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setup.py
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# -*- coding: utf-8 -*-
import os
import sys
import pathlib
import importlib
import glob
import shutil
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
from pathlib import Path
import mesonbuild
import platform
suffix = importlib.machinery.EXTENSION_SUFFIXES[0]
package_dir = \
{'': 'src'}
packages = \
['tallem', 'tallem.extensions']
package_data = \
{'': ['*'], 'tallem.extensions': ['*.so', '*.pyd', 'extensions/*.so', 'extensions/*.pyd'] }
install_requires = \
['numpy>=1.21.3,<2.0.0', 'scipy>=1.6']
extras_require = \
{'autograd': ['autograd'],
'pymanopt': ['pymanopt>=0.2.5'],
'scikit-learn': ['scikit-learn>=1.0']}
# From: https://stackoverflow.com/questions/51108256/how-to-take-a-pathname-string-with-wildcards-and-resolve-the-glob-with-pathlib
def expandpath(path_pattern):
p = Path(path_pattern).expanduser()
parts = p.parts[p.is_absolute():]
return Path(p.root).glob(str(Path(*parts)))
def build_extensions(setup_kwargs):
print(f"Building extensions with suffix: {suffix}")
home_dir = os.getcwd()
existing_modules = list(expandpath(f"{home_dir}/src/tallem/extensions/*{suffix}"))
if len(existing_modules) > 0:
print("Removing existing modules for a clean build")
## Remove existing extension modules
for m in existing_modules: os.remove(m)
import numpy as np
print("\n==== NUMPY INCLUDES ====\n")
print(f"{np.get_include()}")
## Recompile
print("\n==== Printing compiler version ====\n")
os.system("c++ --version")
## Check if build exists, and if it does remove it
if os.path.isdir(f"{home_dir}/build"):
print(f"\n==== Removing directory {home_dir}/build ====\n")
shutil.rmtree(f"{home_dir}/build")
print("\n==== Starting meson build ====\n")
os.system("python3 -m mesonbuild.mesonmain build")
os.system("python3 -m mesonbuild.mesonmain compile -vC build")
## Linux CI servers raise tty exception on meson install, so do manual copy instead
os.system("python3 -m mesonbuild.mesonmain install -C build")
target_path = next(expandpath(f"{home_dir}/src/tallem/extensions/")).resolve()
print(f"\n==== Extension module install path: {target_path} ====\n")
for file in glob.glob(f"build/*{suffix}"):
print(f"Installing {file} to: {target_path} \n")
shutil.copy(file, target_path)
print("\n==== Finished meson build ====\n")
## Check if they now exist
num_so = len([p.name for p in expandpath(f"{home_dir}/src/tallem/extensions/*{suffix}")])
if num_so > 0:
return(0)
else:
print("ERROR: Did not detect native python extensions; Exiting build")
sys.exit(-1)
# Boilerplate from https://stackoverflow.com/questions/63350376/place-pre-compiled-extensions-in-root-folder-of-non-pure-python-wheel-package
# because setuptools/distutils are archaic tools
# class CustomDistribution(Distribution):
# def iter_distribution_names(self):
# for pkg in self.packages or ():
# yield pkg
# for module in self.py_modules or ():
# yield module
class CustomExtension(Extension):
def __init__(self, path):
self.path = path
super().__init__(pathlib.PurePath(path).name, [])
class build_CustomExtensions(build_ext):
def run(self):
for ext in (x for x in self.extensions if isinstance(x, CustomExtension)):
source = f"{ext.path}{suffix}"
build_dir = pathlib.PurePath(self.get_ext_fullpath(ext.name)).parent
os.makedirs(f"{build_dir}/{pathlib.PurePath(ext.path).parent}", exist_ok = True)
shutil.copy(f"{source}", f"{build_dir}/{source}")
def find_extensions(directory):
extensions = []
for path, _, filenames in os.walk(directory):
for filename in filenames:
filename = pathlib.PurePath(filename)
if pathlib.PurePath(filename).suffix == suffix:
extensions.append(CustomExtension(os.path.join(path, filename.stem)))
return extensions
setup_kwargs = {
'name': 'tallem',
'version': '0.2.2',
'description': 'Topological Assembly of Locally Euclidean Models',
'long_description': '# Topological Assembly of Local Euclidean Models \n\nThis repository implements TALLEM - a topologically inspired non-linear dimensionality reduction method.\n\nGiven some data set *X* and a map <img class=\'latex-inline math\' style="background: white; vertical-align:-0.105206pt;" src="https://render.githubusercontent.com/render/math?math=\\large f%20%3A%20X%20%5Cto%20B&mode=inline"> onto some topological space _B_ which captures the topology/nonlinearity of _X_, TALLEM constructs a map <img style="background: white; vertical-align:-0.105206pt" class=\'latex-inline math\' src="https://render.githubusercontent.com/render/math?math=\\large F%20%3A%20X%20%5Cto%20%5Cmathbb%7BR%7D%5ED%20&mode=inline"> mapping _X_ to a _D_-dimensional space. \n\nTODO: describe TALLEM more\n\n## Installing + Dependencies \n\n`tallem`\'s run-time dependencies are fairly minimal. They include: \n\n1. _Python >= 3.8.0_ \n2. *NumPy (>= 1.20)* and *SciPy* *(>=1.6)*\n\nThe details of the rest of package requirements are listed in [pyproject.toml](https://github.com/peekxc/tallem/blob/main/pyproject.toml). These are automatically downloaded and installed via `pip`: \n\n\n\nSome functions which extend TALLEM\'s core functionality require additional dependencies to be called---they include *autograd*, *pymanopt*, *scikit-learn*, and *bokeh*. These packages are completely optional, i.e. they are not needed to get the resulting embedding. Nonetheless, if you would like these package as well, use: \n\n\n\n\n\n###Installing from cibuildwheels\n\nTODO\n\n### Installing from source\n\nTo install `tallem` from source, clone the repository and install the package via: \n\n```bash\npython -m pip install .\n```\n\n`tallem` relies on a few package dependencies in order to compile correctly when building from source. These libraries include: \n\n* [Armadillo](http://arma.sourceforge.net/) >= 10.5.2 ([see here for installation options](http://arma.sourceforge.net/download.html))\n* [Poetry](https://python-poetry.org/) (for building the [source](https://packaging.python.org/glossary/#term-Source-Distribution-or-sdist) and [binary](https://packaging.python.org/glossary/#term-Wheel) distributions)\n* [Meson](https://mesonbuild.com/) and [Ninja](https://ninja-build.org/) (for building the [extension modules](https://docs.python.org/3/glossary.html#term-extension-module))\n\nAn install attempt of these external dependencies is made if they are not available prior to call to `pip`, however these may require manual installation. Additionally, the current source files are written in [C++17](https://en.wikipedia.org/wiki/C%2B%2B17), so a [C++17 compliant compiler](https://en.cppreference.com/w/cpp/compiler_support/17) will be needed. If you have an installation problems or questions, feel free to [make a new issue](https://github.com/peekxc/tallem/issues).\n\n## Usage \n\nBelow is some example code showcasing TALLEMs ability to handle topological obstructions to dimensionality reduction like non-orientability. \n\n```python\nfrom tallem import TALLEM\nfrom tallem.cover import IntervalCover\nfrom tallem.datasets import mobius_band\n\n## Get mobius band data + its parameter space\nX, B = mobius_band()\nB_polar = B[:,[1]]\n\n## Construct a cover over the polar coordinate\nm_dist = lambda x,y: np.sum(np.minimum(abs(x - y), (2*np.pi) - abs(x - y)))\ncover = IntervalCover(B_polar, n_sets = 10, overlap = 0.30, metric = m_dist)\n\n## Parameterize TALLEM + transform the data to the obtain the coordinization\nemb = TALLEM(cover=cover, local_map="cmds2", n_components=3).fit_transform(X, B_polar)\n\n## Draw the coordinates via 3D projection, colored by the polar coordinate\nimport matplotlib.pyplot as plt\nfig = plt.figure()\nax = fig.add_subplot(projection=\'3d\')\nax.scatter(*emb.T, marker=\'o\', c=B_polar)\n```\n\n\n\n',
'author': 'Matt Piekenbrock',
'author_email': 'matt.piekenbrock@gmail.com',
'maintainer': None,
'maintainer_email': None,
'url': 'https://github.com/peekxc/tallem',
'package_dir': package_dir,
'packages': packages,
'package_data': package_data,
'install_requires': install_requires,
'extras_require': extras_require,
'python_requires': '>=3.8,<3.10',
'ext_modules': find_extensions("src/tallem"),
'cmdclass': {'build_ext': build_CustomExtensions},
# 'distclass': CustomDistribution
}
# Build first, then invoke setup
build_extensions(setup_kwargs)
setup(**setup_kwargs)