Develop

.gitignore

@@ -128,3 +128,9 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+
+
+local_testing.ipynb
+.vscode/
+settings.json

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
+requires = ["setuptools>=42", "wheel", "pybind11>=2.5.0"]
+build-backend = "setuptools.build_meta"
 
 [project]
 name = "topapprox"
-version = "0.0.2"
+version = "0.0.4"
 authors = [
   { name="Matias de Jong van Lier", email="[email protected]" },
   { name="Shizuo Kaji", email="[email protected]"},
@@ -19,6 +19,9 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
+dependencies = [
+  "pybind11>=2.5.0",
+  ]
 
 [project.urls]
 Homepage = "https://github.com/mvlier/topapprox"

setup.py

@@ -0,0 +1,34 @@
+# run
+# python setup.py build_ext --inplace
+
+from setuptools import setup, Extension, find_packages
+import pybind11
+from pybind11.setup_helpers import Pybind11Extension
+
+import os
+import platform
+
+compiler = os.environ.get('CXX', 'g++')
+if platform.system() == 'Darwin':  # macOS
+    extra_compile_args = ['-std=c++11', '-mmacosx-version-min=10.9']
+else:
+    extra_compile_args = ['-std=c++11']
+
+ext_modules = [
+    Pybind11Extension(
+        'topapprox.link_reduce_cpp',
+        ['topapprox/link_reduce_cpp.cpp'],
+        include_dirs=[pybind11.get_include()],
+        language='c++',
+        extra_compile_args = extra_compile_args + ['-O3', '-Wall', '-shared'],
+    ),
+]
+
+setup(
+    name='topapprox',
+    author='Matias de Jong van Lier, Junyan Chu, Sebastían Elías Graiff Zurita, Shizuo Kaji',
+    description='A module for topological low persistence filter',
+    packages=find_packages(),
+    ext_modules=ext_modules,
+    zip_safe=False,  # Ensure package is not installed as a zip
+)

test_log.txt

@@ -0,0 +1,65 @@
+
+2024-10-10, at 15:26:42
+Test test_1D_simple_python took 0.00 seconds
+Test test_1D_simple_numba took 1.95 seconds
+Test test_1D_simple_numba2 took 0.00 seconds
+Test test_1D_simple_cpp took 0.00 seconds
+Test test_2D_simple_python took 0.00 seconds
+Test test_2D_simple_numba took 0.41 seconds
+Test test_2D_simple_numba2 took 0.00 seconds
+Test test_2D_simple_cpp took 0.00 seconds
+Test test_pagoda took 82.52 seconds
+
+2024-10-10, at 14:35:17
+Test test_pagoda took 79.14 seconds
+
+2024-10-10, at 14:33:58
+Test test_2D_simple_cpp took 0.00 seconds
+
+2024-10-10, at 14:33:58
+Test test_2D_simple_numba2 took 0.00 seconds
+
+2024-10-10, at 14:33:58
+Test test_2D_simple_numba took 0.42 seconds
+
+2024-10-10, at 14:33:58
+Test test_2D_simple_python took 0.00 seconds
+
+2024-10-10, at 14:33:58
+Test test_1D_simple_cpp took 0.00 seconds
+
+2024-10-10, at 14:33:58
+Test test_1D_simple_numba2 took 0.00 seconds
+
+2024-10-10, at 14:33:58
+Test test_1D_simple_numba took 1.95 seconds
+
+2024-10-10, at 14:33:56
+Test test_1D_simple_python took 0.00 seconds
+
+2024-10-10, at 14:14:21
+Test test_pagoda took 78.81 seconds
+
+2024-10-10, at 14:13:02
+Test test_2D_simple_cpp took 0.00 seconds
+
+2024-10-10, at 14:13:02
+Test test_2D_simple_numba2 took 0.00 seconds
+
+2024-10-10, at 14:13:02
+Test test_2D_simple_numba took 0.41 seconds
+
+2024-10-10, at 14:13:01
+Test test_2D_simple_python took 0.00 seconds
+
+2024-10-10, at 14:13:01
+Test test_1D_simple_cpp took 0.00 seconds
+
+2024-10-10, at 14:13:01
+Test test_1D_simple_numba2 took 0.00 seconds
+
+2024-10-10, at 14:13:01
+Test test_1D_simple_numba took 1.69 seconds
+
+2024-10-10, at 14:13:00
+Test test_1D_simple_python took 0.00 seconds

tests/benchmark_log.txt

@@ -0,0 +1,153 @@
+
+    2024-10-20 16:55:45 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 1.0693 seconds.
+
+
+
+    2024-10-20 16:55:44 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 0.4753 seconds.
+
+
+
+    2024-10-20 16:55:43 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 1.2607 seconds.
+
+
+
+    2024-10-20 16:55:42 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 1.2896 seconds.
+
+
+
+    2024-10-20 16:55:40 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 3.1409 seconds.
+
+
+
+    2024-10-20 16:55:37 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 1.8618 seconds.
+
+
+
+    2024-10-20 16:53:51 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 3.1500 seconds.
+
+
+
+    2024-10-20 16:53:48 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 1.8611 seconds.
+
+
+
+    2024-10-20 16:51:56 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 3.3071 seconds.
+
+
+
+    2024-10-20 16:51:52 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 1.8582 seconds.
+
+
+
+    2024-10-18 11:22:12 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 1.1844 seconds.
+
+
+
+    2024-10-18 11:22:11 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 0.4455 seconds.
+
+
+
+    2024-10-18 11:22:10 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 1.2929 seconds.
+
+
+
+    2024-10-18 11:22:09 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 1.1587 seconds.
+
+
+
+    2024-10-18 11:22:07 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 3.1428 seconds.
+
+
+
+    2024-10-18 11:22:04 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 1.8629 seconds.
+
+
+
+    2024-10-15 12:35:28 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 4.9423 seconds.
+
+
+
+    2024-10-15 12:35:23 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=cpp
+    in 2.4064 seconds.
+
+
+
+    2024-10-15 12:35:20 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 5.1913 seconds.
+
+
+
+    2024-10-15 12:35:15 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=numba
+    in 3.0674 seconds.
+
+
+
+    2024-10-15 12:35:11 - Benchmark Results:
+    Filtered 1-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 7.1421 seconds.
+
+
+
+    2024-10-15 12:35:04 - Benchmark Results:
+    Filtered 0-PH below threshold 0.2
+    from pagoda.npy with method=python
+    in 4.0870 seconds.
+