Restructuring for package to submit to PyPA.

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools >= 42", "wheel", "Cython", "numpy"]
+requires = ["setuptools >= 42", "wheel", "numpy"]
 build-backend = "setuptools.build_meta"

requirements.txt

@@ -1,24 +1,40 @@
 alabaster==0.7.12
 Babel==2.9.1
+bleach==4.1.0
+build==0.7.0
 certifi==2021.5.30
+cffi==1.14.6
 charset-normalizer==2.0.6
+colorama==0.4.4
+cryptography==3.4.8
 cycler==0.10.0
+Cython==0.29.24
 docutils==0.17.1
 idna==3.2
 imagesize==1.2.0
+importlib-metadata==4.8.1
+jeepney==0.7.1
 Jinja2==3.0.1
+keyring==23.2.1
 kiwisolver==1.3.2
 MarkupSafe==2.0.1
 matplotlib==3.4.3
 numpy==1.21.2
 packaging==21.0
+pep517==0.11.0
 Pillow==8.3.2
+pkginfo==1.7.1
+pycparser==2.20
 Pygments==2.10.0
 pyparsing==2.4.7
 python-dateutil==2.8.2
 pytz==2021.1
+readme-renderer==29.0
 requests==2.26.0
+requests-toolbelt==0.9.1
+rfc3986==1.5.0
 scipy==1.7.1
+SecretStorage==3.3.1
 six==1.16.0
 snowballstemmer==2.1.0
 Sphinx==4.2.0
@@ -29,5 +45,9 @@ sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
--e git+git@github.com:ksjdragon/packsim.git@e2f25182310c1f9a950df55c0219165366466e9b#egg=squish
+tomli==1.2.1
+tqdm==4.62.3
+twine==3.4.2
 urllib3==1.26.6
+webencodings==0.5.1
+zipp==3.5.0

setup.cfg

@@ -1,10 +1,10 @@
 [metadata]
-name = squish-ksjdragon
+name = squish
 version = 0.1
 author = Kenneth Jao
 author_email = ksjdragon@gmail.com
 description = squish is Python program which perform simulations for the flow of 'soft' or 'compressible' objects under some energy in a periodic domain.
-long_description = file: README.md
+long_description = file: README.rst
 long_description_content_type = text/markdown
 url = https://github.com/ksjdragon/squish
 project_urls =
@@ -18,19 +18,13 @@ classifiers =
 
 [options]
 zip_safe = False
-package_dir =
+packages = squish
-	= src
-pacakges = find:
 python_requires = >= 3.8
 install_requires =
 	numpy == 1.21.2
 	scipy == 1.7.1
 	matplotlib == 3.4.3
 
-[options.packages.find]
-	where = src
-
-
 [options.entry_points]
 console_scripts =
 	squish = squish.squish:pre

setup.py

@@ -1,20 +1,31 @@
 from setuptools import Extension, setup
-from Cython.Build import cythonize
 import numpy
 
-ext_modules = [
+try:
-    Extension(
+	from Cython.Build import cythonize
-        "_squish",
+	USE_CYTHON = True
-        ["src/_squish/_squish.pyx"],
+except ImportError:
-        extra_compile_args=['-fopenmp'],
+	USE_CYTHON = False
-        extra_link_args=['-fopenmp']
+
-    )
+if USE_CYTHON:
+	ext_modules = cythonize([
+		Extension(
+			"_squish",
+			["squish/_squish/_squish.pyx"],
+			extra_compile_args=['-fopenmp'],
+			extra_link_args=['-fopenmp']
+		)
+	],
+	compiler_directives={
+		'language_level': 3, 'boundscheck' : False, 'wraparound': False, 'cdivision' : True
+	})
+else:
+	ext_modules = [
+	Extension('squish._squish', ["squish/_squish/_squish.c"])
 ]
 
+#annotate='fullc'
 setup(
-    name="squish",
+	ext_modules = ext_modules,
-    ext_modules = cythonize(ext_modules, compiler_directives={
+	include_dirs = [numpy.get_include()]
-        'language_level': 3, 'boundscheck' : False, 'wraparound': False, 'cdivision' : True
-    }),
-    include_dirs = [numpy.get_include()]
 )

squish/_squish/energy.pyx

@@ -40,7 +40,7 @@ cdef class AreaEnergy(VoronoiContainer):
 			if i < self.n:
 				energy += xi.cache.energy(&xi, NAN)
 			
-			for j in prange(xi.edge_num(&xi)):
+			for j in range(xi.edge_num(&xi)):
 				em, ep = e.prev(&e), e.next(&e)
 				vdiff = em.origin(&em)
 				vdiff.self.vsub(&vdiff, ep.origin(&ep))
@@ -71,7 +71,7 @@ cdef class AreaEnergy(VoronoiContainer):
 			xi = init.Site(i, &info)
 			e = xi.edge(&xi)
 			edge_set = init.BitSet(num_edges)
-			for j in prange(xi.edge_num(&xi)):	# Looping through site edges.
+			for j in range(xi.edge_num(&xi)):	# Looping through site edges.
 				f = e
 				while True:	# Circling this vertex.
 					if not edge_set.add(&edge_set, f.arr_index):
@@ -166,7 +166,7 @@ cdef class RadialTEnergy(VoronoiContainer):
 		for i in prange(self.sites.shape[0], nogil=True):
 			xi = init.Site(i, &info)
 			e = xi.edge(&xi)
-			for j in prange(xi.edge_num(&xi)):
+			for j in range(xi.edge_num(&xi)):
 				em = e.prev(&e)
 				e.cache.H(&e, VoronoiContainer.calc_H(em, e))
 				t = Calc.phi(e)
@@ -186,7 +186,7 @@ cdef class RadialTEnergy(VoronoiContainer):
 
 			# For looping again to calculate integrals.
 			em = xi.edge(&xi)
-			for j in prange(xi.edge_num(&xi)):
+			for j in range(xi.edge_num(&xi)):
 				e = em.next(&em)
 				B = em.cache.B(&em, NAN)
 				t, tp = em.cache.phi(&em, NAN), e.cache.phi(&e, NAN)
@@ -234,7 +234,7 @@ cdef class RadialTEnergy(VoronoiContainer):
 			e = xi.edge(&xi)
 			edge_set = init.BitSet(num_edges)
 
-			for j in prange(xi.edge_num(&xi)):	# Looping through site edges.
+			for j in range(xi.edge_num(&xi)):	# Looping through site edges.
 				f = e
 				while True:	# Circling this vertex.
 					fm = f.prev(&f)

squish/_squish/voronoi_dcel.pyx

@@ -537,7 +537,7 @@ cdef class VoronoiContainer:
 		for i in prange(self.sites.shape[0], nogil=True):
 			xi = init.Site(i, &info)
 			em = xi.edge(&xi)
-			for j in prange(xi.edge_num(&xi)):
+			for j in range(xi.edge_num(&xi)):
 				ep = em.next(&em)
 				p, q = em.origin(&em), ep.origin(&ep)
 				la, da = q.copy.vsub(&q, p), p.copy.vsub(&p, xi.vec(&xi))	# vp - vm, vm - xi

squish/common.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 from typing import List, Union, Optional, Iterator, Generator
 import pickle, numpy as np
 from pathlib import Path
-from _squish import AreaEnergy, RadialALEnergy, RadialTEnergy
+from ._squish import AreaEnergy, RadialALEnergy, RadialTEnergy
 
 OUTPUT_DIR = Path("squish_output")
 OUTPUT_DIR.mkdir(exist_ok=True)

squish/simulation.py

@@ -298,7 +298,7 @@ class Search(Simulation):
 
 		for i in range(self.count):
 			# Get to equilibrium.
-			sim = Flow(self.domain, self.energy, self.thres, self.step_size, self.accel)
+			sim = Flow(self.domain, self.energy, self.step_size, self.thres, self.accel)
 			sim.add_frame(new_sites)
 			sim.run(False, log, log_steps)
 
@@ -382,7 +382,7 @@ class Shrink(Simulation):
 		while width >= self.stop_width:
 			# Get to equilibrium.
 			new_domain = DomainParams(self.domain.n, width, self.domain.h, self.domain.r)
-			sim = Flow(new_domain, self.energy, self.thres, self.step_size, self.accel)
+			sim = Flow(new_domain, self.energy, self.step_size, self.thres, self.accel)
 			sim.add_frame(new_sites)
 			sim.run(False, log, log_steps)
 			new_sites = sim[-1].site_arr