arguments
+    "COM819", # conflicts with ruff-format
+    "TRY003", # require implement multiple exception class
+    "RUF005", # problem with numpy compatybility, see https://github.com/charliermarsh/ruff/issues/2142#issuecomment-1451038741
+    "W191", "Q000", "Q001", "Q002", "Q003", "ISC001", # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+]
+
+[tool.ruff.lint.flake8-quotes]
+docstring-quotes = "double"
+inline-quotes = "single"
+multiline-quotes = "double"
+
+[tool.ruff.lint.per-file-ignores]
+"src/tests/**.py" = ["B011", "INP001", "TRY301", "B018", "RUF012"]
+"notebooks/**" = ["FA100", "INP001", "A001"]
+"docs/conf.py" = ["INP001", "A001"]
+
+[tool.ruff.lint.flake8-tidy-imports]
+# Disallow all relative imports.
+ban-relative-imports = "all"
+
+[tool.codespell]
+skip = "notebooks/*"

partsegcore_compiled_backend-0.15.9/src/PartSegCore_compiled_backend/calc_bounds.pyi

@@ -0,0 +1,3 @@
+import numpy as np
+
+def calc_bounds(labels: np.ndarray, components_num: int | None = None): ...

{partsegcore_compiled_backend-0.15.7 → partsegcore_compiled_backend-0.15.9}/src/PartSegCore_compiled_backend/calc_bounds.pyx

@@ -45,7 +45,7 @@ def calc_bounds(labels: np.ndarray, components_num: Optional[int]=None):
     }[labels.ndim](labels, components_num)
 
 
-def calc_bounds5(cnp.ndarray[label_types, ndim=5] labels, components_num: Py_ssize_t):
+def calc_bounds5(cnp.ndarray[label_types, ndim=5] labels, Py_ssize_t components_num):
     """
     Calculate the bounds of the specified labels in a 5-dimensional array.
 
@@ -94,7 +94,7 @@ def calc_bounds5(cnp.ndarray[label_types, ndim=5] labels, components_num: Py_ssi
     return min_bound, max_bound
 
 
-def calc_bounds4(cnp.ndarray[label_types, ndim=4] labels, components_num: Py_ssize_t):
+def calc_bounds4(cnp.ndarray[label_types, ndim=4] labels, Py_ssize_t components_num):
     """
     Calculate the bounds of the specified labels in a 4-dimensional array.
 
@@ -137,7 +137,7 @@ def calc_bounds4(cnp.ndarray[label_types, ndim=4] labels, components_num: Py_ssi
                     max_bound[label_val, 3] = max(max_bound[label_val, 3], x)
     return min_bound, max_bound
 
-def calc_bounds3(cnp.ndarray[label_types, ndim=3] labels, components_num: Py_ssize_t):
+def calc_bounds3(cnp.ndarray[label_types, ndim=3] labels, Py_ssize_t components_num):
     """
     Calculate the bounds of the specified labels in a 3-dimensional array.
 
@@ -178,7 +178,7 @@ def calc_bounds3(cnp.ndarray[label_types, ndim=3] labels, components_num: Py_ssi
     return min_bound, max_bound
 
 
-def calc_bounds2(cnp.ndarray[label_types, ndim=2] labels, components_num: Py_ssize_t):
+def calc_bounds2(cnp.ndarray[label_types, ndim=2] labels, Py_ssize_t components_num):
     """
     Calculate the bounds of the specified labels in a 2-dimensional array.
 

{partsegcore_compiled_backend-0.15.7 → partsegcore_compiled_backend-0.15.9}/src/PartSegCore_compiled_backend/fast_unique.py

@@ -9,7 +9,7 @@ For benchmark please see https://github.com/4DNucleome/PartSegCore-compiled-back
 
 import numpy as np
 
-from ._fast_unique import unique1d, unique2d, unique3d
+from PartSegCore_compiled_backend._fast_unique import unique1d, unique2d, unique3d
 
 
 def label_unique(array, numpy_fallback=False) -> np.ndarray:

partsegcore_compiled_backend-0.15.9/src/PartSegCore_compiled_backend/multiscale_opening/__init__.py

@@ -0,0 +1,3 @@
+from PartSegCore_compiled_backend.multiscale_opening.mso_bind import MuType, PyMSO, calculate_mu, calculate_mu_mid
+
+__all__ = ('MuType', 'PyMSO', 'calculate_mu', 'calculate_mu_mid')