Merge branch 'main' into recipe_test_workflow_prototype

* main: (31 commits) Update environment: pin `iris>=3.11`, unpin `cartopy` and allow for `numpy >=2` (#3811) Fix issue related to removal/change of private function imported in `diag_scripts/shared/_supermeans.py` (deprecation in iris=3.11) (#3810) Remove recipe filler utility (#3777) [Condalock] Update Linux condalock file (#3809) change authors name (#3806) [Condalock] Update Linux condalock file (#3798) Fix contourf plots for masked data (#3797) [Condalock] Update Linux condalock file (#3796) Add next release schedule (#3794) Use `transform_first=True` for contourf plots with Robinson projection to avoid cartopy bug (#3789) Pin pys2index >=0.1.5 in osx environment (#3792) Adding a CMORiser for CMAP data for pr (#3766) Adding pr, tauu, tauv, tos to NCEP2 CMORISer (#3765) Readthedocs configuration/builds: revert to miniconda before miniforge is available (#3785) Adapt ESMValTool to new configuration (#3761) Adding pr, tauu, tauv NOAA-CIRES-20CR-V2 CMORISER (#3763) update comment in conda lock creation Github action (#3788) [Condalock] Update Linux condalock file (#3786) update Docker builds badge in README (#3783) Pin mamba<2 for conda-lock: solution by Ben Mares @maresb (#3771) ...
ESMValGroup · Nov 19, 2024 · 09490de · 09490de
2 parents ca80ce0 + de43833
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Showing 154 changed files with 2,087 additions and 3,875 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -158,7 +158,7 @@ jobs:
   test_installation_from_source_test_mode:
     # Test installation from source
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/miniforge3:latest
     resource_class: large
     steps:
       - test_installation_from_source:
@@ -167,7 +167,7 @@ jobs:
   test_installation_from_source_develop_mode:
     # Test development installation
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/miniforge3:latest
     resource_class: large
     steps:
       - test_installation_from_source:
@@ -179,7 +179,7 @@ jobs:
     # purpose of this test to discover backward-incompatible changes early on in
     # the development cycle.
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/miniforge3:latest
     resource_class: large
     steps:
       - run:
@@ -216,8 +216,8 @@ jobs:
             conda activate esmvaltool
             mkdir -p ~/climate_data
             esmvaltool config get_config_user
-            echo "search_esgf: when_missing" >> ~/.esmvaltool/config-user.yml
-            cat ~/.esmvaltool/config-user.yml
+            echo "search_esgf: when_missing" >> ~/.config/esmvaltool/config-user.yml
+            cat ~/.config/esmvaltool/config-user.yml
             for recipe in esmvaltool/recipes/testing/recipe_*.yml; do
               esmvaltool run "$recipe"
             done
@@ -233,7 +233,7 @@ jobs:
   build_documentation:
     # Test building documentation
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/miniforge3:latest
     resource_class: medium
     steps:
       - checkout
@@ -257,7 +257,7 @@ jobs:
   test_installation_from_conda:
     # Test conda package installation
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/miniforge3:latest
     resource_class: large
     steps:
       - run:

diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
@@ -27,17 +27,18 @@ jobs:
         with:
           auto-update-conda: true
           activate-environment: esmvaltool-fromlock
-          python-version: "3.11"
+          python-version: "3.12"
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - name: Show conda config
         run: |
           conda update -n base -c conda-forge conda
           conda --version
           # setup-miniconda@v3 installs an old conda and mamba
           # forcing a modern mamba updates both mamba and conda
-          conda install -c conda-forge "mamba>=1.4.8"
+          # unpin mamba after conda-lock=3 release
+          # see github.com/ESMValGroup/ESMValTool/issues/3782
+          conda install -c conda-forge "mamba>=1.4.8,<2"
           conda config --show-sources
           conda config --show
           conda --version

diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -20,14 +20,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p conda_install_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/install-from-condalock-file.yml b/.github/workflows/install-from-condalock-file.yml
@@ -30,7 +30,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:

diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
@@ -19,7 +19,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -32,7 +32,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p source_install_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/pypi-build-and-deploy.yml b/.github/workflows/pypi-build-and-deploy.yml
@@ -17,10 +17,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v1
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - name: Install pep517
         run: >-
           python -m

diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
@@ -35,7 +35,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p test_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions
@@ -67,7 +66,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         architecture: ["x64"]  # need to force Intel, arm64 builds have issues
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
@@ -82,7 +81,6 @@ jobs:
           environment-file: environment_osx.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       # - name: Install libomp with homebrew
       #   run: brew install libomp

diff --git a/.github/workflows/test-development.yml b/.github/workflows/test-development.yml
@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
@@ -38,7 +38,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p develop_test_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
@@ -32,7 +32,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p test_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions
@@ -45,6 +44,8 @@ jobs:
         run: conda list
       - name: Install ESMValTool
         run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - name: Examine conda environment
+        run: conda list
       - name: Install Julia dependencies
         run: esmvaltool install Julia
       - name: Export Python minor version
@@ -72,7 +73,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         architecture: ["x64"]  # need to force Intel, arm64 builds have issues
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
@@ -87,7 +88,6 @@ jobs:
           environment-file: environment_osx.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       # - name: Install libomp with homebrew
       #   run: brew install libomp

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,20 +7,13 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    # updated and deployed from Aug 1, 2023
-    python: "mambaforge-22.9"
+    # try miniforge3 when available? see github.com/ESMValGroup/ESMValTool/issues/3779
+    # DO NOT use mambaforge-*; that is currently sunsetted
+    python: "miniconda-latest"
   jobs:
-    pre_create_environment:
-      # update mamba just in case
-      - mamba update --yes --quiet --name=base mamba 'zstd=1.5.2'
-      - mamba --version
-      - mamba list --name=base
     post_create_environment:
-      - conda run -n ${CONDA_DEFAULT_ENV} mamba list
-      # use conda run executable wrapper to have all env variables
-      - conda run -n ${CONDA_DEFAULT_ENV} mamba --version
       - conda run -n ${CONDA_DEFAULT_ENV} pip install . --no-deps
 
 # Declare the requirements required to build your docs

diff --git a/CITATION.cff b/CITATION.cff
@@ -291,6 +291,11 @@ authors:
     family-names: Phillips
     given-names: Adam
     orcid: "https://orcid.org/0000-0003-4859-8585"
+  -
+    affiliation: "ACCESS-NRI, Australia"
+    family-names: Proft
+    given-names: Max
+    orcid: "https://orcid.org/0009-0003-1611-9516"
   -
     affiliation: "University of Arizona, USA"
     family-names: Russell

diff --git a/README.md b/README.md
@@ -6,11 +6,11 @@
 [![CircleCI](https://circleci.com/gh/ESMValGroup/ESMValTool/tree/main.svg?style=svg)](https://circleci.com/gh/ESMValGroup/ESMValTool/tree/main)
 [![Test in Full Development Mode](https://github.com/ESMValGroup/ESMValTool/actions/workflows/test-development.yml/badge.svg)](https://github.com/ESMValGroup/ESMValTool/actions/workflows/test-development.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/79bf6932c2e844eea15d0fb1ed7e415c)](https://app.codacy.com/gh/ESMValGroup/ESMValTool/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
-[![Docker Build Status](https://img.shields.io/docker/cloud/build/esmvalgroup/esmvaltool.svg)](https://hub.docker.com/r/esmvalgroup/esmvaltool/)
+[![Docker Build Status](https://img.shields.io/docker/automated/esmvalgroup/esmvaltool)](https://hub.docker.com/r/esmvalgroup/esmvaltool/)
 [![Anaconda-Server Badge](https://img.shields.io/conda/vn/conda-forge/ESMValTool?color=blue&label=conda-forge&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/esmvaltool)
 ![stand with Ukraine](https://badgen.net/badge/stand%20with/UKRAINE/?color=0057B8&labelColor=FFD700)
 
-![esmvaltoollogo](https://raw.githubusercontent.com/ESMValGroup/ESMValTool/main/doc/sphinx/source/figures/ESMValTool-logo-2.png)
+![esmvaltoollogo](https://raw.githubusercontent.com/ESMValGroup/ESMValTool/main/doc/sphinx/source/figures/ESMValTool-logo-2-glow.png)
 
 - [**Documentation**](https://docs.esmvaltool.org/en/latest/)
 - [**ESMValTool Website**](https://www.esmvaltool.org/)