Bump version requirements (#4312)

Description of changes:
- require Python 3.7+, scipy 1.4.0+, numpy 1.17.4+ (as per #3421, fixes #4258)
- require Boost 1.69+ (enables #3638)
- remove OpenSUSE job from CI (Leap 15.3 doesn't package Python3 and Boost, Leap 15.2 is outdated)

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:063f945eb434f6900402fd412f28a4486288c82b
+image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:08d67d67a4d3c3279cacee975b68c02ec89b2a21
 
 stages:
   - prepare
@@ -127,7 +127,7 @@ no_rotation:
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:e583d4b2eb8eedd10068957f952bd67008475ee5
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:08d67d67a4d3c3279cacee975b68c02ec89b2a21
   variables:
      myconfig: 'maxset'
      with_cuda: 'false'
@@ -145,22 +145,7 @@ ubuntu:wo-dependencies:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/debian:d372d95f6906c16abd9b47b994034a22981a9ff2
-  variables:
-     with_cuda: 'false'
-     myconfig: 'maxset'
-     make_check_python: 'false'
-     with_stokesian_dynamics: 'true'
-  script:
-    - bash maintainer/CI/build_cmake.sh
-  tags:
-    - docker
-    - linux
-
-opensuse:15.2:
-  <<: *global_job_definition
-  stage: build
-  image: docker.pkg.github.com/espressomd/docker/opensuse:d496478230db4e5c286680e3bdc1621af1fccffc
+  image: docker.pkg.github.com/espressomd/docker/debian:08d67d67a4d3c3279cacee975b68c02ec89b2a21
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -175,7 +160,7 @@ opensuse:15.2:
 fedora:32:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/fedora:4f126520866e84a4883355ffe8710040bf20051c
+  image: docker.pkg.github.com/espressomd/docker/fedora:08d67d67a4d3c3279cacee975b68c02ec89b2a21
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -231,7 +216,7 @@ clang-sanitizer:
 cuda11-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/cuda:d372d95f6906c16abd9b47b994034a22981a9ff2
+  image: docker.pkg.github.com/espressomd/docker/cuda:08d67d67a4d3c3279cacee975b68c02ec89b2a21
   variables:
      CC: 'gcc-9'
      CXX: 'g++-9'

CMakeLists.txt

@@ -164,10 +164,10 @@ if(WITH_CUDA)
   endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.6 REQUIRED)
+find_package(PythonInterp 3.7 REQUIRED)
 
 if(WITH_PYTHON)
-  find_package(Cython 0.29 REQUIRED)
+  find_package(Cython 0.29.14 REQUIRED)
   find_package(PythonHeaders REQUIRED)
   find_package(NumPy REQUIRED)
   find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
@@ -281,15 +281,7 @@ if(WITH_TESTS)
   list(APPEND BOOST_COMPONENTS unit_test_framework)
 endif()
 
-set(BOOST_MINIMUM_VERSION "1.66.0")
-
-# old Boost.MPI versions contain a use-after-free bug that seems to only cause
-# crashes on 32-bit architectures
-if(CMAKE_SIZEOF_VOID_P EQUAL 4)
-  set(BOOST_MINIMUM_VERSION "1.67.0")
-endif()
-
-find_package(Boost ${BOOST_MINIMUM_VERSION} REQUIRED ${BOOST_COMPONENTS})
+find_package(Boost 1.69.0 REQUIRED ${BOOST_COMPONENTS})
 
 #
 # Paths

doc/sphinx/installation.rst

@@ -44,7 +44,7 @@ C++ Compiler
 
 Boost
     A number of advanced C++ features used by |es| are provided by Boost.
-    We strongly recommend to use at least Boost 1.67.
+    We strongly recommend to use at least Boost 1.71.
 
 FFTW
     For some algorithms (P\ :math:`^3`\ M), |es| needs the FFTW library
@@ -86,8 +86,8 @@ are required:
 
 .. code-block:: bash
 
-    sudo apt install python3-matplotlib python3-scipy python3-pint ipython3 jupyter-notebook
-    pip3 install --user 'jupyter_contrib_nbextensions==0.5.1' \
+    sudo apt install python3-matplotlib python3-pint ipython3 jupyter-notebook
+    pip3 install --user 'jupyter_contrib_nbextensions==0.5.1' 'python3-scipy>=1.4.0' \
                         'sphinx>=1.6.7,!=2.1.0,!=3.0.0' 'sphinxcontrib-bibtex>=0.3.5' \
                         'MDAnalysis>=1.0.0'
     jupyter contrib nbextension install --user
@@ -182,7 +182,7 @@ Run the following commands:
 .. code-block:: bash
 
     sudo port selfupdate
-    sudo port install cmake python37 py37-cython py37-numpy \
+    sudo port install cmake python37 py37-cython py37-numpy py37-scipy \
       openmpi-default fftw-3 +openmpi boost +openmpi +python37 \
       doxygen py37-opengl py37-sphinx gsl hdf5 +openmpi \
       py37-matplotlib py37-ipython py37-jupyter
@@ -199,7 +199,7 @@ Run the following commands:
 .. code-block:: bash
 
     brew install cmake python cython boost boost-mpi fftw \
-      doxygen gsl numpy ipython jupyter
+      doxygen gsl numpy scipy ipython jupyter
     brew install hdf5-mpi
     brew link --force cython
     pip install PyOpenGL matplotlib

requirements.txt

@@ -1,8 +1,8 @@
 # required scientific packages
-numpy>=1.16.2
+numpy>=1.17.4
 h5py>=2.7.1
 # optional scientific packages
-scipy>=1.1.0
+scipy>=1.4.0
 MDAnalysis>=1.0.0
 pint>=0.10.1
 # optional packages for graphics and external devices

src/core/unit_tests/EspressoSystemStandAlone_test.cpp

@@ -56,16 +56,6 @@ namespace utf = boost::unit_test;
 #include <unordered_map>
 #include <vector>
 
-/* Guard against a bug in Boost versions < 1.68 where fixtures used to skip
- * test are not propagated correctly to the testsuite, causing skipped tests
- * to trigger a failure of the complete testsuite without any error message.
- * More details in ticket https://svn.boost.org/trac10/ticket/12095
- */
-#include <boost/serialization/version.hpp>
-#if BOOST_VERSION / 100000 == 1 && BOOST_VERSION / 100 % 1000 < 68
-int main(int argc, char **argv) {}
-#else
-
 namespace espresso {
 // ESPResSo system instance
 std::unique_ptr<EspressoSystemStandAlone> system;
@@ -329,4 +319,3 @@ int main(int argc, char **argv) {
 
   return boost::unit_test::unit_test_main(init_unit_test, argc, argv);
 }
-#endif // Boost version >= 1.68

src/python/espressomd/__init__.py

@@ -55,9 +55,9 @@ def missing_features(*args):
 
     if len(args) == 1 and not isinstance(
             args[0], str) and hasattr(args[0], "__iter__"):
-        return set(args[0]) - set(features())
+        return sorted(set(args[0]) - set(features()))
 
-    return set(args) - set(features())
+    return sorted(set(args) - set(features()))
 
 
 def assert_features(*args):

testsuite/python/CMakeLists.txt

@@ -218,6 +218,7 @@ python_test(FILE observable_chain.py MAX_NUM_PROC 4)
 python_test(FILE mpiio.py MAX_NUM_PROC 4)
 python_test(FILE gpu_availability.py MAX_NUM_PROC 2 LABELS gpu)
 python_test(FILE features.py MAX_NUM_PROC 1)
+python_test(FILE decorators.py MAX_NUM_PROC 1)
 python_test(FILE galilei.py MAX_NUM_PROC 32)
 python_test(FILE linear_momentum.py MAX_NUM_PROC 4)
 python_test(FILE linear_momentum_lb.py MAX_NUM_PROC 2 LABELS gpu)

testsuite/python/decorators.py

@@ -0,0 +1,84 @@
+# Copyright (C) 2021 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import espressomd
+import unittest as ut
+import unittest_decorators as utx
+import numpy as np
+
+
+class Tests(ut.TestCase):
+
+    def get_skip_reason(self, decorator):
+        try:
+            decorator(lambda: None)()
+        except ut.case.SkipTest as err:
+            return err.args
+
+    def test_version_requirements(self):
+        fun = utx.skipIfUnmetModuleVersionRequirement
+        decorator = fun('numpy___', '>' + np.__version__)
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(
+            args, ('Skipping test: missing python module numpy___',))
+        decorator = fun('numpy', '>1' + np.__version__)
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(
+            args, ('Skipping test: version requirement not met for module numpy',))
+        decorator = fun('numpy', '==' + np.__version__)
+        args = self.get_skip_reason(decorator)
+        self.assertIsNone(args)
+
+    def test_missing_modules(self):
+        err_msg = 'Skipping test: missing python '
+        decorator = utx.skipIfMissingModules('numpy___')
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, (err_msg + 'module numpy___',))
+        decorator = utx.skipIfMissingModules('numpy___', 'scipy___')
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, (err_msg + 'modules numpy___, scipy___',))
+        decorator = utx.skipIfMissingModules(['numpy___', 'scipy___'])
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, (err_msg + 'modules numpy___, scipy___',))
+
+    def test_missing_gpu(self):
+        espressomd.gpu_available = lambda: False
+        decorator = utx.skipIfMissingGPU()
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, ('Skipping test: no GPU available',))
+        espressomd.gpu_available = lambda: True
+        decorator = utx.skipIfMissingGPU()
+        args = self.get_skip_reason(decorator)
+        self.assertIsNone(args)
+
+    def test_missing_features(self):
+        err_msg = 'Skipping test: missing features '
+        espressomd.has_features = lambda x: False
+        decorator = utx.skipIfMissingFeatures('UNKNOWN')
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, (err_msg + 'UNKNOWN',))
+        decorator = utx.skipIfMissingFeatures(['UNKNOWN1', 'UNKNOWN2'])
+        args = self.get_skip_reason(decorator)
+        self.assertEqual(args, (err_msg + 'UNKNOWN1, UNKNOWN2',))
+        espressomd.has_features = lambda x: True
+        decorator = utx.skipIfMissingFeatures('KNOWN')
+        args = self.get_skip_reason(decorator)
+        self.assertIsNone(args)
+
+
+if __name__ == '__main__':
+    ut.main()

testsuite/python/rotation.py

@@ -17,18 +17,12 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 import numpy as np
+import scipy.spatial.transform
 import unittest as ut
 
-try:
-    import scipy.spatial.transform as sst
-except ImportError:
-    pass
-
 import espressomd.rotation
-import unittest_decorators as utx
 
 
-@utx.skipIfUnmetModuleVersionRequirement('scipy', '>=1.4.0')
 class TestRotation(ut.TestCase):
     """
     Tests for the rotation utility functions.
@@ -39,7 +33,7 @@ def setUp(self):
         angle = 2.0 * np.pi * np.random.random()
         quat = [np.sin(angle / 2.0), np.sin(angle / 2.0),
                 np.sin(angle / 2.0), np.cos(angle / 2.0)]
-        self.rotation = sst.Rotation.from_quat(quat)
+        self.rotation = scipy.spatial.transform.Rotation.from_quat(quat)
 
     def test_quat_from_matrix(self):
         """
@@ -50,7 +44,7 @@ def test_quat_from_matrix(self):
         rotated_vector_ref = self.rotation.apply(v_x)
         quat_from_matrix = espressomd.rotation.matrix_to_quat(
             self.rotation.as_matrix())
-        rotated_vector_matrix = sst.Rotation.from_quat(
+        rotated_vector_matrix = scipy.spatial.transform.Rotation.from_quat(
             np.roll(quat_from_matrix, shift=-1)).apply(v_x)
         self.assertAlmostEqual(
             np.dot(rotated_vector_ref, rotated_vector_matrix), 1.0)
@@ -162,7 +156,6 @@ def test_right_handedness_eigenvectormatrix(self):
             np.testing.assert_allclose(
                 np.cross(ev[0], ev[1]), ev[2], atol=1e-7)
 
-    @utx.skipIfUnmetModuleVersionRequirement('scipy', '>1.2.0')
     def test_inertia_tensor_rotated_cuboid(self):
         """
         Rotate the samples and check that the principal axes return by the
@@ -172,7 +165,7 @@ def test_inertia_tensor_rotated_cuboid(self):
         angle = 2.0 * np.pi * np.random.random()
         quat = [np.sin(angle / 2.0), np.sin(angle / 2.0),
                 np.sin(angle / 2.0), np.cos(angle / 2.0)]
-        rotation = sst.Rotation.from_quat(quat)
+        rotation = scipy.spatial.transform.Rotation.from_quat(quat)
         rotated_samples = rotation.apply(self.samples)
         _, eigenvectors = espressomd.rotation.diagonalized_inertia_tensor(
             rotated_samples, self.masses)

testsuite/python/unittest_decorators.py

@@ -42,10 +42,10 @@ def skipIfMissingModules(*args):
         args = set(args[0])
     else:
         args = set(args)
-    missing_modules = set(args) - set(sys.modules.keys())
+    missing_modules = sorted(set(args) - set(sys.modules.keys()))
     if missing_modules:
         return unittest.skip("Skipping test: missing python module{} {}".format(
-            's' if missing_modules else '', ', '.join(missing_modules)))
+            's' if len(missing_modules) > 1 else '', ', '.join(missing_modules)))
     return no_skip
 
 

testsuite/scripts/tutorials/test_active_matter.py

@@ -18,8 +18,6 @@
 import unittest as ut
 import importlib_wrapper
 import numpy as np
-import scipy
-import setuptools
 
 tutorial, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
     "@TUTORIALS_DIR@/active_matter/active_matter.py", 
@@ -55,8 +53,6 @@ def test_hydrodynamics(self):
             tutorial.system.analysis.linear_momentum(
                 include_particles=False)[2], 0)
 
-    @ut.skipIf(not setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet('>=1.4.0').contains(
-        scipy.__version__), "Skipping test: scipy version requirement (>=1.4.0) not met")
     def test_quaternion(self):
         """ Check the quaternion function is correctly implemented
         """