modularitypruning 1.4.0__tar.gz → 1.5.0__tar.gz

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/PKG-INFO

@@ -1,10 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: modularitypruning
-Version: 1.4.0
-Summary: Pruning tool to identify small subsets of network partitions that are significant from the perspective of stochastic block model inference.
-Home-page: https://github.com/ragibson/ModularityPruning
-Author: Ryan Gibson
-Author-email: ryan.alex.gibson@gmail.com
+Version: 1.5.0
+Summary: Pruning tool to identify small subsets of network partitions that are significant from the perspective
+Author-email: Ryan Gibson <ryan.alex.gibson@gmail.com>
+License: MIT
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Programming Language :: Python :: 3
@@ -13,9 +12,11 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: License :: OSI Approved :: MIT License
-Requires-Python: >=3.8, <4
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: leidenalg
@@ -27,6 +28,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: scipy>=1.7
 Requires-Dist: seaborn
 Requires-Dist: tqdm
+Dynamic: license-file
 
 # ModularityPruning
 
@@ -47,6 +49,7 @@ https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-022-20142-6/Media
 ).
 
 ## Installation
+
 This project is on [PyPI](https://pypi.org/project/modularitypruning/) and can
 be installed with
 
@@ -61,6 +64,7 @@ Alternatively, you can install it from this repository directly:
     python3 setup.py install
 
 <a name = "Basic Usage"></a>
+
 ## Basic Usage
 
 This package interfaces directly with python-igraph. A simple example of its

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/README.md

@@ -17,6 +17,7 @@ https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-022-20142-6/Media
 ).
 
 ## Installation
+
 This project is on [PyPI](https://pypi.org/project/modularitypruning/) and can
 be installed with
 
@@ -31,6 +32,7 @@ Alternatively, you can install it from this repository directly:
     python3 setup.py install
 
 <a name = "Basic Usage"></a>
+
 ## Basic Usage
 
 This package interfaces directly with python-igraph. A simple example of its

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/modularitypruning.egg-info/PKG-INFO

@@ -1,10 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: modularitypruning
-Version: 1.4.0
-Summary: Pruning tool to identify small subsets of network partitions that are significant from the perspective of stochastic block model inference.
-Home-page: https://github.com/ragibson/ModularityPruning
-Author: Ryan Gibson
-Author-email: ryan.alex.gibson@gmail.com
+Version: 1.5.0
+Summary: Pruning tool to identify small subsets of network partitions that are significant from the perspective
+Author-email: Ryan Gibson <ryan.alex.gibson@gmail.com>
+License: MIT
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Programming Language :: Python :: 3
@@ -13,9 +12,11 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: License :: OSI Approved :: MIT License
-Requires-Python: >=3.8, <4
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: leidenalg
@@ -27,6 +28,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: scipy>=1.7
 Requires-Dist: seaborn
 Requires-Dist: tqdm
+Dynamic: license-file
 
 # ModularityPruning
 
@@ -47,6 +49,7 @@ https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-022-20142-6/Media
 ).
 
 ## Installation
+
 This project is on [PyPI](https://pypi.org/project/modularitypruning/) and can
 be installed with
 
@@ -61,6 +64,7 @@ Alternatively, you can install it from this repository directly:
     python3 setup.py install
 
 <a name = "Basic Usage"></a>
+
 ## Basic Usage
 
 This package interfaces directly with python-igraph. A simple example of its

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/modularitypruning.egg-info/SOURCES.txt

@@ -1,6 +1,6 @@
 LICENSE
 README.md
-setup.py
+pyproject.toml
 modularitypruning.egg-info/PKG-INFO
 modularitypruning.egg-info/SOURCES.txt
 modularitypruning.egg-info/dependency_links.txt

modularitypruning-1.5.0/pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools >= 75.3.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "modularitypruning"
+version = "1.5.0"
+description = """Pruning tool to identify small subsets of network partitions that are significant from the perspective
+of stochastic block model inference."""
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "MIT" }
+authors = [
+    { name = "Ryan Gibson", email = "ryan.alex.gibson@gmail.com" }
+]
+
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "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 :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3 :: Only",
+    "License :: OSI Approved :: MIT License"
+]
+dependencies = [
+    "leidenalg",
+    "matplotlib",
+    "numpy",
+    "psutil",
+    "igraph",
+    "scikit-learn",
+    "scipy>=1.7",
+    "seaborn",
+    "tqdm"
+]
+
+[tool.setuptools]
+packages = ["modularitypruning"]
+
+[tool.setuptools.package-dir]
+modularitypruning = "utilities"

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_champ_coefficients_2D.py

@@ -1,9 +1,11 @@
-from .shared_testing_functions import generate_connected_ER, generate_random_values, generate_random_partitions, \
-    generate_igraph_famous
+import unittest
+from random import seed
+
 from modularitypruning.champ_utilities import partition_coefficients_2D
 from modularitypruning.leiden_utilities import leiden_part_with_membership, repeated_leiden_from_gammas
-from random import seed
-import unittest
+
+from .shared_testing_functions import generate_connected_ER, generate_random_values, generate_random_partitions, \
+    generate_igraph_famous
 
 
 class TestCHAMPCoefficients2D(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_champ_coefficients_3D.py

@@ -1,8 +1,10 @@
-from .shared_testing_functions import generate_connected_multilayer_ER, generate_random_partitions
+import unittest
+from random import seed
+
 from modularitypruning.champ_utilities import partition_coefficients_3D
 from modularitypruning.leiden_utilities import multilayer_leiden_part_with_membership, leiden_part_with_membership
-from random import seed
-import unittest
+
+from .shared_testing_functions import generate_connected_multilayer_ER, generate_random_partitions
 
 
 class TestCHAMPCoefficients3D(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_champ_usage_2D.py

@@ -1,9 +1,11 @@
-from .shared_testing_functions import generate_connected_ER, generate_random_values, generate_random_partitions, \
-    generate_igraph_famous
+import unittest
+from random import seed
+
 from modularitypruning.champ_utilities import CHAMP_2D
 from modularitypruning.leiden_utilities import leiden_part_with_membership, repeated_leiden_from_gammas
-from random import seed
-import unittest
+
+from .shared_testing_functions import generate_connected_ER, generate_random_values, generate_random_partitions, \
+    generate_igraph_famous
 
 
 class TestCHAMP2D(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_champ_usage_3D.py

@@ -1,10 +1,12 @@
-from .shared_testing_functions import generate_connected_multilayer_ER, generate_random_values, \
-    generate_random_partitions
+import unittest
+from random import seed
+
 from modularitypruning.champ_utilities import CHAMP_3D
 from modularitypruning.leiden_utilities import multilayer_leiden_part_with_membership
 from numpy import mean
-from random import seed
-import unittest
+
+from .shared_testing_functions import generate_connected_multilayer_ER, generate_random_values, \
+    generate_random_partitions
 
 
 def point_is_inside_champ_domain(gamma, omega, domain_vertices):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_deprecated_louvain_names.py

@@ -1,6 +1,7 @@
-import pytest
 import unittest
 
+import pytest
+
 
 class TestDeprecatedLouvainNames(unittest.TestCase):
     def test_deprecated_louvain_module(self):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_documentation_examples.py

@@ -3,6 +3,12 @@ This set of tests checks that the examples from the documentation still work cor
 
 Sometimes this is simply checking that the code produces the intended output or runs without errors.
 """
+import unittest
+from random import seed, random
+
+import igraph as ig
+import matplotlib.pyplot as plt
+import numpy as np
 from modularitypruning import prune_to_stable_partitions, prune_to_multilayer_stable_partitions
 from modularitypruning.champ_utilities import CHAMP_2D, CHAMP_3D
 from modularitypruning.leiden_utilities import (repeated_parallel_leiden_from_gammas,
@@ -11,11 +17,6 @@ from modularitypruning.parameter_estimation_utilities import domains_to_gamma_om
 from modularitypruning.partition_utilities import num_communities
 from modularitypruning.plotting import (plot_2d_domains_with_estimates, plot_2d_domains, plot_2d_domains_with_ami,
                                         plot_2d_domains_with_num_communities, plot_estimates, plot_multiplex_community)
-from random import seed, random
-import igraph as ig
-import matplotlib.pyplot as plt
-import numpy as np
-import unittest
 
 
 class TestDocumentationExamples(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_monolayer_parameter_estimation.py

@@ -1,13 +1,15 @@
-from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_igraph_famous, \
-    generate_random_partition
-import igraph as ig
+import unittest
 from math import log
-from numpy import mean
+from random import seed
+
+import igraph as ig
 from modularitypruning.parameter_estimation import iterative_monolayer_resolution_parameter_estimation
 from modularitypruning.parameter_estimation_utilities import gamma_estimate
 from modularitypruning.partition_utilities import all_degrees
-from random import seed
-import unittest
+from numpy import mean
+
+from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_igraph_famous, \
+    generate_random_partition
 
 
 class TestMonolayerParameterEstimation(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_multiplex_parameter_estimation.py

@@ -1,14 +1,16 @@
-from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_random_partition, \
-    generate_multilayer_intralayer_SBM
-import igraph as ig
+import unittest
 from math import log
-from numpy import mean
+from random import seed
+
+import igraph as ig
 from modularitypruning.leiden_utilities import repeated_leiden_from_gammas_omegas
 from modularitypruning.parameter_estimation import iterative_multilayer_resolution_parameter_estimation
 from modularitypruning.parameter_estimation_utilities import gamma_omega_estimate
 from modularitypruning.partition_utilities import num_communities, all_degrees
-from random import seed
-import unittest
+from numpy import mean
+
+from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_random_partition, \
+    generate_multilayer_intralayer_SBM
 
 
 class TestMultiplexParameterEstimation(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_parallel_leiden_performance.py

@@ -1,16 +1,19 @@
-from .shared_testing_functions import generate_connected_ER, generate_multilayer_intralayer_SBM
-from modularitypruning.leiden_utilities import (repeated_leiden_from_gammas, repeated_parallel_leiden_from_gammas,
-                                                repeated_leiden_from_gammas_omegas,
-                                                repeated_parallel_leiden_from_gammas_omegas)
+import functools
+import unittest
+import warnings
 from multiprocessing import Pool, cpu_count
 from random import seed
-from time import time, sleep
-import functools
+from time import time
+
 import igraph as ig
 import numpy as np
 import psutil
-import unittest
-import warnings
+import pytest
+from modularitypruning.leiden_utilities import (repeated_leiden_from_gammas, repeated_parallel_leiden_from_gammas,
+                                                repeated_leiden_from_gammas_omegas,
+                                                repeated_parallel_leiden_from_gammas_omegas)
+
+from .shared_testing_functions import generate_connected_ER, generate_multilayer_intralayer_SBM
 
 # this set of tests ensures that we achieve >= 75% parallel performance compared to perfect scaling of
 # single-threaded jobs to multiple cores (with no memory contention). This threshold will be decreased in
@@ -38,8 +41,7 @@ def determine_target_parallelization_speedup(num_calculations=32):
     """
     global PERFORMANCE_TARGET_RELATIVE_TO_PERFECT_SCALING
 
-    sleep(5)  # sleep to increase stability of the CPU utilization check
-    cpu_utilization = psutil.cpu_percent()
+    cpu_utilization = psutil.cpu_percent(interval=5)
     if cpu_utilization > 20:
         PERFORMANCE_TARGET_RELATIVE_TO_PERFECT_SCALING = 0.5
         warnings.warn(f"System CPU utilization is non-negligible during parallel performance test! "
@@ -60,6 +62,7 @@ def determine_target_parallelization_speedup(num_calculations=32):
     return num_pool_calculations / num_calculations * base_duration / pool_duration
 
 
+@pytest.mark.serial  # these tests have to run serially for the parallel performance comparisons to make sense
 class TestParallelLeidenPerformance(unittest.TestCase):
     @staticmethod
     def run_singlelayer_graph_parallelization(G, gammas):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/tests/test_temporal_multilevel_parameter_estimation.py

@@ -1,14 +1,16 @@
-from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_random_partition, \
-    generate_multilayer_intralayer_SBM
-import igraph as ig
+import unittest
 from math import log
-from numpy import mean
+from random import seed
+
+import igraph as ig
 from modularitypruning.leiden_utilities import repeated_leiden_from_gammas_omegas
 from modularitypruning.parameter_estimation import iterative_multilayer_resolution_parameter_estimation
 from modularitypruning.parameter_estimation_utilities import gamma_omega_estimate
 from modularitypruning.partition_utilities import num_communities, all_degrees
-from random import seed
-import unittest
+from numpy import mean
+
+from .shared_testing_functions import assert_almost_equal_or_both_none_or_nan, generate_random_partition, \
+    generate_multilayer_intralayer_SBM
 
 
 class TestTemporalAndMultilevelParameterEstimation(unittest.TestCase):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/champ_utilities.py

@@ -1,14 +1,16 @@
-from .partition_utilities import all_degrees, in_degrees, out_degrees, membership_to_communities, \
-    membership_to_layered_communities
+import warnings
 from collections import defaultdict
-import numpy as np
-from numpy.random import choice
 from math import floor
 from multiprocessing import Pool, cpu_count
-from scipy.spatial import HalfspaceIntersection
+
+import numpy as np
+from numpy.random import choice
 from scipy.linalg import LinAlgWarning
 from scipy.optimize import linprog, OptimizeWarning
-import warnings
+from scipy.spatial import HalfspaceIntersection
+
+from .partition_utilities import all_degrees, in_degrees, out_degrees, membership_to_communities, \
+    membership_to_layered_communities
 
 
 def get_interior_point(halfspaces, initial_num_sampled=50, full_retry_limit=10):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/leiden_utilities.py

@@ -1,11 +1,10 @@
 import functools
+from multiprocessing import Pool, cpu_count
+
 import igraph as ig
 import leidenalg
-from math import ceil
-from multiprocessing import Pool, cpu_count
-from tqdm import tqdm
 import numpy as np
-import psutil
+from tqdm import tqdm
 
 LOW_MEMORY_THRESHOLD = 1e9  # 1 GB
 

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/louvain_utilities.py

@@ -6,14 +6,16 @@ module ``modularitypruning.louvain_utilities`` now shims single-layer functions
 in ``modularitypruning.leiden_utilities`` (though it still contains the legacy multi-layer functions since they can be
 faster in general -- leidenalg does not efficiently implement multilayer optimization).
 """
-from . import leiden_utilities
-from .leiden_utilities import sorted_tuple, LOW_MEMORY_THRESHOLD
-from .progress import Progress
+import warnings
 from math import ceil
 from multiprocessing import Pool, cpu_count
+
 import numpy as np
 import psutil
-import warnings
+
+from . import leiden_utilities
+from .leiden_utilities import sorted_tuple, LOW_MEMORY_THRESHOLD
+from .progress import Progress
 
 try:
     import louvain  # import louvain if possible

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/parameter_estimation.py

@@ -1,8 +1,9 @@
+import leidenalg
+
 from .leiden_utilities import singlelayer_leiden, multilayer_leiden
 from .parameter_estimation_utilities import leiden_part_with_membership, estimate_singlelayer_SBM_parameters, \
     gamma_estimate_from_parameters, omega_function_from_model, estimate_multilayer_SBM_parameters
 from .partition_utilities import in_degrees
-import leidenalg
 
 
 def iterative_monolayer_resolution_parameter_estimation(G, gamma=1.0, tol=1e-2, max_iter=25, verbose=False,

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/parameter_estimation_utilities.py

@@ -1,12 +1,14 @@
-from .leiden_utilities import leiden_part_with_membership, sorted_tuple
-from .champ_utilities import CHAMP_2D, CHAMP_3D
-from .partition_utilities import num_communities
+import warnings
+from math import log
+
 import igraph as ig
 import leidenalg
-from math import log
 import numpy as np
 from scipy.optimize import fsolve
-import warnings
+
+from .champ_utilities import CHAMP_2D, CHAMP_3D
+from .leiden_utilities import leiden_part_with_membership, sorted_tuple
+from .partition_utilities import num_communities
 
 
 def estimate_singlelayer_SBM_parameters(G, partition, m=None):

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/partition_utilities.py

@@ -1,4 +1,5 @@
 from collections import defaultdict
+
 from sklearn.metrics import adjusted_mutual_info_score, normalized_mutual_info_score
 
 

{modularitypruning-1.4.0 → modularitypruning-1.5.0}/utilities/plotting.py

@@ -1,12 +1,14 @@
-from .partition_utilities import num_communities, ami
 from collections import defaultdict
 from random import sample, shuffle
-import numpy as np
+
 import matplotlib
-from matplotlib.patches import Polygon
-from matplotlib.collections import PatchCollection
 import matplotlib.pyplot as plt
+import numpy as np
 import seaborn as sbn
+from matplotlib.collections import PatchCollection
+from matplotlib.patches import Polygon
+
+from .partition_utilities import num_communities, ami
 
 
 def plot_adjacency(adj):

modularitypruning-1.4.0/setup.py

@@ -1,38 +0,0 @@
-from setuptools import setup
-import os
-
-here = os.path.abspath(os.path.dirname(__file__))
-
-# Get the long description from the README file
-with open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
-
-setup(
-    name='modularitypruning',
-    version='1.4.0',
-    package_dir={'modularitypruning': 'utilities'},
-    packages=['modularitypruning'],
-    url='https://github.com/ragibson/ModularityPruning',
-    license='',
-    author='Ryan Gibson',
-    author_email='ryan.alex.gibson@gmail.com',
-    description='Pruning tool to identify small subsets of network partitions that are '
-                'significant from the perspective of stochastic block model inference.',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Topic :: Scientific/Engineering :: Information Analysis',
-        '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',
-        'License :: OSI Approved :: MIT License'
-    ],
-    python_requires='>=3.8, <4',
-    install_requires=['leidenalg', 'matplotlib', "numpy", 'psutil', 'igraph',
-                      "scikit-learn", "scipy>=1.7", 'seaborn', 'tqdm']
-)