h5netcdf 1.8.1__tar.gz

h5netcdf-1.8.1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: mixed-line-ending
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.14.1'
+    hooks:
+      - id: ruff
+        args: [ "--fix" ]
+  - repo: https://github.com/psf/black
+    rev: 25.9.0
+    hooks:
+      - id: black
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.20.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==23.9.1
+
+ci:
+  autoupdate_commit_msg: 'MNT: update pre-commit hooks'

h5netcdf-1.8.1/AUTHORS.txt

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+The h5netcdf developers:
+
+* Stephan Hoyer <shoyer@gmail.com> (main h5netcdf author)
+* Kai Mühlbauer <kmuehlbauer@wradlib.org> (current maintainer)
+* Developers that have contributed to the h5netcdf repository:
+  <https://github.com/h5netcdf/h5netcdf/graphs/contributors>

h5netcdf-1.8.1/CHANGELOG.rst

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+Change Log
+----------
+
+Version 1.8.1 (January 23rd, 2026):
+
+- Add numpy to default dependencies, update install section to highlight backend installation, update error message on missing backend (:issue:`310`, :pull:`311`) by `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.8.0 (January 16st, 2026):
+
+- Fix ros3 test (:issue:`295`, :pull:`296`).
+  By `Ezequiel Cimadevilla Alvarez <https://github.com/zequihg50>`_
+- Update pre-commit.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Fix h5py3 hdf5 1.10 CI run (:pull:`303`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Support pyfive as an alternative backend ({pull}`273`).
+  By `Bryan Lawrence <https://github.com/bnlawrence>`_, `David Hassell
+  <https://github.com/davidhassell>`_, `Valeriu Predoi
+  <https://github.com/valeriupredoi>`_, `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ and `Stephan Hoyer <https://github.com/shoyer>`_
+- Add support for ``filters()`` for ``Variables`` to match netCDF4 python API.
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_.
+
+Version 1.7.3 (October 21st, 2025):
+
+- Fix indexing with empty arrays and lists (:pull:`297`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.7.2 (October 17th, 2025):
+
+- Fix regression where format was requested from group instance instead of _root. Simplify logic to check and raise ``CompatibilityError``. (:issue:`293`, :pull:`294`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+
+Version 1.7.1 (October 16th, 2025):
+
+- Fix regression where attributes with list of strings were written with h5py low-level API instead of high-level API (:issue:`291`, :pull:`292`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.7.0 (October 15th, 2025):
+
+- Fix unintentional changes in test suite (:pull:`277`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Create ENUM with low level API to keep order-by-value, add h5dump based tests (:pull:`285`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ and `David Huard <https://github.com/huard>`_
+- Fix interoperability issues between netcdf4/h5netcdf, namely resizing variables using partial slices,
+creating string attributes with NULLTERM, proper attachment of _Netcdf4Coordinates and _Netcdf4Dimid as well as special string type fillvalues (:pull:`286`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ and `David Huard <https://github.com/huard>`_
+- Add the `format` argument to `h5netcdf.File` and support for the `NETCDF4_CLASSIC` format (:issue:`280`, :pull:`283`).
+  By `David Huard <https://github.com/huard>`_
+- Do not return padded arrays for slices larger than variable shape (:issue:`287`, :pull:`288`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.6.4 (August 5th, 2025):
+
+- Cleanup: pyupgrade --py39-plus (:pull:`272`).
+  By `Kurt Schwehr <https://github.com/schwehr>`_
+- Add better error messages when operating on a closed file (:issue:`274`, :pull:`275`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.6.3 (June 30th, 2025):
+
+- fix invalid string format specifier, match raises/warns with messages in test suite,
+  remove tests for h5py < 3.7, fix sphinx issue and pr roles in CHANGELOG.rst (:issue:`269`, :pull:`270`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.6.2 (June 26th, 2025):
+
+- Codespell fixes (:pull:`261`).
+  By `Kurt Schwehr <https://github.com/schwehr>`_
+- Fix hsds/h5pyd test fixture spinup issues (:pull:`265`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Fix and add circular referrer tests for Python 3.14 and update CI matrix (:pull:`264`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Avoid opening h5pyd file to check if there is a preexisting file,
+  instead remap mode "a" -> "r+", resort to "w" if file doesn't exist (:issue:`262`, :pull:`266`).
+  By `Jonas Grönberg <https://github.com/JonasGronberg>`_ and `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+- Reduce CI time by installing available scientific-python-nightly-wheels and using pip cache (:pull:`267`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+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.
+  By `Ezequiel Cimadevilla Alvarez <https://github.com/zequihg50>`_
+- Code and CI maintenance.
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_ and
+  `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 1.2.0 (June 2nd, 2023):
+
+- Remove h5py2 compatibility code, remove h5py2 CI runs, mention NEP29 as
+  upstream dependency support strategy.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ and
+  `Mark Harfouche <https://github.com/hmaarrfk>`_.
+- Update to pyproject.toml-only build process, adapt CI, use `ruff` for linting, add .pre-commit-config.yaml.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Maintenance CI (use setup-micromamba), fix hsds, fix tests, fix license.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Raise early with h5py-error.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Add simple test to ensure that the shape is stored in the coordinates.
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_.
+
+Version 1.1.0 (November 23rd, 2022):
+
+- Rework adding _FillValue-attribute, add tests.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Add special add_phony method for creating phony dimensions, add test.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Rewrite _unlabeled_dimension_mix (labeled/unlabeled), add tests.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Add default netcdf fillvalues, pad only if necessary, adapt tests.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Fix regression in padding algorithm, add test.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Set ``track_order=True`` by default in created files if h5py 3.7.0 or
+  greater is detected to help compatibility with netCDF4-c programs.
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_.
+
+Version 1.0.2 (August 2nd, 2022):
+
+- Adapt boolean indexing as h5py 3.7.0 started supporting it.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Fix several tests to work with new h5py 3.7.0.
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_ and `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 1.0.1 (June 27th, 2022):
+
+- Fix failing tests when using netCDF4 4.9.0.
+  Reported and patch submitted by `Bas Couwenberg <https://github.com/sebastic>`_.
+
+Version 1.0.0 (March 31st, 2022):
+
+- Add HSDS pytest-fixture, make tests work with h5ypd.
+  By `Aleksandar Jelenak <https://github.com/ajelenak>`_.
+- Remove `_NCProperties` from existing file if writing invalid netcdf features.
+  Warn users if `.nc` file extension is used writing invalid netcdf features.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Remove deprecated code (eg. remove deprecated code (eg. handling mode,
+  chunking_heuristics, decode_vlen_strings), adapt LICENSE/AUTHOR.txt,
+  prepare repository for release 1.0.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.15.0 (March 18th, 2022):
+
+- Add documentation to ``h5netcdf``, merging current available documentation
+  available as ``.rst``-files, in the repo-wiki and new API-docs into one document
+  using ``sphinx-doc`` and ``sphinx-book-theme``.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.14.1 (March 2nd, 2022):
+
+- Directly return non-string ``Empty``-type attributes as empty numpy-ndarray.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.14.0 (February 25, 2022):
+
+- Add ``chunking_heuristic`` keyword and custom heuristic ``chunking_heuristic="h5netcdf"``
+  with better handling of unlimited dimensions.
+  By `Dion Häfner <https://github.com/dionhaefner>`_.
+- Return group name instead of full group path for legacy API.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Add ``endian`` keyword argument ``legacyapi.Dataset.createVariable``.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Resize Dimensions when writing to variables (legacy API only), return padded arrays.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Allow 1D boolean indexers in legacy API.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Revert order tracking by default to avoid a bug in ``h5py`` (Closes Issue
+  #136). By `Mark Harfouche <https://github.com/hmaarrfk>`_.
+- Implement Dimension-class.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Return items from 0-dim and one-element 1-dim array attributes. Return multi-element
+  attributes as lists. Return string attributes as Python strings decoded from their respective
+  encoding (`utf-8`, `ascii`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.13.0 (January 12, 2022):
+
+- Assign dimensions at creation time, instead of at sync/flush (file-close).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Create/attach dimension scales on the fly, instead of at sync/flush (file-close).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Ensure order tracking is true for newly created netcdf4 files as required
+  by the netcdf4 standard. This enables files created by h5netcdf to be
+  appended to by netCDF4 library users (Closes Issue #128).
+  By `Mark Harfouche <https://github.com/hmaarrfk>`_.
+
+Version 0.12.0 (December 20, 2021):
+
+- Added ``FutureWarning`` to use ``mode='r'`` as default when opening files.
+  By `Ryan Grout <https://github.com/groutr>`_.
+- Moved handling of ``_nc4_non_coord_`` to ``h5netcdf.BaseVariable``.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Write ``_NCProperties`` when overwriting existing files.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Create/Attach dimension scales on append (``mode="r+"``)
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Create/Attach/Detach dimension scales only if necessary.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Switch warning into error when using invalid netCDF features.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Avoid circular references to objects referencing h5py objects.
+  By `Tom Augspurger <https://github.com/TomAugspurger>`_.
+
+Version 0.11.0 (April 20, 2021):
+
+- Included ``h5pyd.Dataset`` objects as netCDF variables.
+  By `Aleksandar Jelenak <https://github.com/ajelenak>`_.
+- Added automatic PyPI upload on creation of github release.
+- Moved Changelog to CHANGELOG.rst.
+- Updated ``decode_vlen_strings`` ``FutureWarning``.
+- Support for ``h5py.Empty`` strings.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.10.0 (February 11, 2021):
+
+- Replaced ``decode_strings`` with ``decode_vlen_strings``.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.9.0 (February 7, 2021):
+
+- Special thanks to `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ for
+  stepping up as a co-maintainer!
+- Support for ``decode_strings``, to restore old behavior with h5py 3.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+
+Version 0.8.1 (July 17, 2020):
+
+- Fix h5py deprecation warning in test suite.
+
+Version 0.8.0 (February 4, 2020):
+
+- Support for reading Datasets with missing dimension scales.
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Fixed a bug where ``Datatype`` objects were treated as ``Datasets``.
+- Fixed several issues with upstream deprecations.
+
+Version 0.7.4 (June 1, 2019):
+
+- Fixed a flakey test on Python 2.7 and 3.4.
+
+Version 0.7.3 (May 20, 2019):
+
+- Fixed another bug that could result in reusing dimension IDs, when modifying
+  existing files.
+
+Version 0.7.1 (Mar 16, 2019):
+
+- Fixed a bug where h5netcdf could write invalid netCDF files with reused
+  dimension IDs when dimensions are written in multiple groups.
+  netCDF-C 4.6.2 will crash when reading these files, but you can still read
+  these files with older versions of the netcdf library (or h5netcdf).
+- Updated to use version 2 of ``_NCProperties`` attribute.
+
+Version 0.7 (Feb 26, 2019):
+
+- Support for reading and writing file-like objects (requires h5py 2.9 or
+  newer).
+  By `Scott Henderson <https://github.com/scottyhq>`_.
+
+Version 0.6.2 (Aug 19, 2018):
+
+- Fixed a bug that prevented creating variables with the same name as
+  previously created dimensions in reopened files.
+
+Version 0.6.1 (Jun 8, 2018):
+
+- Compression with arbitrary filters no longer triggers warnings about invalid
+  netCDF files, because this is now
+  `supported by netCDF <https://github.com/Unidata/netcdf-c/pull/399>`__.
+
+Version 0.6 (Jun 7, 2018):
+
+- Support for reading and writing data to remote HDF5 files via the HDF5 REST
+  API using the ``h5pyd`` package. Any file "path" starting with either
+  ``http://``, ``https://``, or ``hdf5://`` will automatically trigger the use
+  of this package.
+  By `Aleksandar Jelenak <https://github.com/ajelenak>`_.
+
+Version 0.5.1 (Apr 11, 2018):
+
+- Bug fix for files with an unlimited dimension with no associated variables.
+  By `Aleksandar Jelenak <https://github.com/ajelenak>`_.
+
+Version 0.5 (Oct 17, 2017):
+
+- Support for creating unlimited dimensions.
+  By `Lion Krischer <https://github.com/krischer>`_.
+
+Version 0.4.3 (Oct 10, 2017):
+
+- Fix test suite failure with recent versions of netCDF4-Python.
+
+Version 0.4.2 (Sep 12, 2017):
+
+- Raise ``AttributeError`` rather than ``KeyError`` when attributes are not
+  found using the legacy API. This fixes an issue that prevented writing to
+  h5netcdf with dask.
+
+Version 0.4.1 (Sep 6, 2017):
+
+- Include tests in source distribution on pypi.
+
+Version 0.4 (Aug 30, 2017):
+
+- Add ``invalid_netcdf`` argument. Warnings are now issued by default when
+  writing an invalid NetCDF file. See the "Invalid netCDF files" section of the
+  README for full details.
+
+Version 0.3.1 (Sep 2, 2016):
+
+- Fix garbage collection issue.
+- Add missing ``.flush()`` method for groups.
+- Allow creating dimensions of size 0.
+
+Version 0.3.0 (Aug 7, 2016):
+
+- Datasets are now loaded lazily. This should increase performance when opening
+  files with a large number of groups and/or variables.
+- Support for writing arrays of variable length unicode strings with
+  ``dtype=str`` via the legacy API.
+- h5netcdf now writes the ``_NCProperties`` attribute for identifying netCDF4
+  files.

h5netcdf-1.8.1/LICENSE

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+Copyright (c) 2015, h5netcdf developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.