Provide user the possibility to pip install the ClearMap project (graph-tool is installed separately)

ClearMap3pip.yml

@@ -0,0 +1,11 @@
+name: ClearMap3pip
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - graph-tool<=2.45
+  - mkl<2024.1
+variables:
+  PYTHONNOUSERSITE: 1
+  TMPDIR: /data/tmp

build_ext_custom.py

@@ -0,0 +1,66 @@
+# build_ext_custom.py
+from setuptools.command.build_ext import build_ext as _build_ext
+from setuptools.extension import Extension
+from Cython.Build import cythonize
+import numpy as np
+import os
+import subprocess
+from pathlib import Path
+import platform
+
+os_name = platform.system().lower()
+
+DEFAULT_COMPILE_ARGS = []
+DEFAULT_LIBRARIES = []
+DEFAULT_LINK_ARGS = []
+
+if not os_name.startswith('windows'):
+    DEFAULT_COMPILE_ARGS += ['-w', '-O3']
+    DEFAULT_LIBRARIES += ['m']
+
+if os_name.startswith('linux'):
+    try:
+        out = subprocess.check_output(['gcc', '--help=common']).decode('utf-8')
+        if '-flarge-source-files' in out:
+            DEFAULT_COMPILE_ARGS += ['-flarge-source-files']
+    except Exception:
+        pass
+
+USE_OPENMP = True
+if os_name.startswith('darwin'):
+    try:
+        cpp_version = subprocess.check_output(['c++', '--version']).decode('ascii')
+        USE_OPENMP = 'g++' in cpp_version
+    except Exception:
+        USE_OPENMP = False
+
+extra_args = ['-fopenmp'] if USE_OPENMP else []
+if os_name.startswith('windows'):
+    extra_args = [arg.replace('-f', '/') for arg in extra_args]
+    DEFAULT_COMPILE_ARGS = [arg.replace('-m', '/') for arg in DEFAULT_COMPILE_ARGS]
+    DEFAULT_LINK_ARGS = [arg.replace('-m', '/') for arg in DEFAULT_LINK_ARGS]
+
+extra_link_args = extra_args
+compile_args = DEFAULT_COMPILE_ARGS + extra_args
+link_args = DEFAULT_LINK_ARGS + extra_link_args
+
+
+extension_paths = [str(p) for p in Path('ClearMap').rglob('*.pyx')
+                   if not any(excl in str(p) for excl in ['_Old', '_Todo', 'StatisticsPointListCode', 'flow', 'OrientationCode'])]
+
+extensions = [
+    Extension(
+        name=os.path.splitext(p)[0].replace(os.sep, '.'),
+        sources=[p],
+        libraries=DEFAULT_LIBRARIES,
+        language='c++',
+        include_dirs=[np.get_include(), os.path.dirname(os.path.abspath(p))],
+        extra_compile_args=compile_args,
+        extra_link_args=link_args
+    ) for p in extension_paths
+]
+
+ext_modules = cythonize(extensions, quiet=True)
+
+class build_ext(_build_ext):
+    pass

pyproject.toml

@@ -0,0 +1,103 @@
+# pyproject.toml for ClearMap using setuptools and PEP 621
+
+[build-system]
+requires = [
+    "setuptools>=61",
+    "wheel",
+    "cython",
+    "numpy"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ClearMap"
+version = "3.0.0"
+description = "3D cell counting and vasculature analysis for lightsheet microscopy"
+license = "MIT"
+license-files = ["LICENSE", "LICENSE.txt"]
+authors = [
+    {name = "Christoph Kirst"},
+    {name = "Sophie Skriabine"},
+    {name = "Charly Rousseau"},
+    {name = "Etienne Doumazane"},
+    {name = "Gael Cousin"},
+]
+dependencies = [
+    "cython",
+    "ipython",
+    "jupyter",
+    "ipywidgets",
+    "numpy",
+    "scipy",
+    "pandas<2",
+    "pyarrow",
+    "scikit-image",
+    "scikit-learn",
+    "opencv-python",
+    "configobj",
+    "natsort",
+    "tqdm",
+    "matplotlib",
+    "seaborn",
+    "tifffile",
+    "pyqt5<6",
+    "pyqtwebengine",
+    "qtpy",
+    "pyqtgraph==0.12.*",
+    "pygments",
+    "qdarkstyle",
+    "vispy",
+    "pyvista",
+    "vtk",
+    "PyOpenGL",
+    "napari",
+    "python-igraph",
+    "torch<=2.2",
+    "xmltodict",
+    "psutil",
+    "mpld3",
+    "lxml<5.2",
+    "itk-elastix",
+]
+requires-python = ">=3.8"
+
+[project.urls]
+Homepage = "https://github.com/ClearAnatomics/ClearMap"
+
+[project.optional-dependencies]
+# Define extras if needed later
+
+[project.scripts]
+cell_map = "ClearMap.Scripts.cell_map_new_api:main"
+clearmap-utils = "ClearMap.Scripts.clearmap_utils:main"
+
+[project.gui-scripts]
+clearmap-ui = "ClearMap.gui.run_gui:entry_point"
+
+[tool.setuptools]
+packages = ["ClearMap"]
+
+[tool.setuptools.package-data]
+"ClearMap.config" = ["*.cfg"]
+"ClearMap.gui" = [
+  "creator/*.ui",
+  "creator/*.qrc",
+  "creator/graphics_resources/*.png",
+  "creator/graphics_resources/*.jpg",
+  "creator/graphics_resources/*.svg",
+  "creator/icons/*.png",
+  "creator/icons/*.jpg",
+  "creator/icons/*.svg"
+]
+
+[tool.setuptools.data-files]
+"" = ["start_gui.sh"]
+"ClearMap/External/elastix" = []
+"ClearMap/External/geodesic_distance" = []
+"ClearMap/Resources" = []
+"ClearMap/ImageProcessing/Skeletonization" = []
+"ClearMap/ImageProcessing/Binary" = []
+"ClearMap/ImageProcessing/machine_learning/vessel_filling/resources" = []
+
+[tool.setuptools.cmdclass]
+build_ext = "build_ext_custom.build_ext"