fix: add setup.py

Co-authored-by: Copilot <copilot@github.com>

Author: Teranis

.gitignore

@@ -41,7 +41,6 @@ setup.cfg
 
 # Starting from pip 21.3 setup.py is not needed anymore
 # and we rely only on setup.cfg for env
-setup.py
 environment.yml
 # requirements.txt
 conda_env_list_commands.txt

setup.py

@@ -0,0 +1,28 @@
+# only needed for cython extensions, not needed to run normally
+import sys
+from setuptools import setup, Extension
+from Cython.Build import cythonize
+import numpy as np
+
+setup(
+    ext_modules=cythonize(
+        Extension(
+            "cellacdc.regionprops_helper",
+            sources=["cellacdc/regionprops_helper.pyx"],
+            include_dirs=[np.get_include()],
+        ),
+        annotate=True,
+        build_dir="build/cython",  # .c and .html files go here
+    )
+)
+# move compiled binary to precompiled/
+import shutil
+import os
+
+src_dir = "cellacdc"
+for filename in os.listdir(src_dir):
+    if filename.startswith("regionprops_helper") and (filename.endswith(".so") or filename.endswith(".pyd")):
+        target_path = os.path.join("cellacdc", "precompiled", filename)
+        shutil.move(os.path.join(src_dir, filename), target_path)
+        print(f"Moved {filename} to {target_path}")
+