Merge branch 'main' into fix_race_condition_cleanup

.github/workflows/run-tests.yml

@@ -15,7 +15,7 @@ name: Test
 
 # runs on a push on main and at the end of every day
 on:
-  # triggering on push without branch name will run tests everytime
+  # triggering on push without branch name will run tests every time
   # there is a push on any branch
   # turn it on only if needed
   push:

doc/changelog.rst

@@ -232,7 +232,7 @@ Highlights
 
 -  The new preprocessor :func:`~esmvalcore.preprocessor.extract_location` can extract arbitrary locations on the Earth using the `geopy <https://pypi.org/project/geopy/>`__ package that connects to OpenStreetMap. For details, see :ref:`Extract location <extract_location>`.
 -  Time ranges can now be extracted using the `ISO 8601 format <https://en.wikipedia.org/wiki/ISO_8601>`_. In addition, wildcards are allowed, which makes the time selection much more flexible. For details, see :ref:`Recipe section: Datasets <Datasets>`.
--  The new preprocessor :func:`~esmvalcore.preprocessor.ensemble_statistics` can calculate arbitrary statitics over all ensemble members of a simulation. In addition, the preprocessor :func:`~esmvalcore.preprocessor.multi_model_statistics` now accepts the keyword ``groupy``, which allows the calculation of multi-model statistics over arbitrary multi-model ensembles. For details, see :ref:`Ensemble statistics <ensemble statistics>` and :ref:`Multi-model statistics <multi-model statistics>`.
+-  The new preprocessor :func:`~esmvalcore.preprocessor.ensemble_statistics` can calculate arbitrary statistics over all ensemble members of a simulation. In addition, the preprocessor :func:`~esmvalcore.preprocessor.multi_model_statistics` now accepts the keyword ``groupy``, which allows the calculation of multi-model statistics over arbitrary multi-model ensembles. For details, see :ref:`Ensemble statistics <ensemble statistics>` and :ref:`Multi-model statistics <multi-model statistics>`.
 
 This release includes
 
@@ -327,7 +327,7 @@ Automatic testing
 -  Switch to Mambaforge in Github Actions tests (`#1438 <https://github.com/ESMValGroup/ESMValCore/pull/1438>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  Turn off conda lock file creation on any push on `main` branch from Github Action test (`#1489 <https://github.com/ESMValGroup/ESMValCore/pull/1489>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  Add DRS path test for IPSLCM files (`#1490 <https://github.com/ESMValGroup/ESMValCore/pull/1490>`__) `Stéphane Sénési <https://github.com/senesis>`__
--  Add a test module that runs tests of `iris` I/O everytime we notice serious bugs there (`#1510 <https://github.com/ESMValGroup/ESMValCore/pull/1510>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+-  Add a test module that runs tests of `iris` I/O every time we notice serious bugs there (`#1510 <https://github.com/ESMValGroup/ESMValCore/pull/1510>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  [Github Actions] Trigger Github Actions tests (`run-tests.yml` workflow) from a comment in a PR (`#1520 <https://github.com/ESMValGroup/ESMValCore/pull/1520>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  Update Linux condalock file (various pull requests) github-actions[bot]
 
@@ -617,7 +617,7 @@ Automatic testing
 -  Report coverage for tests that run on any pull request (`#994 <https://github.com/ESMValGroup/ESMValCore/pull/994>`__) `Bouwe Andela <https://github.com/bouweandela>`__
 -  Install ESMValTool sample data from PyPI (`#998 <https://github.com/ESMValGroup/ESMValCore/pull/998>`__) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
 -  Fix tests for multi-processing with spawn method (i.e. macOSX with Python>3.8) (`#1003 <https://github.com/ESMValGroup/ESMValCore/pull/1003>`__) `Barbara Vreede <https://github.com/bvreede>`__
--  Switch to running the Github Action test workflow every 3 hours in single thread mode to observe if Sementation Faults occur (`#1022 <https://github.com/ESMValGroup/ESMValCore/pull/1022>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+-  Switch to running the Github Action test workflow every 3 hours in single thread mode to observe if Segmentation Faults occur (`#1022 <https://github.com/ESMValGroup/ESMValCore/pull/1022>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  Revert to original Github Actions test workflow removing the 3-hourly test run with -n 1 (`#1025 <https://github.com/ESMValGroup/ESMValCore/pull/1025>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
 -  Avoid stale cache for multimodel statistics regression tests (`#1030 <https://github.com/ESMValGroup/ESMValCore/pull/1030>`__) `Bouwe Andela <https://github.com/bouweandela>`__
 -  Add newer Python versions in OSX to Github Actions (`#1035 <https://github.com/ESMValGroup/ESMValCore/pull/1035>`__) `Barbara Vreede <https://github.com/bvreede>`__

doc/quickstart/configure.rst

@@ -53,38 +53,40 @@ omitted in the file.
   # Includes log files and performance stats.
   output_dir: ~/esmvaltool_output
 
-  # Directory for storing downloaded climate data
-  download_dir: ~/climate_data
-
-  # Disable automatic downloads --- [true]/false
-  # Disable the automatic download of missing CMIP3, CMIP5, CMIP6, CORDEX,
-  # and obs4MIPs data from ESGF by default. This is useful if you are working
-  # on a computer without an internet connection.
-  offline: true
-
-  # Search ESGF for files even when files are available locally --- true/[false]
-  # This option is useful to make sure you have the latest version of all files.
-  # Remember to set ``offline: false`` if this option is set to ``true``.
-  always_search_esgf: false
-
   # Auxiliary data directory
   # Used by some recipes to look for additional datasets.
   auxiliary_data_dir: ~/auxiliary_data
 
+  # Automatic data download from ESGF --- [never]/when_missing/always
+  # Use automatic download of missing CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs
+  # data from ESGF. ``never`` disables this feature, which is useful if you are
+  # working on a computer without an internet connection, or if you have limited
+  # disk space. ``when_missing`` enables the automatic download for files that
+  # are not available locally. ``always`` will always check ESGF for the latest
+  # version of a file, and will only use local files if they correspond to that
+  # latest version.
+  search_esgf: never
+
+  # Directory for storing downloaded climate data
+  # Make sure to use a directory where you can store multiple GBs of data. Your
+  # home directory on a HPC is usually not suited for this purpose, so please
+  # change the default value in this case!
+  download_dir: ~/climate_data
+
   # Rootpaths to the data from different projects
-  # This default setting will work if files have been downloaded by the
-  # ESMValTool via ``offline=False``. Lists are also possible. For
-  # site-specific entries, see the default ``config-user.yml`` file that can be
-  # installed with the command ``esmvaltool config get_config_user``. For each
-  # project, this can be either a single path or a list of paths. Comment out
-  # these when using a site-specific path.
+  # This default setting will work if files have been downloaded by ESMValTool
+  # via ``search_esgf``. Lists are also possible. For site-specific entries,
+  # see the default ``config-user.yml`` file that can be installed with the
+  # command ``esmvaltool config get_config_user``. For each project, this can
+  # be either a single path or a list of paths. Comment out these when using a
+  # site-specific path.
   rootpath:
     default: ~/climate_data
 
   # Directory structure for input data --- [default]/ESGF/BADC/DKRZ/ETHZ/etc.
-  # This default setting will work if files have been downloaded by the
-  # ESMValTool via ``offline=False``. See ``config-developer.yml`` for
-  # definitions. Comment out/replace as per needed.
+  # This default setting will work if files have been downloaded by ESMValTool
+  # via ``search_esgf``. See ``config-developer.yml`` for definitions. Comment
+  # out/replace as per needed.
   drs:
     CMIP3: ESGF
     CMIP5: ESGF
@@ -136,11 +138,19 @@ omitted in the file.
   # ``config-developer.yml`` for an example. Set to ``null`` to use the default.
   config_developer_file: null
 
-The ``offline`` setting can be used to disable or enable automatic downloads from ESGF.
-If ``offline`` is set to ``false``, the tool will automatically download
-any CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs data that is required to run a recipe
-but not available locally and store it in ``download_dir`` using the ``ESGF``
+The ``search_esgf`` setting can be used to disable or enable automatic
+downloads from ESGF.
+If ``search_esgf`` is set to ``never``, the tool does not download any data
+from the ESGF.
+If ``search_esgf`` is set to ``when_missing``, the tool will download any CMIP3,
+CMIP5, CMIP6, CORDEX, and obs4MIPs data that is required to run a recipe but
+not available locally and store it in ``download_dir`` using the ``ESGF``
 directory structure defined in the :ref:`config-developer`.
+If ``search_esgf`` is set to ``always``, the tool will first check the ESGF for
+the needed data, regardless of any local data availability; if the data found
+on ESGF is newer than the local data (if any) or the user specifies a version
+of the data that is available only from the ESGF, then that data will be
+downloaded; otherwise, local data will be used.
 
 The ``auxiliary_data_dir`` setting is the path to place any required
 additional auxiliary data files. This is necessary because certain
@@ -199,9 +209,10 @@ The ``esmvaltool run`` command can automatically download the files required
 to run a recipe from ESGF for the projects CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs.
 The downloaded files will be stored in the ``download_dir`` specified in the
 :ref:`user configuration file`.
-To enable automatic downloads from ESGF, set ``offline: false`` in
-the :ref:`user configuration file` or provide the command line argument
-``--offline=False`` when running the recipe.
+To enable automatic downloads from ESGF, set ``search_esgf: when_missing`` or
+``search_esgf: always`` in the :ref:`user configuration file`, or provide the
+corresponding command line arguments ``--search_esgf=when_missing`` or
+``--search_esgf=always`` when running the recipe.
 
 .. note::
 

doc/quickstart/find_data.rst

@@ -483,9 +483,12 @@ retrieval parameters is explained below.
 
 Enabling automatic downloads from the ESGF
 ------------------------------------------
-To enable automatic downloads from ESGF, set ``offline: false`` in
-the :ref:`user configuration file` or provide the command line argument
-``--offline=False`` when running the recipe.
+To enable automatic downloads from ESGF, set ``search_esgf: when_missing`` (use
+local files whenever possible) or ``search_esgf: always`` (always search ESGF
+for latest version of files and only use local data if it is the latest
+version) in the :ref:`user configuration file`, or provide the corresponding
+command line arguments ``--search_esgf=when_missing`` or
+``--search_esgf=always`` when running the recipe.
 The files will be stored in the ``download_dir`` set in
 the :ref:`user configuration file`.
 

doc/quickstart/run.rst

@@ -60,12 +60,20 @@ It is also possible to explicitly change values from the config file using flags
 	esmvaltool run --argument_name argument_value recipe_example.yml
 
 To automatically download the files required to run a recipe from ESGF, set
-``offline`` to ``false`` in the :ref:`user configuration file`
-or run the tool with the command
+``search_esgf`` to ``when_missing`` (use local files whenever possible) or
+``always`` (always search ESGF for latest version of files and only use local
+data if it is the latest version) in the :ref:`user configuration file` or run
+the tool with the corresponding commands
 
 .. code:: bash
 
-    esmvaltool run --offline=False recipe_example.yml
+    esmvaltool run --search_esgf=when_missing recipe_example.yml
+
+or
+
+.. code:: bash
+
+    esmvaltool run --search_esgf=always recipe_example.yml
 
 This feature is available for projects that are hosted on the ESGF, i.e.
 CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs.

doc/recipe/overview.rst

@@ -129,10 +129,10 @@ Reading facet values from file names is not yet supported.
 See :ref:`CMOR-DRS` for more information on this kind of file organization.
 
 When (some) files are available locally, the tool will not automatically look
-for more files on ESGF. To populate a recipe with all available datasets from
-ESGF, ``offline`` should be set to ``false`` and ``always_search_esgf`` should
-be set to ``true`` in the
-:ref:`user configuration file<user configuration file>`.
+for more files on ESGF.
+To populate a recipe with all available datasets from ESGF, ``search_esgf``
+should be set to ``always`` in the :ref:`user configuration file<user
+configuration file>`.
 
 For more control over which datasets are selected, it is recommended to use
 a Python script or `Jupyter notebook <https://jupyter.org/>`_ to compose

environment.yml

@@ -26,6 +26,7 @@ dependencies:
   - nested-lookup
   - netcdf4
   - numpy
+  - packaging
   - pandas
   - pillow
   - pip!=21.3

esmvalcore/_main.py

@@ -329,6 +329,7 @@ def run(self,
             max_years=None,
             skip_nonexistent=None,
             offline=None,
+            search_esgf=None,
             diagnostics=None,
             check_level=None,
             **kwargs):
@@ -357,6 +358,19 @@ def run(self,
             If True, the run will not fail if some datasets are not available.
         offline: bool, optional
             If True, the tool will not download missing data from ESGF.
+
+            .. deprecated:: 2.8.0
+                This option has been deprecated in ESMValCore version 2.8.0 and
+                is scheduled for removal in version 2.10.0. Please use the
+                options `search_esgf=never` (for `offline=True`) or
+                `search_esgf=when_missing` (for `offline=False`). These are
+                exact replacements.
+        search_esgf: str, optional
+            If `never`, disable automatic download of data from the ESGF. If
+            `when_missing`, enable the automatic download of files that are not
+            available locally. If `always`, always check ESGF for the latest
+            version of a file, and only use local files if they correspond to
+            that latest version.
         diagnostics: list(str), optional
             Only run the selected diagnostics from the recipe. To provide more
             than one diagnostic to filter use the syntax 'diag1 diag2/script1'
@@ -384,12 +398,16 @@ def run(self,
             session['max_years'] = max_years
         if offline is not None:
             session['offline'] = offline
+        if search_esgf is not None:
+            session['search_esgf'] = search_esgf
         if skip_nonexistent is not None:
             session['skip_nonexistent'] = skip_nonexistent
         session['resume_from'] = parse_resume(resume_from, recipe)
         session.update(kwargs)
 
         self._run(recipe, session)
+        # Print warnings about deprecated configuration options again:
+        CFG.reload()
 
     @staticmethod
     def _create_session_dir(session):
@@ -421,7 +439,7 @@ def _run(self, recipe: Path, session) -> None:
                                       console_log_level=session['log_level'])
         self._log_header(session['config_file'], log_files)
 
-        if not session['offline']:
+        if session['search_esgf'] != 'never':
             from .esgf._logon import logon
             logon()
 

esmvalcore/_recipe/recipe.py

@@ -946,21 +946,22 @@ def _set_use_legacy_supplementaries(self):
                 logger.info("Running with --use-legacy-supplementaries=True")
                 self.session['use_legacy_supplementaries'] = True
 
-        # Also set the global config because it is used to check if
-        # mismatching shapes should be ignored when attaching
+        # Also adapt the global config if necessary because it is used to check
+        # if mismatching shapes should be ignored when attaching
         # supplementary variables in `esmvalcore.preprocessor.
         # _supplementary_vars.add_supplementary_variables` to avoid having to
         # introduce a new function argument that is immediately deprecated.
-        option = 'use_legacy_supplementaries'
-        CFG[option] = self.session[option]
+        session_use_legacy_supp = self.session['use_legacy_supplementaries']
+        if session_use_legacy_supp is not None:
+            CFG['use_legacy_supplementaries'] = session_use_legacy_supp
 
     def _log_recipe_errors(self, exc):
         """Log a message with recipe errors."""
         logger.error(exc.message)
         for task in exc.failed_tasks:
             logger.error(task.message)
 
-        if self.session['offline'] and any(
+        if self.session['search_esgf'] == 'never' and any(
                 isinstance(err, InputFilesNotFound)
                 for err in exc.failed_tasks):
             logger.error(
@@ -972,8 +973,10 @@ def _log_recipe_errors(self, exc):
                 "configuration file %s", self.session['config_file'])
             logger.error(
                 "To automatically download the required files to "
-                "`download_dir: %s`, set `offline: false` in %s or run the "
-                "recipe with the extra command line argument --offline=False",
+                "`download_dir: %s`, set `search_esgf: when_missing` or "
+                "`search_esgf: always` in %s, or run the recipe with the "
+                "extra command line argument --search_esgf=when_missing or "
+                "--search_esgf=always",
                 self.session['download_dir'],
                 self.session['config_file'],
             )
@@ -1299,7 +1302,7 @@ def run(self):
         filled_recipe = self.write_filled_recipe()
 
         # Download required data
-        if not self.session['offline']:
+        if self.session['search_esgf'] != 'never':
             esgf.download(self._download_files, self.session['download_dir'])
 
         self.tasks.run(max_parallel_tasks=self.session['max_parallel_tasks'])