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feat: update python-h5netcdf to 1.6.1-1 #2

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10 changes: 5 additions & 5 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
rev: v4.6.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
Expand All @@ -9,17 +9,17 @@ repos:
- id: check-yaml
- id: debug-statements
- id: mixed-line-ending
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: 'v0.0.291'
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: 'v0.5.0'
hooks:
- id: ruff
args: [ "--fix" ]
- repo: https://github.com/psf/black
rev: 23.9.1
rev: 24.4.2
hooks:
- id: black
- repo: https://github.com/adamchainz/blacken-docs
rev: "1.16.0"
rev: "1.18.0"
hooks:
- id: blacken-docs
additional_dependencies:
Expand Down
46 changes: 46 additions & 0 deletions CHANGELOG.rst
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@@ -1,6 +1,52 @@
Change Log
----------

Version 1.6.1 (March 7th, 2025):

- Let Variable.chunks return None for scalar variables, independent of what the underlying
h5ds object returns ({pull}`259`).
By `Rickard Holmberg <https://github.com/rho-novatron>`_

Version 1.6.0 (March 7th, 2025):

- Allow specifying `h5netcdf.File(driver="h5pyd")` to force the use of h5pyd ({issue}`255`, {pull}`256`).
By `Rickard Holmberg <https://github.com/rho-novatron>`_
- Add pytest-mypy-plugins for xarray nightly test ({pull}`257`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_

Version 1.5.0 (January 26th, 2025):

- Update CI to new versions (Python 3.13, 3.14 alpha), remove numpy 1 from h5pyd runs ({pull}`250`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- Update CI and reinstate h5pyd/hsds test runs ({pull}`247`).
By `John Readey <https://github.com/jreadey>`_
- Allow ``zlib`` to be used as an alias for ``gzip`` for enhanced compatibility with h5netcdf's API and xarray.
By `Mark Harfouche <https://github.com/hmaarrfk>`_

Version 1.4.1 (November 13th, 2024):

- Add CI run for hdf5 1.10.6, fix complex tests, fix enum/user type tests ({pull}`244`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_


Version 1.4.0 (October 7th, 2024):

- Add UserType class, add EnumType ({pull}`229`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- Refactor fillvalue and dtype handling for user types, enhance sanity checks and tests ({pull}`230`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- Add VLType and CompoundType, commit complex compound type to file. Align with nc-complex ({pull}`227`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- Update h5pyd testing.
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- CI and lint maintenance ({pull}`235`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
- Support wrapping an h5py ``File`` object. Closing the h5netcdf file object
does not close the h5py file ({pull}`238`).
By `Thomas Kluyver <https://github.com/takluyver>`_
- CI and lint maintenance (format README.rst, use more f-strings, change Python 3.9 to 3.10 in CI) ({pull}`239`).
By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_

Version 1.3.0 (November 7th, 2023):

- Add ros3 support by checking `driver`-kwarg.
Expand Down
51 changes: 25 additions & 26 deletions PKG-INFO
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@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Metadata-Version: 2.2
Name: h5netcdf
Version: 1.3.0
Version: 1.6.1
Summary: netCDF4 via h5py
Author-email: Stephan Hoyer <[email protected]>, Kai Mühlbauer <[email protected]>
Maintainer-email: h5netcdf developers <[email protected]>
Expand Down Expand Up @@ -45,6 +45,7 @@ Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
Expand Down Expand Up @@ -138,32 +139,32 @@ design is an adaptation of h5py to the netCDF data model. For example:
import h5netcdf
import numpy as np

with h5netcdf.File('mydata.nc', 'w') as f:
with h5netcdf.File("mydata.nc", "w") as f:
# set dimensions with a dictionary
f.dimensions = {'x': 5}
f.dimensions = {"x": 5}
# and update them with a dict-like interface
# f.dimensions['x'] = 5
# f.dimensions.update({'x': 5})

v = f.create_variable('hello', ('x',), float)
v = f.create_variable("hello", ("x",), float)
v[:] = np.ones(5)

# you don't need to create groups first
# you also don't need to create dimensions first if you supply data
# with the new variable
v = f.create_variable('/grouped/data', ('y',), data=np.arange(10))
v = f.create_variable("/grouped/data", ("y",), data=np.arange(10))

# access and modify attributes with a dict-like interface
v.attrs['foo'] = 'bar'
v.attrs["foo"] = "bar"

# you can access variables and groups directly using a hierarchical
# keys like h5py
print(f['/grouped/data'])
print(f["/grouped/data"])

# add an unlimited dimension
f.dimensions['z'] = None
f.dimensions["z"] = None
# explicitly resize a dimension and all variables using it
f.resize_dimension('z', 3)
f.resize_dimension("z", 3)

Notes:

Expand All @@ -184,22 +185,23 @@ The legacy API is designed for compatibility with `netCDF4-python`_. To use it,
.. code-block:: python

import h5netcdf.legacyapi as netCDF4

# everything here would also work with this instead:
# import netCDF4
import numpy as np

with netCDF4.Dataset('mydata.nc', 'w') as ds:
ds.createDimension('x', 5)
v = ds.createVariable('hello', float, ('x',))
with netCDF4.Dataset("mydata.nc", "w") as ds:
ds.createDimension("x", 5)
v = ds.createVariable("hello", float, ("x",))
v[:] = np.ones(5)

g = ds.createGroup('grouped')
g.createDimension('y', 10)
g.createVariable('data', 'i8', ('y',))
v = g['data']
g = ds.createGroup("grouped")
g.createDimension("y", 10)
g.createVariable("data", "i8", ("y",))
v = g["data"]
v[:] = np.arange(10)
v.foo = 'bar'
print(ds.groups['grouped'].variables['data'])
v.foo = "bar"
print(ds.groups["grouped"].variables["data"])

The legacy API is designed to be easy to try-out for netCDF4-python users, but it is not an
exact match. Here is an incomplete list of functionality we don't include:
Expand All @@ -222,9 +224,6 @@ h5py implements some features that do not (yet) result in valid netCDF files:

- Data types:
- Booleans
- Complex values
- Non-string variable length types
- Enum types
- Reference types
- Arbitrary filters:
- Scale-offset filters
Expand All @@ -239,11 +238,11 @@ when creating a file:
.. code-block:: python

# avoid the .nc extension for non-netcdf files
f = h5netcdf.File('mydata.h5', invalid_netcdf=True)
f = h5netcdf.File("mydata.h5", invalid_netcdf=True)
...

# works with the legacy API, too, though compression options are not exposed
ds = h5netcdf.legacyapi.Dataset('mydata.h5', invalid_netcdf=True)
ds = h5netcdf.legacyapi.Dataset("mydata.h5", invalid_netcdf=True)
...

In such cases the `_NCProperties` attribute will not be saved to the file or be removed
Expand Down Expand Up @@ -281,7 +280,7 @@ phony dimensions according to `netCDF`_ behaviour.
.. code-block:: python

# mimic netCDF-behaviour for non-netcdf files
f = h5netcdf.File('mydata.h5', mode='r', phony_dims='sort')
f = h5netcdf.File("mydata.h5", mode="r", phony_dims="sort")
...

Note, that this iterates once over the whole group-hierarchy. This has affects
Expand All @@ -292,7 +291,7 @@ to group access time. The created phony dimension naming will differ from

.. code-block:: python

f = h5netcdf.File('mydata.h5', mode='r', phony_dims='access')
f = h5netcdf.File("mydata.h5", mode="r", phony_dims="access")
...

.. rubric:: Footnotes
Expand Down
46 changes: 22 additions & 24 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -80,32 +80,32 @@ design is an adaptation of h5py to the netCDF data model. For example:
import h5netcdf
import numpy as np

with h5netcdf.File('mydata.nc', 'w') as f:
with h5netcdf.File("mydata.nc", "w") as f:
# set dimensions with a dictionary
f.dimensions = {'x': 5}
f.dimensions = {"x": 5}
# and update them with a dict-like interface
# f.dimensions['x'] = 5
# f.dimensions.update({'x': 5})

v = f.create_variable('hello', ('x',), float)
v = f.create_variable("hello", ("x",), float)
v[:] = np.ones(5)

# you don't need to create groups first
# you also don't need to create dimensions first if you supply data
# with the new variable
v = f.create_variable('/grouped/data', ('y',), data=np.arange(10))
v = f.create_variable("/grouped/data", ("y",), data=np.arange(10))

# access and modify attributes with a dict-like interface
v.attrs['foo'] = 'bar'
v.attrs["foo"] = "bar"

# you can access variables and groups directly using a hierarchical
# keys like h5py
print(f['/grouped/data'])
print(f["/grouped/data"])

# add an unlimited dimension
f.dimensions['z'] = None
f.dimensions["z"] = None
# explicitly resize a dimension and all variables using it
f.resize_dimension('z', 3)
f.resize_dimension("z", 3)

Notes:

Expand All @@ -126,22 +126,23 @@ The legacy API is designed for compatibility with `netCDF4-python`_. To use it,
.. code-block:: python

import h5netcdf.legacyapi as netCDF4

# everything here would also work with this instead:
# import netCDF4
import numpy as np

with netCDF4.Dataset('mydata.nc', 'w') as ds:
ds.createDimension('x', 5)
v = ds.createVariable('hello', float, ('x',))
with netCDF4.Dataset("mydata.nc", "w") as ds:
ds.createDimension("x", 5)
v = ds.createVariable("hello", float, ("x",))
v[:] = np.ones(5)

g = ds.createGroup('grouped')
g.createDimension('y', 10)
g.createVariable('data', 'i8', ('y',))
v = g['data']
g = ds.createGroup("grouped")
g.createDimension("y", 10)
g.createVariable("data", "i8", ("y",))
v = g["data"]
v[:] = np.arange(10)
v.foo = 'bar'
print(ds.groups['grouped'].variables['data'])
v.foo = "bar"
print(ds.groups["grouped"].variables["data"])

The legacy API is designed to be easy to try-out for netCDF4-python users, but it is not an
exact match. Here is an incomplete list of functionality we don't include:
Expand All @@ -164,9 +165,6 @@ h5py implements some features that do not (yet) result in valid netCDF files:

- Data types:
- Booleans
- Complex values
- Non-string variable length types
- Enum types
- Reference types
- Arbitrary filters:
- Scale-offset filters
Expand All @@ -181,11 +179,11 @@ when creating a file:
.. code-block:: python

# avoid the .nc extension for non-netcdf files
f = h5netcdf.File('mydata.h5', invalid_netcdf=True)
f = h5netcdf.File("mydata.h5", invalid_netcdf=True)
...

# works with the legacy API, too, though compression options are not exposed
ds = h5netcdf.legacyapi.Dataset('mydata.h5', invalid_netcdf=True)
ds = h5netcdf.legacyapi.Dataset("mydata.h5", invalid_netcdf=True)
...

In such cases the `_NCProperties` attribute will not be saved to the file or be removed
Expand Down Expand Up @@ -223,7 +221,7 @@ phony dimensions according to `netCDF`_ behaviour.
.. code-block:: python

# mimic netCDF-behaviour for non-netcdf files
f = h5netcdf.File('mydata.h5', mode='r', phony_dims='sort')
f = h5netcdf.File("mydata.h5", mode="r", phony_dims="sort")
...

Note, that this iterates once over the whole group-hierarchy. This has affects
Expand All @@ -234,7 +232,7 @@ to group access time. The created phony dimension naming will differ from

.. code-block:: python

f = h5netcdf.File('mydata.h5', mode='r', phony_dims='access')
f = h5netcdf.File("mydata.h5", mode="r", phony_dims="access")
...

.. rubric:: Footnotes
Expand Down
59 changes: 59 additions & 0 deletions debian/changelog
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@@ -1,3 +1,62 @@
python-h5netcdf (1.6.1-1) unstable; urgency=medium

* Team upload.
* New upstream release
* Standards-Version: 4.7.2

-- Drew Parsons <[email protected]> Fri, 04 Apr 2025 12:06:33 +0200

python-h5netcdf (1.5.0-1) unstable; urgency=medium

* Team upload.
* New upstream release

-- Drew Parsons <[email protected]> Thu, 20 Feb 2025 20:12:37 +0100

python-h5netcdf (1.4.1-1) unstable; urgency=medium

* Team upload.
* New upstream release
- applies debian patch fix_tests_PR244.patch

-- Drew Parsons <[email protected]> Sun, 24 Nov 2024 23:17:49 +0100

python-h5netcdf (1.4.0-3) unstable; urgency=medium

* Team upload.
* replace debian patches 32bit_skip_complex_type_creation.patch and
test_h5py_TypeError.patch with fix_tests_PR244.patch, applying
upstream PR#244 to fix tests. Closes: #1087199.

-- Drew Parsons <[email protected]> Wed, 13 Nov 2024 00:08:15 +0100

python-h5netcdf (1.4.0-2) unstable; urgency=medium

* Team upload.
* debian patch 32bit_skip_complex_type_creation.patch works around
32-bit complex type test failure. See Bug#1087199.

-- Drew Parsons <[email protected]> Sat, 09 Nov 2024 15:30:00 +0100

python-h5netcdf (1.4.0-1) unstable; urgency=medium

* Team upload.
* New upstream release.
- Build-Depends: python3-packaging
* use pybuild build_dir to build docs
* ignore pycache dir in doc build if it wasn't created
* add debian patches
- doc_no_sphinx_book_theme.patch disables use of sphinx-book-theme
in docs. sphinx-book-theme is essentially unusable, requiring a
specific nodejs version which is not available.
- test_h5py_TypeError.patch catches h5py exception as TypeError
not KeyError. See upstream Issue#236.
* remove generated test files after buildtime testing
* Standards-Version: 4.7.0
* debian/tests: run tests with and without internet access (ros3)

-- Drew Parsons <[email protected]> Fri, 08 Nov 2024 14:18:45 +0100

python-h5netcdf (1.3.0-1) unstable; urgency=medium

* Team upload.
Expand Down
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