Bump Python and CMake versions (#3878)

Description of changes:
- bump CMake version requirement from 3.10 to 3.11 to get full support for imported targets
    * fixes a cryptic error message when compiling ESPResSo with FFTW3 using CMake 3.10
- bump Python version requirement from 3.5 to 3.6 (NEP 29, see drop table in #3421)
    * enables f-strings
- fix flaw in `espressomd.utils.check_type_or_throw_except()` that lead to subtle errors when arrays had the wrong size
- add tests for functions in `espressomd.utils`

CMakeLists.txt

@@ -18,7 +18,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.11)
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 if(POLICY CMP0076)
   # make target_sources() convert relative paths to absolute
@@ -166,7 +166,7 @@ if(WITH_CUDA)
   endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.5 REQUIRED)
+find_package(PythonInterp 3.6 REQUIRED)
 
 if(WITH_PYTHON)
   find_package(Cython 0.26 REQUIRED)
@@ -278,7 +278,6 @@ endif(WITH_STOKESIAN_DYNAMICS)
 if(WITH_STOKESIAN_DYNAMICS)
   set(CMAKE_INSTALL_LIBDIR
       "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
-  cmake_minimum_required(VERSION 3.11)
   include(FetchContent)
   FetchContent_Declare(
     stokesian_dynamics

src/python/espressomd/actors.pyx

@@ -57,7 +57,7 @@ cdef class Actor:
             if k in self.valid_keys():
                 self._params[k] = kwargs[k]
             else:
-                raise KeyError("%s is not a valid key" % k)
+                raise KeyError(f"{k} is not a valid key")
 
     def _activate(self):
         inter = self._get_interaction_type()

src/python/espressomd/analyze.pyx

@@ -186,12 +186,12 @@ class Analysis:
             for i in range(len(p1)):
                 if not is_valid_type(p1[i], int):
                     raise TypeError(
-                        "Particle types in p1 have to be of type int, got: " + repr(p1[i]))
+                        f"Particle types in p1 have to be of type int, got: {repr(p1[i])}")
 
             for i in range(len(p2)):
                 if not is_valid_type(p2[i], int):
                     raise TypeError(
-                        "Particle types in p2 have to be of type int, got: " + repr(p2[i]))
+                        f"Particle types in p2 have to be of type int, got: {repr(p2[i])}")
 
             return analyze.mindist(analyze.partCfg(), p1, p2)
 
@@ -249,7 +249,7 @@ class Analysis:
                 "The p_type keyword argument must be provided (particle type)")
         check_type_or_throw_except(p_type, 1, int, "p_type has to be an int")
         if p_type < 0 or p_type >= analyze.max_seen_particle_type:
-            raise ValueError("Particle type {} does not exist!".format(p_type))
+            raise ValueError(f"Particle type {p_type} does not exist!")
 
         return analyze.centerofmass(analyze.partCfg(), p_type)
 
@@ -736,8 +736,7 @@ class Analysis:
             check_type_or_throw_except(
                 ptype, 1, int, "particle type has to be an int")
             if ptype < 0 or ptype >= analyze.max_seen_particle_type:
-                raise ValueError(
-                    "Particle type {} does not exist!".format(ptype))
+                raise ValueError(f"Particle type {ptype} does not exist!")
         selection = self._system.part.select(lambda p: (p.type in p_type))
         cm = np.mean(selection.pos, axis=0)
         mat = np.zeros(shape=(3, 3))
@@ -787,7 +786,7 @@ class Analysis:
                 "The p_type keyword argument must be provided (particle type)")
         check_type_or_throw_except(p_type, 1, int, "p_type has to be an int")
         if p_type < 0 or p_type >= analyze.max_seen_particle_type:
-            raise ValueError("Particle type {} does not exist!".format(p_type))
+            raise ValueError(f"Particle type {p_type} does not exist!")
 
         analyze.momentofinertiamatrix(
             analyze.partCfg(), p_type, MofImatrix)

src/python/espressomd/cellsystem.pyx

@@ -137,8 +137,8 @@ cdef class CellSystem:
 
         def __set__(self, _node_grid):
             if not np.prod(_node_grid) == n_nodes:
-                raise ValueError("Number of available nodes " + str(
-                    n_nodes) + " and imposed node grid " + str(_node_grid) + " do not agree.")
+                raise ValueError(
+                    f"Number of available nodes {n_nodes} and imposed node grid {_node_grid} do not agree.")
             else:
                 node_grid[0] = _node_grid[0]
                 node_grid[1] = _node_grid[1]

src/python/espressomd/checkpointing.py

@@ -67,7 +67,7 @@ def __init__(self, checkpoint_id=None, checkpoint_path="."):
         # update checkpoint counter
         self.counter = 0
         while os.path.isfile(os.path.join(
-                self.checkpoint_dir, "{}.checkpoint".format(self.counter))):
+                self.checkpoint_dir, f"{self.counter}.checkpoint")):
             self.counter += 1
 
         # init signals
@@ -134,11 +134,11 @@ def register(self, *args):
             # if not a in dir(self.calling_module):
             if not self.__hasattr_submodule(self.calling_module, a):
                 raise KeyError(
-                    "The given object '{}' was not found in the current scope.".format(a))
+                    f"The given object '{a}' was not found in the current scope.")
 
             if a in self.checkpoint_objects:
                 raise KeyError(
-                    "The given object '{}' is already registered for checkpointing.".format(a))
+                    f"The given object '{a}' is already registered for checkpointing.")
 
             self.checkpoint_objects.append(a)
 
@@ -154,7 +154,7 @@ def unregister(self, *args):
         for a in args:
             if not isinstance(a, str) or a not in self.checkpoint_objects:
                 raise KeyError(
-                    "The given object '{}' was not registered for checkpointing yet.".format(a))
+                    f"The given object '{a}' was not registered for checkpointing yet.")
 
             self.checkpoint_objects.remove(a)
 
@@ -204,7 +204,7 @@ def save(self, checkpoint_index=None):
         if checkpoint_index is None:
             checkpoint_index = self.counter
         filename = os.path.join(
-            self.checkpoint_dir, "{}.checkpoint".format(checkpoint_index))
+            self.checkpoint_dir, f"{checkpoint_index}.checkpoint")
 
         tmpname = filename + ".__tmp__"
         with open(tmpname, "wb") as checkpoint_file:
@@ -226,7 +226,7 @@ def load(self, checkpoint_index=None):
             checkpoint_index = self.get_last_checkpoint_index()
 
         filename = os.path.join(
-            self.checkpoint_dir, "{}.checkpoint".format(checkpoint_index))
+            self.checkpoint_dir, f"{checkpoint_index}.checkpoint")
         with open(filename, "rb") as f:
             checkpoint_data = pickle.load(f)
 
@@ -288,7 +288,7 @@ def register_signal(self, signum=None):
 
         if signum in self.checkpoint_signals:
             raise KeyError(
-                "The signal {} is already registered for checkpointing.".format(signum))
+                f"The signal {signum} is already registered for checkpointing.")
 
         signal.signal(signum, self.__signal_handler)
         self.checkpoint_signals.append(signum)

src/python/espressomd/collision_detection.pyx

@@ -216,7 +216,7 @@ class CollisionDetection(ScriptInterfaceHelper):
         for key in self._int_mode:
             if self._int_mode[key] == int_mode:
                 return key
-        raise Exception("Unknown integer collision mode %d" % int_mode)
+        raise Exception(f"Unknown integer collision mode {int_mode}")
 
     # Pickle support
     def __reduce__(self):

src/python/espressomd/electrokinetics.pyx

@@ -43,7 +43,7 @@ IF ELECTROKINETICS:
                     return ElectrokineticsRoutines(np.array(key))
             else:
                 raise Exception(
-                    "%s is not a valid key. Should be a point on the nodegrid e.g. ek[0,0,0]," % key)
+                    f"{key} is not a valid key. Should be a point on the nodegrid e.g. ek[0,0,0].")
 
         def validate_params(self):
             """
@@ -431,7 +431,7 @@ IF ELECTROKINETICS:
                     return SpecieRoutines(np.array(key), self.id)
             else:
                 raise Exception(
-                    "%s is not a valid key. Should be a point on the nodegrid e.g. species[0,0,0]," % key)
+                    f"{key} is not a valid key. Should be a point on the nodegrid e.g. species[0,0,0].")
 
         def __init__(self, **kwargs):
             Species.py_number_of_species += 1
@@ -449,7 +449,7 @@ IF ELECTROKINETICS:
                 if k in self.valid_keys():
                     self._params[k] = kwargs[k]
                 else:
-                    raise KeyError("%s is not a valid key" % k)
+                    raise KeyError(f"{k} is not a valid key")
 
         def valid_keys(self):
             """

src/python/espressomd/highlander.py

@@ -25,8 +25,7 @@ def __init__(self, cls):
         self._cls = cls
 
     def __str__(self):
-        return "There can only be one instance of '{}' at any time.".format(
-            self._cls)
+        return f"There can only be one instance of '{self._cls}' at any time."
 
 
 def highlander(klass):

src/python/espressomd/interactions.pyx

@@ -1825,37 +1825,37 @@ class BondedInteractionNotDefined:
             self.__class__.__name__ + " not compiled into ESPResSo core")
 
     def type_number(self):
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def type_name(self):
         """Name of interaction type.
 
         """
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def valid_keys(self):
         """All parameters that can be set.
 
         """
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def required_keys(self):
         """Parameters that have to be set.
 
         """
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def set_default_params(self):
         """Sets parameters that are not required to their default value.
 
         """
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def _get_params_from_es_core(self):
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
     def _set_params_in_es_core(self):
-        raise Exception(("%s has to be defined in myconfig.hpp.") % self.name)
+        raise Exception(f"{self.name} has to be defined in myconfig.hpp.")
 
 
 class FeneBond(BondedInteraction):
@@ -2591,8 +2591,8 @@ class TabulatedAngle(_TabulatedBase):
         """
         phi = [self._params["min"], self._params["max"]]
         if abs(phi[0] - 0.) > 1e-5 or abs(phi[1] - self.pi) > 1e-5:
-            raise ValueError("Tabulated angle expects forces/energies "
-                             "within the range [0, pi], got " + str(phi))
+            raise ValueError(f"Tabulated angle expects forces/energies "
+                             f"within the range [0, pi], got {phi}")
 
 
 class TabulatedDihedral(_TabulatedBase):
@@ -2631,8 +2631,8 @@ class TabulatedDihedral(_TabulatedBase):
         """
         phi = [self._params["min"], self._params["max"]]
         if abs(phi[0] - 0.) > 1e-5 or abs(phi[1] - 2 * self.pi) > 1e-5:
-            raise ValueError("Tabulated dihedral expects forces/energies "
-                             "within the range [0, 2*pi], got " + str(phi))
+            raise ValueError(f"Tabulated dihedral expects forces/energies "
+                             f"within the range [0, 2*pi], got {phi}")
 
 
 IF TABULATED == 1:
@@ -3313,7 +3313,7 @@ class BondedInteractions:
         # Check if the bonded interaction exists in ESPResSo core
         if bond_type == -1:
             raise ValueError(
-                "The bonded interaction with the id " + str(key) + " is not yet defined.")
+                f"The bonded interaction with the id {key} is not yet defined.")
 
         # Find the appropriate class representing such a bond
         bond_class = bonded_interaction_classes[bond_type]

src/python/espressomd/lb.pyx

@@ -57,7 +57,7 @@ cdef class HydrodynamicInteraction(Actor):
                 return LBFluidRoutines(np.array(key))
         else:
             raise Exception(
-                "%s is not a valid key. Should be a point on the nodegrid e.g. lbf[0,0,0]," % key)
+                f"{key} is not a valid key. Should be a point on the nodegrid e.g. lbf[0,0,0].")
 
     # validate the given parameters on actor initialization
     ####################################################