Merge branch 'main' into misc-lazy

ESMValGroup · Nov 13, 2024 · a4139bf · a4139bf
2 parents b34c3ae + a328578
commit a4139bf
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Showing 129 changed files with 1,562 additions and 1,361 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -21,14 +21,18 @@ commands:
               circleci step halt
             fi
   test_and_report:
+    parameters:
+      args:
+        type: string
+        default: ""
     steps:
       - run:
           name: Run tests
           command: |
             mkdir -p test-reports
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            pytest -n 4 --junitxml=test-reports/report.xml
+            pytest -n 4 --junitxml=test-reports/report.xml << parameters.args >>
             esmvaltool version
       - store_test_results:
           path: test-reports/report.xml
@@ -127,8 +131,9 @@ jobs:
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
             conda activate esmvaltool
-            pip install .[test] |& tee -a /logs/install.txt
-      - test_and_report
+            pip install .[test] > /logs/install.txt 2>&1
+      - test_and_report:
+          args: --cov
       - save_cache:
           key: test-{{ .Branch }}-{{ checksum "cache_key.txt" }}
           paths:
@@ -149,15 +154,15 @@ jobs:
   test_installation_from_source_test_mode:
     # Test installation from source
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     resource_class: large
     steps:
       - test_installation_from_source
 
   test_installation_from_source_develop_mode:
     # Test development installation
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     resource_class: large
     steps:
       - test_installation_from_source:
@@ -167,7 +172,7 @@ jobs:
   test_with_upstream_developments:
     # Test with development versions of upstream packages
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     resource_class: large
     steps:
       - test_installation_from_source:
@@ -187,7 +192,7 @@ jobs:
     # Test conda package installation
     working_directory: /esmvaltool
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     resource_class: medium
     steps:
       - run:
@@ -209,7 +214,7 @@ jobs:
   build_documentation:
     # Test building documentation
     docker:
-      - image: condaforge/mambaforge
+      - image: condaforge/miniforge3
     resource_class: medium
     steps:
       - checkout

diff --git a/.circleci/install_triggers b/.circleci/install_triggers
@@ -1,5 +1,3 @@
 ^\.circleci/
 ^environment\.yml$
 ^pyproject.toml$
-^setup\.py$
-^setup\.cfg$
diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
@@ -29,7 +29,6 @@ jobs:
           activate-environment: esmvaltool-fromlock
           python-version: "3.12"
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - name: Update and show conda config
         run: |
@@ -40,7 +39,9 @@ jobs:
           conda config --show
           # 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 --version
           mamba --version
       - name: Gather Python info

diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -49,7 +49,6 @@ jobs:
         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
@@ -85,7 +84,6 @@ jobs:
           architecture: ${{ matrix.architecture }}
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p conda_install_osx_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/install-from-pypi.yml b/.github/workflows/install-from-pypi.yml
@@ -52,7 +52,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p pip_install_linux_artifacts_python_${{ matrix.python-version }}
       - name: Record versions
@@ -90,7 +89,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p pip_install_osx_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
@@ -50,7 +50,6 @@ 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
@@ -89,7 +88,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p source_install_osx_artifacts_python_${{ matrix.python-version }}
       - name: Record versions

diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -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 }}
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
@@ -70,7 +69,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p test_osx_artifacts_python_${{ matrix.python-version }}
       - run: conda --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -52,7 +52,6 @@ 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 }}
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
@@ -90,7 +89,6 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
-          miniforge-variant: Mambaforge
           use-mamba: true
       - run: mkdir -p test_osx_artifacts_python_${{ matrix.python-version }}
       - run: conda --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -33,13 +33,13 @@ repos:
       - id: codespell
         additional_dependencies: [tomli]  # required for Python 3.10
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.7.3"
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.11.2'
+    rev: 'v1.13.0'
     hooks:
       - id: mypy
         additional_dependencies:

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/ESMValCore/issues/2557
+    # 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