Merge pull request silx-kit#347 from t20100/lint

Added standard formatting/linting

Author: t20100

.flake8

@@ -1,3 +1,6 @@
 [flake8]
 max-line-length = 88
 extend-ignore = E203,E501,E701
+extend-exclude =
+    build,
+    lib

.github/workflows/ci.yml

@@ -17,8 +17,11 @@ jobs:
         with:
           python-version: '3.12'
           cache: 'pip'
-      - run: python -m pip install --upgrade pip bandit build twine
+      - run: python -m pip install --upgrade pip bandit black build flake8 isort twine
       - run: bandit -c pyproject.toml -r .
+      - run: black --check .
+      - run: flake8
+      - run: isort --check .
       - run: python -m build --sdist
       - run: python -m twine check dist/*
       # Build documentation

doc/conf.py

@@ -17,9 +17,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "hdf5plugin"
-copyright = (
-    "2016-2024, European Synchrotron Radiation Facility, Grenoble"
-)
+copyright = "2016-2025, European Synchrotron Radiation Facility, Grenoble"
 author = "ESRF"
 
 # -- General configuration ---------------------------------------------------

doc/contribute.rst

@@ -24,12 +24,26 @@ To also run tests relying on actual HDF5 files, run from the source directory::
 
 This tests the installed version of `hdf5plugin`.
 
-Linting
-=======
+Formatting/Linting
+==================
+
+From the source directory:
+
+* Format code with `black <https://black.readthedocs.io/>`_::
+
+    black .
+
+* Sort imports with `isort <https://pycqa.github.io/isort/>`_::
+
+    isort .
+
+* Check code with `flake8 <https://flake8.pycqa.org/>`_::
+
+    flake8
 
-Run `bandit <https://github.com/PyCQA/bandit/>_` security linter from the source directory::
+* Check code with `bandit <https://bandit.readthedocs.io/>`_ security linter::
 
-   bandit -c pyproject.toml -r .
+    bandit -c pyproject.toml -r .
 
 Building documentation
 ======================

doc/hdf5plugin_EuropeanHUG2023/benchmark.py

@@ -7,12 +7,11 @@
 import sys
 import tempfile
 import time
-from typing import Optional, NamedTuple
+from typing import NamedTuple, Optional
 
 import h5py
 import numpy
 
-
 # Set affinity and env. var. before importing hdf5plugin
 
 if len(sys.argv) >= 2:
@@ -28,13 +27,14 @@
 # Directory where to run read/write benchmarks
 DIRECTORY = "/dev/shm"
 
+
 # Function to get data to use for tests
 def get_data():
     with h5py.File("/dev/shm/kevlar.h5") as h5file:
         return h5file["/entry/data/data"][::10]  # Take 100 frames
 
 
-import hdf5plugin
+import hdf5plugin  # noqa: E402
 
 
 class Result(NamedTuple):
@@ -46,21 +46,18 @@ class Result(NamedTuple):
     read_duration: float
     chunks: tuple[int]
 
-    compression_rate = property(
-        lambda self: self.raw_nbytes / self.compressed_nbytes)
+    compression_rate = property(lambda self: self.raw_nbytes / self.compressed_nbytes)
     write_speed = property(
         lambda self: (self.raw_nbytes / 1024**2) / self.write_duration,
-        doc="Unit: MB/sec")
+        doc="Unit: MB/sec",
+    )
     read_speed = property(
         lambda self: (self.raw_nbytes / 1024**2) / self.read_duration,
-        doc="Unit: MB/sec")
-
-    
-def benchmark(
-    data: numpy.ndarray,
-    directory: Optional[str] = None,
-    **kwargs
-) -> Result:
+        doc="Unit: MB/sec",
+    )
+
+
+def benchmark(data: numpy.ndarray, directory: Optional[str] = None, **kwargs) -> Result:
     """Run benchmark for given conditions
 
     :param data: Dataset to use
@@ -73,15 +70,16 @@ def benchmark(
     else:
         dirname = directory
 
-    filename = os.path.join(dirname, 'hdf5plugin_benchmark.h5')
+    filename = os.path.join(dirname, "hdf5plugin_benchmark.h5")
 
     if os.path.exists(filename):
         os.remove(filename)
 
     # Compression
     with h5py.File(filename, "w") as h5file:
         dataset = h5file.create_dataset(
-            "data", shape=data.shape, dtype=data.dtype, **kwargs)
+            "data", shape=data.shape, dtype=data.dtype, **kwargs
+        )
         start_write_time = time.perf_counter()
         dataset[:] = data
         dataset.flush()
@@ -91,16 +89,18 @@ def benchmark(
     with h5py.File(filename, "r") as h5file:
         dataset = h5file["data"]
         start_time = time.perf_counter()
-        read_data = dataset[()]
+        dataset[()]
         read_duration = time.perf_counter() - start_time
         storage_size = dataset.id.get_storage_size()
         chunks = dataset.chunks
-    
+
     os.remove(filename)
 
-    return Result(data.nbytes, storage_size, write_duration, read_duration, chunks=chunks)
+    return Result(
+        data.nbytes, storage_size, write_duration, read_duration, chunks=chunks
+    )
+
 
-    
 DEFAULT_FILTERS = {  # Filters available with h5py/libhdf5
     "Raw": None,
     "GZip": "gzip",
@@ -114,28 +114,34 @@ def benchmark(
 }
 
 BITSHUFFLE_FILTERS = {
-    "Bitshuffle-lz4": hdf5plugin.Bitshuffle(cname='lz4'),
-    "Bitshuffle-zstd": hdf5plugin.Bitshuffle(cname='zstd'),
+    "Bitshuffle-lz4": hdf5plugin.Bitshuffle(cname="lz4"),
+    "Bitshuffle-zstd": hdf5plugin.Bitshuffle(cname="zstd"),
 }
-    
+
 BLOSC_FILTERS = {}
-for cname in ('lz4', 'blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd'):
-    for shuffle_name, shuffle in [('NoShuffle', hdf5plugin.Blosc.NOSHUFFLE),
-                                  ('Shuffle', hdf5plugin.Blosc.SHUFFLE),
-                                  ('BitShuffle', hdf5plugin.Blosc.BITSHUFFLE)]:
-        for clevel in [5]: #(1, 3, 5, 9):
+for cname in ("lz4", "blosclz", "lz4", "lz4hc", "snappy", "zlib", "zstd"):
+    for shuffle_name, shuffle in [
+        ("NoShuffle", hdf5plugin.Blosc.NOSHUFFLE),
+        ("Shuffle", hdf5plugin.Blosc.SHUFFLE),
+        ("BitShuffle", hdf5plugin.Blosc.BITSHUFFLE),
+    ]:
+        for clevel in [5]:  # (1, 3, 5, 9):
             BLOSC_FILTERS[f"Blosc-{cname}-{shuffle_name}-{clevel}"] = hdf5plugin.Blosc(
-                cname=cname, clevel=clevel, shuffle=shuffle)
+                cname=cname, clevel=clevel, shuffle=shuffle
+            )
 
 
 BLOSC2_FILTERS = {}
-for cname in ('lz4', 'blosclz', 'lz4', 'lz4hc', 'zlib', 'zstd'):
-    for filters_name, filters in [('NoFilter', hdf5plugin.Blosc2.NOFILTER),
-                                ('Shuffle', hdf5plugin.Blosc2.SHUFFLE),
-                                ('BitShuffle', hdf5plugin.Blosc2.BITSHUFFLE)]:
-        for clevel in [5]: # (1, 3, 5, 9):
-            BLOSC2_FILTERS[f"Blosc2-{cname}-{filters_name}-{clevel}"] = hdf5plugin.Blosc2(
-                cname=cname, clevel=clevel, filters=filters)
+for cname in ("lz4", "blosclz", "lz4", "lz4hc", "zlib", "zstd"):
+    for filters_name, filters in [
+        ("NoFilter", hdf5plugin.Blosc2.NOFILTER),
+        ("Shuffle", hdf5plugin.Blosc2.SHUFFLE),
+        ("BitShuffle", hdf5plugin.Blosc2.BITSHUFFLE),
+    ]:
+        for clevel in [5]:  # (1, 3, 5, 9):
+            BLOSC2_FILTERS[f"Blosc2-{cname}-{filters_name}-{clevel}"] = (
+                hdf5plugin.Blosc2(cname=cname, clevel=clevel, filters=filters)
+            )
 
 
 FILTERS = {

pyproject.toml

@@ -45,6 +45,13 @@ test = [
     "blosc2>=2.5.1",
     "blosc2-grok>=0.2.2",
 ]
+dev = [
+    "hdf5plugin[doc,test]",
+    "bandit",
+    "black",
+    "flake8",
+    "isort",
+]
 
 [tool.setuptools]
 packages = ["hdf5plugin"]
@@ -62,3 +69,15 @@ exclude_dirs = [
 
 [tool.bandit.assert_used]
 skips = ["*test.py"]
+
+[tool.black]
+extend-exclude = '''
+(
+    lib
+    | .*\.ipynb
+)
+'''
+
+[tool.isort]
+profile = "black"
+skip_glob = ["lib"]