Merge branch 'main' into depr-eagerly-compute-group

Author: dcherian

ci/minimum_versions.py

@@ -20,6 +20,12 @@
 
 channels = ["conda-forge"]
 platforms = ["noarch", "linux-64"]
+# these packages don't fail the CI, but will be printed in the report
+ignore_failure_packages = [
+    # remove when we can pin to pydap 3.5.1 without error
+    "pydap",
+]
+# these packages are completely ignored
 ignored_packages = [
     "coveralls",
     "pip",
@@ -171,7 +177,11 @@ def compare_versions(environments, policy_versions):
     status = {}
     for env, specs in environments.items():
         env_status = any(
-            spec.version > policy_versions[spec.name].version for spec in specs
+            (
+                (spec.version > policy_versions[spec.name].version)
+                and (spec.name not in ignore_failure_packages)
+            )
+            for spec in specs
         )
         status[env] = env_status
     return status

ci/requirements/min-all-deps.yml

@@ -42,7 +42,7 @@ dependencies:
   - pandas=2.1
   - pint=0.22
   - pip
-  - pydap=3.4
+  - pydap=3.5
   - pytest
   - pytest-cov
   - pytest-env

doc/api-hidden.rst

@@ -530,6 +530,10 @@
    Index.rename
    Index.copy
 
+   indexes.RangeIndex.start
+   indexes.RangeIndex.stop
+   indexes.RangeIndex.step
+
    backends.NetCDF4DataStore.close
    backends.NetCDF4DataStore.encode
    backends.NetCDF4DataStore.encode_attribute

doc/api.rst

@@ -1573,6 +1573,7 @@ Custom Indexes
    :toctree: generated/
 
    CFTimeIndex
+   indexes.RangeIndex
 
 Creating custom indexes
 -----------------------
@@ -1582,6 +1583,8 @@ Creating custom indexes
    cftime_range
    date_range
    date_range_like
+   indexes.RangeIndex.arange
+   indexes.RangeIndex.linspace
 
 Tutorial
 ========

doc/internals/time-coding.rst

@@ -535,3 +535,20 @@ To opt-out of timedelta decoding (see issue `Undesired decoding to timedelta64 <
 .. note::
     Note that in the future the default value of ``decode_timedelta`` will be
     ``False`` rather than ``None``.
+
+
+
+.. ipython:: python
+    :suppress:
+
+    # Cleanup
+    import os
+
+    for f in [
+        "test-datetimes1.nc",
+        "test-datetimes2.nc",
+        "test-timedeltas1.nc",
+        "test-timedeltas2.nc",
+    ]:
+        if os.path.exists(f):
+            os.remove(f)

doc/user-guide/io.rst

@@ -1245,37 +1245,44 @@ over the network until we look at particular values:
 
 .. image:: ../_static/opendap-prism-tmax.png
 
-Some servers require authentication before we can access the data. For this
-purpose we can explicitly create a :py:class:`backends.PydapDataStore`
-and pass in a `Requests`__ session object. For example for
-HTTP Basic authentication::
+Some servers require authentication before we can access the data. Pydap uses
+a `Requests`__ session object (which the user can pre-define), and this
+session object can recover `authentication`__` credentials from a locally stored
+``.netrc`` file. For example, to connect to a server that requires NASA's
+URS authentication, with the username/password credentials stored on a locally
+accessible ``.netrc``, access to OPeNDAP data should be as simple as this::
 
     import xarray as xr
     import requests
 
-    session = requests.Session()
-    session.auth = ('username', 'password')
+    my_session = requests.Session()
 
-    store = xr.backends.PydapDataStore.open('http://example.com/data',
-                                            session=session)
-    ds = xr.open_dataset(store)
+    ds_url = 'https://gpm1.gesdisc.eosdis.nasa.gov/opendap/hyrax/example.nc'
 
-`Pydap's cas module`__ has functions that generate custom sessions for
-servers that use CAS single sign-on. For example, to connect to servers
-that require NASA's URS authentication::
+    ds = xr.open_dataset(ds_url, session=my_session, engine="pydap")
 
-  import xarray as xr
-  from pydata.cas.urs import setup_session
+Moreover, a bearer token header can be included in a `Requests`__ session
+object, allowing for token-based authentication which  OPeNDAP servers can use
+to avoid some redirects.
 
-  ds_url = 'https://gpm1.gesdisc.eosdis.nasa.gov/opendap/hyrax/example.nc'
 
-  session = setup_session('username', 'password', check_url=ds_url)
-  store = xr.backends.PydapDataStore.open(ds_url, session=session)
+Lastly, OPeNDAP servers may provide endpoint URLs for different OPeNDAP protocols,
+DAP2 and DAP4. To specify which protocol between the two options to use, you can
+replace the scheme of the url with the name of the protocol. For example::
 
-  ds = xr.open_dataset(store)
+    # dap2 url
+    ds_url = 'dap2://gpm1.gesdisc.eosdis.nasa.gov/opendap/hyrax/example.nc'
+
+    # dap4 url
+    ds_url = 'dap4://gpm1.gesdisc.eosdis.nasa.gov/opendap/hyrax/example.nc'
+
+While most OPeNDAP servers implement DAP2, not all servers implement DAP4. It
+is recommended to check if the URL you are using `supports DAP4`__ by checking the
+URL on a browser.
 
 __ https://docs.python-requests.org
-__ https://www.pydap.org/en/latest/client.html#authentication
+__ https://pydap.github.io/pydap/en/notebooks/Authentication.html
+__ https://pydap.github.io/pydap/en/faqs/dap2_or_dap4_url.html
 
 .. _io.pickle:
 
@@ -1356,7 +1363,10 @@ To export just the dataset schema without the data itself, use the
     # However, `ds` (rather than the unpickled dataset) refers to the open file.  Delete
     # `ds` to close the file.
     del ds
-    os.remove("saved_on_disk.nc")
+
+    for f in ["saved_on_disk.nc", "saved_on_disk.h5"]:
+        if os.path.exists(f):
+            os.remove(f)
 
 This can be useful for generating indices of dataset contents to expose to
 search indices or other automated data discovery tools.

doc/whats-new.rst

@@ -24,10 +24,20 @@ New Features
 
 - Added `scipy-stubs <https://github.com/scipy/scipy-stubs>`_ to the ``xarray[types]`` dependencies.
   By `Joren Hammudoglu <https://github.com/jorenham>`_.
+- Improved compatibility with OPeNDAP DAP4 data model for backend engine ``pydap``. This
+  includes ``datatree`` support, and removing slashes from dimension names. By
+  `Miguel Jimenez-Urias <https://github.com/Mikejmnez>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
+- The minimum versions of some dependencies were changed
+
+  ===================== =========  =======
+   Package                    Old      New
+  ===================== =========  =======
+    pydap                    3.4     3.5.0
+  ===================== =========  =======
 
 Deprecations
 ~~~~~~~~~~~~
@@ -50,6 +60,8 @@ Documentation
 
 - Fix references to core classes in docs (:issue:`10195`, :pull:`10207`).
   By `Mattia Almansi <https://github.com/malmans2>`_.
+- Fix references to point to updated pydap documentation (:pull:`10182`).
+  By `Miguel Jimenez-Urias <https://github.com/Mikejmnez>`_.
 
 Internal Changes
 ~~~~~~~~~~~~~~~~
@@ -65,9 +77,11 @@ Andrecho, Deepak Cherian, Ian Hunt-Isaak, Karl Krauth, Mathias Hauser, Maximilia
 
 New Features
 ~~~~~~~~~~~~
-
 - Allow setting a ``fill_value`` for Zarr format 3 arrays. Specify ``fill_value`` in ``encoding`` as usual.
   (:issue:`10064`). By `Deepak Cherian <https://github.com/dcherian>`_.
+- Added :py:class:`indexes.RangeIndex` as an alternative, memory saving Xarray index representing
+  a 1-dimensional bounded interval with evenly spaced floating values (:issue:`8473`, :pull:`10076`).
+  By `Benoit Bovy <https://github.com/benbovy>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~

pyproject.toml

@@ -346,6 +346,8 @@ filterwarnings = [
   "default:the `pandas.MultiIndex` object:FutureWarning:xarray.tests.test_variable",
   "default:Using a non-tuple sequence for multidimensional indexing is deprecated:FutureWarning",
   "default:Duplicate dimension names present:UserWarning:xarray.namedarray.core",
+  # Zarr 2 V3 implementation
+  "ignore:Zarr-Python is not in alignment with the final V3 specification",
   # TODO: this is raised for vlen-utf8, consolidated metadata, U1 dtype
   "ignore:is currently not part .* the Zarr version 3 specification.",
   # TODO: remove once we know how to deal with a changed signature in protocols