fix merge conflict

Author: bettina-gier

.circleci/config.yml

@@ -41,10 +41,10 @@ commands:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            mamba --version
             pytest -n 4 --junitxml=test-reports/report.xml
             esmvaltool version
             esmvaltool -- --help
+            esmvaltool develop compare -- --help
             ncl -V
             cdo --version
       - store_test_results:
@@ -96,7 +96,6 @@ commands:
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
             pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
-            esmvaltool install Julia > /logs/install_julia.txt 2>&1
             if [[ "<<parameters.flags>>" != *'--editable'* ]]
             then
               rm -r esmvaltool
@@ -137,7 +136,6 @@ jobs:
             conda activate esmvaltool
             mkdir /logs
             pip install .[test] > /logs/install.txt 2>&1
-            esmvaltool install Julia > /logs/install_julia.txt 2>&1
       - run:
           name: Check Python code style and mistakes
           command: |
@@ -209,7 +207,6 @@ jobs:
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
             pip install --editable .[develop]
-            esmvaltool install Julia > /logs/install_julia.txt 2>&1
             git clone https://github.com/ESMValGroup/ESMValCore $HOME/ESMValCore
             pip install --editable $HOME/ESMValCore[develop]
       - log_versions
@@ -272,11 +269,9 @@ jobs:
             # Install prerequisites
             mkdir /logs
             # Install ESMValTool in a new conda environment
-            mamba create -y --name esmvaltool -c conda-forge esmvaltool julia 'python=3.11' >> /logs/conda.txt 2>&1
+            mamba create -y --name esmvaltool -c conda-forge esmvaltool 'python=3.11' >> /logs/conda.txt 2>&1
             # Activate the environment
             set +x; conda activate esmvaltool; set -x
-            # install the Julia dependencies
-            esmvaltool install Julia > /logs/install_Julia.txt 2>&1
             # Log versions
             mamba env export > /logs/environment.yml
             # Test installation

.circleci/install_triggers

@@ -1,6 +1,5 @@
 ^\.circleci/
 ^environment\.yml$
-^esmvaltool/install/
 ^pyproject.toml$
 ^setup\.py$
 ^setup\.cfg$

.codacy.yml

@@ -24,4 +24,5 @@ exclude_paths: [
     'esmvaltool/cmor/tables/**',
     'tests/**',
     'esmvaltool/utils/recipe_test_workflow/app/configure/bin/test_configure.py',
+    'esmvaltool/utils/recipe_test_workflow/app/generate_report/bin/test_generate_html_report.py',
 ]

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the default location of `.github/workflows`
+    # You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/check-rtw.yml

@@ -36,7 +36,7 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job
       # can access it
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup Cylc
         uses: cylc/setup-cylc@v1

.github/workflows/citation_file_validator.yml

@@ -17,7 +17,7 @@ jobs:
     if: github.event_name != 'schedule' || github.repository == 'ESMValGroup/ESMValTool' # avoid scheduled GHAs in forks
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0

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

@@ -21,28 +21,20 @@ jobs:
     runs-on: 'ubuntu-latest'
     if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           activate-environment: esmvaltool-fromlock
-          python-version: "3.12"
+          python-version: "3.13"
           miniforge-version: "latest"
           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
-          # 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
           mamba --version
       - name: Python info
         run: |
@@ -81,7 +73,7 @@ jobs:
       # Automated PR
       # see https://github.com/marketplace/actions/create-pull-request
       - name: Create Automated PR if conda lock file has changed
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Updating Linux condalock file

.github/workflows/cron_esmvalbot_test.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: 'ubuntu-latest'
     if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Create empty commit on branch

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

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.11", "3.12"]  # add "3.13" when pkg built
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: conda-incubator/setup-miniconda@v3
@@ -72,7 +72,7 @@ jobs:
 #      - run: which conda 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/conda_path.txt
 #      - run: python -V 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
 #      # ncurses needs to be from conda-forge and not main channel
-#      # for now it's turned off since we're not testing R/Julia installs
+#      # for now it's turned off since we're not testing R installs
 #      # - run: conda uninstall -y ncurses
 #      # - run: conda list ncurses
 #      # - run: conda install -y conda-forge::ncurses

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

@@ -31,11 +31,11 @@ jobs:
     if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     strategy:
       matrix:
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v3