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Merged
t20100 merged 6 commits into from
Jun 25, 2026
Merged

Use ruff instead of bandit, black, flake8, isort #400

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1f466fb
Switch config from bandit, black, isort, flake8 to ruff
t20100 Jun 25, 2026
2ecc6ae
Apply ruff to src/ and test/
t20100 Jun 25, 2026
8e58918
apply ruff to notebooks
t20100 Jun 25, 2026
910cbfd
use ruff in CI
t20100 Jun 25, 2026
722de46
update documentation to use ruff
t20100 Jun 25, 2026
48744c8
update dev dependencies
t20100 Jun 25, 2026
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6 changes: 0 additions & 6 deletions .flake8
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8 changes: 3 additions & 5 deletions .github/workflows/ci.yml
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Expand Up @@ -17,11 +17,9 @@ jobs:
with:
python-version: '3.12'
cache: 'pip'
- run: python -m pip install --upgrade pip bandit black build flake8 isort mypy numpy twine
- run: bandit -c pyproject.toml -r .
- run: black --check .
- run: flake8
- run: isort --check .
- run: python -m pip install --upgrade build mypy numpy pip ruff twine
- run: ruff format --check
- run: ruff check
- run: mypy
- run: python -m build --sdist
- run: python -m twine check dist/*
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6 changes: 4 additions & 2 deletions .github/workflows/release.yml
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Expand Up @@ -16,8 +16,10 @@ jobs:
with:
python-version: '3.12'
cache: 'pip'
- run: python -m pip install --upgrade pip bandit build twine
- run: bandit -c pyproject.toml -r .
- run: python -m pip install --upgrade build mypy numpy pip ruff twine
- run: ruff format --check
- run: ruff check
- run: mypy
- run: python -m build --sdist
- run: python -m twine check dist/*
- run: pip install --pre "$(ls dist/hdf5plugin*.tar.gz)[test]"
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18 changes: 5 additions & 13 deletions doc/contribute.rst
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Expand Up @@ -29,23 +29,15 @@ Formatting/Linting

From the source directory:

* Format code with `black <https://black.readthedocs.io/>`_::
* To format the code, use `ruff format <https://docs.astral.sh/ruff/formatter/>`_::

black .
ruff format

* Sort imports with `isort <https://pycqa.github.io/isort/>`_::
* To check (lint) the code, use `ruff check <https://docs.astral.sh/ruff/linter/>`_::

isort .
ruff check

* Check code with `flake8 <https://flake8.pycqa.org/>`_::

flake8

* Check code with `bandit <https://bandit.readthedocs.io/>`_ security linter::

bandit -c pyproject.toml -r .

* Check typing with `mypy <https://mypy.readthedocs.io>`_::
* To check typing, use `mypy <https://mypy.readthedocs.io>`_::

mypy

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37 changes: 23 additions & 14 deletions doc/hdf5plugin_EuropeanHUG2021.ipynb
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Expand Up @@ -51,12 +51,14 @@
"%matplotlib inline\n",
"\n",
"# Creates data.h5 used for demos\n",
"import urllib.request\n",
"\n",
"import numpy\n",
"from matplotlib import pyplot as plt\n",
"from PIL import Image\n",
"\n",
"import h5py\n",
"import hdf5plugin\n",
"import numpy\n",
"from PIL import Image\n",
"import urllib.request\n",
"\n",
"url = \"https://www.eiroforum.org/wp-content/uploads/pg-esrf-01.jpg\"\n",
"filename = urllib.request.urlretrieve(url)[0]\n",
Expand All @@ -67,7 +69,9 @@
"h5file[\"copyright\"] = \"P.Ginter/ESRF\"\n",
"h5file.attrs[\"url\"] = url\n",
"h5file.create_dataset(\"/data\", data=image)\n",
"h5file.create_dataset(\"/compressed_data_bitshuffle_lz4\", data=image, **hdf5plugin.Bitshuffle())\n",
"h5file.create_dataset(\n",
" \"/compressed_data_bitshuffle_lz4\", data=image, **hdf5plugin.Bitshuffle()\n",
")\n",
"h5file.close()\n",
"\n",
"# Restart kernel once the file is created!"
Expand Down Expand Up @@ -334,6 +338,7 @@
],
"source": [
"from h5glance import H5Glance # Browsing HDF5 files\n",
"\n",
"H5Glance(\"data.h5\")"
]
},
Expand Down Expand Up @@ -373,8 +378,9 @@
"import h5py # Pythonic HDF5 wrapper: https://docs.h5py.org/\n",
"\n",
"h5file = h5py.File(\"data.h5\", mode=\"r\") # Open HDF5 file in read mode\n",
"data = h5file[\"/data\"][()] # Access HDF5 dataset \"/data\"\n",
"plt.imshow(data); plt.colorbar() # Display data"
"data = h5file[\"/data\"][()] # Access HDF5 dataset \"/data\"\n",
"plt.imshow(data) # Display data\n",
"plt.colorbar()"
]
},
{
Expand Down Expand Up @@ -506,7 +512,8 @@
],
"source": [
"data = h5file[\"/compressed_data_bitshuffle_lz4\"][()] # Access datset\n",
"plt.imshow(data); plt.colorbar() # Display data"
"plt.imshow(data) # Display data\n",
"plt.colorbar()"
]
},
{
Expand Down Expand Up @@ -567,7 +574,7 @@
" \"/compressed_data_bitshuffle_lz4\",\n",
" data=data,\n",
" compression=32008, # bitshuffle/lz4 HDF5 filter identifier\n",
" compression_opts=(0, 2) # options: default number of elements/block, enable LZ4\n",
" compression_opts=(0, 2), # options: default number of elements/block, enable LZ4\n",
")\n",
"h5file.close()"
]
Expand Down Expand Up @@ -597,7 +604,7 @@
"h5file.create_dataset(\n",
" \"/compressed_data_bitshuffle_lz4\",\n",
" data=data,\n",
" **hdf5plugin.Bitshuffle() # Or: **hdf5plugin.BitShuffle(lz4=True)\n",
" **hdf5plugin.Bitshuffle(), # Or: **hdf5plugin.BitShuffle(lz4=True)\n",
")\n",
"h5file.close()"
]
Expand Down Expand Up @@ -847,7 +854,8 @@
],
"source": [
"h5file = h5py.File(\"new_file_bitshuffle_lz4.h5\", mode=\"r\")\n",
"plt.imshow(h5file[\"/compressed_data_bitshuffle_lz4\"][()]); plt.colorbar()\n",
"plt.imshow(h5file[\"/compressed_data_bitshuffle_lz4\"][()])\n",
"plt.colorbar()\n",
"h5file.close()"
]
},
Expand Down Expand Up @@ -914,7 +922,8 @@
"source": [
"h5file = h5py.File(\"new_file_shuffle_gzip.h5\", mode=\"w\")\n",
"h5file.create_dataset(\n",
" \"/compressed_data_shuffle_gzip\", data=data, shuffle=True, compression=\"gzip\")\n",
" \"/compressed_data_shuffle_gzip\", data=data, shuffle=True, compression=\"gzip\"\n",
")\n",
"h5file.close()"
]
},
Expand Down Expand Up @@ -947,7 +956,7 @@
"h5file.create_dataset(\n",
" \"/compressed_data_blosc\",\n",
" data=data,\n",
" **hdf5plugin.Blosc(cname='zlib', clevel=5, shuffle=hdf5plugin.Blosc.SHUFFLE)\n",
" **hdf5plugin.Blosc(cname=\"zlib\", clevel=5, shuffle=hdf5plugin.Blosc.SHUFFLE),\n",
")\n",
"h5file.close()"
]
Expand Down Expand Up @@ -1098,7 +1107,7 @@
}
],
"source": [
"!h5dump -d /compressed_data_bitshuffle_lz4 -s \"0,0\" -c \"5,10\" data.h5 "
"!h5dump -d /compressed_data_bitshuffle_lz4 -s \"0,0\" -c \"5,10\" data.h5"
]
},
{
Expand Down Expand Up @@ -1137,7 +1146,7 @@
"outputs": [],
"source": [
"# Retrieve hdf5plugin.PLUGINS_PATH from the command line\n",
"!python3 -c \"import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)\" "
"!python3 -c \"import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)\""
]
},
{
Expand Down
35 changes: 18 additions & 17 deletions doc/hdf5plugin_EuropeanHUG2022.ipynb
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Expand Up @@ -30,7 +30,7 @@
"source": [
"# Notebook requirements\n",
"# A recent version of Pillow is required!\n",
"#%pip install numpy h5py hdf5plugin h5glance rise jupyterlab matplotlib ipympl Pillow"
"# %pip install numpy h5py hdf5plugin h5glance rise jupyterlab matplotlib ipympl Pillow"
]
},
{
Expand All @@ -47,12 +47,14 @@
"%matplotlib inline\n",
"\n",
"# Creates data.h5 used for demos\n",
"import urllib.request\n",
"\n",
"import numpy\n",
"from matplotlib import pyplot as plt\n",
"from PIL import Image\n",
"\n",
"import h5py\n",
"import hdf5plugin\n",
"import numpy\n",
"from PIL import Image\n",
"import urllib.request\n",
"\n",
"url = \"https://www.iter.org/doc/www/content/com/Lists/WebText_2014/Attachments/236/platform_view_north_1.jpg\"\n",
"filename = urllib.request.urlretrieve(url)[0]\n",
Expand All @@ -66,7 +68,7 @@
"h5file.create_dataset(\n",
" \"/compressed_data\",\n",
" data=image,\n",
" **hdf5plugin.Blosc('lz4', shuffle=hdf5plugin.Blosc.BITSHUFFLE)\n",
" **hdf5plugin.Blosc(\"lz4\", shuffle=hdf5plugin.Blosc.BITSHUFFLE),\n",
")\n",
"h5file.close()"
]
Expand All @@ -93,6 +95,7 @@
"outputs": [],
"source": [
"import os\n",
"\n",
"os._exit(0) # Makes the kernel restart"
]
},
Expand All @@ -110,6 +113,7 @@
"%matplotlib inline\n",
"from matplotlib import pyplot as plt\n",
"\n",
"\n",
"def imshow(image):\n",
" plt.imshow(image)\n",
" plt.colorbar()"
Expand Down Expand Up @@ -360,6 +364,7 @@
],
"source": [
"from h5glance import H5Glance # Browsing HDF5 files\n",
"\n",
"H5Glance(\"data.h5\")"
]
},
Expand Down Expand Up @@ -389,8 +394,8 @@
"import h5py # Pythonic HDF5 wrapper: https://docs.h5py.org/\n",
"\n",
"h5file = h5py.File(\"data.h5\", mode=\"r\") # Open HDF5 file in read mode\n",
"data = h5file[\"/data\"][()] # Access HDF5 dataset \"/data\"\n",
"imshow(data) # Display data"
"data = h5file[\"/data\"][()] # Access HDF5 dataset \"/data\"\n",
"imshow(data) # Display data"
]
},
{
Expand Down Expand Up @@ -536,7 +541,7 @@
],
"source": [
"data = h5file[\"/compressed_data\"][()] # Access datset\n",
"imshow(data) # Display data"
"imshow(data) # Display data"
]
},
{
Expand Down Expand Up @@ -598,7 +603,7 @@
" data=data,\n",
" compression=32001, # blosc HDF5 filter identifier\n",
" # options: 0, 0, 0, 0, level, shuffle, compression\n",
" compression_opts=(0, 0, 0, 0, 5, 2, 1) \n",
" compression_opts=(0, 0, 0, 0, 5, 2, 1),\n",
")\n",
"h5file.close()"
]
Expand Down Expand Up @@ -628,10 +633,7 @@
"h5file.create_dataset(\n",
" \"/compressed_data\",\n",
" data=data,\n",
" **hdf5plugin.Blosc(\n",
" cname='lz4',\n",
" clevel=5,\n",
" shuffle=hdf5plugin.Blosc.BITSHUFFLE),\n",
" **hdf5plugin.Blosc(cname=\"lz4\", clevel=5, shuffle=hdf5plugin.Blosc.BITSHUFFLE),\n",
")\n",
"h5file.close()"
]
Expand Down Expand Up @@ -1071,7 +1073,8 @@
"source": [
"h5file = h5py.File(\"new_file_shuffle_gzip.h5\", mode=\"w\")\n",
"h5file.create_dataset(\n",
" \"/compressed_data_shuffle_gzip\", data=data, shuffle=True, compression=\"gzip\")\n",
" \"/compressed_data_shuffle_gzip\", data=data, shuffle=True, compression=\"gzip\"\n",
")\n",
"h5file.close()"
]
},
Expand Down Expand Up @@ -1102,9 +1105,7 @@
"source": [
"h5file = h5py.File(\"new_file_bitshuffle_lz4.h5\", mode=\"w\")\n",
"h5file.create_dataset(\n",
" \"/compressed_data_bitshuffle_lz4\",\n",
" data=data,\n",
" **hdf5plugin.Bitshuffle()\n",
" \"/compressed_data_bitshuffle_lz4\", data=data, **hdf5plugin.Bitshuffle()\n",
")\n",
"h5file.close()"
]
Expand Down
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