Merge remote-tracking branch 'upstream/master' into rwp_typing

.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

.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

.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: ${{ github.workspace }}/..
       NETCDF_EXTRA_CONFIG: --enable-pnetcdf
       CC: mpicc.mpich
@@ -35,18 +35,19 @@ jobs:
         pushd pnetcdf-${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-${NETCDF_VERSION}.tar.gz
+        #wget https://downloads.unidata.ucar.edu/netcdf-c/${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${NETCDF_DIR}/include"
         export LDFLAGS="-L${NETCDF_DIR}/lib"
         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

.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@v2.21.3
       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:
@@ -135,7 +133,7 @@ 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

.github/workflows/miniconda.yml

@@ -16,7 +16,7 @@ jobs:
         os: [windows-latest, ubuntu-latest, macos-latest]
         platform: [x64, x32]
         exclude:
-          - os: macos-latest  
+          - os: macos-latest
             platform: x32
       fail-fast: false
     defaults:
@@ -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
@@ -63,13 +63,13 @@ 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
         create-args: >-
           python=${{ matrix.python-version }}
-          numpy cython pip pytest mpi4py hdf5=*=mpi* libnetcdf=*=mpi* cftime zlib certifi typing-extensions
+          numpy cython pip pytest openmpi mpi4py hdf5=*=mpi* libnetcdf=*=mpi* cftime zlib certifi typing-extensions
           --channel conda-forge
 
     - name: Install netcdf4-python with mpi
@@ -82,7 +82,7 @@ jobs:
       run: |
         cd test && python run_all.py
         cd ../examples
-        export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" 
+        export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH"
         which mpirun
         mpirun --version
         mpirun -np 4 --oversubscribe python mpi_example.py # for openmpi

Changelog

@@ -2,6 +2,9 @@
 ===============================
  * 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 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)
 ===============================
@@ -22,7 +25,7 @@
 
  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 +344,7 @@
  * 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 +418,7 @@
    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 +961,7 @@
    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 +1199,7 @@ 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 +1210,7 @@ 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 +1379,7 @@ 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).

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.