Remove PseudoNetCDF (#8446)

dcherian · web-flow · commit 49bd63a8332c · 2023-11-13T21:53:56.000Z
diff --git a/ci/requirements/all-but-dask.yml b/ci/requirements/all-but-dask.yml
@@ -28,7 +28,6 @@ dependencies:
   - pandas
   - pint>=0.22
   - pip
-  - pseudonetcdf
   - pydap
   - pytest
   - pytest-cov
diff --git a/ci/requirements/environment-py311.yml b/ci/requirements/environment-py311.yml
@@ -32,7 +32,6 @@ dependencies:
   - pip
   - pooch
   - pre-commit
-  - pseudonetcdf
   - pydap
   - pytest
   - pytest-cov
diff --git a/ci/requirements/environment-windows-py311.yml b/ci/requirements/environment-windows-py311.yml
@@ -28,7 +28,6 @@ dependencies:
   - pint>=0.22
   - pip
   - pre-commit
-  - pseudonetcdf
   - pydap
   - pytest
   - pytest-cov
diff --git a/ci/requirements/environment-windows.yml b/ci/requirements/environment-windows.yml
@@ -28,7 +28,6 @@ dependencies:
   - pint>=0.22
   - pip
   - pre-commit
-  - pseudonetcdf
   - pydap
   - pytest
   - pytest-cov
diff --git a/ci/requirements/environment.yml b/ci/requirements/environment.yml
@@ -33,7 +33,6 @@ dependencies:
   - pip
   - pooch
   - pre-commit
-  - pseudonetcdf
   - pydap
   - pytest
   - pytest-cov
diff --git a/ci/requirements/min-all-deps.yml b/ci/requirements/min-all-deps.yml
@@ -37,7 +37,6 @@ dependencies:
   - pandas=1.4
   - pint=0.22
   - pip
-  - pseudonetcdf=3.2
   - pydap=3.3
   - pytest
   - pytest-cov
diff --git a/doc/api-hidden.rst b/doc/api-hidden.rst
@@ -591,20 +591,6 @@
    backends.H5netcdfBackendEntrypoint.guess_can_open
    backends.H5netcdfBackendEntrypoint.open_dataset
 
-   backends.PseudoNetCDFDataStore.close
-   backends.PseudoNetCDFDataStore.get_attrs
-   backends.PseudoNetCDFDataStore.get_dimensions
-   backends.PseudoNetCDFDataStore.get_encoding
-   backends.PseudoNetCDFDataStore.get_variables
-   backends.PseudoNetCDFDataStore.open
-   backends.PseudoNetCDFDataStore.open_store_variable
-   backends.PseudoNetCDFDataStore.ds
-
-   backends.PseudoNetCDFBackendEntrypoint.description
-   backends.PseudoNetCDFBackendEntrypoint.url
-   backends.PseudoNetCDFBackendEntrypoint.guess_can_open
-   backends.PseudoNetCDFBackendEntrypoint.open_dataset
-
    backends.PydapDataStore.close
    backends.PydapDataStore.get_attrs
    backends.PydapDataStore.get_dimensions
diff --git a/doc/api.rst b/doc/api.rst
@@ -1117,7 +1117,6 @@ arguments for the ``load_store`` and ``dump_to_store`` Dataset methods:
 
    backends.NetCDF4DataStore
    backends.H5NetCDFStore
-   backends.PseudoNetCDFDataStore
    backends.PydapDataStore
    backends.ScipyDataStore
    backends.ZarrStore
@@ -1133,7 +1132,6 @@ used filetypes in the xarray universe.
 
    backends.NetCDF4BackendEntrypoint
    backends.H5netcdfBackendEntrypoint
-   backends.PseudoNetCDFBackendEntrypoint
    backends.PydapBackendEntrypoint
    backends.ScipyBackendEntrypoint
    backends.StoreBackendEntrypoint
diff --git a/doc/getting-started-guide/installing.rst b/doc/getting-started-guide/installing.rst
@@ -38,9 +38,6 @@ For netCDF and IO
 - `cftime <https://unidata.github.io/cftime>`__: recommended if you
   want to encode/decode datetimes for non-standard calendars or dates before
   year 1678 or after year 2262.
-- `PseudoNetCDF <http://github.com/barronh/pseudonetcdf/>`__: recommended
-  for accessing CAMx, GEOS-Chem (bpch), NOAA ARL files, ICARTT files
-  (ffi1001) and many other.
 - `iris <https://github.com/scitools/iris>`__: for conversion to and from iris'
   Cube objects
 
diff --git a/doc/user-guide/io.rst b/doc/user-guide/io.rst
@@ -1308,27 +1308,6 @@ We recommend installing PyNIO via conda::
 .. _PyNIO backend is deprecated: https://github.com/pydata/xarray/issues/4491
 .. _PyNIO is no longer maintained: https://github.com/NCAR/pynio/issues/53
 
-.. _io.PseudoNetCDF:
-
-Formats supported by PseudoNetCDF
----------------------------------
-
-Xarray can also read CAMx, BPCH, ARL PACKED BIT, and many other file
-formats supported by PseudoNetCDF_, if PseudoNetCDF is installed.
-PseudoNetCDF can also provide Climate Forecasting Conventions to
-CMAQ files. In addition, PseudoNetCDF can automatically register custom
-readers that subclass PseudoNetCDF.PseudoNetCDFFile. PseudoNetCDF can
-identify readers either heuristically, or by a format specified via a key in
-`backend_kwargs`.
-
-To use PseudoNetCDF to read such files, supply
-``engine='pseudonetcdf'`` to :py:func:`open_dataset`.
-
-Add ``backend_kwargs={'format': '<format name>'}`` where `<format name>`
-options are listed on the PseudoNetCDF page.
-
-.. _PseudoNetCDF: https://github.com/barronh/PseudoNetCDF
-
 
 CSV and other formats supported by pandas
 -----------------------------------------
diff --git a/doc/whats-new.rst b/doc/whats-new.rst
@@ -34,7 +34,7 @@ Breaking changes
 
 Deprecations
 ~~~~~~~~~~~~
-
+- The PseudoNetCDF backend has been removed. By `Deepak Cherian <https://github.com/dcherian>`_.
 - Supplying dimension-ordered sequences to :py:meth:`DataArray.chunk` &
   :py:meth:`Dataset.chunk` is deprecated in favor of supplying a dictionary of
   dimensions, or a single ``int`` or ``"auto"`` argument covering all
@@ -4530,7 +4530,7 @@ Enhancements
 
 - New PseudoNetCDF backend for many Atmospheric data formats including
   GEOS-Chem, CAMx, NOAA arlpacked bit and many others. See
-  :ref:`io.PseudoNetCDF` for more details.
+  ``io.PseudoNetCDF`` for more details.
   By `Barron Henderson <https://github.com/barronh>`_.
 
 - The :py:class:`Dataset` constructor now aligns :py:class:`DataArray`
diff --git a/pyproject.toml b/pyproject.toml
@@ -109,7 +109,6 @@ module = [
   "opt_einsum.*",
   "pandas.*",
   "pooch.*",
-  "PseudoNetCDF.*",
   "pydap.*",
   "pytest.*",
   "scipy.*",
diff --git a/xarray/backends/__init__.py b/xarray/backends/__init__.py
@@ -13,10 +13,6 @@
 from xarray.backends.memory import InMemoryDataStore
 from xarray.backends.netCDF4_ import NetCDF4BackendEntrypoint, NetCDF4DataStore
 from xarray.backends.plugins import list_engines, refresh_engines
-from xarray.backends.pseudonetcdf_ import (
-    PseudoNetCDFBackendEntrypoint,
-    PseudoNetCDFDataStore,
-)
 from xarray.backends.pydap_ import PydapBackendEntrypoint, PydapDataStore
 from xarray.backends.pynio_ import NioDataStore
 from xarray.backends.scipy_ import ScipyBackendEntrypoint, ScipyDataStore
@@ -37,10 +33,8 @@
     "ScipyDataStore",
     "H5NetCDFStore",
     "ZarrStore",
-    "PseudoNetCDFDataStore",
     "H5netcdfBackendEntrypoint",
     "NetCDF4BackendEntrypoint",
-    "PseudoNetCDFBackendEntrypoint",
     "PydapBackendEntrypoint",
     "ScipyBackendEntrypoint",
     "StoreBackendEntrypoint",
diff --git a/xarray/backends/api.py b/xarray/backends/api.py
@@ -59,7 +59,7 @@
     T_NetcdfEngine = Literal["netcdf4", "scipy", "h5netcdf"]
     T_Engine = Union[
         T_NetcdfEngine,
-        Literal["pydap", "pynio", "pseudonetcdf", "zarr"],
+        Literal["pydap", "pynio", "zarr"],
         type[BackendEntrypoint],
         str,  # no nice typing support for custom backends
         None,
@@ -78,7 +78,6 @@
     "pydap": backends.PydapDataStore.open,
     "h5netcdf": backends.H5NetCDFStore.open,
     "pynio": backends.NioDataStore,
-    "pseudonetcdf": backends.PseudoNetCDFDataStore.open,
     "zarr": backends.ZarrStore.open_group,
 }
 
@@ -420,7 +419,7 @@ def open_dataset(
         scipy.io.netcdf (only netCDF3 supported). Byte-strings or file-like
         objects are opened by scipy.io.netcdf (netCDF3) or h5py (netCDF4/HDF).
     engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "pynio", \
-        "pseudonetcdf", "zarr", None}, installed backend \
+        "zarr", None}, installed backend \
         or subclass of xarray.backends.BackendEntrypoint, optional
         Engine to use when reading files. If not provided, the default engine
         is chosen based on available dependencies, with a preference for
@@ -452,8 +451,7 @@ def open_dataset(
         taken from variable attributes (if they exist).  If the `_FillValue` or
         `missing_value` attribute contains multiple values a warning will be
         issued and all array values matching one of the multiple values will
-        be replaced by NA. mask_and_scale defaults to True except for the
-        pseudonetcdf backend. This keyword may not be supported by all the backends.
+        be replaced by NA. This keyword may not be supported by all the backends.
     decode_times : bool, optional
         If True, decode times encoded in the standard NetCDF datetime format
         into datetime objects. Otherwise, leave them encoded as numbers.
@@ -523,7 +521,7 @@ def open_dataset(
           relevant when using dask or another form of parallelism. By default,
           appropriate locks are chosen to safely read and write files with the
           currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
-          "scipy", "pynio", "pseudonetcdf".
+          "scipy", "pynio".
 
         See engine open function for kwargs accepted by each specific engine.
 
@@ -628,7 +626,7 @@ def open_dataarray(
         scipy.io.netcdf (only netCDF3 supported). Byte-strings or file-like
         objects are opened by scipy.io.netcdf (netCDF3) or h5py (netCDF4/HDF).
     engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "pynio", \
-        "pseudonetcdf", "zarr", None}, installed backend \
+        "zarr", None}, installed backend \
         or subclass of xarray.backends.BackendEntrypoint, optional
         Engine to use when reading files. If not provided, the default engine
         is chosen based on available dependencies, with a preference for
@@ -658,8 +656,7 @@ def open_dataarray(
         taken from variable attributes (if they exist).  If the `_FillValue` or
         `missing_value` attribute contains multiple values a warning will be
         issued and all array values matching one of the multiple values will
-        be replaced by NA. mask_and_scale defaults to True except for the
-        pseudonetcdf backend. This keyword may not be supported by all the backends.
+        be replaced by NA. This keyword may not be supported by all the backends.
     decode_times : bool, optional
         If True, decode times encoded in the standard NetCDF datetime format
         into datetime objects. Otherwise, leave them encoded as numbers.
@@ -729,7 +726,7 @@ def open_dataarray(
           relevant when using dask or another form of parallelism. By default,
           appropriate locks are chosen to safely read and write files with the
           currently active dask scheduler. Supported by "netcdf4", "h5netcdf",
-          "scipy", "pynio", "pseudonetcdf".
+          "scipy", "pynio".
 
         See engine open function for kwargs accepted by each specific engine.
 
@@ -869,7 +866,7 @@ def open_mfdataset(
         You can find the file-name from which each dataset was loaded in
         ``ds.encoding["source"]``.
     engine : {"netcdf4", "scipy", "pydap", "h5netcdf", "pynio", \
-        "pseudonetcdf", "zarr", None}, installed backend \
+        "zarr", None}, installed backend \
         or subclass of xarray.backends.BackendEntrypoint, optional
         Engine to use when reading files. If not provided, the default engine
         is chosen based on available dependencies, with a preference for
diff --git a/xarray/backends/pseudonetcdf_.py b/xarray/backends/pseudonetcdf_.py
diff --git a/xarray/tests/__init__.py b/xarray/tests/__init__.py
diff --git a/xarray/tests/test_backends.py b/xarray/tests/test_backends.py
diff --git a/xarray/tests/test_plugins.py b/xarray/tests/test_plugins.py
diff --git a/xarray/util/print_versions.py b/xarray/util/print_versions.py
