From f7b87f5c5753358b0a82ed00bc23074101bba773 Mon Sep 17 00:00:00 2001 From: Randall Pittman Date: Thu, 25 Jul 2024 08:58:30 -0700 Subject: [PATCH 01/36] [docs] Add link to auth page on rc files. Incidentally pdoc re-inserted missing date2index and date2num stuff. --- docs/index.html | 17 ++++++++++++----- src/netCDF4/_netCDF4.pyx | 6 +++++- 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/docs/index.html b/docs/index.html index 730c955d7..377e45741 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1173,7 +1173,8 @@

Functions

def date2index(dates, nctime, calendar=None, select='exact', has_year_zero=None)
-

Return indices of a netCDF time variable corresponding to the given dates.

+

date2index(dates, nctime, calendar=None, select=u'exact', has_year_zero=None)

+

Return indices of a netCDF time variable corresponding to the given dates.

dates: A datetime object or a sequence of datetime objects. The datetime objects should not include a time-zone offset.

nctime: A netCDF time variable object. The nctime object must have a @@ -1212,7 +1213,8 @@

Functions

def date2num(dates, units, calendar=None, has_year_zero=None, longdouble=False)
-

Return numeric time values given datetime objects. The units +

date2num(dates, units, calendar=None, has_year_zero=None, longdouble=False)

+

Return numeric time values given datetime objects. The units of the numeric time values are described by the units argument and the calendar keyword. The datetime objects must be in UTC with no time-zone offset. @@ -1292,7 +1294,8 @@

Functions

def num2date(times, units, calendar='standard', only_use_cftime_datetimes=True, only_use_python_datetimes=False, has_year_zero=None)
-

Return datetime objects given numeric time values. The units +

num2date(times, units, calendar=u'standard', only_use_cftime_datetimes=True, only_use_python_datetimes=False, has_year_zero=None)

+

Return datetime objects given numeric time values. The units of the numeric time values are described by the units argument and the calendar keyword. The returned datetime objects represent UTC with no time-zone offset, even if the specified @@ -1348,14 +1351,18 @@

Functions

rc_get(key)

-

Returns the internal netcdf-c rc table value corresponding to key.

+

Returns the internal netcdf-c rc table value corresponding to key. +See https://docs.unidata.ucar.edu/netcdf-c/current/auth.html +for more information on rc files and values.

def rc_set(key, value)

rc_set(key, value)

-

Sets the internal netcdf-c rc table value corresponding to key.

+

Sets the internal netcdf-c rc table value corresponding to key. +See https://docs.unidata.ucar.edu/netcdf-c/current/auth.html +for more information on rc files and values.

def set_alignment(threshold, alignment) diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx index 9bbc3aaf6..c31ab3f72 100644 --- a/src/netCDF4/_netCDF4.pyx +++ b/src/netCDF4/_netCDF4.pyx @@ -1323,6 +1323,8 @@ def rc_get(key): **```rc_get(key)```** Returns the internal netcdf-c rc table value corresponding to key. +See +for more information on rc files and values. """ cdef int ierr cdef char *keyc @@ -1345,7 +1347,9 @@ def rc_set(key, value): **```rc_set(key, value)```** Sets the internal netcdf-c rc table value corresponding to key. - """ +See +for more information on rc files and values. +""" cdef int ierr cdef char *keyc cdef char *valuec From 3a6d94425dfc7bec0613d8b8897095122a5999d5 Mon Sep 17 00:00:00 2001 From: Randall Pittman Date: Thu, 25 Jul 2024 09:05:36 -0700 Subject: [PATCH 02/36] (minor) simplify diff --- src/netCDF4/_netCDF4.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx index c31ab3f72..d4c6f7d53 100644 --- a/src/netCDF4/_netCDF4.pyx +++ b/src/netCDF4/_netCDF4.pyx @@ -1349,7 +1349,7 @@ def rc_set(key, value): Sets the internal netcdf-c rc table value corresponding to key. See for more information on rc files and values. -""" + """ cdef int ierr cdef char *keyc cdef char *valuec From 9996c01f14cbdf1729a79a83e5816ad21f5ff071 Mon Sep 17 00:00:00 2001 From: Randall Pittman Date: Mon, 29 Jul 2024 09:17:02 -0700 Subject: [PATCH 03/36] Correct auth link --- docs/index.html | 4 ++-- src/netCDF4/_netCDF4.pyx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/index.html b/docs/index.html index 377e45741..f120d187c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1352,7 +1352,7 @@

Functions

rc_get(key)

Returns the internal netcdf-c rc table value corresponding to key. -See https://docs.unidata.ucar.edu/netcdf-c/current/auth.html +See https://docs.unidata.ucar.edu/netcdf-c/current/md_auth.html for more information on rc files and values.

@@ -1361,7 +1361,7 @@

Functions

rc_set(key, value)

Sets the internal netcdf-c rc table value corresponding to key. -See https://docs.unidata.ucar.edu/netcdf-c/current/auth.html +See https://docs.unidata.ucar.edu/netcdf-c/current/md_auth.html for more information on rc files and values.

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx index d4c6f7d53..6023406c9 100644 --- a/src/netCDF4/_netCDF4.pyx +++ b/src/netCDF4/_netCDF4.pyx @@ -1323,7 +1323,7 @@ def rc_get(key): **```rc_get(key)```** Returns the internal netcdf-c rc table value corresponding to key. -See +See for more information on rc files and values. """ cdef int ierr @@ -1347,7 +1347,7 @@ def rc_set(key, value): **```rc_set(key, value)```** Sets the internal netcdf-c rc table value corresponding to key. -See +See for more information on rc files and values. """ cdef int ierr From 0a777315e9f436412819b14606550fcd4de57826 Mon Sep 17 00:00:00 2001 From: Masahiro Sakai Date: Thu, 1 Aug 2024 10:13:47 +0900 Subject: [PATCH 04/36] fix not to use iendian when the return value of nc_inq_var_endian() is not NC_NOERR iendian is left uninitialized when nc_inq_var_endian() returns NC_ENOTNC4. --- src/netCDF4/_netCDF4.pyx | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx index 6023406c9..2f49870fe 100644 --- a/src/netCDF4/_netCDF4.pyx +++ b/src/netCDF4/_netCDF4.pyx @@ -2062,10 +2062,11 @@ cdef _get_vars(group, bint auto_complex=False): endianness = None with nogil: ierr = nc_inq_var_endian(_grpid, varid, &iendian) - if ierr == NC_NOERR and iendian == NC_ENDIAN_LITTLE: - endianness = '<' - elif iendian == NC_ENDIAN_BIG: - endianness = '>' + if ierr == NC_NOERR: + if iendian == NC_ENDIAN_LITTLE: + endianness = '<' + elif iendian == NC_ENDIAN_BIG: + endianness = '>' # check to see if it is a supported user-defined type. try: datatype = _nctonptype[xtype] From 892717312a2290ad3625e67611fc138a328210e0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 5 Aug 2024 03:19:05 +0000 Subject: [PATCH 05/36] Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 in the github-actions group Bumps the github-actions group with 1 update: [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel). Updates `pypa/cibuildwheel` from 2.19.2 to 2.20.0 - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](https://github.com/pypa/cibuildwheel/compare/v2.19.2...v2.20.0) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] --- .github/workflows/cibuildwheel.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml index 5eb8bb975..558c65685 100644 --- a/.github/workflows/cibuildwheel.yml +++ b/.github/workflows/cibuildwheel.yml @@ -92,7 +92,7 @@ jobs: echo "Setting CIBW_SKIP=$CIBW_SKIP" - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels" - uses: pypa/cibuildwheel@v2.19.2 + uses: pypa/cibuildwheel@v2.20.0 env: CIBW_SKIP: ${{ env.CIBW_SKIP }} CIBW_ARCHS: ${{ matrix.arch }} From 3ebb93b7684544464f14e535984b617e17e98784 Mon Sep 17 00:00:00 2001 From: Filipe Fernandes Date: Tue, 13 Aug 2024 16:03:48 +0200 Subject: [PATCH 06/36] all wheels are built with cibuildwheel now --- README.wheels.md | 100 ----------------------------------------------- 1 file changed, 100 deletions(-) delete mode 100644 README.wheels.md diff --git a/README.wheels.md b/README.wheels.md deleted file mode 100644 index 83626b78f..000000000 --- a/README.wheels.md +++ /dev/null @@ -1,100 +0,0 @@ -# Building and uploading wheels - -## For OSX - -We automate OSX wheel building using a custom github repository that builds on -the travis-ci OSX machines. - -The travis-ci interface for the builds is : -https://travis-ci.org/MacPython/netcdf4-python-wheels - -The driving github repository is : -https://github.com/MacPython/netcdf4-python-wheels - -### How it works - -The wheel-building repository: - -* does a fresh build of the required C / C++ libraries; -* builds a netcdf4-python wheel, linking against these fresh builds; -* processes the wheel using [delocate](https://pypi.python.org/pypi/delocate). - `delocate` copies the required dynamic libraries into the wheel and relinks - the extension modules against the copied libraries; -* uploads the built wheel to http://wheels.scipy.org (a Rackspace container - kindly donated by Rackspace to scikit-learn). - -The resulting wheel is therefore self-contained and does not need any external -dynamic libraries apart from those provided as standard by OSX. - -### Triggering a build - -You will need write permission to the github repository to trigger new builds -on the travis-ci interface. Contact us on the mailing list if you need this. - -You can trigger a build by: - -* making a commit to the `netcdf4-python-wheels` repository (e.g. with `git - commit --allow-empty`); or -* clicking on the circular arrow icon towards the top right of the travis-ci - page, to rerun the previous build. - -In general, it is better to trigger a build with a commit, because this makes -a new set of build products and logs, keeping the old ones for reference. -Keeping the old build logs helps us keep track of previous problems and -successful builds. - -### Which netcdf4-python commit does the repository build? - -By default, the `netcd4-python-wheels` repository is usually set up to build -the latest git tag. To check whether this is so have a look around line 5 of -`.travis.yml` in the `netcdf4-python-wheels` repository. You should see -something like: - -``` -- BUILD_COMMIT='latest-tag' -``` - -If this is commented out, then the repository is set up to build the current -commit in the `netcdf4-python` submodule of the repository. If it is set to -another value then it will be specifying a commit to build. - -You can therefore build any arbitrary commit by specificying the commit hash -or branch name or tag name in this line of the `.travis.yml` file. - -### Uploading the built wheels to pypi - -Be careful, http://wheels.scipy.org points to a container on a distributed -content delivery network. It can take up to 15 minutes for the new wheel file -to get updated into the container at http://wheels.scipy.org. - -When the wheels are updated, you can of course just download them to your -machine manually, and then upload them manually to pypi, or by using -[twine][twine]. You can also use a script for doing this, housed at : -https://github.com/MacPython/terryfy/blob/master/wheel-uploader - -You'll need [twine][twine] and [beautiful soup 4][bs4]. - -You will typically have a directory on your machine where you store wheels, -called a `wheelhouse`. The typical call for `wheel-uploader` would then -be something like: - -``` -wheel-uploader -v -w ~/wheelhouse netCDF4 1.1.8 -``` - -where: - -* `-v` means give verbose messages; -* `-w ~/wheelhouse` means download the wheels from https://wheels.scipy.org to - the directory `~/wheelhouse`; -* `netCDF4` is the root name of the wheel(s) to download / upload; -* `1.1.8` is the version to download / upload. - -So, in this case, `wheel-uploader` will download all wheels starting with -`netCDF4-1.1.8-` from http://wheels.scipy.org to `~/wheelhouse`, then upload -them to pypi. - -Of course, you will need permissions to upload to pypi, for this to work. - -[twine]: https://pypi.python.org/pypi/twine -[bs4]: https://pypi.python.org/pypi/beautifulsoup4 From 2aeb78b5416e23f305331f98fffa46f07976a64a Mon Sep 17 00:00:00 2001 From: Filipe Fernandes Date: Tue, 13 Aug 2024 16:04:16 +0200 Subject: [PATCH 07/36] fix minor typos --- Changelog | 14 +++++++------- README.md | 2 +- docs/index.html | 8 ++++---- examples/reading_netCDF.ipynb | 2 +- examples/writing_netCDF.ipynb | 2 +- include/membuf.pyx | 2 +- include/netCDF4.pxi | 4 ++-- setup.cfg | 2 +- setup.py | 2 +- src/netCDF4/_netCDF4.pyx | 8 ++++---- test/test_alignment.py | 2 +- 11 files changed, 24 insertions(+), 24 deletions(-) diff --git a/Changelog b/Changelog index f1e82e2b3..4015f67a1 100644 --- a/Changelog +++ b/Changelog @@ -22,7 +22,7 @@ version 1.6.5 (tag v1.6.5rel) =============================== - * fix for issue #1271 (mask ignored if bool MA assinged to uint8 var) + * fix for issue #1271 (mask ignored if bool MA assigned to uint8 var) * include information on specific object when reporting errors from netcdf-c * python 3.12 wheels added, support for python 3.7 removed. @@ -341,7 +341,7 @@ * Fix for auto scaling and masking when _Unsigned attribute set (create view as unsigned type after scaling and masking). Issue #671. * Always mask values outside valid_min, valid_max (not just when - missing_value attribue present). Issue #672. + missing_value attribute present). Issue #672. * Fix setup.py so pip install doesn't fail if cython not installed. setuptools >= 18.0 now required for installation (Issue #666). @@ -415,7 +415,7 @@ reading, a vlen string array attribute is returned as a list of strings. To write, use var.setncattr_string("name", ["two", "strings"]).) * Fix for issue #596 - julian day calculations wrong for negative years, - caused incorrect rountrip num2date(date2num(date)) roundtrip for dates with year + caused incorrect roundtrip num2date(date2num(date)) roundtrip for dates with year < 0. * Make sure negative years work in utime.num2date (issue #596). * raise NotImplementedError when trying to pickle Dataset, Variable, @@ -958,7 +958,7 @@ lib after the 4.2 release). Controlled by kwarg 'diskless' to netCDF4.Dataset (default False). diskless=True when creating a file results in a file that exists only in memory, closing the file - makes the data disapper, except if persist=True keyword given in + makes the data disappear, except if persist=True keyword given in which case it is persisted to a disk file on close. diskless=True when opening a file creates an in-memory copy of the file for faster access. @@ -1196,7 +1196,7 @@ version 0.8.1 (svn revision 744) * Experimental variable-length (vlen) data type support added. - * changes to accomodate compound types in netcdf-4.1-beta snapshots. + * changes to accommodate compound types in netcdf-4.1-beta snapshots. Compound types now work correctly for snapshots >= 20090603. * Added __len__ method and 'size' property to Variable class. @@ -1207,7 +1207,7 @@ version 0.8.1 (svn revision 744) * Fixed bug occurring when indexing with a numpy array of length 1. - * Fixed bug that occured when -1 was used as a variable index. + * Fixed bug that occurred when -1 was used as a variable index. * enabled 'shared access' mode for NETCDF3 formatted files (mode='ws', 'r+s' or 'as'). Writes in shared mode are unbuffered, which can @@ -1376,7 +1376,7 @@ version 0.7.3 (svn revision 501) to work as slice indices. * (netCDF4_classic only) try to make sure file is not left in 'define mode' - when execption is raised. + when exception is raised. * if slicing a variable results in a array with shape (1,), just return a scalar (except for compound types). diff --git a/README.md b/README.md index 59cf74311..8fa99985b 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ For details on the latest updates, see the [Changelog](https://github.com/Unidat 06/13/2024: Version [1.7.0](https://pypi.python.org/pypi/netCDF4/1.7.0) released. Add support for complex numbers via `auto_complex` keyword to `Dataset` ([PR #1295](https://github.com/Unidata/netcdf4-python/pull/1295)) 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), +Fix for issue #1271 (mask ignored if bool MA assigned to uint8 var), support for python 3.12 (removal of python 3.7 support), more informative error messages. diff --git a/docs/index.html b/docs/index.html index f120d187c..29e5a7c3c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -289,7 +289,7 @@

Dimensions in a netCDF file

<class 'netCDF4._netCDF4.Dimension'>: name = 'lon', size = 144

Dimension names can be changed using the -Datatset.renameDimension method of a Dataset or +Dataset.renameDimension method of a Dataset or Group instance.

Variables in a netCDF file

netCDF variables behave much like python multidimensional array objects @@ -901,7 +901,7 @@

Parallel IO

The optional comm keyword may be used to specify a particular MPI communicator (MPI_COMM_WORLD is used by default). Each process (or rank) -can now write to the file indepedently. +can now write to the file independently. In this example the process rank is written to a different variable index on each task

>>> d = nc.createDimension('dim',4)
@@ -1164,7 +1164,7 @@ 
Functions

 Will be converted to a array of strings, where each string has a fixed
 length of b.shape[-1] characters.

 
optional kwarg encoding can be used to specify character encoding (default
-utf-8). If encoding is 'none' or 'bytes', a numpy.string_ btye array is
+utf-8). If encoding is 'none' or 'bytes', a numpy.string_ byte array is
 returned.

 
returns a numpy string array with datatype 'UN' (or 'SN') and shape
 b.shape[:-1] where where N=b.shape[-1].

@@ -2884,7 +2884,7 @@ 
Methods

 The value of _Encoding
 is the unicode encoding that is used to decode the bytes into strings.

 
When numpy string data is written to a variable it is converted back to
-indiviual bytes, with the number of bytes in each string equalling the
+individual bytes, with the number of bytes in each string equalling the
 rightmost dimension of the variable.

 
The default value of chartostring() is True
 (automatic conversions are performed).

diff --git a/examples/reading_netCDF.ipynb b/examples/reading_netCDF.ipynb
index 670b06340..95d33957d 100644
--- a/examples/reading_netCDF.ipynb
+++ b/examples/reading_netCDF.ipynb
@@ -479,7 +479,7 @@
     "### Finding the latitude and longitude indices of 50N, 140W\n",
     "\n",
     "- The `X` and `Y` dimensions don't look like longitudes and latitudes\n",
-    "- Use the auxilary coordinate variables named in the `coordinates` variable attribute, `Latitude` and `Longitude`"
+    "- Use the auxiliary coordinate variables named in the `coordinates` variable attribute, `Latitude` and `Longitude`"
    ]
   },
   {
diff --git a/examples/writing_netCDF.ipynb b/examples/writing_netCDF.ipynb
index 2e2fef5ef..61927929f 100644
--- a/examples/writing_netCDF.ipynb
+++ b/examples/writing_netCDF.ipynb
@@ -710,7 +710,7 @@
     "\n",
     "netCDF version 4 added support for organizing data in hierarchical groups.\n",
     "\n",
-    "- analagous to directories in a filesystem. \n",
+    "- analogous to directories in a filesystem. \n",
     "- Groups serve as containers for variables, dimensions and attributes, as well as other groups. \n",
     "- A `netCDF4.Dataset` creates a special group, called the 'root group', which is similar to the root directory in a unix filesystem. \n",
     "\n",
diff --git a/include/membuf.pyx b/include/membuf.pyx
index b964453e9..21a916db4 100644
--- a/include/membuf.pyx
+++ b/include/membuf.pyx
@@ -12,7 +12,7 @@ cdef memview_fromptr(void *memory, size_t size):
     buf.size = size # size of pointer in bytes
     return memoryview(buf)
 
-# private extension type that implements buffer protocal.
+# private extension type that implements buffer protocol.
 cdef class _MemBuf:
     cdef const void *memory
     cdef size_t size
diff --git a/include/netCDF4.pxi b/include/netCDF4.pxi
index f748bf82c..62b9be609 100644
--- a/include/netCDF4.pxi
+++ b/include/netCDF4.pxi
@@ -55,7 +55,7 @@ cdef extern from "netcdf.h":
         NC_NETCDF4 # Use netCDF-4/HDF5 format 
         NC_CLASSIC_MODEL # Enforce strict netcdf-3 rules. 
         # Use these 'mode' flags for both nc_create and nc_open.
-        NC_SHARE # Share updates, limit cacheing 
+        NC_SHARE # Share updates, limit caching 
         # The following flag currently is ignored, but use in
         # nc_open() or nc_create() may someday support use of advisory
         # locking to prevent multiple writers from clobbering a file 
@@ -111,7 +111,7 @@ cdef extern from "netcdf.h":
         NC_FILL
         NC_NOFILL
         # Starting with version 3.6, there are different format netCDF
-        # files. 4.0 instroduces the third one. These defines are only for
+        # files. 4.0 introduces the third one. These defines are only for
         # the nc_set_default_format function.
         NC_FORMAT_CLASSIC 
         NC_FORMAT_64BIT   
diff --git a/setup.cfg b/setup.cfg
index 55736d8b9..c0afd570c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,7 @@ use_ncconfig=True
 # use szip_libdir and szip_incdir.
 #szip_dir = /usr/local
 # if netcdf lib was build statically with HDF4 support,
-# uncomment and set to hdf4 lib (libmfhdf and libdf) nstall location.
+# uncomment and set to hdf4 lib (libmfhdf and libdf) install location.
 # If the libraries and include files are installed in separate locations,
 # use hdf4_libdir and hdf4_incdir.
 #hdf4_dir = /usr/local
diff --git a/setup.py b/setup.py
index c23eb0348..b17f09ef5 100644
--- a/setup.py
+++ b/setup.py
@@ -182,7 +182,7 @@ def extract_version(CYTHON_FNAME):
     HAS_NCCONFIG = False
 
 # make sure USE_NCCONFIG from environment takes
-# precendence over use_ncconfig from setup.cfg (issue #341).
+# precedence over use_ncconfig from setup.cfg (issue #341).
 if use_ncconfig and not USE_NCCONFIG:
     USE_NCCONFIG = use_ncconfig
 elif not USE_NCCONFIG:
diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 6023406c9..b8573270d 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -285,7 +285,7 @@ and whether it is unlimited.
 ```
 
 `Dimension` names can be changed using the
-`Datatset.renameDimension` method of a `Dataset` or
+`Dataset.renameDimension` method of a `Dataset` or
 `Group` instance.
 
 ## Variables in a netCDF file
@@ -997,7 +997,7 @@ use the `parallel` keyword to enable parallel access.
 
 The optional `comm` keyword may be used to specify a particular
 MPI communicator (`MPI_COMM_WORLD` is used by default).  Each process (or rank)
-can now write to the file indepedently.  In this example the process rank is
+can now write to the file independently.  In this example the process rank is
 written to a different variable index on each task
 
 ```python
@@ -5625,7 +5625,7 @@ of the the rightmost dimension of the variable).  The value of `_Encoding`
 is the unicode encoding that is used to decode the bytes into strings.
 
 When numpy string data is written to a variable it is converted back to
-indiviual bytes, with the number of bytes in each string equalling the
+individual bytes, with the number of bytes in each string equalling the
 rightmost dimension of the variable.
 
 The default value of `chartostring` is `True`
@@ -6751,7 +6751,7 @@ Will be converted to a array of strings, where each string has a fixed
 length of `b.shape[-1]` characters.
 
 optional kwarg `encoding` can be used to specify character encoding (default
-`utf-8`). If `encoding` is 'none' or 'bytes', a `numpy.string_` btye array is
+`utf-8`). If `encoding` is 'none' or 'bytes', a `numpy.string_` byte array is
 returned.
 
 returns a numpy string array with datatype `'UN'` (or `'SN'`) and shape
diff --git a/test/test_alignment.py b/test/test_alignment.py
index 3f7333cd6..39c437535 100644
--- a/test/test_alignment.py
+++ b/test/test_alignment.py
@@ -134,7 +134,7 @@ def test_setting_alignment(self):
         for line in h5ls_results.split('\n'):
             if not line.startswith(' '):
                 data_variable = line.split(' ')[0]
-            # only process the data variables we care to inpsect
+            # only process the data variables we care to inspect
             if data_variable not in addresses:
                 continue
             line = line.strip()

From b2e1c0b15b2fe388a80c8b1242fc3b2e0d4f2eed Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 17 Sep 2024 04:02:42 +0000
Subject: [PATCH 08/36] Bump pypa/cibuildwheel in the github-actions group
 across 1 directory

Bumps the github-actions group with 1 update in the / directory: [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel).


Updates `pypa/cibuildwheel` from 2.20.0 to 2.21.1
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.20.0...v2.21.1)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: github-actions
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/cibuildwheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 558c65685..5284f428e 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -92,7 +92,7 @@ jobs:
         echo "Setting CIBW_SKIP=$CIBW_SKIP"
 
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.20.0
+      uses: pypa/cibuildwheel@v2.21.1
       env:
         CIBW_SKIP: ${{ env.CIBW_SKIP }}
         CIBW_ARCHS: ${{ matrix.arch }}

From 324dacca7faa427d99072f83d6635286396ced25 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 22 Sep 2024 09:40:49 -0600
Subject: [PATCH 09/36] fix for compiling with netcdf-c 4.7.4 (issue #1363)

---
 .github/workflows/build_old.yml      | 2 +-
 external/nc_complex/src/nc_complex.c | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_old.yml b/.github/workflows/build_old.yml
index eeaa61c3b..2c7233819 100644
--- a/.github/workflows/build_old.yml
+++ b/.github/workflows/build_old.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       PNETCDF_VERSION: 1.12.1
-      NETCDF_VERSION: 4.8.1
+      NETCDF_VERSION: 4.7.4
       NETCDF_DIR: ${{ github.workspace }}/..
       NETCDF_EXTRA_CONFIG: --enable-pnetcdf
       CC: mpicc.mpich
diff --git a/external/nc_complex/src/nc_complex.c b/external/nc_complex/src/nc_complex.c
index 68decb02c..4063d4fdc 100644
--- a/external/nc_complex/src/nc_complex.c
+++ b/external/nc_complex/src/nc_complex.c
@@ -9,6 +9,11 @@
 
 #include "nc_complex_version.h"
 
+// to enable compilation with older versions of netcdf-c
+#ifndef NC_FORMATX_NCZARR
+#define NC_FORMATX_NCZARR    (10)
+#endif
+
 // NOLINTBEGIN(bugprone-assignment-in-if-condition)
 #define CHECK(func)           \
     do {                      \

From 72a45b7e80ed0d68f16671756e8609e06add9fdf Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 22 Sep 2024 09:50:45 -0600
Subject: [PATCH 10/36] use sudo for make install

---
 .github/workflows/build_latest.yml | 4 ++--
 .github/workflows/build_master.yml | 2 +-
 .github/workflows/build_old.yml    | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_latest.yml b/.github/workflows/build_latest.yml
index 079774710..bd797bd1e 100644
--- a/.github/workflows/build_latest.yml
+++ b/.github/workflows/build_latest.yml
@@ -35,7 +35,7 @@ jobs:
         pushd pnetcdf-${PNETCDF_VERSION}
         ./configure --prefix $NETCDF_DIR --enable-shared --disable-fortran --disable-cxx
         make -j 2
-        make install
+        sudo make install
         popd
         echo "Download and build netCDF version ${NETCDF_VERSION}"
         wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
@@ -46,7 +46,7 @@ jobs:
         export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
         ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 $NETCDF_EXTRA_CONFIG
         make -j 2
-        make install
+        sudo make install
         popd
 
 #   - name: The job has failed
diff --git a/.github/workflows/build_master.yml b/.github/workflows/build_master.yml
index f8f841636..48f901648 100644
--- a/.github/workflows/build_master.yml
+++ b/.github/workflows/build_master.yml
@@ -35,7 +35,7 @@ jobs:
         autoreconf -i
         ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 
         make -j 2
-        make install
+        sudo make install
         popd
 
 #   - name: The job has failed
diff --git a/.github/workflows/build_old.yml b/.github/workflows/build_old.yml
index 2c7233819..18a9ad187 100644
--- a/.github/workflows/build_old.yml
+++ b/.github/workflows/build_old.yml
@@ -35,7 +35,7 @@ jobs:
         pushd pnetcdf-${PNETCDF_VERSION}
         ./configure --prefix $NETCDF_DIR --enable-shared --disable-fortran --disable-cxx
         make -j 2
-        make install
+        sudo make install
         popd
         echo "Download and build netCDF version ${NETCDF_VERSION}"
         wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
@@ -46,7 +46,7 @@ jobs:
         export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
         ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 $NETCDF_EXTRA_CONFIG
         make -j 2
-        make install
+        sudo make install
         popd
 
 #   - name: The job has failed

From a0ff68a050759c834045e15543275fa7540a269b Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 22 Sep 2024 10:03:40 -0600
Subject: [PATCH 11/36] get netcdf-c 4.7.4 from a mirror

---
 .github/workflows/build_old.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_old.yml b/.github/workflows/build_old.yml
index 18a9ad187..484a627e2 100644
--- a/.github/workflows/build_old.yml
+++ b/.github/workflows/build_old.yml
@@ -38,7 +38,8 @@ jobs:
         sudo make install
         popd
         echo "Download and build netCDF version ${NETCDF_VERSION}"
-        wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
+        #wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
+        wget https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-${NETCDF_VERSION}.tar.gz
         tar -xzf netcdf-c-${NETCDF_VERSION}.tar.gz
         pushd netcdf-c-${NETCDF_VERSION}
         export CPPFLAGS="-I/usr/include/hdf5/mpich -I${NETCDF_DIR}/include"

From b33dad5fee079334d0c20a35fc548ace60c59887 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 22 Sep 2024 10:18:49 -0600
Subject: [PATCH 12/36] specify openmpi

---
 .github/workflows/miniconda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/miniconda.yml b/.github/workflows/miniconda.yml
index a79c8e572..ac20f1ec8 100644
--- a/.github/workflows/miniconda.yml
+++ b/.github/workflows/miniconda.yml
@@ -69,7 +69,7 @@ jobs:
         init-shell: bash
         create-args: >-
           python=${{ matrix.python-version }}
-          numpy cython pip pytest mpi4py hdf5=*=mpi* libnetcdf=*=mpi* cftime zlib certifi
+          numpy cython pip pytest openmpi mpi4py hdf5=*=mpi* libnetcdf=*=mpi* cftime zlib certifi
           --channel conda-forge
 
     - name: Install netcdf4-python with mpi

From 91d6e98d7b9df516aaf75a41c4233347a40b213a Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 22 Sep 2024 16:56:30 -0600
Subject: [PATCH 13/36] update cibuildwheel

---
 .github/workflows/cibuildwheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 558c65685..5284f428e 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -92,7 +92,7 @@ jobs:
         echo "Setting CIBW_SKIP=$CIBW_SKIP"
 
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.20.0
+      uses: pypa/cibuildwheel@v2.21.1
       env:
         CIBW_SKIP: ${{ env.CIBW_SKIP }}
         CIBW_ARCHS: ${{ matrix.arch }}

From 6e11ed9598ebe66eb672250d8676c9e7e64614ff Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 4 Oct 2024 03:25:23 +0000
Subject: [PATCH 14/36] Bump the github-actions group across 1 directory with 2
 updates

Bumps the github-actions group with 2 updates in the / directory: [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) and [mamba-org/setup-micromamba](https://github.com/mamba-org/setup-micromamba).


Updates `pypa/cibuildwheel` from 2.21.1 to 2.21.2
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.21.1...v2.21.2)

Updates `mamba-org/setup-micromamba` from 1 to 2
- [Release notes](https://github.com/mamba-org/setup-micromamba/releases)
- [Commits](https://github.com/mamba-org/setup-micromamba/compare/v1...v2)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: github-actions
- dependency-name: mamba-org/setup-micromamba
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: github-actions
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/cibuildwheel.yml | 4 ++--
 .github/workflows/miniconda.yml    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 5284f428e..acd0fb855 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -92,7 +92,7 @@ jobs:
         echo "Setting CIBW_SKIP=$CIBW_SKIP"
 
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.21.1
+      uses: pypa/cibuildwheel@v2.21.2
       env:
         CIBW_SKIP: ${{ env.CIBW_SKIP }}
         CIBW_ARCHS: ${{ matrix.arch }}
@@ -135,7 +135,7 @@ jobs:
           python-version: 3.x
 
       - name: Setup Micromamba Python ${{ matrix.python-version }}
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: build
           init-shell: bash
diff --git a/.github/workflows/miniconda.yml b/.github/workflows/miniconda.yml
index ac20f1ec8..893e60cf5 100644
--- a/.github/workflows/miniconda.yml
+++ b/.github/workflows/miniconda.yml
@@ -29,7 +29,7 @@ jobs:
         submodules: true
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -63,7 +63,7 @@ jobs:
         submodules: true
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash

From 2e8118600b56ab63646e8533473903719c8bd42c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Oct 2024 03:27:17 +0000
Subject: [PATCH 15/36] Bump pypa/cibuildwheel from 2.21.2 to 2.21.3 in the
 github-actions group

Bumps the github-actions group with 1 update: [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel).


Updates `pypa/cibuildwheel` from 2.21.2 to 2.21.3
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.21.2...v2.21.3)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: github-actions
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/cibuildwheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index acd0fb855..c7f025676 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -92,7 +92,7 @@ jobs:
         echo "Setting CIBW_SKIP=$CIBW_SKIP"
 
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.21.2
+      uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_SKIP: ${{ env.CIBW_SKIP }}
         CIBW_ARCHS: ${{ matrix.arch }}

From 2728bcf679958076600680f7355f06f8457b2f97 Mon Sep 17 00:00:00 2001
From: Filipe Fernandes 
Date: Thu, 10 Oct 2024 10:43:19 +0200
Subject: [PATCH 16/36] remove bad OPeNDAP URL

---
 .github/workflows/cibuildwheel.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index acd0fb855..15a87d6ef 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -92,7 +92,7 @@ jobs:
         echo "Setting CIBW_SKIP=$CIBW_SKIP"
 
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.21.2
+      uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_SKIP: ${{ env.CIBW_SKIP }}
         CIBW_ARCHS: ${{ matrix.arch }}
@@ -107,8 +107,6 @@ jobs:
         CIBW_TEST_COMMAND: >
           python -c "import netCDF4; print(f'netCDF4 v{netCDF4.__version__}')"
           && pytest -s -rxs -v {project}/test
-          && URL="https://icdc.cen.uni-hamburg.de/thredds/dodsC/ftpthredds/hamtide/m2.hamtide11a.nc"
-          && python -c "from netCDF4 import Dataset; nc=Dataset(\"${URL}\"); print(nc)"
 
     - uses: actions/upload-artifact@v4
       with:

From 459dd04357c85c76691e42178a89ad75bfde561a Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Oct 2024 13:59:03 -0600
Subject: [PATCH 17/36] add method to return variable _FillValue
 (get_fill_value)

---
 src/netCDF4/_netCDF4.pyx | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 8679706ba..d7e3af767 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4638,6 +4638,27 @@ behavior is similar to Fortran or Matlab, but different than numpy.
 return the group that this `Variable` is a member of."""
         return self._grp
 
+    def get_fill_value(self):
+        """
+**`get_fill_value(self)`**
+
+return the `_FillValue` associated with this `Variable` (None if data is not
+pre-filled)."""
+        cdef int ierr, no_fill
+        with nogil:
+            ierr = nc_inq_var_fill(self._grpid,self._varid,&no_fill,NULL)
+        _ensure_nc_success(ierr)
+        if no_fill == 1:
+            return None
+        else:
+            try:
+                fillval = self._FillValue
+            except AttributeError:
+                if self._isprimitive:
+                    return default_fillvals[self.dtype.str[1:]]
+                else:
+                    return None
+
     def ncattrs(self):
         """
 **`ncattrs(self)`**

From 61121e525c3ec45ec8a5665ed5e3d731446f56cf Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Oct 2024 14:03:59 -0600
Subject: [PATCH 18/36] add comments

---
 src/netCDF4/_netCDF4.pyx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index d7e3af767..d155600c9 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4648,15 +4648,18 @@ pre-filled)."""
         with nogil:
             ierr = nc_inq_var_fill(self._grpid,self._varid,&no_fill,NULL)
         _ensure_nc_success(ierr)
-        if no_fill == 1:
+        if no_fill == 1: # no filling for this variable
             return None
         else:
             try:
                 fillval = self._FillValue
             except AttributeError:
+                # _FillValue attribute not set, use default _FillValue
+                # for primite datatypes.
                 if self._isprimitive:
-                    return default_fillvals[self.dtype.str[1:]]
+                    return np.asarray(default_fillvals[self.dtype.str[1:]],self.dtype)
                 else:
+                    # no default filling for non-primitive datatypes.
                     return None
 
     def ncattrs(self):

From 821c74086608c03935ffe99f7099baa820cbc703 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Oct 2024 14:09:50 -0600
Subject: [PATCH 19/36] update

---
 src/netCDF4/_netCDF4.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index d155600c9..df196d2a0 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4657,7 +4657,7 @@ pre-filled)."""
                 # _FillValue attribute not set, use default _FillValue
                 # for primite datatypes.
                 if self._isprimitive:
-                    return np.asarray(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    return np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
                 else:
                     # no default filling for non-primitive datatypes.
                     return None

From 1668b9900867d107fcc42cba4e7dabbddfc9c483 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Oct 2024 14:27:26 -0600
Subject: [PATCH 20/36] update

---
 src/netCDF4/_netCDF4.pyx | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index df196d2a0..7e3c397a4 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4654,12 +4654,17 @@ pre-filled)."""
             try:
                 fillval = self._FillValue
             except AttributeError:
-                # _FillValue attribute not set, use default _FillValue
-                # for primite datatypes.
-                if self._isprimitive:
+                # _FillValue attribute not set, see if we can retrieve _FillValue.
+                # for primitive data types.
+                if self._isprimitive
                     return np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    #fillval = np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    #with nogil:
+                    #    ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,fillval)
+                    #_ensure_nc_success(ierr)
+                    #return fillval
                 else:
-                    # no default filling for non-primitive datatypes.
+                    # no default filling for non-primitive data types.
                     return None
 
     def ncattrs(self):

From 365fbab2d582fcd0d88070539a98ade3d797aa2d Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Oct 2024 14:32:01 -0600
Subject: [PATCH 21/36] update

---
 src/netCDF4/_netCDF4.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 7e3c397a4..babc6d242 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4660,7 +4660,7 @@ pre-filled)."""
                     return np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
                     #fillval = np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
                     #with nogil:
-                    #    ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,fillval)
+                    #    ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,PyArray_DATA(fillval))
                     #_ensure_nc_success(ierr)
                     #return fillval
                 else:

From 33da47badf0a10b135d586cd28cde9dfbd58f99b Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 09:57:50 -0600
Subject: [PATCH 22/36] use C API to get default fill values

---
 src/netCDF4/_netCDF4.pyx | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index babc6d242..5f5728775 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4656,13 +4656,12 @@ pre-filled)."""
             except AttributeError:
                 # _FillValue attribute not set, see if we can retrieve _FillValue.
                 # for primitive data types.
-                if self._isprimitive
-                    return np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
-                    #fillval = np.array(default_fillvals[self.dtype.str[1:]],self.dtype)
-                    #with nogil:
-                    #    ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,PyArray_DATA(fillval))
-                    #_ensure_nc_success(ierr)
-                    #return fillval
+                if self._isprimitive:
+                    #return numpy.array(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    fillval = numpy.array(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,PyArray_DATA(fillval))
+                    _ensure_nc_success(ierr)
+                    return fillval
                 else:
                     # no default filling for non-primitive data types.
                     return None

From d2099dcb92f8bdddc57bcfb231f0260c637ca031 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:01:38 -0600
Subject: [PATCH 23/36] update

---
 src/netCDF4/_netCDF4.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 5f5728775..56cc62207 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4658,7 +4658,7 @@ pre-filled)."""
                 # for primitive data types.
                 if self._isprimitive:
                     #return numpy.array(default_fillvals[self.dtype.str[1:]],self.dtype)
-                    fillval = numpy.array(default_fillvals[self.dtype.str[1:]],self.dtype)
+                    fillval = numpy.empty((),self.dtype)
                     ierr=nc_inq_var_fill(self._grpid,self._varid,&no_fill,PyArray_DATA(fillval))
                     _ensure_nc_success(ierr)
                     return fillval

From 0deeb124e583f28f90859cab3db0eb36aa2acf57 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:14:50 -0600
Subject: [PATCH 24/36] update

---
 src/netCDF4/_netCDF4.pyx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 56cc62207..2f53efdc1 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4653,6 +4653,7 @@ pre-filled)."""
         else:
             try:
                 fillval = self._FillValue
+                return fillval
             except AttributeError:
                 # _FillValue attribute not set, see if we can retrieve _FillValue.
                 # for primitive data types.

From 3d9b9d9323a03a87e68d6b32fbe21e480fa201a1 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:26:28 -0600
Subject: [PATCH 25/36] add test case

---
 test/test_get_fill_value.py | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 test/test_get_fill_value.py

diff --git a/test/test_get_fill_value.py b/test/test_get_fill_value.py
new file mode 100644
index 000000000..0e588c0bc
--- /dev/null
+++ b/test/test_get_fill_value.py
@@ -0,0 +1,36 @@
+import unittest, os, tempfile
+import netCDF4
+from numpy.testing import assert_array_equal
+import numpy as np
+
+fill_val = np.array(9.9e31)
+
+class TestGetFillValue(unittest.TestCase):
+    def setUp(self):
+        self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
+        f = netCDF4.Dataset(self.testfile, 'w')
+        dim = f.createDimension('x',10)
+        for dt in netCDF4.default_fillvals.keys():
+            if not dt.startswith('c'):
+                v = f.createVariable(dt+'_var',dt,dim)
+        v = f.createVariable('float_var',np.float64,dim,fill_value=fill_val)
+        f.close()
+        
+    def tearDown(self):
+        os.remove(self.testfile)
+
+    def runTest(self):
+        f = netCDF4.Dataset(self.testfile, "r")
+        # no _FillValue set, test that default fill value returned
+        for dt in netCDF4.default_fillvals.keys():
+            if not dt.startswith('c'):
+                fillval = np.array(netCDF4.default_fillvals[dt])
+                if dt == 'S1': fillval = fillval.astype(dt)
+                v = f[dt+'_var']
+                assert_array_equal(fillval, v.get_fill_value())
+        # _FillValue attribute is set.
+        v = f['float_var']
+        assert_array_equal(fill_val, v.get_fill_value())
+
+if __name__ == '__main__':
+    unittest.main()

From b4b6eee4162dbcdd664e5179c777adeafe1e4f28 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:27:04 -0600
Subject: [PATCH 26/36] update

---
 test/test_get_fill_value.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/test_get_fill_value.py b/test/test_get_fill_value.py
index 0e588c0bc..79591b803 100644
--- a/test/test_get_fill_value.py
+++ b/test/test_get_fill_value.py
@@ -5,6 +5,8 @@
 
 fill_val = np.array(9.9e31)
 
+# test Variable.get_fill_value
+
 class TestGetFillValue(unittest.TestCase):
     def setUp(self):
         self.testfile = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name

From d16a91fd3f4aea30ad2194eae1e8f4ee9eda1aa7 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:34:23 -0600
Subject: [PATCH 27/36] update docstring

---
 src/netCDF4/_netCDF4.pyx | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 2f53efdc1..f3d0a2f91 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4039,7 +4039,11 @@ behavior is similar to Fortran or Matlab, but different than numpy.
         value that the variable gets filled with before any data is written to it)
         is replaced with this value.  If fill_value is set to `False`, then
         the variable is not pre-filled. The default netCDF fill values can be found
-        in the dictionary `netCDF4.default_fillvals`.
+        in the dictionary `netCDF4.default_fillvals`. If not set, the netCDF default
+        `_FillValue` will be used but no `_FillValue` attribute will be created
+        (this is the default behavior of the netcdf-c library). `Variable.get_fill_value`
+        can be used to retrieve the fill value, even if the `_FillValue` attribute is
+        not set.
 
         **`chunk_cache`**: If specified, sets the chunk cache size for this variable.
         Persists as long as Dataset is open. Use `set_var_chunk_cache` to
@@ -4642,8 +4646,9 @@ return the group that this `Variable` is a member of."""
         """
 **`get_fill_value(self)`**
 
-return the `_FillValue` associated with this `Variable` (None if data is not
-pre-filled)."""
+return the fill value associated with this `Variable` (None if data is not
+pre-filled). Works even if default fill value was used, and `_FillValue` attribute
+does not exist."""
         cdef int ierr, no_fill
         with nogil:
             ierr = nc_inq_var_fill(self._grpid,self._varid,&no_fill,NULL)

From d740b0a98430d27ae510a437e60a1d1a809e96b9 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 10:37:05 -0600
Subject: [PATCH 28/36] update

---
 src/netCDF4/_netCDF4.pyx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index f3d0a2f91..5e083ea49 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4035,12 +4035,12 @@ behavior is similar to Fortran or Matlab, but different than numpy.
         Ignored if `significant_digts` not specified. If 'BitRound' is used, then
         `significant_digits` is interpreted as binary (not decimal) digits.
 
-        **`fill_value`**:  If specified, the default netCDF `_FillValue` (the
+        **`fill_value`**:  If specified, the default netCDF fill value (the
         value that the variable gets filled with before any data is written to it)
-        is replaced with this value.  If fill_value is set to `False`, then
-        the variable is not pre-filled. The default netCDF fill values can be found
-        in the dictionary `netCDF4.default_fillvals`. If not set, the netCDF default
-        `_FillValue` will be used but no `_FillValue` attribute will be created
+        is replaced with this value, and the `_FillValue` attribute is set.
+        If fill_value is set to `False`, then the variable is not pre-filled.
+        The default netCDF fill values can be found in the dictionary `netCDF4.default_fillvals`.
+        If not set, the default fill value will be used but no `_FillValue` attribute will be created
         (this is the default behavior of the netcdf-c library). `Variable.get_fill_value`
         can be used to retrieve the fill value, even if the `_FillValue` attribute is
         not set.

From f50a70df84be4655d2e4d0a3e70a51ef584bf2cb Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 12:41:45 -0600
Subject: [PATCH 29/36] close file

---
 test/test_get_fill_value.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/test_get_fill_value.py b/test/test_get_fill_value.py
index 79591b803..f325f4456 100644
--- a/test/test_get_fill_value.py
+++ b/test/test_get_fill_value.py
@@ -33,6 +33,7 @@ def runTest(self):
         # _FillValue attribute is set.
         v = f['float_var']
         assert_array_equal(fill_val, v.get_fill_value())
+        f.close()
 
 if __name__ == '__main__':
     unittest.main()

From 5d922e40f16109f7b1cd79b8563400b3e32ced86 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 13:29:41 -0600
Subject: [PATCH 30/36] add get_fill_value to stub

---
 src/netCDF4/__init__.pyi | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/netCDF4/__init__.pyi b/src/netCDF4/__init__.pyi
index 1a709dd35..68e18dcae 100644
--- a/src/netCDF4/__init__.pyi
+++ b/src/netCDF4/__init__.pyi
@@ -465,6 +465,7 @@ class Variable(Generic[T_Datatype]):
     def renameAttribute(self, oldname: str, newname: str) -> None: ...
     def assignValue(self, val: Any) -> None: ...
     def getValue(self) -> Any: ...
+    def get_fill_value(self) -> Any: ...
     def set_auto_chartostring(self, chartostring: bool) -> None: ...
     def use_nc_get_vars(self, use_nc_get_vars: bool) -> None: ...
     def set_auto_maskandscale(self, maskandscale: bool) -> None: ...

From 1f67c941b24a413834bee5f7ecee7c6a7597db6f Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 13:33:37 -0600
Subject: [PATCH 31/36] update

---
 Changelog | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Changelog b/Changelog
index 4015f67a1..4c635ce8f 100644
--- a/Changelog
+++ b/Changelog
@@ -2,6 +2,8 @@
 ===============================
  * add static type hints (PR #1302)
  * Expose nc_rc_set, nc_rc_get (via rc_set, rc_get module functions). (PR #1348)
+ * Add Variable.get_fill_value (issue #1374, PR #1375).
+ * Fix NETCDF3 endian error (issue #1373, PR #1355).
 
  version 1.7.1 (tag v1.7.1rel)
 ===============================

From aa9452a5f49b5098e349fcaed8975f2e1cb2b239 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 14:00:56 -0600
Subject: [PATCH 32/36] add fill_value='default' option

---
 src/netCDF4/_netCDF4.pyx    | 13 ++++++++++---
 test/test_get_fill_value.py |  4 ++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 5e083ea49..341151381 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4041,9 +4041,10 @@ behavior is similar to Fortran or Matlab, but different than numpy.
         If fill_value is set to `False`, then the variable is not pre-filled.
         The default netCDF fill values can be found in the dictionary `netCDF4.default_fillvals`.
         If not set, the default fill value will be used but no `_FillValue` attribute will be created
-        (this is the default behavior of the netcdf-c library). `Variable.get_fill_value`
-        can be used to retrieve the fill value, even if the `_FillValue` attribute is
-        not set.
+        (this is the default behavior of the netcdf-c library). If you want to use the 
+        default fill value, but have the `_FillValue` attribute set, use
+        `fill_value='default'` (note - this only works for primitive data types). ``Variable.get_fill_value`
+        can be used to retrieve the fill value, even if the `_FillValue` attribute is not set.
 
         **`chunk_cache`**: If specified, sets the chunk cache size for this variable.
         Persists as long as Dataset is open. Use `set_var_chunk_cache` to
@@ -4407,6 +4408,12 @@ behavior is similar to Fortran or Matlab, but different than numpy.
                     if ierr != NC_NOERR:
                         if grp.data_model != 'NETCDF4': grp._enddef()
                         _ensure_nc_success(ierr, extra_msg=error_info)
+                elif fill_value == 'default':
+                    if self._isprimitive:
+                        fillval = numpy.array(default_fillvals[self.dtype.str[1:]])
+                        if not fillval.dtype.isnative: fillval.byteswap(True)
+                        _set_att(self._grp, self._varid, '_FillValue',\
+                                 fillval, xtype=xtype)
                 else:
                     if self._isprimitive or self._isenum or \
                        (self._isvlen and self.dtype == str):
diff --git a/test/test_get_fill_value.py b/test/test_get_fill_value.py
index f325f4456..257a3121e 100644
--- a/test/test_get_fill_value.py
+++ b/test/test_get_fill_value.py
@@ -16,6 +16,8 @@ def setUp(self):
             if not dt.startswith('c'):
                 v = f.createVariable(dt+'_var',dt,dim)
         v = f.createVariable('float_var',np.float64,dim,fill_value=fill_val)
+        # test fill_value='default' option (issue #1374)
+        v2 = f.createVariable('float_var2',np.float64,dim,fill_value='default')
         f.close()
         
     def tearDown(self):
@@ -33,6 +35,8 @@ def runTest(self):
         # _FillValue attribute is set.
         v = f['float_var']
         assert_array_equal(fill_val, v.get_fill_value())
+        v = f['float_var2']
+        assert_array_equal(np.array(netCDF4.default_fillvals['f8']), v._FillValue)
         f.close()
 
 if __name__ == '__main__':

From f3eba108e29402fee10c465e5a4727fc76336646 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 14:06:32 -0600
Subject: [PATCH 33/36] update

---
 Changelog | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Changelog b/Changelog
index 4c635ce8f..bc46e06ce 100644
--- a/Changelog
+++ b/Changelog
@@ -2,7 +2,8 @@
 ===============================
  * add static type hints (PR #1302)
  * Expose nc_rc_set, nc_rc_get (via rc_set, rc_get module functions). (PR #1348)
- * Add Variable.get_fill_value (issue #1374, PR #1375).
+ * Add Variable.get_fill_value and allow `fill_value='default'` to 
+   set `_FillValue` using default fill values.  (issue #1374, PR #1375).
  * Fix NETCDF3 endian error (issue #1373, PR #1355).
 
  version 1.7.1 (tag v1.7.1rel)

From 801e7b611f4c015552ab7681b840b359fe562846 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 14:15:52 -0600
Subject: [PATCH 34/36] add warning if fill_value='default' used for non
 primitive data type

---
 src/netCDF4/_netCDF4.pyx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index 341151381..e6d20a7db 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4414,6 +4414,11 @@ behavior is similar to Fortran or Matlab, but different than numpy.
                         if not fillval.dtype.isnative: fillval.byteswap(True)
                         _set_att(self._grp, self._varid, '_FillValue',\
                                  fillval, xtype=xtype)
+                    else:
+                        msg = """
+WARNING: there is no default fill value for this data type, so fill_value='default'
+does not do anything."""
+                        warnings.warn(msg)
                 else:
                     if self._isprimitive or self._isenum or \
                        (self._isvlen and self.dtype == str):

From bff03a4791283076907f7515718cd3092b4ff5fe Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 17:40:03 -0600
Subject: [PATCH 35/36] fix typos in docstrings

---
 src/netCDF4/_netCDF4.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/netCDF4/_netCDF4.pyx b/src/netCDF4/_netCDF4.pyx
index e6d20a7db..7c92f09bd 100644
--- a/src/netCDF4/_netCDF4.pyx
+++ b/src/netCDF4/_netCDF4.pyx
@@ -4043,7 +4043,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
         If not set, the default fill value will be used but no `_FillValue` attribute will be created
         (this is the default behavior of the netcdf-c library). If you want to use the 
         default fill value, but have the `_FillValue` attribute set, use
-        `fill_value='default'` (note - this only works for primitive data types). ``Variable.get_fill_value`
+        `fill_value='default'` (note - this only works for primitive data types). `Variable.get_fill_value`
         can be used to retrieve the fill value, even if the `_FillValue` attribute is not set.
 
         **`chunk_cache`**: If specified, sets the chunk cache size for this variable.
@@ -4658,7 +4658,7 @@ return the group that this `Variable` is a member of."""
         """
 **`get_fill_value(self)`**
 
-return the fill value associated with this `Variable` (None if data is not
+return the fill value associated with this `Variable` (returns `None` if data is not
 pre-filled). Works even if default fill value was used, and `_FillValue` attribute
 does not exist."""
         cdef int ierr, no_fill

From 6e30d7bbe2d550b38cf007397b2d230ed1e8ccf2 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Mon, 21 Oct 2024 17:40:31 -0600
Subject: [PATCH 36/36] update docs

---
 docs/index.html | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/docs/index.html b/docs/index.html
index 29e5a7c3c..8484e66d6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -289,7 +289,7 @@ 
Dimensions in a netCDF file

 <class 'netCDF4._netCDF4.Dimension'>: name = 'lon', size = 144

Dimension names can be changed using the -Dataset.renameDimension method of a Dataset or +Dataset.renameDimension() method of a Dataset or Group instance.

Variables in a netCDF file

netCDF variables behave much like python multidimensional array objects @@ -2676,12 +2676,16 @@

Instance variables

Ignored if significant_digts not specified. If 'BitRound' is used, then significant_digits is interpreted as binary (not decimal) digits.

fill_value: -If specified, the default netCDF _FillValue (the +If specified, the default netCDF fill value (the value that the variable gets filled with before any data is written to it) -is replaced with this value. -If fill_value is set to False, then -the variable is not pre-filled. The default netCDF fill values can be found -in the dictionary netCDF4.default_fillvals.

+is replaced with this value, and the _FillValue attribute is set. +If fill_value is set to False, then the variable is not pre-filled. +The default netCDF fill values can be found in the dictionary netCDF4.default_fillvals. +If not set, the default fill value will be used but no _FillValue attribute will be created +(this is the default behavior of the netcdf-c library). If you want to use the +default fill value, but have the _FillValue attribute set, use +fill_value='default' (note - this only works for primitive data types). Variable.get_fill_value() +can be used to retrieve the fill value, even if the _FillValue attribute is not set.

chunk_cache: If specified, sets the chunk cache size for this variable. Persists as long as Dataset is open. Use set_var_chunk_cache to change it when Dataset is re-opened.

@@ -2806,6 +2810,15 @@

Methods

return a tuple of Dimension instances associated with this Variable.

+
+def get_fill_value(self) +
+
+

get_fill_value(self)

+

return the fill value associated with this Variable (returns None if data is not +pre-filled). Works even if default fill value was used, and _FillValue attribute +does not exist.

+
def get_var_chunk_cache(self)
@@ -3241,6 +3254,7 @@

Variablefilters
  • getValue
  • get_dims
    • +
  • get_fill_value
  • get_var_chunk_cache
  • getncattr
  • group