Merge branch 'main' into lazy-extract-levels

.github/workflows/install-from-conda.yml

@@ -15,12 +15,12 @@ name: Install from conda-forge
 
 # 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:
     branches:
-    - main
+      - main
   # run the test only if the PR is to main
   # turn it on if required
   # pull_request:
@@ -35,9 +35,9 @@ jobs:
     strategy:
       matrix:
         # TODO add "3.11" once we have the package built
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       # fail-fast set to False allows all other tests
-      # in the worflow to run regardless of any fail
+      # in the workflow to run regardless of any fail
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -75,7 +75,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

.github/workflows/install-from-condalock-file.yml

@@ -10,7 +10,7 @@ name: Conda-lock Install
 on:
   push:
     branches:
-    - main
+      - main
   # run the test only if the PR is to main
   # turn it on if required
   #pull_request:
@@ -24,7 +24,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:

.github/workflows/install-from-pypi.yml

@@ -20,7 +20,7 @@ on:
   # turn it on only if needed
   push:
     branches:
-    - main
+      - main
   # run the test only if the PR is to main
   # turn it on if required
   #pull_request:
@@ -35,7 +35,7 @@ jobs:
     strategy:
       matrix:
         # TODO add "3.11" once we have the package built
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       # fail-fast set to False allows all other tests
       # in the workflow to run regardless of any fail
       fail-fast: false
@@ -77,7 +77,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
@@ -103,8 +103,8 @@ jobs:
         run: pip install esmvalcore 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         shell: bash -l {0}
-        run: | 
-          esmvaltool --help 
+        run: |
+          esmvaltool --help
           esmvaltool version 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail

.github/workflows/install-from-source.yml

@@ -13,12 +13,12 @@ name: Install from Source
 
 # 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:
     branches:
-    - main
+      - main
   # run the test only if the PR is to main
   # turn it on if required
   #pull_request:
@@ -32,7 +32,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -73,7 +73,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

.github/workflows/run-tests-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     if: ${{ github.event.issue.pull_request && github.event.comment.body == '@runGAtests' }}
@@ -48,7 +48,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     if: ${{ github.event.issue.pull_request && github.event.comment.body == '@runGAtests' }}

.github/workflows/run-tests-monitor.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -57,7 +57,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

.github/workflows/run-tests.yml

@@ -34,7 +34,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -72,7 +72,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

README.md

@@ -11,7 +11,7 @@
 [![Github Actions Test](https://github.com/ESMValGroup/ESMValCore/actions/workflows/run-tests.yml/badge.svg)](https://github.com/ESMValGroup/ESMValCore/actions/workflows/run-tests.yml)
 [![Github Actions Dashboard](https://api.meercode.io/badge/ESMValGroup/ESMValCore?type=ci-success-rate&branch=main&lastDay=14)](https://meercode.io)
 
-![esmvaltoollogo](https://github.com/ESMValGroup/ESMValCore/blob/main/doc/figures/ESMValTool-logo-2.png)
+![esmvaltoollogo](https://raw.githubusercontent.com/ESMValGroup/ESMValCore/main/doc/figures/ESMValTool-logo-2.png)
 
 ESMValCore: core functionalities for the ESMValTool, a community diagnostic
 and performance metrics tool for routine evaluation of Earth System Models

doc/api/esmvalcore.cmor.rst

@@ -7,6 +7,7 @@ Checking compliance
 -------------------
 
 .. automodule:: esmvalcore.cmor.check
+   :no-inherited-members:
    :member-order: bysource
 
 Automatically fixing issues

doc/conf.py

@@ -67,8 +67,6 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-    # github.com/readthedocs/sphinx_rtd_theme/issues/1451
-    'sphinxcontrib.jquery',
 ]
 
 autodoc_default_options = {

doc/develop/fixing_data.rst

@@ -60,6 +60,17 @@ called by the preprocessor functions
 :py:func:`esmvalcore.preprocessor.fix_metadata`, and
 :py:func:`esmvalcore.preprocessor.fix_data`.
 
+The :class:`~esmvalcore.cmor._fixes.fix.Fix` class provides the following
+attributes:
+
+- :attr:`Fix.vardef`: :class:`~esmvalcore.cmor.table.VariableInfo` object that
+  corresponds to the variable fixed by the fix.
+- :attr:`Fix.extra_facets`: :obj:`dict` that contains all facets of the
+  corresponding dataset fixed by the fix (see
+  :attr:`esmvalcore.dataset.Dataset.facets`).
+- :attr:`Fix.session`: :class:`~esmvalcore.config.Session` object that includes
+  configuration and directory information.
+
 Fixing a dataset
 ================
 

environment.yml

@@ -34,7 +34,7 @@ dependencies:
   - psutil
   - py-cordex
   - pybtex
-  - python>=3.8
+  - python>=3.9
   - python-stratify>=0.3
   - pyyaml
   - requests

esmvalcore/cmor/_fixes/fix.py

@@ -5,29 +5,43 @@
 import inspect
 import tempfile
 from pathlib import Path
+from typing import TYPE_CHECKING, Optional
 
 from ..table import CMOR_TABLES
 
+if TYPE_CHECKING:
+    from ...config import Session
+    from ..table import VariableInfo
+
 
 class Fix:
     """Base class for dataset fixes."""
 
-    def __init__(self, vardef, extra_facets=None):
+    def __init__(
+        self,
+        vardef: VariableInfo,
+        extra_facets: Optional[dict] = None,
+        session: Optional[Session] = None,
+    ):
         """Initialize fix object.
 
         Parameters
         ----------
-        vardef: str
+        vardef: VariableInfo
             CMOR table entry.
         extra_facets: dict, optional
             Extra facets are mainly used for data outside of the big projects
             like CMIP, CORDEX, obs4MIPs. For details, see :ref:`extra_facets`.
+        session: Session, optional
+            Current session which includes configuration and directory
+            information.
 
         """
         self.vardef = vardef
         if extra_facets is None:
             extra_facets = {}
         self.extra_facets = extra_facets
+        self.session = session
 
     def fix_file(
         self,
@@ -136,7 +150,14 @@ def __ne__(self, other):
         return not self.__eq__(other)
 
     @staticmethod
-    def get_fixes(project, dataset, mip, short_name, extra_facets=None):
+    def get_fixes(
+        project: str,
+        dataset: str,
+        mip: str,
+        short_name: str,
+        extra_facets: Optional[dict] = None,
+        session: Optional[Session] = None,
+    ) -> list:
         """Get the fixes that must be applied for a given dataset.
 
         It will look for them at the module
@@ -163,6 +184,9 @@ def get_fixes(project, dataset, mip, short_name, extra_facets=None):
         extra_facets: dict, optional
             Extra facets are mainly used for data outside of the big projects
             like CMIP, CORDEX, obs4MIPs. For details, see :ref:`extra_facets`.
+        session: Session, optional
+            Current session which includes configuration and directory
+            information.
 
         Returns
         -------
@@ -202,13 +226,15 @@ def get_fixes(project, dataset, mip, short_name, extra_facets=None):
                 pass
 
         for fixes_module in fixes_modules:
-            classes = inspect.getmembers(fixes_module, inspect.isclass)
-            classes = dict((name.lower(), value) for name, value in classes)
+            classes = dict(
+                (name.lower(), value) for (name, value) in
+                inspect.getmembers(fixes_module, inspect.isclass)
+            )
             for fix_name in (short_name, mip.lower(), 'allvars'):
-                try:
-                    fixes.append(classes[fix_name](vardef, extra_facets))
-                except KeyError:
-                    pass
+                if fix_name in classes:
+                    fixes.append(classes[fix_name](
+                        vardef, extra_facets=extra_facets, session=session
+                    ))
 
         return fixes