Refactored project setup, added tests to CI, updated Cython.

.github/workflows/test.yml

@@ -0,0 +1,32 @@
+# This workflow will install Python dependencies, run tests and lint with a
+# variety of Python versions For more information see:
+# https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: test
+
+on:
+  push:
+    branches: [ "main"]
+  pull_request:
+    branches: [ "main"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        cd ${GITHUB_WORKSPACE}/scripts && ./setup.sh
+    - name: Run unit tests
+      run: |
+        cd ${GITHUB_WORKSPACE}/scripts && ./test.sh

README.md

@@ -4,7 +4,7 @@ Python wrapper for the [Zeo++ library](http://zeoplusplus.org). Based on the lat
 
 ## Installation
 
-We provide pre-built wheels for most platforms (including Apple Silicon). So in most cases you will want to install the package with `pip`:
+We provide pre-built wheels for several platforms (including Apple Silicon). So in most cases you will want to install the package with `pip`:
 
 ```sh
 pip install pyzeo

pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = 'pyzeo'
+version = '0.1.6'
+description = 'Python interface to Zeo++'
+readme = "README.md"
+authors = [{ name = "Lauri Himanen" }]
+license = { file = "LICENSE" }
+requires-python = ">=3.8"
+dependencies = []
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: C++",
+    "Programming Language :: Cython",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering"
+]
+keywords = ['zeo++', 'porous', 'materials', 'science']
+
+[project.urls]
+Source = "https://github.com/nomad-coe/pyzeo"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+]
+
+[tool.setuptools.package-dir]
+"" = "src"

scripts/setup.sh

@@ -0,0 +1,3 @@
+cd ..
+python -m pip install --upgrade pip
+pip install .[dev]

scripts/test.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+cd ../tests
+pytest

setup.py

@@ -2,7 +2,7 @@
 import platform
 from distutils.ccompiler import new_compiler
 from distutils.sysconfig import customize_compiler
-from setuptools import setup, find_packages
+from setuptools import setup
 from setuptools.extension import Extension
 from subprocess import getoutput
 
@@ -89,35 +89,5 @@ def using_clang():
     from Cython.Build import cythonize
     extensions = cythonize(extensions)
 
-setup(
-    name='pyzeo',
-    version='0.1.5',
-    description="Python interface to Zeo++",
-    long_description="Python interface to Zeo++",
-    url="https://github.com/nomad-coe/pyzeo",
-    author="Lauri Himanen",
-    license="",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Programming Language :: C++",
-        "Programming Language :: Cython",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Programming Language :: Python :: 3 :: Only",
-        "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering"
-    ],
-    # In the Cython build guide it is said that zip_safe should be disabled
-    # when building with setuptools
-    packages=find_packages('src'),
-    package_dir={'': 'src'},
-    zip_safe=False,
-    ext_modules=extensions,
-    keywords="zeo++ porous materials science",
-    python_requires=">=3.8",
-)
+if __name__ == "__main__":
+    setup(ext_modules=extensions)

tests/test_areavol.py

@@ -1,32 +1,33 @@
-from pyzeo.netstorage import AtomNetwork
-from pyzeo.area_volume import volume, surface_area
+def test_areavol():
+    from pyzeo.netstorage import AtomNetwork
+    from pyzeo.area_volume import volume, surface_area
 
-atmnet = AtomNetwork.read_from_CSSR("MgO_vac1.cssr", rad_file="MgO.rad")
-vol_str = volume(atmnet, 0.1, 0.05, 20000)
-lines = vol_str.decode("utf-8").split('\n')
-for line in lines:
-    if "Number_of_pockets" in line:
-        print('---------')
-        print(line)
-        print('---------')
-vol_str, ha_atmnet = volume(atmnet, 0.1, 0.05, 7000, True)
-lines = vol_str.decode("utf-8").split('\n')
-for line in lines:
-    if "Number_of_pockets" in line:
-        print('---------')
-        print(line)
-        print('---------')
-#print("--------")
-#print(vol_str)
-#print("--------")
-sa_str = surface_area(atmnet, 0.1, 0.05, 7000, False)
-lines = sa_str.decode("utf-8").split('\n')
-for line in lines:
-    if "Number_of_pockets" in line:
-        print('---------')
-        print(line.split())
-        print('---------')
-#print("--------")
-#print(sa_str)
-#print("--------")
+    atmnet = AtomNetwork.read_from_CSSR("MgO_vac1.cssr", rad_file="MgO.rad")
+    vol_str = volume(atmnet, 0.1, 0.05, 20000)
+    lines = vol_str.decode("utf-8").split('\n')
+    for line in lines:
+        if "Number_of_pockets" in line:
+            print('---------')
+            print(line)
+            print('---------')
+    vol_str, ha_atmnet = volume(atmnet, 0.1, 0.05, 7000, True)
+    lines = vol_str.decode("utf-8").split('\n')
+    for line in lines:
+        if "Number_of_pockets" in line:
+            print('---------')
+            print(line)
+            print('---------')
+    #print("--------")
+    #print(vol_str)
+    #print("--------")
+    sa_str = surface_area(atmnet, 0.1, 0.05, 7000, False)
+    lines = sa_str.decode("utf-8").split('\n')
+    for line in lines:
+        if "Number_of_pockets" in line:
+            print('---------')
+            print(line.split())
+            print('---------')
+    #print("--------")
+    #print(sa_str)
+    #print("--------")
 

tests/test_cluster.py

@@ -1,17 +1,18 @@
-from pyzeo.netstorage import AtomNetwork
-from pyzeo.cluster import pruned_highaccuracy_voronoi_network, \
-        get_nearest_largest_diameter_highaccuracy_vornode
+def test_cluster():
+    from pyzeo.netstorage import AtomNetwork
+    from pyzeo.cluster import pruned_highaccuracy_voronoi_network, \
+            get_nearest_largest_diameter_highaccuracy_vornode
 
-atmnet = AtomNetwork.read_from_CSSR("MgO.cssr", rad_file="MgO.rad")
-vornet,ecs,fcs = atmnet.perform_voronoi_decomposition()
-vornet.analyze_writeto_XYZ('mgo_low', 0.4, atmnet)
+    atmnet = AtomNetwork.read_from_CSSR("MgO.cssr", rad_file="MgO.rad")
+    vornet, ecs, fcs = atmnet.perform_voronoi_decomposition()
+    vornet.analyze_writeto_XYZ('mgo_low', 0.4, atmnet)
 
-# Pruned high accuracy voronoi network
-ha_vornet = pruned_highaccuracy_voronoi_network(atmnet, 0.7)
-ha_vornet.analyze_writeto_XYZ('mgo_high_prune', 0.4, atmnet)
+    # Pruned high accuracy voronoi network
+    ha_vornet = pruned_highaccuracy_voronoi_network(atmnet, 0.7)
+    ha_vornet.analyze_writeto_XYZ('mgo_high_prune', 0.4, atmnet)
 
-# Reduced high accuracy voronoi network
-ha_red_vornet = get_nearest_largest_diameter_highaccuracy_vornode(atmnet) 
-ha_red_vornet.analyze_writeto_XYZ('mgo_high_red', 0.4, atmnet)
+    # Reduced high accuracy voronoi network
+    ha_red_vornet = get_nearest_largest_diameter_highaccuracy_vornode(atmnet) 
+    ha_red_vornet.analyze_writeto_XYZ('mgo_high_red', 0.4, atmnet)
 
 

tests/test_cycle.py

@@ -1,29 +1,28 @@
-import sys
-from pyzeo.netstorage import AtomNetwork
-from pyzeo.cycle import compute_centroid_4cycles, compute_face_centers
+def test_cycle():
+    from pyzeo.netstorage import AtomNetwork
+    from pyzeo.cycle import compute_centroid_4cycles, compute_face_centers
 
-atmnet = AtomNetwork.read_from_CSSR("MgO.cssr", rad_file="MgO.rad")
-compute_face_centers(atmnet)
-sys.exit()
+    atmnet = AtomNetwork.read_from_CSSR("MgO.cssr", rad_file="MgO.rad")
+    compute_face_centers(atmnet)
 
-vornet = atmnet.perform_voronoi_decomposition()
-oh_interstitials = compute_centroid_4cycles(vornet)
+    vornet, _, _ = atmnet.perform_voronoi_decomposition()
+    oh_interstitials = compute_centroid_4cycles(vornet)
 
-ids_set = set()
-i = 0
-while i < len(oh_interstitials):
-    node_ids = frozenset(oh_interstitials[i]['ids'])
-    if node_ids not in ids_set:
-        ids_set.add(node_ids)
-        i = i+1
-    else:
-        oh_interstitials.pop(i)
-
-print(len(oh_interstitials))
-for inter in oh_interstitials:
-    node_ids = inter['ids']
-    print(node_ids)
-    coord = inter['coords']
-    print(coord.x, coord.y, coord.z)
+    ids_set = set()
+    i = 0
+    while i < len(oh_interstitials):
+        node_ids = frozenset(oh_interstitials[i]['ids'])
+        if node_ids not in ids_set:
+            ids_set.add(node_ids)
+            i = i+1
+        else:
+            oh_interstitials.pop(i)
+            
+    print(len(oh_interstitials))
+    for inter in oh_interstitials:
+        node_ids = inter['ids']
+        print(node_ids)
+        coord = inter['coords']
+        print(coord.x, coord.y, coord.z)