From 111283a0e0184e1674ef29ec0bd873a099574096 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= Date: Tue, 18 Apr 2023 10:46:51 +0200 Subject: [PATCH] python: Update deprecated setuptools functionality Starting with setuptools v67.3.0, the pkg_resources module is being progressively phased out from the setuptools main module. --- doc/tutorials/constant_pH/constant_pH.ipynb | 4 ++-- maintainer/benchmarks/mc_acid_base_reservoir.py | 4 ++-- testsuite/python/unittest_decorators.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/tutorials/constant_pH/constant_pH.ipynb b/doc/tutorials/constant_pH/constant_pH.ipynb index bcfd5bdf993..ca4029465a4 100644 --- a/doc/tutorials/constant_pH/constant_pH.ipynb +++ b/doc/tutorials/constant_pH/constant_pH.ipynb @@ -137,10 +137,10 @@ "plt.rcParams.update({'font.size': 18})\n", "\n", "import numpy as np\n", - "import setuptools\n", + "import pkg_resources\n", "import pint # module for working with units and dimensions\n", "import time\n", - "assert setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \\\n", + "assert pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \\\n", " f'pint version {pint.__version__} is too old: several numpy operations can cast away the unit'\n", "\n", "import espressomd\n", diff --git a/maintainer/benchmarks/mc_acid_base_reservoir.py b/maintainer/benchmarks/mc_acid_base_reservoir.py index 97e465e8c70..a7a7a965f73 100644 --- a/maintainer/benchmarks/mc_acid_base_reservoir.py +++ b/maintainer/benchmarks/mc_acid_base_reservoir.py @@ -24,7 +24,7 @@ import espressomd import espressomd.electrostatics import espressomd.reaction_methods -import setuptools +import pkg_resources import argparse parser = argparse.ArgumentParser(description="Benchmark MC simulations in the grand-reaction ensemble. " @@ -45,7 +45,7 @@ # process and check arguments assert args.particles_per_core >= 100, "you need to use at least 100 particles per core to avoid finite-size effects in the simulation" espressomd.assert_features(['WCA', 'ELECTROSTATICS']) -assert setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \ +assert pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \ f'pint version {pint.__version__} is too old: several numpy operations can cast away the unit' diff --git a/testsuite/python/unittest_decorators.py b/testsuite/python/unittest_decorators.py index 109f89cc8d7..a9a0e5200c4 100644 --- a/testsuite/python/unittest_decorators.py +++ b/testsuite/python/unittest_decorators.py @@ -19,7 +19,7 @@ import sys import importlib -import setuptools +import pkg_resources import unittest import espressomd @@ -74,7 +74,7 @@ def skipIfUnmetModuleVersionRequirement(module, version_requirement): _module = importlib.import_module(module) except ImportError: return skipIfMissingModules(module) - if not setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet( + if not pkg_resources.packaging.specifiers.SpecifierSet( version_requirement).contains(_module.__version__): return unittest.skip( "Skipping test: version requirement not met for module {}".format(module)) From bff5e2703d4371f06f281d48181431558066d566 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= Date: Tue, 20 Dec 2022 19:36:34 +0100 Subject: [PATCH] tests: Replace deprecated numpy option Option 'normed' in numpy.histogramdd was deprecated since 1.15 and removed in 1.24. --- testsuite/python/observable_profile.py | 2 +- testsuite/python/observable_profileLB.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/testsuite/python/observable_profile.py b/testsuite/python/observable_profile.py index 9692449185b..0a7b7eafff5 100644 --- a/testsuite/python/observable_profile.py +++ b/testsuite/python/observable_profile.py @@ -51,7 +51,7 @@ def test_density_profile(self): obs_bin_centers = density_profile.bin_centers() np_hist, np_edges = tests_common.get_histogram( np.copy(self.system.part.all().pos), self.kwargs, 'cartesian', - normed=True) + density=True) np_hist *= len(self.system.part) np.testing.assert_array_almost_equal(obs_data, np_hist) for i in range(3): diff --git a/testsuite/python/observable_profileLB.py b/testsuite/python/observable_profileLB.py index 4a3527035da..6770cea8e50 100644 --- a/testsuite/python/observable_profileLB.py +++ b/testsuite/python/observable_profileLB.py @@ -91,7 +91,7 @@ def test_velocity_profile(self): obs_edges = obs.call_method("edges") _, np_edges = tests_common.get_histogram( np.zeros([1, 3]), LB_VELOCITY_PROFILE_PARAMS, 'cartesian', - normed=True) + density=True) for i in range(3): np.testing.assert_array_almost_equal(obs_edges[i], np_edges[i]) for x in range(obs_data.shape[0]):