[Git][debian-gis-team/netcdf4-python][upstream] New upstream version 1.6.5
Bas Couwenberg (@sebastic)
gitlab at salsa.debian.org
Wed Oct 25 04:32:44 BST 2023
Bas Couwenberg pushed to branch upstream at Debian GIS Project / netcdf4-python
Commits:
b5422974 by Bas Couwenberg at 2023-10-25T05:25:19+02:00
New upstream version 1.6.5
- - - - -
11 changed files:
- .github/workflows/miniconda.yml
- Changelog
- README.md
- create_docs.sh
- docs/index.html
- pyproject.toml
- src/netCDF4/__init__.py
- src/netCDF4/_netCDF4.pyx
- test/tst_masked.py
- test/tst_multifile.py
- test/tst_multifile2.py
Changes:
=====================================
.github/workflows/miniconda.yml
=====================================
@@ -12,7 +12,7 @@ jobs:
# NO_NET: 1
strategy:
matrix:
- python-version: [ "3.7", "3.8", "3.9", "3.10", "3.11" ]
+ python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
os: [windows-latest, ubuntu-latest, macos-latest]
platform: [x64, x32]
exclude:
@@ -79,8 +79,8 @@ jobs:
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH"
which mpirun
mpirun --version
- mpirun -np 4 --oversubscribe python mpi_example.py # for openmpi
- #mpirun -np 4 python mpi_example.py
+ #mpirun -np 4 --oversubscribe python mpi_example.py # for openmpi
+ mpirun -np 4 python mpi_example.py
if [ $? -ne 0 ] ; then
echo "hdf5 mpi test failed!"
exit 1
=====================================
Changelog
=====================================
@@ -1,3 +1,8 @@
+ version 1.6.5 (not yet released)
+===============================
+ * fix for issue #1271 (mask ignored if bool MA assinged to uint8 var)
+ * include information on specific object when reporting errors from netcdf-c
+
version 1.6.4 (tag v1.6.4rel)
===============================
* set path to SSL certificates internally, so https DAP URLs work with wheels
=====================================
README.md
=====================================
@@ -10,9 +10,13 @@
## News
For details on the latest updates, see the [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).
+10/20/2023: Version [1.6.5](https://pypi.python.org/pypi/netCDF4/1.6.5) released.
+Fix for issue #1271 (mask ignored if bool MA assinged to uint8 var), support for python 3.12, more
+informative error messages.
+
6/4/2023: Version [1.6.4](https://pypi.python.org/pypi/netCDF4/1.6.4) released. Now requires
[certifi](https://github.com/certifi/python-certifi) to locate SSL certificates - this allows
-OpenDAP https URLs to work with linux wheels (issue [#1246](https://github.com/Unidata/netcdf4-python/issues/1246).
+OpenDAP https URLs to work with linux wheels (issue [#1246](https://github.com/Unidata/netcdf4-python/issues/1246)).
3/3/2023: Version [1.6.3](https://pypi.python.org/pypi/netCDF4/1.6.3) released.
=====================================
create_docs.sh
=====================================
@@ -1,10 +1,3 @@
-# Uses pdoc (https://github.com/mitmproxy/pdoc)
-# to create html docs from docstrings in Cython source.
-pdoc -o 'docs' netCDF4
-# use resulting docs/netCDF4/_netCDF4.html
-cp docs/netCDF4.html docs/index.html
-sed -i -e 's!href="../netCDF4.html!href="./index.html!g' docs/index.html
-sed -i -e 's!/../netCDF4.html!/index.html!g' docs/index.html
-sed -i -e 's!._netCDF4 API! API!g' docs/index.html
-sed -i -e 's!netCDF4</a>._netCDF4</h1>!netCDF4</a></h1>!g' docs/index.html
-
+# use pdoc (https://pdoc3.github.io/pdoc/) to generate API docs
+pdoc3 --html --config show_source_code=False --force -o 'docs' netCDF4
+/bin/cp -f docs/netCDF4/index.html docs/index.html
=====================================
docs/index.html
=====================================
The diff for this file was not included because it is too large.
=====================================
pyproject.toml
=====================================
@@ -9,14 +9,6 @@ build-backend = "setuptools.build_meta"
[project]
name = "netCDF4"
description = "Provides an object-oriented python interface to the netCDF version 4 library"
-readme = {text = """\
-netCDF version 4 has many features not found in earlier versions of the library,
-such as hierarchical groups, zlib compression, multiple unlimited dimensions,
-and new data types. It is implemented on top of HDF5. This module implements
-most of the new features, and can read and write netCDF files compatible with
-older versions of the library. The API is modelled after Scientific.IO.NetCDF,
-and should be familiar to users of that module.
-""", content-type = "text/x-rst"}
authors = [
{name = "Jeff Whitaker", email = "jeffrey.s.whitaker at noaa.gov"},
]
@@ -47,6 +39,25 @@ dependencies = [
]
dynamic = ["version"]
+[project.optional-dependencies]
+tests = [
+ "Cython",
+ "packaging",
+ "pytest",
+]
+
+
+[project.readme]
+text = """\
+netCDF version 4 has many features not found in earlier versions of the library,
+such as hierarchical groups, zlib compression, multiple unlimited dimensions,
+and new data types. It is implemented on top of HDF5. This module implements
+most of the new features, and can read and write netCDF files compatible with
+older versions of the library. The API is modelled after Scientific.IO.NetCDF,
+and should be familiar to users of that module.
+"""
+content-type = "text/x-rst"
+
[project.scripts]
nc3tonc4 = "netCDF4.utils:nc3tonc4"
nc4tonc3 = "netCDF4.utils:nc4tonc3"
=====================================
src/netCDF4/__init__.py
=====================================
@@ -14,6 +14,9 @@ from ._netCDF4 import (__version__, __netcdf4libversion__, __hdf5libversion__,
import os
__all__ =\
['Dataset','Variable','Dimension','Group','MFDataset','MFTime','CompoundType','VLType','date2num','num2date','date2index','stringtochar','chartostring','stringtoarr','getlibversion','EnumType','get_chunk_cache','set_chunk_cache','set_alignment','get_alignment']
+__pdoc__ = {
+ 'utils': False,
+}
# if HDF5_PLUGIN_PATH not set, point to package path if plugins live there
pluginpath = os.path.join(__path__[0],'plugins')
if 'HDF5_PLUGIN_PATH' not in os.environ and\
=====================================
src/netCDF4/_netCDF4.pyx
=====================================
@@ -1,5 +1,5 @@
"""
-Version 1.6.4
+Version 1.6.5
-------------
# Introduction
@@ -64,8 +64,7 @@ types) are not supported.
so the extra compression algorithms available in netcdf-c >= 4.9.0 will automatically
be available. Otherwise, the user will have to set `HDF5_PLUGIN_PATH` explicitly
to have access to the extra compression plugins.
- - run `python setup.py build`, then `python setup.py install` (as root if
- necessary).
+ - run `pip install -v .` (as root if necessary)
- run the tests in the 'test' directory by running `python run_all.py`.
# Tutorial
@@ -1228,7 +1227,7 @@ from .utils import (_StartCountStride, _quantize, _find_dim, _walk_grps,
import sys
import functools
-__version__ = "1.6.4"
+__version__ = "1.6.5"
# Initialize numpy
import posixpath
@@ -2017,16 +2016,22 @@ cdef _get_vars(group):
free(varids) # free pointer holding variable ids.
return variables
-cdef _ensure_nc_success(ierr, err_cls=RuntimeError, filename=None):
+def _ensure_nc_success(ierr, err_cls=RuntimeError, filename=None, extra_msg=None):
# print netcdf error message, raise error.
- if ierr != NC_NOERR:
- err_str = (<char *>nc_strerror(ierr)).decode('ascii')
- if issubclass(err_cls, OSError):
- if isinstance(filename, bytes):
- filename = filename.decode()
- raise err_cls(ierr, err_str, filename)
- else:
- raise err_cls(err_str)
+ if ierr == NC_NOERR:
+ return
+
+ err_str = (<char *>nc_strerror(ierr)).decode('ascii')
+ if issubclass(err_cls, OSError):
+ if isinstance(filename, bytes):
+ filename = filename.decode()
+ raise err_cls(ierr, err_str, filename)
+
+ if extra_msg:
+ if isinstance(extra_msg, bytes):
+ extra_msg = extra_msg.decode()
+ err_str = f"{err_str}: {extra_msg}"
+ raise err_cls(err_str)
# these are class attributes that
# only exist at the python level (not in the netCDF file).
@@ -4017,6 +4022,10 @@ behavior is similar to Fortran or Matlab, but different than numpy.
cdef size_t sizep, nelemsp
cdef size_t *chunksizesp
cdef float preemptionp
+
+ # Extra information for more helpful error messages
+ error_info = f"(variable '{name}', group '{grp.name}')"
+
# flag to indicate that orthogonal indexing is supported
self.__orthogonal_indexing__ = True
# For backwards compatibility, deprecated zlib kwarg takes
@@ -4060,7 +4069,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
compression = None # if compression evaluates to False, set to None.
pass
else:
- raise ValueError("Unsupported value for compression kwarg")
+ raise ValueError(f"Unsupported value for compression kwarg {error_info}")
self._grpid = grp._grpid
# make a weakref to group to avoid circular ref (issue 218)
# keep strong reference the default behaviour (issue 251)
@@ -4118,14 +4127,15 @@ behavior is similar to Fortran or Matlab, but different than numpy.
'Variable length strings are only supported for the '
'NETCDF4 format. For other formats, consider using '
'netCDF4.stringtochar to convert string arrays into '
- 'character arrays with an additional dimension.')
+ 'character arrays with an additional dimension.'
+ f' {error_info}')
datatype = VLType(self._grp, str, None)
self._vltype = datatype
xtype = datatype._nc_type
# make sure this a valid user defined datatype defined in this Group
with nogil:
ierr = nc_inq_type(self._grpid, xtype, namstring, NULL)
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
# dtype variable attribute is a numpy datatype object.
self.dtype = datatype.dtype
elif datatype.str[1:] in _supportedtypes:
@@ -4136,7 +4146,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
# dtype variable attribute is a numpy datatype object.
self.dtype = datatype
else:
- raise TypeError('illegal primitive data type, must be one of %s, got %s' % (_supportedtypes,datatype))
+ raise TypeError(f'Illegal primitive data type, must be one of {_supportedtypes}, got {datatype} {error_info}')
if 'id' in kwargs:
self._varid = kwargs['id']
else:
@@ -4162,6 +4172,12 @@ behavior is similar to Fortran or Matlab, but different than numpy.
with nogil:
ierr = nc_def_var(self._grpid, varname, xtype, ndims,
NULL, &self._varid)
+
+ if ierr != NC_NOERR:
+ if grp.data_model != 'NETCDF4':
+ grp._enddef()
+ _ensure_nc_success(ierr, extra_msg=error_info)
+
# set chunk cache size if desired
# default is 1mb per var, can cause problems when many (1000's)
# of vars are created. This change only lasts as long as file is
@@ -4170,16 +4186,14 @@ behavior is similar to Fortran or Matlab, but different than numpy.
with nogil:
ierr = nc_get_var_chunk_cache(self._grpid, self._varid, &sizep,
&nelemsp, &preemptionp)
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
# reset chunk cache size, leave other parameters unchanged.
sizep = chunk_cache
with nogil:
ierr = nc_set_var_chunk_cache(self._grpid, self._varid, sizep,
nelemsp, preemptionp)
- _ensure_nc_success(ierr)
- if ierr != NC_NOERR:
- if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
+
# set compression, shuffle, chunking, fletcher32 and endian
# variable settings.
# don't bother for NETCDF3* formats.
@@ -4199,7 +4213,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
ierr = nc_def_var_deflate(self._grpid, self._varid, 0, 1, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
if szip:
IF HAS_SZIP_SUPPORT:
try:
@@ -4212,7 +4226,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
ierr = nc_def_var_szip(self._grpid, self._varid, iszip_coding, iszip_pixels_per_block)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='szip' only works if linked version of hdf5 has szip functionality enabled"""
@@ -4224,7 +4238,7 @@ compression='szip' only works if linked version of hdf5 has szip functionality e
ierr = nc_def_var_zstandard(self._grpid, self._varid, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='zstd' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
@@ -4237,7 +4251,7 @@ version 4.9.0 or higher netcdf-c with zstandard support, and rebuild netcdf4-pyt
ierr = nc_def_var_bzip2(self._grpid, self._varid, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='bzip2' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
@@ -4256,7 +4270,7 @@ version 4.9.0 or higher netcdf-c with bzip2 support, and rebuild netcdf4-python.
iblosc_shuffle)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='blosc_*' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
@@ -4268,7 +4282,7 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.
ierr = nc_def_var_fletcher32(self._grpid, self._varid, 1)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
# set chunking stuff.
if ndims: # don't bother for scalar variable.
if contiguous:
@@ -4296,7 +4310,7 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.
free(chunksizesp)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
# set endian-ness of variable
if endian == 'little':
with nogil:
@@ -4328,17 +4342,17 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.
ELSE:
if significant_digits is not None:
- msg = """
+ msg = f"""
significant_digits kwarg only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
version 4.9.0 or higher netcdf-c, and rebuild netcdf4-python. Otherwise, use least_significant_digit
-kwarg for quantization."""
+kwarg for quantization. {error_info}"""
raise ValueError(msg)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
else:
if endian != 'native':
- msg="only endian='native' allowed for NETCDF3 files"
+ msg=f"only endian='native' allowed for NETCDF3 files {error_info}"
raise RuntimeError(msg)
# set a fill value for this variable if fill_value keyword
# given. This avoids the HDF5 overhead of deleting and
@@ -4355,7 +4369,7 @@ kwarg for quantization."""
ierr = nc_def_var_fill(self._grpid, self._varid, 1, NULL)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
else:
if self._isprimitive or self._isenum or \
(self._isvlen and self.dtype == str):
@@ -4380,7 +4394,7 @@ kwarg for quantization."""
# set ndim attribute (number of dimensions).
with nogil:
ierr = nc_inq_varndims(self._grpid, self._varid, &numdims)
- _ensure_nc_success(ierr)
+ _ensure_nc_success(ierr, extra_msg=error_info)
self.ndim = numdims
self._name = name
# default for automatically applying scale_factor and
@@ -5234,6 +5248,8 @@ rename a `Variable` attribute named `oldname` to `newname`."""
elif hasattr(self, 'add_offset'):
data = data - self.add_offset
if self.dtype.kind in 'iu': data = numpy.around(data)
+ if self.dtype != data.dtype:
+ data = data.astype(self.dtype) # cast data to var type, if necessary.
if ma.isMA(data):
# if underlying data in masked regions of masked array
# corresponds to missing values, don't fill masked array -
@@ -5264,8 +5280,6 @@ rename a `Variable` attribute named `oldname` to `newname`."""
data = numpy.array([fillval],self.dtype)
else:
data = data.filled(fill_value=fillval)
- if self.dtype != data.dtype:
- data = data.astype(self.dtype) # cast data to var type, if necessary.
return data
def _assign_vlen(self, elem, data):
=====================================
test/tst_masked.py
=====================================
@@ -15,6 +15,7 @@ from numpy.ma import masked_all
# create an n1dim by n2dim random ranarr.
FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
FILE_NAME2 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+FILE_NAME3 = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
ndim = 10
ranarr = 100.*uniform(size=(ndim))
ranarr2 = 100.*uniform(size=(ndim))
@@ -41,6 +42,7 @@ class PrimitiveTypesTestCase(unittest.TestCase):
def setUp(self):
self.file = FILE_NAME
self.file2 = FILE_NAME2
+ self.file3 = FILE_NAME3
file = netCDF4.Dataset(self.file,'w')
file.createDimension('n', ndim)
foo = file.createVariable('maskeddata', 'f8', ('n',))
@@ -93,6 +95,19 @@ class PrimitiveTypesTestCase(unittest.TestCase):
data = dataset['v'][:]
dataset.close()
+ # issue #1271 (mask is ignored when assigning bool array to uint8 var)
+ ds = netCDF4.Dataset(self.file3, "w")
+ dim = ds.createDimension('time', 48)
+ var = ds.createVariable('blaat', np.uint8, ('time',),
+ zlib=True, complevel=4, shuffle=True, fletcher32=True,
+ fill_value=240)
+ mask = np.full((48,), False)
+ for x in range(30):
+ mask[x] = True
+ mama = ma.array(np.full((48,), True), mask=mask)
+ var[:] = mama
+ ds.close()
+
def tearDown(self):
# Remove the temporary files
os.remove(self.file)
@@ -148,6 +163,11 @@ class PrimitiveTypesTestCase(unittest.TestCase):
assert var1[:].mask.all()
assert var2[:].mask.any() == False
dataset.close()
+ # issue #1271
+ ds = netCDF4.Dataset(self.file3,"r")
+ var = ds['blaat']
+ assert np.count_nonzero(var[:].mask) == 30
+ ds.close()
if __name__ == '__main__':
unittest.main()
=====================================
test/tst_multifile.py
=====================================
@@ -5,7 +5,7 @@ from numpy.testing import assert_array_equal, assert_equal
from numpy import ma
import tempfile, unittest, os, datetime
import cftime
-from pkg_resources import parse_version
+from packaging.version import Version
nx=100; ydim=5; zdim=10
nfiles = 10
@@ -138,7 +138,7 @@ class NonuniformTimeTestCase(unittest.TestCase):
assert_equal(T.typecode(), t.typecode())
# skip this until cftime pull request #55 is in a released
# version (1.0.1?). Otherwise, fix for issue #808 breaks this
- if parse_version(cftime.__version__) >= parse_version('1.0.1'):
+ if Version(cftime.__version__) >= Version('1.0.1'):
assert_array_equal(cftime.num2date(T[:], T.units, T.calendar), dates)
assert_equal(cftime.date2index(datetime.datetime(1980, 1, 2), T), 366)
f.close()
=====================================
test/tst_multifile2.py
=====================================
@@ -5,7 +5,7 @@ from numpy.testing import assert_array_equal, assert_equal
from numpy import ma
import tempfile, unittest, os, datetime
import cftime
-from pkg_resources import parse_version
+from packaging.version import Version
nx=100; ydim=5; zdim=10
nfiles = 10
@@ -106,7 +106,7 @@ class NonuniformTimeTestCase(unittest.TestCase):
# Get the real dates
# skip this until cftime pull request #55 is in a released
# version (1.0.1?). Otherwise, fix for issue #808 breaks this
- if parse_version(cftime.__version__) >= parse_version('1.0.1'):
+ if Version(cftime.__version__) >= Version('1.0.1'):
dates = []
for file in self.files:
f = Dataset(file)
@@ -126,7 +126,7 @@ class NonuniformTimeTestCase(unittest.TestCase):
assert_equal(T.typecode(), t.typecode())
# skip this until cftime pull request #55 is in a released
# version (1.0.1?). Otherwise, fix for issue #808 breaks this
- if parse_version(cftime.__version__) >= parse_version('1.0.1'):
+ if Version(cftime.__version__) >= Version('1.0.1'):
assert_array_equal(cftime.num2date(T[:], T.units, T.calendar), dates)
assert_equal(cftime.date2index(datetime.datetime(1980, 1, 2), T), 366)
f.close()
View it on GitLab: https://salsa.debian.org/debian-gis-team/netcdf4-python/-/commit/b5422974561958d6f4ab8a30ece5767b040d0d8a
--
View it on GitLab: https://salsa.debian.org/debian-gis-team/netcdf4-python/-/commit/b5422974561958d6f4ab8a30ece5767b040d0d8a
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