Merge remote-tracking branch 'origin/main' into dev_clip_timerange_fx

.github/workflows/build-and-deploy-on-pypi.yml

@@ -13,7 +13,9 @@ jobs:
     name: Build and publish ESMValCore on PyPi
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
@@ -39,6 +41,7 @@ jobs:
       #    repository_url: https://test.pypi.org/legacy/
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
+          user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/citation_file_validator.yml

@@ -16,8 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v2
-
+        uses: actions/checkout@v3
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0
         with:

.github/workflows/create-condalock-file.yml

@@ -15,7 +15,9 @@ jobs:
     name: Create and verify conda lock file for latest Python
     runs-on: 'ubuntu-latest'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true

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

@@ -40,7 +40,6 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.python-version }}
@@ -79,7 +78,6 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.python-version }}

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

@@ -28,7 +28,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool-fromlock

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

@@ -40,7 +40,7 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore
@@ -80,7 +80,7 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore

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

@@ -36,7 +36,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore
@@ -75,7 +77,9 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore

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

@@ -14,7 +14,9 @@ jobs:
     name: Linux Python ${{ matrix.python-version }}
     if: ${{ github.event.issue.pull_request && github.event.comment.body == '@runGAtests' }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore
@@ -51,7 +53,9 @@ jobs:
     name: OSX Python ${{ matrix.python-version }}
     if: ${{ github.event.issue.pull_request && github.event.comment.body == '@runGAtests' }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore

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

@@ -21,7 +21,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore
@@ -63,7 +65,9 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore

.github/workflows/run-tests.yml

@@ -38,7 +38,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore
@@ -74,7 +76,9 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvalcore

CITATION.cff

@@ -188,11 +188,11 @@ authors:
     orcid: "https://orcid.org/0000-0002-5317-1247"
 
 cff-version: 1.2.0
-date-released: 2022-03-14
+date-released: 2022-06-13
 doi: "10.5281/zenodo.3387139"
 license: "Apache-2.0"
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/ESMValGroup/ESMValCore/"
 title: ESMValCore
-version: "v2.5.0"
+version: "v2.6.0rc2"
 ...

doc/changelog.rst

@@ -1,6 +1,109 @@
 Changelog
 =========
 
+
+.. _changelog-v2-6-0:
+
+v2.6.0
+------
+
+Highlights
+~~~~~~~~~~
+
+- A new set of CMOR fixes is now available in order to load native EMAC model output and CMORize it on the fly. For details, see :ref:`Supported native models: EMAC <read_emac>`.
+- The version number of ESMValCore is now automatically generated using `setuptools_scm <https://github.com/pypa/setuptools_scm/#default-versioning-scheme>`__, which extracts Python package versions from git metadata.
+
+This release includes
+
+Bug fixes
+~~~~~~~~~
+
+-  Added `start_year` and `end_year` attributes to derived variables (`#1547 <https://github.com/ESMValGroup/ESMValCore/pull/1547>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Show all results on recipe results webpage (`#1560 <https://github.com/ESMValGroup/ESMValCore/pull/1560>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Regridding regular grids with similar coordinates  (`#1567 <https://github.com/ESMValGroup/ESMValCore/pull/1567>`__) `Tomas Lovato <https://github.com/tomaslovato>`__
+-  Fix timerange wildcard search when deriving variables or downloading files (`#1562 <https://github.com/ESMValGroup/ESMValCore/pull/1562>`__) `sloosvel <https://github.com/sloosvel>`__
+-  Fix `force_derivation` bug (`#1627 <https://github.com/ESMValGroup/ESMValCore/pull/1627>`__) `sloosvel <https://github.com/sloosvel>`__
+
+CMOR standard
+~~~~~~~~~~~~~
+
+-  Added custom CMOR tables used for EMAC CMORizer (`#1599 <https://github.com/ESMValGroup/ESMValCore/pull/1599>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Extended ICON CMORizer (`#1549 <https://github.com/ESMValGroup/ESMValCore/pull/1549>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Add CMOR check exception for a basin coord named sector (`#1612 <https://github.com/ESMValGroup/ESMValCore/pull/1612>`__) `David Hohn <https://github.com/dhohn>`__
+
+Containerization
+~~~~~~~~~~~~~~~~
+
+-  Remove update command in Dockerfile (`#1630 <https://github.com/ESMValGroup/ESMValCore/pull/1630>`__) `sloosvel <https://github.com/sloosvel>`__
+
+Community
+~~~~~~~~~
+
+-  Add David Hohn to contributors' list (`#1586 <https://github.com/ESMValGroup/ESMValCore/pull/1586>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+
+Deprecations
+~~~~~~~~~~~~
+
+-  Deprecate the function `esmvalcore.var_name_constraint` (`#1592 <https://github.com/ESMValGroup/ESMValCore/pull/1592>`__) `Manuel Schlund <https://github.com/schlunma>`__
+
+Documentation
+~~~~~~~~~~~~~
+
+-  [Github Actions Docs] Full explanation on how to use the GA test triggered by PR comment and added docs link for GA hosted runners  (`#1553 <https://github.com/ESMValGroup/ESMValCore/pull/1553>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+-  Update the command for building the documentation (`#1556 <https://github.com/ESMValGroup/ESMValCore/pull/1556>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Update documentation on running the tool (`#1400 <https://github.com/ESMValGroup/ESMValCore/pull/1400>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Add support for DKRZ-Levante (`#1558 <https://github.com/ESMValGroup/ESMValCore/pull/1558>`__) `Rémi Kazeroni <https://github.com/remi-kazeroni>`__
+-  Improved documentation on native dataset support (`#1559 <https://github.com/ESMValGroup/ESMValCore/pull/1559>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Tweak `extract_point` preprocessor: explain what it returns if one point coord outside cube and add explicit test  (`#1584 <https://github.com/ESMValGroup/ESMValCore/pull/1584>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+-  Update CircleCI, readthedocs, and Docker configuration (`#1588 <https://github.com/ESMValGroup/ESMValCore/pull/1588>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Remove support for Mistral in `config-user.yml` (`#1620 <https://github.com/ESMValGroup/ESMValCore/pull/1620>`__) `Rémi Kazeroni <https://github.com/remi-kazeroni>`__
+
+Improvements
+~~~~~~~~~~~~
+
+-  Removed trailing whitespace in custom CMOR tables (`#1564 <https://github.com/ESMValGroup/ESMValCore/pull/1564>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Try searching multiple ESGF index nodes (`#1561 <https://github.com/ESMValGroup/ESMValCore/pull/1561>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Add CMIP6 `amoc` derivation case and add a test (`#1577 <https://github.com/ESMValGroup/ESMValCore/pull/1577>`__) `Valeriu Predoi <https://github.com/valeriupredoi>`__
+-  Added EMAC CMORizer (`#1554 <https://github.com/ESMValGroup/ESMValCore/pull/1554>`__) `Manuel Schlund <https://github.com/schlunma>`__
+
+Fixes for datasets
+~~~~~~~~~~~~~~~~~~
+
+-  Fixes of ocean variables in multiple CMIP6 datasets (`#1566 <https://github.com/ESMValGroup/ESMValCore/pull/1566>`__) `Tomas Lovato <https://github.com/tomaslovato>`__
+-  Ensure lat/lon bounds in FGOALS-l3 atmos variables are contiguous (`#1571 <https://github.com/ESMValGroup/ESMValCore/pull/1571>`__) `sloosvel <https://github.com/sloosvel>`__
+-  Added `AllVars` fix for CMIP6's ICON-ESM-LR (`#1582 <https://github.com/ESMValGroup/ESMValCore/pull/1582>`__) `Manuel Schlund <https://github.com/schlunma>`__
+
+Installation
+~~~~~~~~~~~~
+
+-  Removed `package/meta.yml` (`#1540 <https://github.com/ESMValGroup/ESMValCore/pull/1540>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Pinned iris>=3.2.1 (`#1552 <https://github.com/ESMValGroup/ESMValCore/pull/1552>`__) `Manuel Schlund <https://github.com/schlunma>`__
+-  Use setuptools-scm to automatically generate the version number (`#1578 <https://github.com/ESMValGroup/ESMValCore/pull/1578>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+
+Preprocessor
+~~~~~~~~~~~~
+
+-  Add general `extract_coordinate_points` preprocessor (`#1581 <https://github.com/ESMValGroup/ESMValCore/pull/1581>`__) `sloosvel <https://github.com/sloosvel>`__
+-  Add preprocessor `accumulate_coordinate` (`#1281 <https://github.com/ESMValGroup/ESMValCore/pull/1281>`__) `Javier Vegas-Regidor <https://github.com/jvegreg>`__
+
+Release
+~~~~~~~
+
+-  Increase version number for ESMValCore v2.6.0rc1 (`#1632 <https://github.com/ESMValGroup/ESMValCore/pull/1632>`__) `sloosvel <https://github.com/sloosvel>`__
+
+Automatic testing
+~~~~~~~~~~~~~~~~~
+
+-  Refresh CircleCI cache weekly (`#1597 <https://github.com/ESMValGroup/ESMValCore/pull/1597>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Use correct cache restore key on CircleCI (`#1598 <https://github.com/ESMValGroup/ESMValCore/pull/1598>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Install git and ssh before checking out code on CircleCI (`#1601 <https://github.com/ESMValGroup/ESMValCore/pull/1601>`__) `Bouwe Andela <https://github.com/bouweandela>`__
+-  Fetch all history in Github Action tests (`#1622 <https://github.com/ESMValGroup/ESMValCore/pull/1622>`__) `sloosvel <https://github.com/sloosvel>`__
+
+Variable Derivation
+~~~~~~~~~~~~~~~~~~~
+
+-  Added derivation of `hfns` (`#1594 <https://github.com/ESMValGroup/ESMValCore/pull/1594>`__) `Manuel Schlund <https://github.com/schlunma>`__
+
 .. _changelog-v2-5-0:
 
 v2.5.0

doc/contributing.rst

@@ -734,9 +734,10 @@ to run their favourite recipe using this branch.
 3. Increase the version number
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The version number is stored in ``esmvalcore/_version.py``, ``CITATION.cff``.
-Make sure to update both files.
-Also update the release date in ``CITATION.cff``.
+The version number is automatically generated from the information provided by
+git using [setuptools-scm](https://pypi.org/project/setuptools-scm/), but a
+static version number is stored in ``CITATION.cff``.
+Make sure to update the version number and release date in ``CITATION.cff``.
 See https://semver.org for more information on choosing a version number.
 Make a pull request and get it merged into ``main`` and cherry pick it into
 the release branch.

doc/develop/fixing_data.rst

@@ -110,7 +110,7 @@ Then we have to create the class for the fix deriving from
     from esmvalcore.cmor.fix import Fix
 
     class tas(Fix):
-         """Fixes for tas variable.""""
+         """Fixes for tas variable."""
 
 Next we must choose the method to use between the ones offered by the
 Fix class:
@@ -134,15 +134,15 @@ so we will implement the ``fix_metadata`` method:
     from esmvalcore.cmor.fix import Fix
 
     class tas(Fix):
-        """Fixes for tas variable.""""
+        """Fixes for tas variable."""
 
         def fix_metadata(self, cubes):
             """
             Fix metadata for tas.
 
             Fix the name of the latitude coordinate, which is called altitude
             in the original file.
-            """"
+            """
             # Sometimes Iris will interpret the data as multiple cubes.
             # Good CMOR datasets will only show one but we support the
             # multiple cubes case to be able to fix the errors that are
@@ -196,15 +196,15 @@ derive from the one you just created:
     from esmvalcore.cmor.fix import Fix
 
     class tas(Fix):
-        """Fixes for tas variable.""""
+        """Fixes for tas variable."""
 
         def fix_metadata(self, cubes):
             """
             Fix metadata for tas.
 
             Fix the name of the latitude coordinate, which is called altitude
             in the original file.
-            """"
+            """
             # Sometimes Iris will interpret the data as multiple cubes.
             # Good CMOR datasets will only show one but we support the
             # multiple cubes case to be able to fix the errors that are
@@ -275,7 +275,7 @@ discarding some cubes in the fix metadata step. Just before that warning you
 should see the full list of cubes as read by Iris. If that list contains your
 missing coordinate you can create a fix for this model:
 
-.. code-block:: bash
+.. code-block:: python
 
     def fix_metadata(self, cubes):
         coord_cube = cubes.extract_strict('COORDINATE_NAME')