* [gentoo-commits] repo/gentoo:master commit in: sci-physics/espresso/files/
@ 2017-09-02 14:35 Michael Palimaka
0 siblings, 0 replies; 2+ messages in thread
From: Michael Palimaka @ 2017-09-02 14:35 UTC (permalink / raw
To: gentoo-commits
commit: fe50e58025ef3cd19e2fe572da2de5add50ac442
Author: Michael Mair-Keimberger <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Sun Aug 20 12:57:14 2017 +0000
Commit: Michael Palimaka <kensington <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 14:35:44 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fe50e580
sci-physics/espresso: remove unused patch
.../files/espresso-3.3.0-cython-0.22.patch | 23 ----------------------
1 file changed, 23 deletions(-)
diff --git a/sci-physics/espresso/files/espresso-3.3.0-cython-0.22.patch b/sci-physics/espresso/files/espresso-3.3.0-cython-0.22.patch
deleted file mode 100644
index 22b726b480e..00000000000
--- a/sci-physics/espresso/files/espresso-3.3.0-cython-0.22.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-From 9e6caa3294b0f5f377c16550a07429b73c871ac3 Mon Sep 17 00:00:00 2001
-From: Christoph Junghans <junghans@votca.org>
-Date: Thu, 12 Mar 2015 08:55:51 -0600
-Subject: [PATCH] fix build with cython-0.22
-
----
- src/python/espressomd/particle_data.pxd | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/python/espressomd/particle_data.pxd b/src/python/espressomd/particle_data.pxd
-index fff022b..4cc39e8 100644
---- a/src/python/espressomd/particle_data.pxd
-+++ b/src/python/espressomd/particle_data.pxd
-@@ -185,5 +185,5 @@ cdef class ParticleHandle(object):
- cdef public int id
- cdef bint valid
- cdef Particle particleData
-- cdef int updateParticleData(self)
-+ cdef int updateParticleData(self) except -1
-
---
-2.0.5
-
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-physics/espresso/files/
@ 2025-09-08 19:19 Eli Schwartz
0 siblings, 0 replies; 2+ messages in thread
From: Eli Schwartz @ 2025-09-08 19:19 UTC (permalink / raw
To: gentoo-commits
commit: ff73a7079b041ea3f23dcbc8e1e544cfdaa13157
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 8 19:18:02 2025 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Mon Sep 8 19:19:35 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ff73a707
sci-physics/espresso: add the patches too. oops...
Fixes: 74d3bc3916a6fefac6f5a1f810b855b7046696bb
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
...ing-test-deps-without-running-ctest-indir.patch | 40 ++++
.../files/espresso-4.2.0-test-deprecations.patch | 112 ++++++++++++
.../files/espresso-4.2.0-test-rounding.patch | 201 +++++++++++++++++++++
3 files changed, 353 insertions(+)
diff --git a/sci-physics/espresso/files/0001-allow-building-test-deps-without-running-ctest-indir.patch b/sci-physics/espresso/files/0001-allow-building-test-deps-without-running-ctest-indir.patch
new file mode 100644
index 000000000000..9ae60e5cbdb1
--- /dev/null
+++ b/sci-physics/espresso/files/0001-allow-building-test-deps-without-running-ctest-indir.patch
@@ -0,0 +1,40 @@
+From e0852a7cc236c500cfcd155dd1a58838dbdc438a Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz@gentoo.org>
+Date: Tue, 2 Sep 2025 19:47:46 -0400
+Subject: [PATCH] allow building test deps without running ctest indirectly
+
+---
+ src/CMakeLists.txt | 3 +--
+ testsuite/python/CMakeLists.txt | 3 +--
+ 2 files changed, 2 insertions(+), 4 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 2b80d67..abb251b 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -20,8 +20,7 @@
+
+ # Target for the unit tests
+ add_custom_target(
+- check_unit_tests COMMAND ${CMAKE_CTEST_COMMAND} --timeout ${TEST_TIMEOUT}
+- ${CTEST_ARGS} --output-on-failure)
++ check_unit_tests )
+
+ if(WITH_TESTS)
+ # Run unit tests on check
+diff --git a/testsuite/python/CMakeLists.txt b/testsuite/python/CMakeLists.txt
+index bb057cd..e2107e0 100644
+--- a/testsuite/python/CMakeLists.txt
++++ b/testsuite/python/CMakeLists.txt
+@@ -340,7 +340,6 @@ add_custom_target(
+ add_dependencies(check_python_skip_long pypresso python_test_data)
+
+ add_custom_target(
+- check_python COMMAND ${CMAKE_CTEST_COMMAND} --timeout ${TEST_TIMEOUT}
+- ${CTEST_ARGS} --output-on-failure)
++ check_python )
+ add_dependencies(check_python pypresso python_test_data)
+ add_dependencies(check check_python)
+--
+2.49.1
+
diff --git a/sci-physics/espresso/files/espresso-4.2.0-test-deprecations.patch b/sci-physics/espresso/files/espresso-4.2.0-test-deprecations.patch
new file mode 100644
index 000000000000..e721fb199765
--- /dev/null
+++ b/sci-physics/espresso/files/espresso-4.2.0-test-deprecations.patch
@@ -0,0 +1,112 @@
+From 111283a0e0184e1674ef29ec0bd873a099574096 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
+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?= <jgrad@icp.uni-stuttgart.de>
+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]):
diff --git a/sci-physics/espresso/files/espresso-4.2.0-test-rounding.patch b/sci-physics/espresso/files/espresso-4.2.0-test-rounding.patch
new file mode 100644
index 000000000000..80be45f4647f
--- /dev/null
+++ b/sci-physics/espresso/files/espresso-4.2.0-test-rounding.patch
@@ -0,0 +1,201 @@
+Several files were removed from this patch due to not applying.
+
+Only Ellipsoid_test.cpp actually failed for me without it.
+
+From 18aeab318cbf2df7450d8c2e5e3634802345454c Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
+Date: Mon, 17 Apr 2023 11:58:09 +0200
+Subject: [PATCH] tests: Decrease sensitivity to rounding errors
+
+Expressions involving multiple multiplications can lead to rounding
+errors in the order of 1.5 machine precision, triggering assertions
+on architectures that don't support double extended precision, or
+when fast-math mode is enabled.
+---
+ .../tests/ReactionAlgorithm_test.cpp | 2 +-
+ .../tests/SingleReaction_test.cpp | 4 ++--
+ .../tests/reaction_methods_utils_test.cpp | 2 +-
+ .../unit_tests/EspressoSystemStandAlone_test.cpp | 2 +-
+ src/core/unit_tests/Verlet_list_test.cpp | 2 +-
+ src/core/unit_tests/p3m_test.cpp | 2 +-
+ src/core/unit_tests/periodic_fold_test.cpp | 4 ++--
+ src/core/unit_tests/specfunc_test.cpp | 2 +-
+ src/core/unit_tests/thermostats_test.cpp | 2 +-
+ src/particle_observables/tests/algorithms.cpp | 2 +-
+ src/shapes/unit_tests/Ellipsoid_test.cpp | 2 +-
+ src/shapes/unit_tests/Sphere_test.cpp | 2 +-
+ src/utils/tests/Vector_test.cpp | 5 +++--
+ src/utils/tests/interpolation_test.cpp | 3 ++-
+ src/utils/tests/matrix_vector_product.cpp | 5 +++--
+ src/utils/tests/vec_rotate_test.cpp | 2 +-
+ testsuite/python/analyze_chains.py | 15 ++++++++++-----
+ testsuite/python/integrator_npt_stats.py | 2 +-
+ 18 files changed, 34 insertions(+), 26 deletions(-)
+
+diff --git a/src/core/reaction_methods/tests/SingleReaction_test.cpp b/src/core/reaction_methods/tests/SingleReaction_test.cpp
+index aeae253cec1..41a27b03ae9 100644
+--- a/src/core/reaction_methods/tests/SingleReaction_test.cpp
++++ b/src/core/reaction_methods/tests/SingleReaction_test.cpp
+@@ -32,7 +32,7 @@
+ // and the configurational move probability for a given system state.
+ BOOST_AUTO_TEST_CASE(SingleReaction_test) {
+ using namespace ReactionMethods;
+- constexpr double tol = 100 * std::numeric_limits<double>::epsilon();
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+
+ // create a reaction A -> 3 B + 4 C
+ int const type_A = 0;
+@@ -64,7 +64,7 @@ BOOST_AUTO_TEST_CASE(SingleReaction_test) {
+ std::unordered_map<int, int>{{type_A, i}, {type_B, j}, {type_C, k}};
+ auto const val = calculate_factorial_expression(reaction, p_numbers);
+ auto const ref = g(i, -1) * g(j, 3) * g(k, 4);
+- BOOST_CHECK_CLOSE(val, ref, 5 * tol);
++ BOOST_CHECK_CLOSE(val, ref, 5. * tol);
+ }
+ }
+ }
+diff --git a/src/core/unit_tests/periodic_fold_test.cpp b/src/core/unit_tests/periodic_fold_test.cpp
+index 7346b472c0e..49d69777c94 100644
+--- a/src/core/unit_tests/periodic_fold_test.cpp
++++ b/src/core/unit_tests/periodic_fold_test.cpp
+@@ -106,7 +106,7 @@ BOOST_AUTO_TEST_CASE(with_image_count) {
+ BOOST_CHECK(res.first >= 0.);
+ BOOST_CHECK(res.first <= box);
+ BOOST_CHECK(std::abs(res.first - x + res.second * box) <=
+- std::numeric_limits<double>::epsilon());
++ 4. * std::numeric_limits<double>::epsilon());
+ }
+
+ /* Corner right */
+@@ -117,7 +117,7 @@ BOOST_AUTO_TEST_CASE(with_image_count) {
+ BOOST_CHECK(res.first >= 0.);
+ BOOST_CHECK(res.first < box);
+ BOOST_CHECK(std::abs(res.first - x + res.second * box) <=
+- std::numeric_limits<double>::epsilon());
++ 4. * std::numeric_limits<double>::epsilon());
+ }
+ }
+
+diff --git a/src/core/unit_tests/thermostats_test.cpp b/src/core/unit_tests/thermostats_test.cpp
+index 0edd7f47a44..16d5cbf992c 100644
+--- a/src/core/unit_tests/thermostats_test.cpp
++++ b/src/core/unit_tests/thermostats_test.cpp
+@@ -42,7 +42,7 @@
+
+ // multiply by 100 because BOOST_CHECK_CLOSE takes a percentage tolerance,
+ // and by 6 to account for error accumulation in thermostat functions
+-constexpr auto tol = 6 * 100 * std::numeric_limits<double>::epsilon();
++auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+
+ Particle particle_factory() {
+ Particle p{};
+diff --git a/src/particle_observables/tests/algorithms.cpp b/src/particle_observables/tests/algorithms.cpp
+index 4a1cef824cf..7fabb7c3ef4 100644
+--- a/src/particle_observables/tests/algorithms.cpp
++++ b/src/particle_observables/tests/algorithms.cpp
+@@ -79,7 +79,7 @@ BOOST_AUTO_TEST_CASE(algorithms_integer) {
+ }
+
+ BOOST_AUTO_TEST_CASE(algorithms_double) {
+- auto constexpr tol = 100 * std::numeric_limits<double>::epsilon();
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+ std::vector<double> const values{1., 2., 3., 4.};
+ {
+ auto const res = WeightedAverage<Testing::Identity, Testing::One>()(values);
+diff --git a/src/shapes/unit_tests/Ellipsoid_test.cpp b/src/shapes/unit_tests/Ellipsoid_test.cpp
+index 2f4331a6147..d9d41874bf7 100644
+--- a/src/shapes/unit_tests/Ellipsoid_test.cpp
++++ b/src/shapes/unit_tests/Ellipsoid_test.cpp
+@@ -34,7 +34,7 @@
+
+ BOOST_AUTO_TEST_CASE(dist_function) {
+ // multiply by 100 because BOOST_REQUIRE_CLOSE takes a percentage tolerance
+- auto constexpr tol = std::numeric_limits<double>::epsilon() * 100;
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+ double const semiaxes[3] = {3.1, 2.2, 1.3};
+
+ Shapes::Ellipsoid e;
+diff --git a/src/shapes/unit_tests/Sphere_test.cpp b/src/shapes/unit_tests/Sphere_test.cpp
+index e6eb19aa2f7..61fb916ce7f 100644
+--- a/src/shapes/unit_tests/Sphere_test.cpp
++++ b/src/shapes/unit_tests/Sphere_test.cpp
+@@ -34,7 +34,7 @@ void check_distance_function(Shapes::Sphere &s) {
+ Utils::Vector3d vec;
+ double dist;
+ // multiply by 100 because BOOST_REQUIRE_CLOSE takes a percentage tolerance
+- auto const tol = std::numeric_limits<double>::epsilon() * 100;
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+
+ s.rad() = 1.0;
+ pos = {0., 0., 0.};
+diff --git a/src/utils/tests/Vector_test.cpp b/src/utils/tests/Vector_test.cpp
+index 88bb0ad0ceb..a29709ecfc6 100644
+--- a/src/utils/tests/Vector_test.cpp
++++ b/src/utils/tests/Vector_test.cpp
+@@ -119,10 +119,11 @@ BOOST_AUTO_TEST_CASE(test_norm2) {
+ }
+
+ BOOST_AUTO_TEST_CASE(normalize) {
+- Utils::Vector3d v{1, 2, 3};
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
++ Utils::Vector3d v{1., 2., 3.};
+ v.normalize();
+
+- BOOST_CHECK((v.norm2() - 1.0) <= std::numeric_limits<double>::epsilon());
++ BOOST_CHECK_CLOSE(v.norm2(), 1.0, tol);
+ }
+
+ BOOST_AUTO_TEST_CASE(comparison_operators) {
+diff --git a/src/utils/tests/interpolation_test.cpp b/src/utils/tests/interpolation_test.cpp
+index 701a7456c89..b452ab32e9d 100644
+--- a/src/utils/tests/interpolation_test.cpp
++++ b/src/utils/tests/interpolation_test.cpp
+@@ -135,6 +135,7 @@ BOOST_AUTO_TEST_CASE(sum_of_weights_odd) {
+ }
+
+ BOOST_AUTO_TEST_CASE(nearest_point) {
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+ std::array<int, 3> nmp;
+ double weight;
+ auto save_ind = [&nmp, &weight](const std::array<int, 3> &ind, double w) {
+@@ -145,7 +146,7 @@ BOOST_AUTO_TEST_CASE(nearest_point) {
+ bspline_3d<1>({.1, .2, .3}, save_ind, {0.5, 0.5, 0.5}, {});
+
+ BOOST_CHECK((std::array<int, 3>{{0, 0, 1}} == nmp));
+- BOOST_CHECK_CLOSE(weight, 1., 100. * std::numeric_limits<double>::epsilon());
++ BOOST_CHECK_CLOSE(weight, 1., tol);
+ }
+
+ BOOST_AUTO_TEST_CASE(interpolation_points_3) {
+diff --git a/src/utils/tests/matrix_vector_product.cpp b/src/utils/tests/matrix_vector_product.cpp
+index 8f7d8f1fdec..f98d0f5bd4f 100644
+--- a/src/utils/tests/matrix_vector_product.cpp
++++ b/src/utils/tests/matrix_vector_product.cpp
+@@ -32,10 +32,11 @@ static constexpr std::array<std::array<int, 3>, 3> matrix{
+ {{{1, 2, 9}}, {{8, 41, 6}}, {{31, 15, 99}}}};
+
+ BOOST_AUTO_TEST_CASE(inner_product) {
++ auto constexpr tol = 8. * 100. * std::numeric_limits<double>::epsilon();
+ const std::array<double, 3> vector{{0.5, 1.25, 3.1}};
+ auto const result = Utils::matrix_vector_product<double, 3, matrix>(vector);
+ for (int i = 0; i < 3; ++i) {
+- BOOST_CHECK_CLOSE(result[i], boost::inner_product(matrix[i], vector, 0.0),
+- 100. * std::numeric_limits<double>::epsilon());
++ auto const ref = boost::inner_product(matrix[i], vector, 0.0);
++ BOOST_CHECK_CLOSE(result[i], ref, tol);
+ }
+ }
+diff --git a/src/utils/tests/vec_rotate_test.cpp b/src/utils/tests/vec_rotate_test.cpp
+index c1ad10eabb7..88b2af17983 100644
+--- a/src/utils/tests/vec_rotate_test.cpp
++++ b/src/utils/tests/vec_rotate_test.cpp
+@@ -44,7 +44,7 @@ BOOST_AUTO_TEST_CASE(rotation) {
+ auto const is = Utils::vec_rotate(k, t, v);
+ auto const rel_diff = (expected - is).norm() / expected.norm();
+
+- BOOST_CHECK(rel_diff < std::numeric_limits<double>::epsilon());
++ BOOST_CHECK(rel_diff < 8. * std::numeric_limits<double>::epsilon());
+ }
+
+ BOOST_AUTO_TEST_CASE(angle_between) {
+
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