Add Ruff formatter to pre-commit for Python

.github/workflows/source.yml

@@ -20,7 +20,9 @@ jobs:
     - name: PEP8
       run: |
         python3 -m pip install -U flake8
-        python3 -m flake8 --exclude=thirdParty .
+        # E203: checks that ':' is not preceded by a space
+        # But the Ruff formatter has better logic for that
+        python3 -m flake8 --extend-ignore=E203 --exclude=thirdParty .
 
   static-analysis:
     runs-on: ubuntu-22.04

.pre-commit-config.yaml

@@ -85,13 +85,20 @@ repos:
   - id: pycln
     name: pycln (python)
 
-# Sorts Python imports according to PEP8
-# https://www.python.org/dev/peps/pep-0008/#imports
-- repo: https://github.com/pycqa/isort
-  rev: 7.0.0
+# # Sorts Python imports according to PEP8
+# # https://www.python.org/dev/peps/pep-0008/#imports
+# - repo: https://github.com/pycqa/isort
+#   rev: 7.0.0
+#   hooks:
+#   - id: isort
+#     name: isort (python)
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.1
   hooks:
-  - id: isort
-    name: isort (python)
+  - id: ruff-check
+    args: [ --fix, --exit-non-zero-on-fix ]
+  - id: ruff-format
 
 # Python: Flake8 (checks only, does this support auto-fixes?)
 #- repo: https://github.com/PyCQA/flake8

docs/source/conf.py

@@ -26,7 +26,7 @@
 # -- General configuration ------------------------------------------------
 
 # RTD
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+on_rtd = os.environ.get("READTHEDOCS", None) == "True"
 
 show_authors = True
 
@@ -37,63 +37,67 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.mathjax',
-              'breathe',
-              'sphinx_copybutton',
-              'sphinx_design',
-              'sphinxcontrib.googleanalytics',
-              'sphinxcontrib.programoutput',
-              'sphinxcontrib.rsvgconverter',
-              'matplotlib.sphinxext.plot_directive']
+extensions = [
+    "sphinx.ext.mathjax",
+    "breathe",
+    "sphinx_copybutton",
+    "sphinx_design",
+    "sphinxcontrib.googleanalytics",
+    "sphinxcontrib.programoutput",
+    "sphinxcontrib.rsvgconverter",
+    "matplotlib.sphinxext.plot_directive",
+]
 
 if not on_rtd:
-    extensions.append('sphinx.ext.githubpages')
+    extensions.append("sphinx.ext.githubpages")
 
 # Google Analytics
 googleanalytics_id = "G-3P1ZT3SQQ5"
 googleanalytics_enabled = True
 
 # breathe config
-breathe_projects = {'openPMD-api': '../xml'}
-breathe_default_project = 'openPMD-api'
+breathe_projects = {"openPMD-api": "../xml"}
+breathe_default_project = "openPMD-api"
 
-subprocess.call('cd ..; doxygen;'
-                'mkdir -p source/_static;'
-                'cp -r doxyhtml source/_static/;'
-                'cp openpmd-api-doxygen-web.tag.xml source/_static/doxyhtml/',
-                shell=True)
+subprocess.call(
+    "cd ..; doxygen;"
+    "mkdir -p source/_static;"
+    "cp -r doxyhtml source/_static/;"
+    "cp openpmd-api-doxygen-web.tag.xml source/_static/doxyhtml/",
+    shell=True,
+)
 
 if not on_rtd:
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 source_parsers = {
-    '.md': CommonMarkParser,
+    ".md": CommonMarkParser,
 }
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'openPMD-api'
-copyright = u'Documentation under CC-BY 4.0, The openPMD Community'
-author = u'The openPMD Community'
+project = "openPMD-api"
+copyright = "Documentation under CC-BY 4.0, The openPMD Community"
+author = "The openPMD Community"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'0.18.0'
+version = "0.18.0"
 # The full version, including alpha/beta/rc tags.
-release = u'0.18.0-dev'
+release = "0.18.0-dev"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -108,20 +112,20 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
 
 # -- Options for HTML output ----------------------------------------------
 
-html_logo = 'openPMD.png'
+html_logo = "openPMD.png"
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 numfig = True
 
@@ -134,34 +138,31 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'openPMD-apidoc'
+htmlhelp_basename = "openPMD-apidoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_logo = 'openPMD.png'
+latex_logo = "openPMD.png"
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-    'papersize': 'a4paper',
-
+    "papersize": "a4paper",
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-    'preamble': r'\setcounter{tocdepth}{2}',
-
+    "preamble": r"\setcounter{tocdepth}{2}",
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -171,8 +172,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'openPMD-api.tex', u'openPMD-api Documentation',
-     u'The openPMD Community', 'manual'),
+    (
+        master_doc,
+        "openPMD-api.tex",
+        "openPMD-api Documentation",
+        "The openPMD Community",
+        "manual",
+    ),
 ]
 
 
@@ -181,8 +187,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'openPMD-api', u'openPMD-api Documentation',
-     [author], 1)
+    (master_doc, "openPMD-api", "openPMD-api Documentation", [author], 1)
 ]
 
 
@@ -192,14 +197,19 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'openPMD-api', u'openPMD-api Documentation',
-     author, 'openPMD-api',
-             'C++ and Python APIs for the openPMD meta-standard',
-     """
+    (
+        master_doc,
+        "openPMD-api",
+        "openPMD-api Documentation",
+        author,
+        "openPMD-api",
+        "C++ and Python APIs for the openPMD meta-standard",
+        """
      The openPMD standard, short for open standard for particle-mesh data files
      is not a file format per se. It is a standard for meta data and naming
      schemes.
      openPMD provides naming and attribute conventions that allow to exchange
      particle and mesh based data from scientific simulations and experiments.
-     """),
+     """,
+    ),
 ]

examples/10_streaming_read.py

@@ -5,10 +5,11 @@
 
 # pass-through for ADIOS2 engine parameters
 # https://adios2.readthedocs.io/en/latest/engines/engines.html
-config = {'adios2': {'engine': {}, 'dataset': {}}}
-config['adios2']['engine'] = {'parameters':
-                              {'Threads': '4', 'DataTransport': 'WAN'}}
-config['adios2']['dataset'] = {'operators': [{'type': 'bzip2'}]}
+config = {"adios2": {"engine": {}, "dataset": {}}}
+config["adios2"]["engine"] = {
+    "parameters": {"Threads": "4", "DataTransport": "WAN"}
+}
+config["adios2"]["dataset"] = {"operators": [{"type": "bzip2"}]}
 
 if __name__ == "__main__":
     # this block is for our CI, SST engine is not present on all systems

examples/10_streaming_write.py

@@ -6,10 +6,11 @@
 
 # pass-through for ADIOS2 engine parameters
 # https://adios2.readthedocs.io/en/latest/engines/engines.html
-config = {'adios2': {'engine': {}, 'dataset': {}}}
-config['adios2']['engine'] = {'parameters':
-                              {'Threads': '4', 'DataTransport': 'WAN'}}
-config['adios2']['dataset'] = {'operators': [{'type': 'bzip2'}]}
+config = {"adios2": {"engine": {}, "dataset": {}}}
+config["adios2"]["engine"] = {
+    "parameters": {"Threads": "4", "DataTransport": "WAN"}
+}
+config["adios2"]["dataset"] = {"operators": [{"type": "bzip2"}]}
 
 if __name__ == "__main__":
     # this block is for our CI, SST engine is not present on all systems
@@ -41,8 +42,9 @@
         electronPositions.set_attribute("comment", "I'm a comment")
 
         length = 10
-        local_data = np.arange(i * length, (i + 1) * length,
-                               dtype=np.dtype("double"))
+        local_data = np.arange(
+            i * length, (i + 1) * length, dtype=np.dtype("double")
+        )
         for dim in ["x", "y", "z"]:
             pos = electronPositions[dim]
             pos.reset_dataset(io.Dataset(local_data.dtype, [length]))
@@ -58,12 +60,13 @@
         temperature = iteration.meshes["temperature"]
         temperature.unit_dimension = {io.Unit_Dimension.theta: 1.0}
         temperature.axis_labels = ["x", "y"]
-        temperature.grid_spacing = [1., 1.]
+        temperature.grid_spacing = [1.0, 1.0]
         # temperature has no x,y,z components, so skip the last layer:
         temperature_dataset = temperature
         # let's say we are in a 3x3 mesh
         temperature_dataset.reset_dataset(
-            io.Dataset(np.dtype("double"), [3, 3]))
+            io.Dataset(np.dtype("double"), [3, 3])
+        )
         # temperature is constant
         temperature_dataset.make_constant(273.15)
 

examples/11_particle_dataframe.py

@@ -6,6 +6,7 @@
 Authors: Axel Huebl, Dmitry Ganyushin
 License: LGPLv3+
 """
+
 import sys
 
 import numpy as np
@@ -20,6 +21,7 @@
 found_cudf = False
 try:
     import cudf
+
     found_cudf = True
 except ImportError:
     print("cudf NOT found. Install RAPIDS for CUDA DataFrame example.")
@@ -29,6 +31,7 @@
     import dask
     import dask.array as da
     from dask.delayed import delayed
+
     found_dask = True
 except ImportError:
     print("dask NOT found. Install dask to run the 2nd example.")
@@ -66,7 +69,7 @@
         # the default schedulers are local/threaded, not requiring much.
         # But multi-node, "distributed" and local "processes" need object
         # pickle capabilities, so we test this here:
-        dask.config.set(scheduler='processes')
+        dask.config.set(scheduler="processes")
 
         df = electrons.to_dask(attributes=["particleShape"])
         print(df)
@@ -79,20 +82,23 @@
         print("<momentum_z>={}".format(df["momentum_z"].mean().compute()))
 
         #   example2: momentum histogram
-        h, bins = da.histogram(df["momentum_z"].to_dask_array(), bins=50,
-                               range=[-8.0e-23, 8.0e-23],
-                               weights=df["weighting"].to_dask_array())
+        h, bins = da.histogram(
+            df["momentum_z"].to_dask_array(),
+            bins=50,
+            range=[-8.0e-23, 8.0e-23],
+            weights=df["weighting"].to_dask_array(),
+        )
         print(h.compute())
 
         #   example3: longitudinal phase space (dask 2021.04.0+)
         z_min = df["position_z"].min().compute()
         z_max = df["position_z"].max().compute()
 
         z_pz, z_pz_bins = da.histogramdd(
-            df[['position_z', 'momentum_z']].to_dask_array(),
+            df[["position_z", "momentum_z"]].to_dask_array(),
             bins=[80, 80],
             range=[[z_min, z_max], [-8.0e-23, 8.0e-23]],
-            weights=df["weighting"].to_dask_array()
+            weights=df["weighting"].to_dask_array(),
         )
         print(z_pz.compute())
 
@@ -114,9 +120,15 @@
         Intensity = darr_x * darr_x + darr_y * darr_y + darr_z * darr_z
         Intensity_max = Intensity.max().compute()
         idx_max = da.argwhere(Intensity == Intensity_max).compute()[0]
-        pos_max = 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]))
+        pos_max = (
+            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]
+            )
+        )
 
     s.close()