Merge branch 'main' into cmorise_cci_lst_v3

ESMValGroup · Sep 19, 2024 · 766a025 · 766a025
2 parents 234a21b + 8d15ce2
commit 766a025
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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

diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -20,10 +20,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 }}
@@ -56,12 +56,12 @@ jobs:
 #    runs-on: "macos-latest"
 #    strategy:
 #      matrix:
-#        python-version: ["3.9", "3.10", "3.11"]
+#        python-version: ["3.10", "3.11"]
 #      fail-fast: false
 #    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
@@ -30,14 +30,14 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
       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
@@ -19,14 +19,14 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
       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 }}
@@ -59,12 +59,12 @@ jobs:
 #    runs-on: "macos-latest"
 #    strategy:
 #      matrix:
-#        python-version: ["3.9", "3.10", "3.11"]
+#        python-version: ["3.10", "3.11"]
 #      fail-fast: false
 #    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
@@ -23,13 +23,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 }}
@@ -65,15 +67,17 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 * * *'
 
@@ -27,13 +26,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 * * *'
 
@@ -21,13 +20,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 }}
@@ -69,15 +72,17 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["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 }}