h5netcdf 1.2.0__tar.gz → 1.4.0__tar.gz

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/.pre-commit-config.yaml

@@ -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
@@ -9,12 +9,21 @@ repos:
       - id: check-yaml
       - id: debug-statements
       - id: mixed-line-ending
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.254'
+  - 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: 23.1.0
+    rev: 24.4.2
     hooks:
       - id: black
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.18.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==23.9.1
+
+ci:
+  autoupdate_commit_msg: 'MNT: update pre-commit hooks'

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/CHANGELOG.rst

@@ -1,6 +1,32 @@
 Change Log
 ----------
 
+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

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: h5netcdf
-Version: 1.2.0
+Version: 1.4.0
 Summary: netCDF4 via h5py
 Author-email: Stephan Hoyer <shoyer@gmail.com>, Kai Mühlbauer <kmuehlbauer@wradlib.org>
 Maintainer-email: h5netcdf developers <devteam@h5netcdf.org>
@@ -45,12 +45,17 @@ 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
-Provides-Extra: test
 License-File: LICENSE
 License-File: AUTHORS.txt
+Requires-Dist: h5py
+Requires-Dist: packaging
+Provides-Extra: test
+Requires-Dist: netCDF4; extra == "test"
+Requires-Dist: pytest; extra == "test"
 
 h5netcdf
 ========
@@ -134,32 +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:
 
@@ -180,22 +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:
@@ -218,9 +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
@@ -235,11 +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
@@ -277,7 +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
@@ -288,7 +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

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/README.rst

@@ -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:
 
@@ -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:
@@ -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
@@ -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
@@ -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
@@ -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

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/doc/api.rst

@@ -18,3 +18,6 @@ This page provides an auto-generated summary of h5netcdf's new API.
    Group
    Dimension
    Variable
+   CompoundType
+   EnumType
+   VLType

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/doc/conf.py

@@ -130,7 +130,7 @@ else:
     # extract git revision
     gh_tree_name = version_tuple[-1].split(".")[0][1:]
 
-rel = "`{0} <{1}/h5netcdf/tree/{2}>`__".format(release, url, gh_tree_name)
+rel = f"`{release} <{url}/h5netcdf/tree/{gh_tree_name}>`__"
 
 rst_epilog = ""
 rst_epilog += f"""

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/doc/devguide.rst

@@ -15,6 +15,7 @@ Contributors
 - `Brett Naul <https://github.com/bnaul>`_
 - `Dion Häfner <https://github.com/dionhaefner>`_
 - `Drew Parsons <https://github.com/drew-parsons>`_
+- `Ezequiel Cimadevilla Alvarez <https://github.com/zequihg50>`_
 - `Frédéric Laliberté <https://github.com/laliberte>`_
 - `Ghislain Vaillant <https://github.com/ghisvail>`_
 - `Lion Krischer <https://github.com/krischer>`_
@@ -23,6 +24,7 @@ Contributors
 - `Pierre Augier <https://github.com/paugier>`_
 - `Ryan Grout <https://github.com/groutr>`_
 - `Scott Henderson <https://github.com/scottyhq>`_
+- `Thomas Kluyver <https://github.com/takluyver>`_
 - `Tom Augspurger <https://github.com/TomAugspurger>`_
 
 If you are interested to contribute, just let us know by creating an issue or pull request on github.

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/doc/index.rst

@@ -50,7 +50,7 @@ by Stephan Hoyer. The first `official` ``h5netcdf`` announcement was made by Ste
 `xarray issue tracker`_ only one day later.
 
 The library evolved constantly over the years (fixing bugs and adding enhancements)
-and gained contributions from 15 other :ref:`contributors` so far. The library is widely used,
+and gained contributions from 17 other :ref:`contributors` so far. The library is widely used,
 especially as backend within `xarray`_.
 
 Early 2020 Kai Mühlbauer started to add contributions and after some time he volunteered

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/doc/legacyapi.rst

@@ -18,3 +18,6 @@ This page provides an auto-generated summary of h5netcdf's legacy API.
    Group
    Dimension
    Variable
+   CompoundType
+   EnumType
+   VLType

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/h5netcdf/__init__.py

@@ -5,6 +5,7 @@ h5netcdf
 A Python library for the netCDF4 file-format that directly reads and writes
 HDF5 files via h5py, without using the Unidata netCDF library.
 """
+
 try:
     from ._version import version as __version__
 except Exception:

h5netcdf-1.4.0/h5netcdf/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.4.0'
+__version_tuple__ = version_tuple = (1, 4, 0)

{h5netcdf-1.2.0 → h5netcdf-1.4.0}/h5netcdf/attrs.py

@@ -76,7 +76,7 @@ class Attributes(MutableMapping):
 
     def __setitem__(self, key, value):
         if key in _HIDDEN_ATTRS:
-            raise AttributeError("cannot write attribute with reserved name %r" % key)
+            raise AttributeError(f"cannot write attribute with reserved name {key!r}")
         if hasattr(value, "dtype"):
             dtype = value.dtype
         else:
@@ -98,4 +98,4 @@ class Attributes(MutableMapping):
         return len(self._h5attrs) - hidden_count
 
     def __repr__(self):
-        return "\n".join(["%r" % type(self)] + [f"{k}: {v!r}" for k, v in self.items()])
+        return "\n".join([f"{type(self)!r}"] + [f"{k}: {v!r}" for k, v in self.items()])