ESMValCore 2.13.0rc2__tar.gz → 2.13.0rc4__tar.gz

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.circleci/config.yml

@@ -31,8 +31,10 @@ commands:
             mkdir -p test-reports
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
+            pip check
             pytest -n 4 --junitxml=test-reports/report.xml << parameters.args >>
             esmvaltool version
+            esmvaltool -- --help
       - store_test_results:
           path: test-reports/report.xml
       - store_artifacts:
@@ -54,7 +56,7 @@ commands:
         type: string
         default: "test"
       flags:
-        description: pip install flags
+        description: pip install --no-deps flags
         type: string
         default: ""
       upstream_packages:
@@ -130,7 +132,7 @@ jobs:
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
             conda activate esmvaltool
-            pip install .[test] > /logs/install.txt 2>&1
+            pip install --no-deps .[test] > /logs/install.txt 2>&1
       - test_and_report:
           args: --cov
       - save_cache:
@@ -220,7 +222,8 @@ jobs:
             # Install
             mamba env create -n esmvaltool -f environment.yml
             conda activate esmvaltool
-            pip install .[doc]
+            pip install --no-deps .[doc]
+            pip check
             # Log versions
             dpkg -l | tee /logs/versions.txt
             conda env export | tee /logs/environment.yml

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/create-condalock-file.yml

@@ -61,9 +61,10 @@ jobs:
       - name: Show environment contents
         run: conda list
       - name: Install esmvalcore
-        run: pip install -e .[develop]
+        run: pip install --no-deps -e .[develop]
       - name: Run basic commands
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version
       - name: Run pytests

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/install-from-condalock-file.yml

@@ -49,7 +49,8 @@ jobs:
       - run: conda create --name esmvaltool-fromlock --file conda-linux-64.lock
       - run: which python
       - run: pip --version
-      - run: pip install -e .[develop]
+      - run: pip install --no-deps -e .[develop]
+      - run: pip check
       - run: esmvaltool --help
       - run: esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - run: pytest -n 2 -m "not installation"

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/install-from-pypi.yml

@@ -61,9 +61,10 @@ jobs:
           python -V 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
           pip -V 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/pip_version.txt
       - name: Install
-        run: pip install esmvalcore 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps esmvalcore 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
@@ -99,7 +100,7 @@ jobs:
           python -V 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
           pip -V 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/pip_version.txt
       - name: Install
-        run: pip install esmvalcore 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps esmvalcore 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
           esmvaltool --help

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/install-from-source.yml

@@ -58,9 +58,10 @@ jobs:
           mamba --version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - name: Install
-        run: pip install -e .[develop] 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps -e .[develop] 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
@@ -99,7 +100,7 @@ jobs:
       - name: Force install x64 git
         run: mamba install -c conda-forge git
       - name: Install
-        run: pip install -e .[develop] 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps -e .[develop] 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
           esmvaltool --help

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/run-tests-monitor.yml

@@ -41,7 +41,7 @@ jobs:
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
       - run: python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: pip install pytest-monitor
-      - run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: pytest -n 2 -m "not installation" --db ../.pymon 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - run: python tests/parse_pymon.py
       - name: Upload artifacts
@@ -77,7 +77,7 @@ jobs:
       - run: python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: mamba install -c conda-forge git
       - run: pip install pytest-monitor
-      - run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
       - run: pytest -n 2 -m "not installation" --db ../.pymon 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - run: python tests/parse_pymon.py

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/.github/workflows/run-tests.yml

@@ -58,8 +58,9 @@ jobs:
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
       - run: python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: conda list
-      - run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
+      - run: pip check
       - run: |
           pre-commit install
           pre-commit run -a
@@ -97,7 +98,7 @@ jobs:
       - run: python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: mamba install -c conda-forge git
       - run: conda list
-      - run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
       - run: |
           pre-commit install

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/CITATION.cff

@@ -230,11 +230,11 @@ authors:
     orcid: "https://orcid.org/0000-0002-9949-3989"
 
 cff-version: 1.2.0
-date-released: 2025-08-21
+date-released: 2025-09-23
 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: "v2.13.0rc1"
+version: "v2.13.0rc4"
 ...

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4/ESMValCore.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ESMValCore
-Version: 2.13.0rc2
+Version: 2.13.0rc4
 Summary: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts
 Author-email: ESMValTool Development Team <esmvaltool-dev@listserv.dfn.de>
 License: Apache License, Version 2.0
@@ -79,8 +79,8 @@ Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: ESMValTool_sample_data==0.0.4; extra == "test"
 Provides-Extra: doc
 Requires-Dist: autodocsumm>=0.2.2; extra == "doc"
-Requires-Dist: ipython<9.0; extra == "doc"
-Requires-Dist: nbsphinx>=0.9.7; extra == "doc"
+Requires-Dist: ipython; extra == "doc"
+Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: sphinx>=6.1.3; extra == "doc"
 Requires-Dist: pydata_sphinx_theme; extra == "doc"
 Provides-Extra: develop

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/ESMValCore.egg-info/requires.txt

@@ -44,8 +44,8 @@ vprof
 
 [doc]
 autodocsumm>=0.2.2
-ipython<9.0
-nbsphinx>=0.9.7
+ipython
+myst-nb
 sphinx>=6.1.3
 pydata_sphinx_theme
 

{esmvalcore-2.13.0rc2/ESMValCore.egg-info → esmvalcore-2.13.0rc4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ESMValCore
-Version: 2.13.0rc2
+Version: 2.13.0rc4
 Summary: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts
 Author-email: ESMValTool Development Team <esmvaltool-dev@listserv.dfn.de>
 License: Apache License, Version 2.0
@@ -79,8 +79,8 @@ Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: ESMValTool_sample_data==0.0.4; extra == "test"
 Provides-Extra: doc
 Requires-Dist: autodocsumm>=0.2.2; extra == "doc"
-Requires-Dist: ipython<9.0; extra == "doc"
-Requires-Dist: nbsphinx>=0.9.7; extra == "doc"
+Requires-Dist: ipython; extra == "doc"
+Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: sphinx>=6.1.3; extra == "doc"
 Requires-Dist: pydata_sphinx_theme; extra == "doc"
 Provides-Extra: develop

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/conda-linux-64.lock

@@ -420,7 +420,6 @@ https://conda.anaconda.org/conda-forge/noarch/intake-esm-2025.7.9-pyhd8ed1ab_0.c
 https://conda.anaconda.org/conda-forge/noarch/iris-esmf-regrid-0.12.1-pyhd8ed1ab_0.conda#d2559adb7d967418c23ecd49e55d7301
 https://conda.anaconda.org/conda-forge/noarch/ncdata-0.2.0-pyhd8ed1ab_0.conda#fe1f9b43ee7eb8cb24b3f9821a98f9b7
 https://conda.anaconda.org/conda-forge/noarch/autodocsumm-0.2.14-pyhd8ed1ab_0.conda#351a11ac1215eb4f6c5b82e30070277a
-https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.7-pyhd8ed1ab_0.conda#9a3844478c73b5fe288426d001453261
 https://conda.anaconda.org/conda-forge/noarch/pydata-sphinx-theme-0.16.1-pyhd8ed1ab_0.conda#837aaf71ddf3b27acae0e7e9015eebc6
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-2.0.0-pyhd8ed1ab_1.conda#16e3f039c0aa6446513e94ab18a8784b
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-2.0.0-pyhd8ed1ab_1.conda#910f28a05c178feba832f842155cbfff

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/doc/changelog.rst

@@ -68,6 +68,9 @@ Documentation
 -  Explicitly export LC_ALL for sphinx builds (:pull:`2708`) by :user:`valeriupredoi`
 -  Remove reference to psy-plot recipe in ESMValTool (:pull:`2741`) by :user:`valeriupredoi`
 -  Fix Codecov badge in README (:pull:`2754`) by :user:`valeriupredoi`
+-  Remove mention of Julia in documentation ahead of discontinued support in v2.13 (:pull:`2819`) by :user:`jlenh`
+-  Remove codacy badge (:pull:`2822`) by :user:`bouweandela`
+-  Replace nbsphinx with myst-nb and remove pin on ipython (:pull:`2838`) by :user:`valeriupredoi`
 
 Fixes for datasets
 ~~~~~~~~~~~~~~~~~~
@@ -86,6 +89,7 @@ Installation
 -  Unpin dask, pin iris, in light of solved #2716 (iris saver not working well with latest Dask API) (:pull:`2726`) by :user:`valeriupredoi`
 -  Harmonize environment.yml with pyproject.yml: identical dependencies (:pull:`2756`) by :user:`valeriupredoi`
 -  Install `esmvaltool-sample-data(==0.0.4)` from conda forge not PyPI (:pull:`2795`) by :user:`valeriupredoi`
+-  Use ``pip install --no-deps`` to avoid overwriting packages from the conda environment (:pull:`2829`) by :user:`bouweandela`
 
 Iris
 ~~~~
@@ -101,12 +105,8 @@ Preprocessor
 -  Allow adding supplementary variables from a different project and different dataset (:pull:`2755`) by :user:`valeriupredoi`
 -  Move concatenate preprocessor function to its own module (:pull:`2766`) by :user:`bouweandela`
 -  Add preprocessor `align_metadata` (:pull:`2789`) by :user:`schlunma`
-
-Release
-~~~~~~~
-
--  Use finer current version for pypa PyPI upload github action (:pull:`2804`) by :user:`valeriupredoi`
--  Commenting out ORNL ESGF node in esgf_pyclient config (:pull:`2806`) by :user:`jlenh`
+-  Fix for `add_ancillary_variable` (#2820) (:pull:`2825`) by :user:`jlenh`
+-  Set correct calendar when reading file dates (:pull:`2826`) by :user:`bouweandela`
 
 Automatic testing
 ~~~~~~~~~~~~~~~~~
@@ -121,6 +121,10 @@ Automatic testing
 -  Zarr support (backend, in `esmvalcore.preprocessor._io.py`) (:pull:`2785`) by :user:`valeriupredoi`
 -  Update mamba and python (remove pins and allow for Python 3.13) conda-lock file creation Github Action - via ESMValTool_sample_data being a conda-forge package (:pull:`2792`) by :user:`valeriupredoi`
 -  Automatically open pull requests to update GitHub Actions (:pull:`2799`) by :user:`bouweandela`
+-  Use finer current version for pypa PyPI upload github action (:pull:`2804`) by :user:`valeriupredoi`
+-  Change zarr exception test to GroupNotFoundError (:pull:`2823`) by :user:`jlenh`
+-  Remove failing test `test_load_zarr_local_not_zarr_file` due to zarr version changes (:pull:`2824`) by :user:`jlenh`
+-  Repair gha tests after pip install with no deps and add working reference to ipynb Jupyter notebooks in docs (:pull:`2844`) by :user:`valeriupredoi`
 
 Variable Derivation
 ~~~~~~~~~~~~~~~~~~~
@@ -147,6 +151,10 @@ Improvements
 -  Enable ruff rule that checks unused arguments (:pull:`2809`) by :user:`bouweandela`
 -  Enable ruff rule to prevent print statements (:pull:`2810`) by :user:`bouweandela`
 -  Enable ruff rule that enforces using items() to iterate over dict key/value pairs (:pull:`2811`) by :user:`bouweandela`
+-  Remove use of prospector and related tools and Codacy (:pull:`2818`) by :user:`bouweandela`
+-  Commenting out ORNL ESGF node in esgf_pyclient config (:pull:`2806`) by :user:`jlenh`
+-  Enable ruff rule that prevents overwriting loop variables (:pull:`2813`) by :user:`bouweandela`
+-  Enable ruff rule that checks for commented out code (:pull:`2808`) by :user:`bouweandela`
 
 .. _changelog-v2-12-0:
 

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/doc/conf.py

@@ -57,7 +57,7 @@ if rtd_version not in ["latest", "stable", "doc"]:
 # ones.
 extensions = [
     'autodocsumm',
-    'nbsphinx',
+    'myst_nb',
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.extlinks',
@@ -78,6 +78,9 @@ autodoc_default_options = {
     'autosummary': True,
 }
 
+# Don't execute notebooks
+nb_execution_mode = "off"
+
 # Show type hints in function signature AND docstring
 autodoc_typehints = 'both'
 

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/doc/quickstart/install.rst

@@ -63,11 +63,11 @@ Finally, activate the newly created environment
 
     conda activate esmvalcore
 
-and install ESMValCore as well as any remaining dependencies with the command:
+and install ESMValCore with the command:
 
 .. code-block:: bash
 
-    pip install esmvalcore
+    pip install --no-deps esmvalcore
 
 
 Docker installation
@@ -189,10 +189,10 @@ To install from source for development, follow these instructions.
 -  Create the esmvalcore conda environment
    ``conda env create --name esmvalcore --file environment.yml``
 -  Activate the esmvalcore environment: ``conda activate esmvalcore``
--  Install in development mode: ``pip install -e '.[develop]'``. If you
+-  Install in development mode: ``pip install --no-deps -e '.[develop]'``. If you
    are installing behind a proxy that does not trust the usual pip-urls
    you can declare them with the option ``--trusted-host``,
-   e.g. ``pip install --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org -e .[develop]``
+   e.g. ``pip install --no-deps --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org -e .[develop]``
 -  Test that your installation was successful by running
    ``esmvaltool -h``.
 -  Install the :ref:`esmvaltool:pre-commit` hooks by running:

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/doc/recipe/overview.rst

@@ -137,7 +137,7 @@ To populate a recipe with all available datasets from ESGF, the
 For more control over which datasets are selected, it is recommended to use
 a Python script or `Jupyter notebook <https://jupyter.org/>`_ to compose
 the recipe.
-See :ref:`/notebooks/composing-recipes.ipynb` for an example.
+See the :doc:`/notebooks/composing-recipes` notebook for an example.
 This is particularly useful when specific relations are required between
 datasets, e.g. when a dataset needs to be available for multiple variables
 or experiments.

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/environment.yml

@@ -52,8 +52,8 @@ dependencies:
   - zarr >3
   # Python packages needed for building docs
   - autodocsumm >=0.2.2
-  - ipython <9.0  # github.com/ESMValGroup/ESMValCore/issues/2680
-  - nbsphinx >=0.9.7  # github.com/ESMValGroup/ESMValCore/issues/2669
+  - ipython
+  - myst-nb
   - sphinx >=6.1.3
   - pydata-sphinx-theme
   # Python packages needed for testing

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/esmvalcore/_recipe/from_datasets.py

@@ -334,7 +334,7 @@ def datasets_to_recipe(
 
     Examples
     --------
-    See :ref:`/notebooks/composing-recipes.ipynb` for example use cases.
+    See :doc:`/notebooks/composing-recipes` notebook for example use cases.
 
     Returns
     -------

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/esmvalcore/dataset.py

@@ -307,7 +307,7 @@ class Dataset:
 
         Examples
         --------
-        See :ref:`/notebooks/discovering-data.ipynb` for example use cases.
+        See :doc:`/notebooks/discovering-data` notebook for example use cases.
 
         Yields
         ------

{esmvalcore-2.13.0rc2 → esmvalcore-2.13.0rc4}/pyproject.toml

@@ -91,8 +91,8 @@ test = [
 ]
 doc = [
     "autodocsumm>=0.2.2",
-    "ipython<9.0",  # github.com/ESMValGroup/ESMValCore/issues/2680
-    "nbsphinx>=0.9.7",  # github.com/ESMValGroup/ESMValCore/issues/2669
+    "ipython",
+    "myst-nb",
     "sphinx>=6.1.3",
     "pydata_sphinx_theme",
 ]