[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -66,7 +66,7 @@ repos:
 # clang-format v13
 #   to run manually, use .github/workflows/clang-format/clang-format.sh
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v22.1.5
+  rev: v22.1.8
   hooks:
   - id: clang-format
     # By default, the clang-format hook configures:
@@ -86,7 +86,7 @@ repos:
     name: pycln (python)
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.1
+  rev: v0.16.1
 
   hooks:
   - id: ruff-check

docs/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # This file is execfile()d with the current directory set to its
 # containing dir.
@@ -16,8 +15,8 @@
 import os
 import subprocess
 
-from recommonmark.parser import CommonMarkParser
 import sphinx_rtd_theme
+from recommonmark.parser import CommonMarkParser
 
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))

examples/10_streaming_read.py

@@ -20,7 +20,7 @@
 
     # Read all available iterations and print electron position data.
     for index, iteration in series.snapshots().items():
-        print("Current iteration {}".format(index))
+        print(f"Current iteration {index}")
         electronPositions = iteration.particles["e"]["position"]
         loadedChunks = []
         shapes = []
@@ -42,7 +42,7 @@
         for i in range(3):
             dim = dimensions[i]
             shape = shapes[i]
-            print("dim: {}".format(dim))
+            print(f"dim: {dim}")
             chunk = loadedChunks[i]
             print(chunk)
 

examples/10_streaming_write.py

@@ -2,6 +2,7 @@
 import sys
 
 import numpy as np
+
 import openpmd_api as io
 
 # pass-through for ADIOS2 engine parameters

examples/11_particle_dataframe.py

@@ -10,6 +10,7 @@
 import sys
 
 import numpy as np
+
 import openpmd_api as io
 
 try:
@@ -124,9 +125,7 @@
             E.grid_unit_SI * 1.0e6 * (idx_max * E.grid_spacing + E.grid_global_offset)
         )
         print(
-            "maximum intensity I={} at index={} z={}mu".format(
-                Intensity_max, idx_max, pos_max[2]
-            )
+            f"maximum intensity I={Intensity_max} at index={idx_max} z={pos_max[2]}mu"
         )
 
     s.close()

examples/12_span_write.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import openpmd_api as io
 
 

examples/13_write_dynamic_configuration.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 import numpy as np
+
 import openpmd_api as io
 
 # This example demonstrates how to use JSON/TOML-based dynamic

examples/15_compression.py

@@ -20,6 +20,7 @@
 #
 
 import numpy as np
+
 import openpmd_api as opmd
 
 try:
@@ -68,7 +69,7 @@ def write(filename, config):
 def main():
 
     # We start with two examples for ADIOS2.
-    if "adios2" in opmd.variants and opmd.variants["adios2"]:
+    if opmd.variants.get("adios2"):
         simple_adios2_config = {
             # Backend can either be inferred from the filename ending, or
             # specified explicitly. In the latter case, the filename ending can
@@ -189,7 +190,7 @@ def main():
     # Filters are additionally distinguished by how tightly they integrate with
     # HDF5. The most tightly-integrated filter is Zlib, which has its own API
     # calls and hence also a special JSON/TOML configuration in openPMD:
-    if "hdf5" in opmd.variants and opmd.variants["hdf5"]:
+    if opmd.variants.get("hdf5"):
         hdf5_zlib_config = {
             "backend": "hdf5",
             "hdf5": {

examples/2_read_serial.py

@@ -17,35 +17,35 @@
     )
     print("Read a Series with openPMD standard version %s" % series.openPMD)
 
-    print("The Series contains {0} iterations:".format(len(series.snapshots())))
+    print(f"The Series contains {len(series.snapshots())} iterations:")
     for i in series.snapshots():
-        print("\t {0}".format(i))
-    print("")
+        print(f"\t {i}")
+    print()
 
     # with defer_iteration_parsing, open() must be called explicitly
     i = series.snapshots()[100].open()
-    print("Iteration 100 contains {0} meshes:".format(len(i.meshes)))
+    print(f"Iteration 100 contains {len(i.meshes)} meshes:")
     for m in i.meshes:
-        print("\t {0}".format(m))
-    print("")
-    print("Iteration 100 contains {0} particle species:".format(len(i.particles)))
+        print(f"\t {m}")
+    print()
+    print(f"Iteration 100 contains {len(i.particles)} particle species:")
     for ps in i.particles:
-        print("\t {0}".format(ps))
+        print(f"\t {ps}")
         print("With records:")
         for r in i.particles[ps]:
-            print("\t {0}".format(r))
+            print(f"\t {r}")
 
     # printing a scalar value
     electrons = i.particles["electrons"]
     charge = electrons["charge"]
     series.flush()
-    print("And the first electron particle has a charge {}".format(charge[0]))
-    print("")
+    print(f"And the first electron particle has a charge {charge[0]}")
+    print()
 
     E_x = i.meshes["E"]["x"]
     shape = E_x.shape
 
-    print("Field E.x has shape {0} and datatype {1}".format(shape, E_x.dtype))
+    print(f"Field E.x has shape {shape} and datatype {E_x.dtype}")
 
     chunk_data = E_x[1:3, 1:3, 1:2]
     # print("Queued the loading of a single chunk from disk, "
@@ -65,7 +65,7 @@
     # The iteration can be closed in order to help free up resources.
     # The iteration's content will be flushed automatically.
     i.close()
-    print("Full E/x is of shape {0} and starts with:".format(all_data.shape))
+    print(f"Full E/x is of shape {all_data.shape} and starts with:")
     print(all_data[0, 0, :5])
 
     # The files in 'series' are still open until the series is closed, at which

examples/3_write_serial.py

@@ -8,6 +8,7 @@
 """
 
 import numpy as np
+
 import openpmd_api as io
 
 if __name__ == "__main__":
@@ -17,22 +18,20 @@
     # matrix dataset to write with values 0...size*size-1
     data = np.arange(size * size, dtype=np.double).reshape(3, 3)
 
-    print("Set up a 2D square array ({0}x{1}) that will be written".format(size, size))
+    print(f"Set up a 2D square array ({size}x{size}) that will be written")
 
     # open file for writing
     series = io.Series("../samples/3_write_serial_py.h5", io.Access.create_linear)
 
-    print("Created an empty {0} Series".format(series.iteration_encoding))
+    print(f"Created an empty {series.iteration_encoding} Series")
 
     print(len(series.iterations))
     rho = series.snapshots()[1].meshes["rho"]
 
     dataset = io.Dataset(data.dtype, data.shape)
 
     print(
-        "Created a Dataset of size {0}x{1} and Datatype {2}".format(
-            dataset.extent[0], dataset.extent[1], dataset.dtype
-        )
+        f"Created a Dataset of size {dataset.extent[0]}x{dataset.extent[1]} and Datatype {dataset.dtype}"
     )
 
     rho.reset_dataset(dataset)

examples/3a_write_thetaMode_serial.py

@@ -8,6 +8,7 @@
 """
 
 import numpy as np
+
 import openpmd_api as io
 
 if __name__ == "__main__":
@@ -30,7 +31,7 @@
         num_fields, N_r, N_z
     )
 
-    geometry_parameters = "m={0};imag=+".format(num_modes)
+    geometry_parameters = f"m={num_modes};imag=+"
 
     E = series.snapshots()[0].meshes["E"]
     E.geometry = io.Geometry.thetaMode

examples/3b_write_resizable_particles.py

@@ -8,6 +8,7 @@
 """
 
 import numpy as np
+
 import openpmd_api as io
 
 if __name__ == "__main__":

examples/4_read_parallel.py

@@ -12,6 +12,7 @@
 # on import: calls MPI_Init_thread()
 # exit hook: calls MPI_Finalize()
 from mpi4py import MPI
+
 import openpmd_api as io
 
 if __name__ == "__main__":
@@ -25,7 +26,7 @@
         {"defer_iteration_parsing": True},
     )
     if 0 == comm.rank:
-        print("Read a series in parallel with {} MPI ranks".format(comm.size))
+        print(f"Read a series in parallel with {comm.size} MPI ranks")
 
     # with defer_iteration_parsing, open() must be called explicitly
     # explicit use of open() is recommended for parallel applications
@@ -51,18 +52,14 @@
 
     for i in range(comm.size):
         if i == comm.rank:
-            print("Rank {} - Read chunk contains:".format(i))
+            print(f"Rank {i} - Read chunk contains:")
             for row in range(chunk_extent[0]):
                 for col in range(chunk_extent[1]):
                     print(
-                        "\t({}|{}|1)\t{:e}".format(
-                            row + chunk_offset[0],
-                            col + chunk_offset[1],
-                            chunk_data[row, col, 0],
-                        ),
+                        f"\t({row + chunk_offset[0]}|{col + chunk_offset[1]}|1)\t{chunk_data[row, col, 0]:e}",
                         end="",
                     )
-                print("")
+                print()
 
         # this barrier is not necessary but structures the example output
         comm.Barrier()

examples/5_write_parallel.py

@@ -11,8 +11,9 @@
 # https://mpi4py.readthedocs.io/en/stable/mpi4py.run.html
 # on import: calls MPI_Init_thread()
 # exit hook: calls MPI_Finalize()
-from mpi4py import MPI
 import numpy as np
+from mpi4py import MPI
+
 import openpmd_api as io
 
 try:
@@ -33,8 +34,8 @@
     local_data = np.ones(10 * 300, dtype=np.double).reshape(10, 300) * local_value
     if 0 == comm.rank:
         print(
-            "Set up a 2D array with 10x300 elements per MPI rank ({}x) "
-            "that will be written to disk".format(comm.size)
+            f"Set up a 2D array with 10x300 elements per MPI rank ({comm.size}x) "
+            "that will be written to disk"
         )
 
     # open file for writing
@@ -46,7 +47,7 @@
         comm,
     )
     if 0 == comm.rank:
-        print("Created an empty series in parallel with {} MPI ranks".format(comm.size))
+        print(f"Created an empty series in parallel with {comm.size} MPI ranks")
 
     # In parallel contexts, it's important to explicitly open iterations.
     # However, we use Access mode CREATE_LINEAR, so the Series creates
@@ -65,9 +66,7 @@
 
     if 0 == comm.rank:
         print(
-            "Prepared a Dataset of size {} and Datatype {}".format(
-                dataset.extent, dataset.dtype
-            )
+            f"Prepared a Dataset of size {dataset.extent} and Datatype {dataset.dtype}"
         )
 
     mymesh.reset_dataset(dataset)

examples/7_extended_write_serial.py

@@ -8,6 +8,7 @@
 """
 
 import numpy as np
+
 from openpmd_api import Access, Dataset, Mesh_Record_Component, Series, Unit_Dimension
 
 SCALAR = Mesh_Record_Component.SCALAR

examples/9_particle_write_serial.py

@@ -10,6 +10,7 @@
 from pathlib import Path
 
 import numpy as np
+
 from openpmd_api import Access, Dataset, Series, Unit_Dimension
 
 if __name__ == "__main__":

new_version.py

@@ -8,9 +8,9 @@
 # This file is a maintainer tool to bump the versions inside openPMD-api's
 # source directory at all places where necessary.
 #
-from pathlib import Path
 import re
 import sys
+from pathlib import Path
 
 # Maintainer Inputs ###########################################################
 
@@ -97,7 +97,7 @@
     cmakelists_content = f.read()
     cmakelists_content = re.sub(
         r"^(project.*openPMD.*VERSION *)(.*)(\).*)$",
-        r"\g<1>{}\g<3>".format(VERSION_STR),
+        rf"\g<1>{VERSION_STR}\g<3>",
         cmakelists_content,
         flags=re.MULTILINE,
     )
@@ -165,16 +165,16 @@ def generic_replace(filename, previous, after):
     def replace(key, value):
         global version_hpp_content
         version_hpp_content = re.sub(
-            r"^(#define OPENPMDAPI_VERSION_{}) .*$".format(re.escape(key)),
-            r"\1 {}".format(value),
+            rf"^(#define OPENPMDAPI_VERSION_{re.escape(key)}) .*$",
+            rf"\1 {value}",
             version_hpp_content,
             flags=re.MULTILINE,
         )
 
     replace("MAJOR", MAJOR)
     replace("MINOR", MINOR)
     replace("PATCH", PATCH)
-    replace("LABEL", '"{}"'.format(SUFFIX))
+    replace("LABEL", f'"{SUFFIX}"')
 
 with open(version_hpp_path, "w", encoding="utf-8") as f:
     f.write(version_hpp_content)

setup.py

@@ -178,7 +178,7 @@ def build_extension(self, ext):
     else:
         continue
     if cmake_var:
-        extra_cmake_args.append("-D{0}={1}".format(cmake_var, v))
+        extra_cmake_args.append(f"-D{cmake_var}={v}")
 
 # https://cmake.org/cmake/help/v3.0/command/if.html
 if openPMD_USE_MPI.upper() in ["1", "ON", "TRUE", "YES"]:
@@ -188,7 +188,7 @@ def build_extension(self, ext):
 
 # Get the package requirements from the requirements.txt file
 with open("./requirements.txt") as f:
-    install_requires = [line.strip("\n") for line in f.readlines()]
+    install_requires = [line.strip("\n") for line in f]
     if openPMD_USE_MPI == "ON":
         install_requires.append("mpi4py>=2.1.0")