Merge branch 'main' into update_adjust_time

doc/quickstart/configure.rst

@@ -440,71 +440,6 @@ corresponding command line arguments ``--search_esgf=when_missing`` or
    tool by pressing the ``Ctrl`` and ``C`` keys on your keyboard simultaneously
    several times, edit the recipe so it contains fewer datasets and try again.
 
-For downloading some files, you may need to log in to be able to download the
-data.
-
-See the
-`ESGF user guide <https://esgf.github.io/esgf-user-support/user_guide.html>`_
-for instructions on how to create an ESGF OpenID account if you do not have
-one yet.
-Note that the OpenID account consists of 3 components instead of the usual
-two, in addition a username and password you also need the hostname of the
-provider of the ID; for example
-`esgf-data.dkrz.de <https://esgf-data.dkrz.de/user/add/?next=http://esgf-data.dkrz.de/projects/esgf-dkrz/>`_.
-Even though the account is issued by a particular host, the same OpenID
-account can be used to download data from all hosts in the ESGF.
-
-Next, configure your system so the ``esmvaltool`` can use your credentials.
-This can be done using the keyring_ package or they can be stored in a
-:ref:`configuration file <config_esgf_pyclient>`.
-
-.. _keyring:
-
-Storing credentials in keyring
-------------------------------
-First install the keyring package. Note that this requires a supported
-backend that may not be available on compute clusters, see the
-`keyring documentation <https://pypi.org/project/keyring>`__ for more
-information.
-
-.. code-block:: bash
-
-    pip install keyring
-
-Next, set your username and password by running the commands:
-
-.. code-block:: bash
-
-    keyring set ESGF hostname
-    keyring set ESGF username
-    keyring set ESGF password
-
-for example, if you created an account on the host `esgf-data.dkrz.de`_ with username
-'cookiemonster' and password 'Welcome01', run the command
-
-.. code-block:: bash
-
-    keyring set ESGF hostname
-
-this will display the text
-
-.. code-block:: bash
-
-    Password for 'hostname' in 'ESGF':
-
-type ``esgf-data.dkrz.de`` (the characters will not be shown) and press ``Enter``.
-Repeat the same procedure with ``keyring set ESGF username``, type ``cookiemonster``
-and press ``Enter`` and ``keyring set ESGF password``, type ``Welcome01`` and
-press ``Enter``.
-
-To check that you entered your credentials correctly, run:
-
-.. code-block:: bash
-
-    keyring get ESGF hostname
-    keyring get ESGF username
-    keyring get ESGF password
-
 .. _config_esgf_pyclient:
 
 Configuration file
@@ -514,49 +449,6 @@ An optional configuration file can be created for configuring how the tool uses
 to find and download data.
 The name of this file is ``~/.esmvaltool/esgf-pyclient.yml``.
 
-Logon
-`````
-In the ``logon`` section you can provide arguments that will be passed on to
-:py:meth:`pyesgf.logon.LogonManager.logon`.
-For example, you can store the hostname, username, and password or your OpenID
-account in the file like this:
-
-.. code-block:: yaml
-
-    logon:
-      hostname: "your-hostname"
-      username: "your-username"
-      password: "your-password"
-
-for example
-
-.. code-block:: yaml
-
-    logon:
-      hostname: "esgf-data.dkrz.de"
-      username: "cookiemonster"
-      password: "Welcome01"
-
-if you created an account on the host `esgf-data.dkrz.de`_ with username
-'cookiemonster' and password 'Welcome01'.
-Alternatively, you can configure an interactive log in:
-
-.. code-block:: yaml
-
-    logon:
-      interactive: true
-
-Note that storing your password in plain text in the configuration
-file is less secure.
-On shared systems, make sure the permissions of the file are set so
-only you and administrators can read it, i.e.
-
-.. code-block:: bash
-
-    ls -l ~/.esmvaltool/esgf-pyclient.yml
-
-shows permissions ``-rw-------``.
-
 Search
 ``````
 Any arguments to :py:obj:`pyesgf.search.connection.SearchConnection` can

environment.yml

@@ -18,7 +18,7 @@ dependencies:
   - fire
   - geopy
   - humanfriendly
-  - iris >=3.9.0
+  - iris >=3.10.0
   - iris-esmf-regrid >=0.10.0  # github.com/SciTools-incubator/iris-esmf-regrid/pull/342
   - iris-grib
   - isodate

esmvalcore/_main.py

@@ -444,10 +444,6 @@ def _run(self, recipe: Path, session) -> None:
                                       console_log_level=session['log_level'])
         self._log_header(session['config_file'], log_files)
 
-        if session['search_esgf'] != 'never':
-            from .esgf._logon import logon
-            logon()
-
         # configure resource logger and run program
         from ._task import resource_usage_logger
         resource_log = session.run_dir / 'resource_usage.txt'

esmvalcore/cmor/_fixes/cmip6/awi_esm_1_1_lr.py

@@ -21,9 +21,10 @@ def fix_metadata(self, cubes):
         bad_value = 'days since 0000-01-01 00:00:00'
         for cube in cubes:
             try:
-                if cube.attributes[parent_units] == bad_value:
-                    cube.attributes[parent_units] = 'days since 0001-01-01 ' \
-                        + '00:00:00'
+                if parent_units in cube.attributes:
+                    if cube.attributes[parent_units] == bad_value:
+                        cube.attributes[parent_units] = \
+                            'days since 0001-01-01 00:00:00'
             except AttributeError:
                 pass
         return cubes

esmvalcore/cmor/_fixes/icon/_base_fixes.py

@@ -16,7 +16,7 @@
 import requests
 from iris import NameConstraint
 from iris.cube import Cube, CubeList
-from iris.experimental.ugrid import Connectivity, Mesh
+from iris.mesh import Connectivity, MeshXY
 
 from esmvalcore.cmor._fixes.native_datasets import NativeDatasetFix
 from esmvalcore.local import _get_data_sources
@@ -38,24 +38,24 @@ def __init__(self, *args, **kwargs):
         self._horizontal_grids = {}
         self._meshes = {}
 
-    def _create_mesh(self, cube):
+    def _create_mesh(self, cube: Cube) -> MeshXY:
         """Create mesh from horizontal grid file.
 
         Note
         ----
-        This functions creates a new :class:`iris.experimental.ugrid.Mesh` from
-        the ``clat`` (already present in the cube), ``clon`` (already present
-        in the cube), ``vertex_index``, ``vertex_of_cell``, ``vlat``, and
-        ``vlon`` variables of the horizontal grid file.
-
-        We do not use :func:`iris.experimental.ugrid.Mesh.from_coords` with the
-        existing latitude and longitude coordinates here because this would
-        produce lots of duplicated entries for the node coordinates. The reason
-        for this is that the node coordinates are constructed from the bounds;
-        since each node is contained 6 times in the bounds array (each node is
-        shared by 6 neighboring cells) the number of nodes is 6 times higher
-        with :func:`iris.experimental.ugrid.Mesh.from_coords` compared to using
-        the information already present in the horizontal grid file.
+        This functions creates a new :class:`iris.mesh.MeshXY` from the
+        ``clat`` (already present in the cube), ``clon`` (already present in
+        the cube), ``vertex_index``, ``vertex_of_cell``, ``vlat``, and ``vlon``
+        variables of the horizontal grid file.
+
+        We do not use :func:`iris.mesh.MeshXY.from_coords` with the existing
+        latitude and longitude coordinates here because this would produce lots
+        of duplicated entries for the node coordinates. The reason for this is
+        that the node coordinates are constructed from the bounds; since each
+        node is contained 6 times in the bounds array (each node is shared by 6
+        neighboring cells) the number of nodes is 6 times higher with
+        :func:`iris.mesh.MeshXY.from_coords` compared to using the information
+        already present in the horizontal grid file.
 
         """
         horizontal_grid = self.get_horizontal_grid(cube)
@@ -91,7 +91,7 @@ def _create_mesh(self, cube):
         if not np.allclose(
                 face_lat.bounds,
                 node_lat.points[conn_node_inds],
-                **close_kwargs,
+                **close_kwargs,  # type: ignore
         ):
             logger.warning(
                 "Latitude bounds of the face coordinate ('clat_vertices' in "
@@ -108,7 +108,7 @@ def _create_mesh(self, cube):
         # differ by 360°, which is also okay.
         face_lon_bounds_to_check = face_lon.bounds % 360
         node_lon_conn_to_check = node_lon.points[conn_node_inds] % 360
-        idx_notclose = ~np.isclose(
+        idx_notclose = ~np.isclose(  # type: ignore
             face_lon_bounds_to_check,
             node_lon_conn_to_check,
             **close_kwargs,
@@ -131,7 +131,7 @@ def _create_mesh(self, cube):
             start_index=start_index,
             location_axis=0,
         )
-        mesh = Mesh(
+        mesh = MeshXY(
             topology_dimension=2,
             node_coords_and_axes=[(node_lat, 'y'), (node_lon, 'x')],
             connectivities=[connectivity],
@@ -429,8 +429,8 @@ def get_mesh(self, cube):
 
         Returns
         -------
-        iris.experimental.ugrid.Mesh
-            Mesh.
+        iris.mesh.MeshXY
+            Mesh of the cube.
 
         Raises
         ------

esmvalcore/config/_esgf_pyclient.py

@@ -1,53 +1,20 @@
 """esgf-pyclient configuration.
 
 The configuration is read from the file ~/.esmvaltool/esgf-pyclient.yml.
-
-There are four sections in the configuration file:
-
-logon: contains keyword arguments to :func:`pyesgf.logon.LogonManager.logon`
-search_connection: contains keyword arguments to
-    :class:`pyesgf.search.connection.SearchConnection`
 """
-import importlib
 import logging
 import os
 import stat
 from functools import lru_cache
 from pathlib import Path
-from types import ModuleType
-from typing import Optional
 
 import yaml
 
-keyring: Optional[ModuleType] = None
-try:
-    keyring = importlib.import_module('keyring')
-except ModuleNotFoundError:
-    pass
-
 logger = logging.getLogger(__name__)
 
 CONFIG_FILE = Path.home() / '.esmvaltool' / 'esgf-pyclient.yml'
 
 
-def get_keyring_credentials():
-    """Load credentials from keyring."""
-    logon = {}
-    if keyring is None:
-        return logon
-
-    for key in ['hostname', 'username', 'password']:
-        try:
-            value = keyring.get_password('ESGF', key)
-        except keyring.errors.NoKeyringError:
-            # No keyring backend is available
-            return logon
-        if value is not None:
-            logon[key] = value
-
-    return logon
-
-
 def read_config_file():
     """Read the configuration from file."""
     if CONFIG_FILE.exists():
@@ -77,12 +44,6 @@ def read_config_file():
 def load_esgf_pyclient_config():
     """Load the esgf-pyclient configuration."""
     cfg = {
-        # Arguments to
-        # https://esgf-pyclient.readthedocs.io/en/latest/api.html#pyesgf.logon.LogonManager.logon
-        'logon': {
-            'interactive': False,
-            'bootstrap': True,
-        },
         # Arguments to
         # https://esgf-pyclient.readthedocs.io/en/latest/api.html#pyesgf.search.connection.SearchConnection
         'search_connection': {
@@ -105,11 +66,8 @@ def load_esgf_pyclient_config():
         },
     }
 
-    keyring_cfg = get_keyring_credentials()
-    cfg['logon'].update(keyring_cfg)
-
     file_cfg = read_config_file()
-    for section in ['logon', 'search_connection']:
+    for section in ['search_connection']:
         cfg[section].update(file_cfg.get(section, {}))
 
     if 'cache' in cfg['search_connection']:

esmvalcore/esgf/_download.py

@@ -22,7 +22,6 @@
 from esmvalcore.typing import Facets
 
 from ..local import LocalFile
-from ._logon import get_credentials
 from .facets import DATASET_MAP, FACETS
 
 logger = logging.getLogger(__name__)
@@ -460,10 +459,7 @@ def _download(self, local_file, url):
 
         logger.debug("Downloading %s to %s", url, tmp_file)
         start_time = datetime.datetime.now()
-        response = requests.get(url,
-                                stream=True,
-                                timeout=TIMEOUT,
-                                cert=get_credentials())
+        response = requests.get(url, stream=True, timeout=TIMEOUT)
         response.raise_for_status()
         with tmp_file.open("wb") as file:
             # Specify chunk_size to avoid