Merge branch 'main' of github.com:ESMValGroup/ESMValCore into disable…

…-coverage-by-default
ESMValGroup · Sep 26, 2024 · 9fe2d82 · 9fe2d82
2 parents 7ef0796 + 4b0dd41
commit 9fe2d82
Show file tree

Hide file tree

Showing 565 changed files with 29,768 additions and 23,679 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,8 +2,8 @@
 version: 2.1
 
 orbs:
-  coverage-reporter: codacy/coverage-reporter@13.16.5
-  codecov: codecov/codecov@3.2.5
+  coverage-reporter: codacy/coverage-reporter@14.0.0
+  codecov: codecov/codecov@4.1.0
 
 commands:
   check_changes:
@@ -32,7 +32,6 @@ commands:
             mkdir -p test-reports
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            flake8 -j 4
             pytest -n 4 --junitxml=test-reports/report.xml << parameters.args >>
             esmvaltool version
       - store_test_results:
@@ -52,8 +51,15 @@ commands:
   test_installation_from_source:
     parameters:
       extra:
+        description: pip "extra"s to install
         type: string
+        default: "test"
       flags:
+        description: pip install flags
+        type: string
+        default: ""
+      upstream_packages:
+        description: List of packages that will be installed with pip.
         type: string
         default: ""
     steps:
@@ -78,20 +84,25 @@ commands:
               - r-yaml
               - ncl
             " >> environment.yml
+            # Installation of development version of packages requires compilers
+            if [[ "<< parameters.upstream_packages >>" ]]; then
+                echo "  - compilers" >> environment.yml
+            fi
             # Install
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
-            mamba env create >> /logs/conda.txt 2>&1
+            mamba env create |& tee /logs/conda.txt
+            git stash  # Restore repository state to get clean version number.
             conda activate esmvaltool
-            pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
+            pip install << parameters.flags >> ".[<<parameters.extra>>]" << parameters.upstream_packages >> |& tee /logs/install.txt
       - run:
           name: Log versions
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            dpkg -l > /logs/versions.txt
-            conda env export > /logs/environment.yml
-            pip freeze > /logs/requirements.txt
+            dpkg -l | tee /logs/versions.txt
+            conda env export | tee /logs/environment.yml
+            pip freeze | tee /logs/requirements.txt
       - test_and_report
       - save_cache:
           key: install-<< parameters.extra >>-{{ .Branch }}-{{ checksum "cache_key.txt" }}
@@ -146,8 +157,7 @@ jobs:
       - image: condaforge/mambaforge
     resource_class: large
     steps:
-      - test_installation_from_source:
-          extra: test
+      - test_installation_from_source
 
   test_installation_from_source_develop_mode:
     # Test development installation
@@ -159,6 +169,25 @@ jobs:
           extra: develop
           flags: "--editable"
 
+  test_with_upstream_developments:
+    # Test with development versions of upstream packages
+    docker:
+      - image: condaforge/mambaforge
+    resource_class: large
+    steps:
+      - test_installation_from_source:
+          upstream_packages: >-
+            git+https://github.com/esgf/esgf-pyclient
+            git+https://github.com/euro-cordex/py-cordex
+            git+https://github.com/SciTools/cartopy
+            git+https://github.com/SciTools/cf-units
+            git+https://github.com/SciTools/iris
+            git+https://github.com/SciTools/iris-grib
+            git+https://github.com/SciTools/nc-time-axis
+            git+https://github.com/SciTools-incubator/iris-esmf-regrid
+            git+https://github.com/SciTools-incubator/python-stratify
+            git+https://github.com/Toblerity/Fiona
+
   test_installation_from_conda:
     # Test conda package installation
     working_directory: /esmvaltool
@@ -172,14 +201,13 @@ jobs:
             set -x
             # Install prerequisites
             mkdir /logs
-            # conda update -y conda > /logs/conda.txt 2>&1
             # Create and activate conda environment
             mamba create -y --name esmvaltool 'python=3.11'
             set +x; conda activate esmvaltool; set -x
             # Install
             mamba install -y esmvalcore
             # Log versions
-            conda env export > /logs/environment.yml
+            conda env export | tee /logs/environment.yml
             # Test installation
             esmvaltool version
 
@@ -199,9 +227,9 @@ jobs:
             conda activate esmvaltool
             pip install .[doc]
             # Log versions
-            dpkg -l > /logs/versions.txt
-            conda env export > /logs/environment.yml
-            pip freeze > /logs/requirements.txt
+            dpkg -l | tee /logs/versions.txt
+            conda env export | tee /logs/environment.yml
+            pip freeze | tee /logs/requirements.txt
             # Test building documentation
             MPLBACKEND=Agg sphinx-build -W doc doc/build
       - store_artifacts:
@@ -211,8 +239,9 @@ workflows:
   commit:
     jobs:
       - run_tests
-      - test_installation_from_source_test_mode
       - test_installation_from_source_develop_mode
+      - test_installation_from_source_test_mode
+      - test_with_upstream_developments
 
   nightly:
     triggers:
@@ -223,8 +252,9 @@ workflows:
               only:
                 - main
     jobs:
-      - run_tests
-      - test_installation_from_source_test_mode
       - build_documentation
-      - test_installation_from_source_develop_mode
+      - run_tests
       - test_installation_from_conda
+      - test_installation_from_source_develop_mode
+      - test_installation_from_source_test_mode
+      - test_with_upstream_developments
diff --git a/.editorconfig b/.editorconfig
@@ -27,4 +27,3 @@ indent_size = 2
 
 [*.{md,Rmd}]
 trim_trailing_whitespace = false
-
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -1,3 +1 @@
-esmvalcore/cmor @jvegasbsc
 .github/workflows @valeriupredoi
-
diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
@@ -71,8 +71,6 @@ jobs:
         run: |
           esmvaltool --help
           esmvaltool version
-      - name: Run flake8
-        run: flake8
       - name: Run pytests
         run: pytest -n 2 -m "not installation"
       # Automated PR

diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -39,7 +39,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       # fail-fast set to False allows all other tests
       # in the workflow to run regardless of any fail
       fail-fast: false
@@ -75,7 +75,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        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 }}

diff --git a/.github/workflows/install-from-condalock-file.yml b/.github/workflows/install-from-condalock-file.yml
@@ -29,7 +29,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -51,7 +51,6 @@ jobs:
       - run: pip install -e .[develop]
       - run: esmvaltool --help
       - run: esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
-      - run: flake8
       - run: pytest -n 2 -m "not installation"
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail

diff --git a/.github/workflows/install-from-pypi.yml b/.github/workflows/install-from-pypi.yml
@@ -39,7 +39,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       # fail-fast set to False allows all other tests
       # in the workflow to run regardless of any fail
       fail-fast: false
@@ -77,7 +77,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        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 }}

diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
@@ -37,7 +37,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -74,7 +74,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        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 }}

diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -55,7 +55,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        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 }}

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -39,7 +39,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -60,7 +60,9 @@ jobs:
       - run: conda list
       - run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
-      - run: flake8
+      - run: |
+          pre-commit install
+          pre-commit run -a
       - 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
@@ -73,7 +75,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         architecture: ["x64"]  # need to force Intel, arm64 builds have issues
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
@@ -97,7 +99,9 @@ jobs:
       - run: conda list
       - run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
-      - run: flake8
+      - run: |
+          pre-commit install
+          pre-commit run -a
       - 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

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,19 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 ---
+ci:
+  autofix_prs: false
+
 exclude: |
   (?x)
   ^doc/conf.py|
   ^esmvalcore/cmor/tables/|
-  ^esmvalcore/preprocessor/ne_masks/
+  ^esmvalcore/preprocessor/ne_masks/|
+  ^esmvalcore/preprocessor/shapefiles/
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -19,33 +24,22 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/adrienverge/yamllint
-    rev: 'v1.31.0'
+    rev: 'v1.35.1'
     hooks:
       - id: yamllint
   - repo: https://github.com/codespell-project/codespell
-    rev: 'v2.2.4'
+    rev: 'v2.3.0'
     hooks:
       - id: codespell
-  - repo: https://github.com/PyCQA/isort
-    rev: '5.12.0'
+        additional_dependencies: [tomli]  # required for Python 3.10
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.6.8"
     hooks:
-      - id: isort
-  - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: 'v0.32.0'
-    hooks:
-      - id: yapf
-        additional_dependencies:
-          - 'toml'
-  - repo: https://github.com/myint/docformatter
-    rev: 'v1.6.5'
-    hooks:
-      - id: docformatter
-  - repo: https://github.com/pycqa/flake8
-    rev: '6.0.0'
-    hooks:
-      - id: flake8
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.2.0'
+    rev: 'v1.11.2'
     hooks:
       - id: mypy
         additional_dependencies:

diff --git a/.prospector.yml b/.prospector.yml
@@ -10,16 +10,21 @@ test-warnings: true
 member-warnings: false
 
 pyroma:
-    run: true
+  run: true
 
 pep8:
-    full: true
+  full: true
+  # ignore rules that conflict with ruff formatter
+  # E203: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#slices
+  # E501: https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+  # W503: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
+  disable: ['E203', 'E501', 'W503']
 
 mypy:
   run: true
 
 pep257:
-    # disable rules that are allowed by the numpy convention
-    # see https://github.com/PyCQA/pydocstyle/blob/master/src/pydocstyle/violations.py
-    # and http://pydocstyle.readthedocs.io/en/latest/error_codes.html
-    disable: ['D107', 'D203', 'D212', 'D213', 'D402', 'D413', 'D416']
+  # disable rules that are allowed by the numpy convention
+  # see https://github.com/PyCQA/pydocstyle/blob/master/src/pydocstyle/violations.py
+  # and http://pydocstyle.readthedocs.io/en/latest/error_codes.html
+  disable: ['D107', 'D203', 'D212', 'D213', 'D402', 'D413', 'D416']