Merge branch 'main' of https://github.com/ESMValGroup/ESMValTool into…

… spy4cast
ESMValGroup · Jun 11, 2024 · d989578 · d989578
2 parents 9c3c20a + ae00a53
commit d989578
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Showing 103 changed files with 3,433 additions and 764 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -258,7 +258,7 @@ jobs:
     # Test conda package installation
     docker:
       - image: condaforge/mambaforge:latest
-    resource_class: medium
+    resource_class: large
     steps:
       - run:
           command: |

diff --git a/.github/workflows/citation_file_validator.yml b/.github/workflows/citation_file_validator.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]

diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
@@ -20,10 +20,10 @@ jobs:
     name: Create conda lock file for latest Python
     runs-on: 'ubuntu-latest'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           activate-environment: esmvaltool-fromlock
@@ -35,7 +35,7 @@ jobs:
         run: |
           conda update -n base -c conda-forge conda
           conda --version
-          # setup-miniconda@v2 installs an old conda and mamba
+          # 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"
           conda config --show-sources
@@ -97,7 +97,4 @@ jobs:
             automatedPR
           assignees: valeriupredoi
           reviewers: valeriupredoi
-          team-reviewers: |
-            owners
-            maintainers
           draft: false
diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
@@ -44,7 +44,7 @@ jobs:
           esmvaltool version 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Conda_Install_Linux_python_${{ matrix.python-version }}
           path: conda_install_linux_artifacts_python_${{ matrix.python-version }}
@@ -61,7 +61,7 @@ jobs:
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:
 #      - uses: actions/checkout@v2
-#      - uses: conda-incubator/setup-miniconda@v2
+#      - uses: conda-incubator/setup-miniconda@v3
 #        with:
 #          python-version: ${{ matrix.python-version }}
 #          miniconda-version: "latest"
@@ -82,7 +82,7 @@ jobs:
 #      - run: esmvaltool version 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/version.txt
 #      - name: Upload artifacts
 #        if: ${{ always() }}  # upload artifacts even if fail
-#        uses: actions/upload-artifact@v2
+#        uses: actions/upload-artifact@v4
 #        with:
 #          name: Conda_Install_OSX_python_${{ matrix.python-version }}
 #          path: conda_install_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/install-from-condalock-file.yml b/.github/workflows/install-from-condalock-file.yml
@@ -34,10 +34,10 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: esmvaltool-fromlock
           python-version: ${{ matrix.python-version }}
@@ -57,7 +57,7 @@ jobs:
       - run: pytest -n 2 -m "not installation"
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Source_Install_Linux_python_${{ matrix.python-version }}
           path: source_install_linux_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
@@ -23,10 +23,10 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -47,7 +47,7 @@ jobs:
           esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Source_Install_Linux_python_${{ matrix.python-version }}
           path: source_install_linux_artifacts_python_${{ matrix.python-version }}
@@ -64,7 +64,7 @@ jobs:
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:
 #      - uses: actions/checkout@v2
-#      - uses: conda-incubator/setup-miniconda@v2
+#      - uses: conda-incubator/setup-miniconda@v3
 #        with:
 #          activate-environment: esmvaltool
 #          environment-file: environment.yml
@@ -79,7 +79,7 @@ jobs:
 #      - run: esmvaltool version 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/version.txt
 #      - name: Upload artifacts
 #        if: ${{ always() }}  # upload artifacts even if fail
-#        uses: actions/upload-artifact@v2
+#        uses: actions/upload-artifact@v4
 #        with:
 #          name: Source_Install_OSX_python_${{ matrix.python-version }}
 #          path: source_install_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/pypi-build-and-deploy.yml b/.github/workflows/pypi-build-and-deploy.yml
@@ -14,7 +14,7 @@ jobs:
     name: Build and publish ESMValTool on PyPi
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python 3.11

diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -26,10 +26,10 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -42,6 +42,8 @@ jobs:
         run: |
           mamba --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - name: Inspect environment
+        run: conda list
       - name: Install pytest-monitor
         run: pip install pytest-monitor
       - name: Install ESMValTool
@@ -56,7 +58,7 @@ jobs:
         run: python tests/parse_pymon.py
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Test_Linux_python_${{ matrix.python-version }}
           path: test_linux_artifacts_python_${{ matrix.python-version }}
@@ -66,14 +68,16 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
+        architecture: ["x64"]  # need to force Intel, arm64 builds have issues
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
+          architecture: ${{ matrix.architecture }}
           activate-environment: esmvaltool
           environment-file: environment_osx.yml
           python-version: ${{ matrix.python-version }}
@@ -87,6 +91,10 @@ jobs:
         run: |
           mamba --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - name: Inspect environment
+        run: conda list
+      - name: Install git
+        run: mamba install -c conda-forge git
       - name: Install pytest-monitor
         run: pip install pytest-monitor
       - name: Install ESMValTool
@@ -101,7 +109,7 @@ jobs:
         run: python tests/parse_pymon.py
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Test_OSX_python_${{ matrix.python-version }}
           path: test_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/test-development.yml b/.github/workflows/test-development.yml
@@ -12,7 +12,6 @@ on:
   push:
     branches:
       - main
-      - fix_recipe_filler_bkwds_incompatibility
   schedule:
     - cron: '0 0 * * *'
 
@@ -30,10 +29,10 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -62,7 +61,7 @@ jobs:
         run: pytest -n 2 -m "not installation" 2>&1 | tee develop_test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Develop_Test_Linux_python_${{ matrix.python-version }}
           path: develop_test_linux_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -6,7 +6,6 @@ on:
   push:
     branches:
       - main
-      - fix_recipe_filler_bkwds_incompatibility
   schedule:
     - cron: '0 0 * * *'
 
@@ -24,10 +23,10 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -42,6 +41,8 @@ jobs:
           python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
           # this is how to export variables to the GITHUB var environment
           echo "pver0=$(python -V)" >> $GITHUB_ENV
+      - name: Inspect environment
+        run: conda list
       - name: Install ESMValTool
         run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Install Julia dependencies
@@ -54,13 +55,15 @@ jobs:
           echo "Python minor version changed after Julia install"
           python -V
           exit 1
+      - name: Inspect environment
+        run: conda list
       - name: Run flake8
         run: flake8
       - name: Run tests
         run: pytest -n 2 -m "not installation" 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Test_Linux_python_${{ matrix.python-version }}
           path: test_linux_artifacts_python_${{ matrix.python-version }}
@@ -70,14 +73,16 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
+        architecture: ["x64"]  # need to force Intel, arm64 builds have issues
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
+          architecture: ${{ matrix.architecture }}
           activate-environment: esmvaltool
           environment-file: environment_osx.yml
           python-version: ${{ matrix.python-version }}
@@ -91,15 +96,25 @@ jobs:
         run: |
           mamba --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - name: Inspect environment
+        run: conda list
+      - name: Determine if git
+        run: |
+          which git
+          git --version
+      - name: Install git
+        run: mamba install -c conda-forge git
       - name: Install ESMValTool
         run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - name: Inspect environment
+        run: conda list
       - name: Run flake8
         run: flake8
       - name: Run tests
         run: pytest -n 2 -m "not installation" 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Test_OSX_python_${{ matrix.python-version }}
           path: test_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/CITATION.cff b/CITATION.cff
@@ -175,6 +175,11 @@ authors:
     family-names: Hagemann
     given-names: Stefan
     orcid: "https://orcid.org/0000-0001-5444-2945"
+  -
+    affiliation: "University of Canterbury, New Zealand"
+    family-names: Hardacre
+    given-names: Catherine
+    orcid: "https://orcid.org/0000-0001-9093-4656"
   -
     affiliation: "ISAC-CNR, Italy"
     name-particle: von

diff --git a/README.md b/README.md
@@ -5,8 +5,7 @@
 [![Chat on Matrix](https://matrix.to/img/matrix-badge.svg)](https://matrix.to/#/#ESMValGroup_Lobby:gitter.im)
 [![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/Coverage/79bf6932c2e844eea15d0fb1ed7e415c)](https://www.codacy.com/gh/ESMValGroup/ESMValTool?utm_source=github.com&utm_medium=referral&utm_content=ESMValGroup/ESMValTool&utm_campaign=Badge_Coverage)
-[![Codacy Badge](https://app.codacy.com/project/badge/Grade/79bf6932c2e844eea15d0fb1ed7e415c)](https://www.codacy.com/gh/ESMValGroup/ESMValTool?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ESMValGroup/ESMValTool&amp;utm_campaign=Badge_Grade)
+[![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/)
 [![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)