Reduce formatting changes

Author: Klaus Zimmermann

doc/develop/fixing_data.rst

@@ -10,11 +10,11 @@ data that is read using
 ESMValCore also allows for some departures with compliance (see
 :ref:`cmor_check_strictness`). Beyond that situation, some datasets
 (either model or observations) contain (known) errors that would
-normally prevent them from being processed. The issues can be in the
-metadata describing the dataset and/or in the actual data.  Typical
-examples of such errors are missing or wrong attributes (e.g.
-attribute ''units'' says 1e-9 but data are actually in 1e-6), missing
-or mislabeled coordinates (e.g. ''lev'' instead of ''plev'' or missing
+normally prevent them from being processed. The issues can be in
+the metadata describing the dataset and/or in the actual data.
+Typical examples of such errors are missing or wrong attributes (e.g.
+attribute ''units'' says 1e-9 but data are actually in 1e-6), missing or
+mislabeled coordinates (e.g. ''lev'' instead of ''plev'' or missing
 coordinate bounds like ''lat_bnds'') or problems with the actual data
 (e.g. cloud liquid water only instead of sum of liquid + ice as
 specified by the CMIP data request).
@@ -23,10 +23,19 @@ As an extreme case, some others data sources simply are not NetCDF
 files and must go through other data load function.
 
 The ESMValCore can apply on the fly fixes to such datasets when
-issues can be fixed automatically.  This is implemented for a set
-of `Natively supported non-CMIP datasets`_.  The following provide
+issues can be fixed automatically. This is implemented for a set
+of `Natively supported non-CMIP datasets`_. The following provide
 details on how to design such fixes.
 
+.. note::
+
+  **CMORizer scripts**. Support for many observational and reanalysis
+  datasets is also possible through a priori reformatting by
+  :ref:`CMORizer scripts in the ESMValTool <esmvaltool:new-dataset>`,
+  which are rather relevant for datasets of small volume
+
+.. _fix_structure:
+
 .. note::
 
   **CMORizer scripts**.  Support for many observational and reanalysis
@@ -337,14 +346,23 @@ Natively supported non-CMIP datasets
 Some fixed datasets and native models formats are supported through
 the ``native6`` project or through a dedicated project.
 
-.. _fixing_native_models:
+ERA5 and MSWEP datasets
+-----------------------
+Put the files containing the data in the directory that you have configured
+for the ``native6`` project in your :ref:`user configuration file`, in a
+subdirectory called ``Tier{tier}/{dataset}/{version}/{frequency}/{short_name}``.
+Replace the items in curly braces by the values used in the variable/dataset
+definition in the :ref:`recipe <recipe_overview>`.
+Below is a list of datasets currently supported.
+
+ERA5
+~~~~
 
 Native models : IPSL-CM6,... 
 -----------------------------
 
-The following models are natively supported through the procedure
-described above (:ref:`fix_structure`) and at
-:ref:`configure_native_models`:
+MSWEP
+~~~~~
 
   - **IPSL-CM6** : both output formats (i.e. the ``Output`` and the
     ``Analyse / Time series`` formats) are supported, and should be
@@ -402,6 +420,40 @@ datasets currently supported :
 
     For more info: http://www.gloh2o.org/
 
+.. _fixing_native_models:
+
+Native models : IPSL-CM6,...
+-----------------------------
+
+The following models are natively supported through the procedure
+described above (:ref:`fix_structure`) and at
+:ref:`configure_native_models`:
+
+  - **IPSL-CM6** : both output formats (i.e. the ``Output`` and the
+    ``Analyse / Time series`` formats) are supported, and should be
+    configured in recipes as e.g.:
+
+    .. code-block:: yaml
+
+      datasets:
+        - {simulation: CM61-LR-hist-03.1950, exp: piControl, freq: Analyse/TS_MO,
+           account: p86caub,  status: PROD, dataset: IPSL-CM6, project: IPSLCM,
+           root: /thredds/tgcc/store}
+        - {simulation: CM61-LR-hist-03.1950, exp: historical, freq: Output/MO,
+           account: p86caub,  status: PROD, dataset: IPSL-CM6, project: IPSLCM,
+           root: /thredds/tgcc/store}
+
+    .. _ipslcm_extra_facets_example:
+
+    The ``Output`` format is an example of a case where variables are
+    grouped in multi-variable files, which name cannot be computed
+    directly from datasets attributes alone but requires to use an
+    extra_facets file, which principles are explained in
+    :ref:`extra_facets`, and which content is :download:`available here
+    </../esmvalcore/_config/extra_facets/ipslcm-mappings.yml>`. These
+    multi-variable files must also undergo some data selection, which
+    may involve an external process for performance purpose.
+
 .. _extra-facets-fixes:
 
 Use of extra facets in fixes

doc/quickstart/configure.rst

@@ -176,8 +176,8 @@ It will be installed along with ESMValCore and can also be viewed on GitHub:
 `esmvalcore/config-developer.yml
 <https://github.com/ESMValGroup/ESMValCore/blob/main/esmvalcore/config-developer.yml>`_.
 This configuration file describes the file system structure and CMOR tables for several
-key projects (CMIP6, CMIP5, obs4mips, OBS6, OBS) on several key machines (e.g.
-BADC, CP4CDS, DKRZ, ETHZ, SMHI, BSC), and for native output data for some
+key projects (CMIP6, CMIP5, obs4mips, OBS6, OBS) on several key machines (e.g. BADC, CP4CDS, DKRZ,
+ETHZ, SMHI, BSC), and for native output data for some
 models (IPSL, ... see :ref:`configure_native_models`).
 CMIP data is stored as part of the Earth System Grid
 Federation (ESGF) and the standards for file naming and paths to files are set
@@ -293,13 +293,13 @@ related to CMOR table settings available:
   Defaults to the value provided in ``cmor_type``.
 
 .. _configure_native_models:
-  
+
 Configuring native models and observation data sets
 ----------------------------------------------------
 
 ESMValCore can be configured for handling native model output formats
 and specific
-observation data sets without preliminary reformating. You can choose
+observation data sets without preliminary reformatting. You can choose
 to host this new data source either under a dedicated project or under
 project ``native6``; when choosing the latter, such a configuration
 involves the following steps:
@@ -314,9 +314,9 @@ involves the following steps:
 
       .. code-block:: yaml
 
-	native6:
-  	  ...
-	  input_dir:
+        native6:
+          ...
+          input_dir:
              default: 'Tier{tier}/{dataset}/{latestversion}/{frequency}/{short_name}'
              MY_DATA_ORG: '{model}/{exp}/{simulation}/{version}/{type}'
           input_file:

doc/quickstart/find_data.rst

@@ -50,7 +50,7 @@ section.
 
 Native model data
 ---------------------------------------------------------
-Support for native model data that is not formatted according to a CMIP 
+Support for native model data that is not formatted according to a CMIP
 data request is quite easy using basic
 :ref:`ESMValCore fix procedure <fixing_data>` and has been implemented
 for some models :ref:`as described here <fixing_native_models>`