Bump formatters and linters requirements

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
         always_run: false
         files: '.*\.(py|pyx|pxd)'
         exclude: '\.pylintrc|.*.\.py\.in|^libs/'
-        args: ["--ignore=E266,E402,E701,W291,W293", "--in-place", "--aggressive"]
+        args: ["--ignore=E266,E402,E701,W291,W293", "--in-place"]
 
     -   id: cmake-format
         name: cmake-format

maintainer/benchmarks/benchmarks.py

@@ -84,7 +84,7 @@ def get_timings(system, n_steps, n_iterations, verbose=True):
             energy = system.analysis.energy()["total"]
             verlet = system.cell_system.get_state()["verlet_reuse"]
             print(
-                f"step {i}, time: {1000*t:.1f} ms, verlet: {verlet:.2f}, energy: {energy:.2e}")
+                f"step {i}, time: {1000 * t:.1f} ms, verlet: {verlet:.2f}, energy: {energy:.2e}")
     return np.array(timings)
 
 
@@ -131,7 +131,7 @@ def write_report(filepath, n_proc, timings, n_steps, label=''):
     cmd = " ".join(x for x in sys.argv[1:] if not x.startswith("--output"))
     avg, ci = get_average_time(timings)
     header = '"script","arguments","cores","mean","ci","nsteps","duration","label"\n'
-    report = f'"{script}","{cmd}",{n_proc},{avg:.3e},{ci:.3e},{n_steps},{np.sum(timings):.1f},"{label}"\n'
+    report = f'"{script}","{cmd}",{n_proc},{avg:.3e},{ci:.3e},{n_steps},{np.sum(timings):.1f},"{label}"\n'  # nopep8
     if pathlib.Path(filepath).is_file():
         header = ''
     with open(filepath, "a") as f:

maintainer/benchmarks/mc_acid_base_reservoir.py

@@ -93,7 +93,7 @@ def calc_donnan_coefficient(c_acid, I_res, charge=-1):
 NUM_SAMPLES = 100
 INTEGRATION_STEPS_PER_SAMPLE = 100
 assert TOTAL_NUM_MC_STEPS % NUM_SAMPLES == 0, \
-    f"Total number of MC steps must be divisible by total number of samples, got {TOTAL_NUM_MC_STEPS} and {NUM_SAMPLES}"
+    f"Total number of MC steps must be divisible by total number of samples, got {TOTAL_NUM_MC_STEPS} and {NUM_SAMPLES}"  # nopep8
 MC_STEPS_PER_SAMPLE = TOTAL_NUM_MC_STEPS // NUM_SAMPLES
 
 # definitions of reduced units
@@ -266,7 +266,8 @@ def report_progress(system, i, next_i):
     n_All = len(system.part)
     if i == next_i:
         print(
-            f"run {i:d} time {system.time:.3g} completed {i / NUM_SAMPLES * 100:.0f}%",
+            f"run {i:d} time {system.time:.3g} completed "
+            f"{i / NUM_SAMPLES * 100:.0f}%",
             f"instantaneous values: All {n_All:d}  Na {n_Na:d}  Cl {n_Cl:d}",
             f"A {n_A:d}  alpha {n_A / N_ACID:.3f}")
         if i == 0:
@@ -308,7 +309,8 @@ def report_progress(system, i, next_i):
         energy = system.analysis.energy()["total"]
         verlet = system.cell_system.get_state()["verlet_reuse"]
         print(
-            f"step {i}, time MD: {t_MD:.2e}, time MC: {t_MC:.2e}, verlet: {verlet:.2f}, energy: {energy:.2e}")
+            f"step {i}, time MD: {t_MD:.2e}, time MC: {t_MC:.2e}, "
+            f"verlet: {verlet:.2f}, energy: {energy:.2e}")
 
     # average time
     avg_MC, ci_MC = benchmarks.get_average_time(timings_MC)

maintainer/format/autopep8.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
+#
 # Copyright (C) 2018-2022 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -15,10 +16,11 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 
 
-AUTOPEP8_VER=1.6.0
-PYCODESTYLE_VER=2.8.0
+AUTOPEP8_VER=2.1.0
+PYCODESTYLE_VER=2.11.1
 
 python3 -m autopep8 --help 2>&1 > /dev/null
 if [ "$?" = "0" ]; then

maintainer/format/clang-format.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
+#
 # Copyright (C) 2018-2022 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -15,8 +16,9 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 
-CLANG_FORMAT_VER=14.0
+CLANG_FORMAT_VER=18.1
 if hash clang-format-${CLANG_FORMAT_VER} 2>/dev/null; then
     CLANGFORMAT="$(which clang-format-${CLANG_FORMAT_VER})"
 elif hash clang-format-${CLANG_FORMAT_VER%.*} 2>/dev/null; then

maintainer/format/cmake-format.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
+#
 # Copyright (C) 2018-2022 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -15,6 +16,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 
 CMAKE_FORMAT_VER=0.6.13
 python3 -m cmakelang.format 2>&1 > /dev/null

maintainer/format/ex_flag.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
+#
 # Copyright (C) 2018-2022 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -15,6 +16,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
+#
 
 chmod -x "$@"

maintainer/lint/pre_commit.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
+#
 # Copyright (C) 2018-2022 The ESPResSo project
 #
 # This file is part of ESPResSo.
@@ -15,9 +16,9 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 
-
-python3 -m pre_commit 2>&1 >/dev/null
+pre-commit 2>&1 >/dev/null
 if [ "$?" = "0" ]; then
     precommit="python3 -m pre_commit"
 else

maintainer/lint/pylint.sh

@@ -1,5 +1,6 @@
 #!/bin/sh
-# Copyright (C) 2018-2022 The ESPResSo project
+#
+# Copyright (C) 2018-2024 The ESPResSo project
 #
 # This file is part of ESPResSo.
 #
@@ -15,6 +16,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 
 
 python3 -m pylint --help 2>&1 > /dev/null

maintainer/walberla_kernels/code_generation_context.py

@@ -48,7 +48,7 @@ def new_generate_members(*args, **kwargs):
             if token in output:
                 i = output.index(token)
                 vartype = output[:i].split("\n")[-1].strip()
-                output += f"\nstd::function<void(IBlock *, {vartype}&, {vartype}&, {vartype}&)> block_offset_generator = [](IBlock * const, {vartype}&, {vartype}&, {vartype}&) {{ }};"
+                output += f"\nstd::function<void(IBlock *, {vartype}&, {vartype}&, {vartype}&)> block_offset_generator = [](IBlock * const, {vartype}&, {vartype}&, {vartype}&) {{ }};"  # nopep8
             return output
 
         def new_generate_refs_for_kernel_parameters(*args, **kwargs):
@@ -83,12 +83,13 @@ def earmark_generated_kernels():
             walberla_commit = f.read()
     token = "// kernel generated with"
     earmark = (
-        f"{token} pystencils v{pystencils.__version__}, lbmpy v{lbmpy.__version__}, "
-        f"lbmpy_walberla/pystencils_walberla from waLBerla commit {walberla_commit}"
+        f"{token} pystencils v{pystencils.__version__}, "
+        f"lbmpy v{lbmpy.__version__}, "
+        f"lbmpy_walberla/pystencils_walberla from "
+        f"waLBerla commit {walberla_commit}"
     )
     for filename in os.listdir("."):
-        if not filename.endswith(
-                ".tmpl.h") and filename.endswith((".h", ".cpp", ".cu")):
+        if filename.endswith((".h", ".cpp", ".cu", ".cuh")):
             with open(filename, "r+") as f:
                 content = f.read()
                 if token not in content:
@@ -100,7 +101,7 @@ def earmark_generated_kernels():
                         pos = content.find("//=====", 5)
                         pos = content.find("\n", pos) + 1
                     f.seek(pos)
-                    f.write(f"\n{earmark}\n{content[pos:]}")
+                    f.write(f"\n{earmark}\n{content[pos:].rstrip()}\n")
 
 
 def guard_generated_kernels_clang_format():
@@ -117,9 +118,9 @@ def guard_generated_kernels_clang_format():
             if not all_ns:
                 continue
             for ns in all_ns:
-                content = re.sub(rf"(?<=[^a-zA-Z0-9_]){ns}(?=[^a-zA-Z0-9_])",
-                                 f"internal_{hashlib.md5(ns.encode('utf-8')).hexdigest()}",
-                                 content)
+                ns_hash = hashlib.md5(ns.encode('utf-8')).hexdigest()
+                content = re.sub(f"(?<=[^a-zA-Z0-9_]){ns}(?=[^a-zA-Z0-9_])",
+                                 f"internal_{ns_hash}", content)
             with open(filename, "w") as f:
                 f.write(content)
 

maintainer/walberla_kernels/custom_additional_extensions.py

@@ -88,10 +88,8 @@ def __call__(self, field, direction_symbol, index_field, **kwargs):
         conds = [
             sp.Equality(
                 direction_symbol,
-                ps.typing.CastFunc(
-                    d + 1,
-                    np.int32)) for d in range(
-                len(accesses))]
+                ps.typing.CastFunc(d + 1, np.int32))
+            for d in range(len(accesses))]
 
         # use conditional
         conditional = None
@@ -137,8 +135,7 @@ def __init__(self, stencil, boundary_object):
 
     @property
     def constructor_arguments(self):
-        return f", std::function<{self.data_type}(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)>& " \
-               "dirichletCallback "
+        return f", std::function<{self.data_type}(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)>& dirichletCallback "
 
     @property
     def initialiser_list(self):
@@ -153,15 +150,15 @@ def additional_parameters_for_fill_function(self):
         return " const shared_ptr<StructuredBlockForest> &blocks, "
 
     def data_initialisation(self, _):
-        init_list = [f"{self.data_type} InitialisatonAdditionalData = elementInitaliser(Cell(it.x(), it.y(), it.z()), "
-                     "blocks, *block);", "element.value = InitialisatonAdditionalData;"]
+        init_list = [
+            f"{self.data_type} InitialisatonAdditionalData = elementInitaliser(Cell(it.x(), it.y(), it.z()), blocks, *block);",
+            "element.value = InitialisatonAdditionalData;"]
 
         return "\n".join(init_list)
 
     @property
     def additional_member_variable(self):
-        return f"std::function<{self.data_type}(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)> " \
-               "elementInitaliser; "
+        return f"std::function<{self.data_type}(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)> elementInitaliser; "
 
 
 class FluxAdditionalDataHandler(
@@ -174,8 +171,7 @@ def __init__(self, stencil, boundary_object):
 
     @property
     def constructor_arguments(self):
-        return f", std::function<Vector3<{self.data_type}>(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)>& " \
-               "fluxCallback "
+        return f", std::function<Vector3<{self.data_type}>(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)>& fluxCallback "
 
     @property
     def initialiser_list(self):
@@ -193,8 +189,8 @@ def data_initialisation(self, direction):
         dirVec = self.stencil_info[direction][1]
 
         init_list = [
-            f"Vector3<{self.data_type}> InitialisatonAdditionalData = elementInitaliser(Cell(it.x() + {dirVec[0]}, it.y() + {dirVec[1]}, it.z() + {dirVec[2]}), "
-            "blocks, *block);", "element.flux_0 = InitialisatonAdditionalData[0];",
+            f"Vector3<{self.data_type}> InitialisatonAdditionalData = elementInitaliser(Cell(it.x() + {dirVec[0]}, it.y() + {dirVec[1]}, it.z() + {dirVec[2]}), blocks, *block);",
+            "element.flux_0 = InitialisatonAdditionalData[0];",
             "element.flux_1 = InitialisatonAdditionalData[1];"]
         if self._dim == 3:
             init_list.append(
@@ -204,13 +200,11 @@ def data_initialisation(self, direction):
 
     @property
     def additional_member_variable(self):
-        return f"std::function<Vector3<{self.data_type}>(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)> " \
-               "elementInitaliser; "
+        return f"std::function<Vector3<{self.data_type}>(const Cell &, const shared_ptr<StructuredBlockForest>&, IBlock&)> elementInitaliser; "
 
 
-# this custom boundary generator is necessary because our boundary
-# condition writes to several fields at once which is impossible with the
-# shipped one
+# this custom boundary generator is necessary because our boundary condition
+# writes to several fields at once which is impossible with the shipped one
 def generate_boundary(
         generation_context,
         stencil,
@@ -250,9 +244,8 @@ def generate_boundary(
         index_struct_dtype,
         layout=[0],
         shape=(
-            ps.typing.TypedSymbol(
-                "indexVectorSize", ps.typing.BasicType(np.int32)
-            ),
+            ps.typing.TypedSymbol("indexVectorSize",
+                                  ps.typing.BasicType(np.int32)),
             1,
         ),
         strides=(1, 1),

maintainer/walberla_kernels/walberla_lbm_generation.py

@@ -106,7 +106,7 @@ def equations_to_code(equations, variable_prefix="",
 
 def substitute_force_getter_cpp(code):
     field_getter = "force->"
-    assert field_getter in code is not None, f"pattern '{field_getter} not found in '''\n{code}\n'''"
+    assert field_getter in code is not None, f"pattern '{field_getter} not found in '''\n{code}\n'''"  # nopep8
     return code.replace(field_getter, "force_field->")
 
 

requirements.txt

@@ -35,10 +35,11 @@ nbformat==5.1.3
 nbconvert==6.5.1
 tqdm>=4.57.0
 # linters and their dependencies
-autopep8==1.6.0
-pycodestyle==2.8.0
-pylint>=2.12.2
-astroid>=2.9.3
+pep8==1.7.1
+autopep8==2.1.0
+pycodestyle==2.11.1
+pylint>=3.0.3
+astroid>=3.0.2
 isort>=5.6.4
-pre-commit>=2.17.0
+pre-commit>=3.6.2
 cmakelang==0.6.13

samples/reaction_ensemble_complex_reaction.py

@@ -148,7 +148,9 @@ def equations(variables):
 
 print("concentrations sampled with the reaction ensemble vs. analytical solutions:")
 for ptype in types:
-    print(f"  type {types_name[ptype]}: {concentrations[ptype]:.4f} +/- {concentrations_95ci[ptype]:.4f} mol/l (95% CI), expected: {concentrations_numerical[ptype]:.4f} mol/l")
+    print(f"  type {types_name[ptype]}: {concentrations[ptype]:.4f} "
+          f"+/- {concentrations_95ci[ptype]:.4f} mol/l (95% CI), "
+          f"expected: {concentrations_numerical[ptype]:.4f} mol/l")
 
 K_sim = ((concentrations[type_C] / c_ref_in_mol_per_l)**nu_C
          * (concentrations[type_D] / c_ref_in_mol_per_l)**nu_D

samples/visualization_cellsystem.py

@@ -47,7 +47,7 @@
 system.time_step = 0.0005
 system.cell_system.set_regular_decomposition(use_verlet_lists=True)
 system.cell_system.skin = 0.4
-#system.cell_system.node_grid = [i, j, k]
+# system.cell_system.node_grid = [i, j, k]
 
 for i in range(100):
     system.part.add(pos=box * np.random.random(3))

src/core/BondList.hpp

@@ -108,13 +108,13 @@ class BondList {
   template <class Archive> void serialize(Archive &ar, long int /* version */) {
     if (Archive::is_loading::value) {
       std::size_t size{};
-      ar &size;
+      ar & size;
       m_storage.resize(size);
     }
 
     if (Archive::is_saving::value) {
       auto size = m_storage.size();
-      ar &size;
+      ar & size;
     }
 
     ar &boost::serialization::make_array(m_storage.data(), m_storage.size());

src/core/MpiCallbacks.hpp

@@ -271,7 +271,7 @@ class MpiCallbacks {
     if (m_comm.rank() == 0) {
       try {
         abort_loop();
-      } catch (...) {
+      } catch (...) { // NOLINT(bugprone-empty-catch)
       }
     }
   }