Merge branch 'main' into enso_diagnostics

Author: rbeucher

.circleci/config.yml

@@ -90,7 +90,9 @@ commands:
             # Install
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
-            mamba env create
+            mamba --version
+            mamba install -c conda-forge "mamba>=2"  # mamba<2 can't solve env
+            mamba env create -n esmvaltool -f environment.yml
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
             pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
@@ -105,7 +107,7 @@ commands:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            flake8 -j 4
+            pre-commit run --all
       - test_and_report
       - save_cache:
           key: install-<< parameters.extra >>-{{ .Branch }}-{{ checksum "cache_key.txt" }}
@@ -141,7 +143,7 @@ jobs:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            flake8 -j 4
+            pre-commit run --all
       - run:
           name: Remove source code to test the installed software
           command: rm -r esmvaltool
@@ -202,7 +204,8 @@ jobs:
             # https://docs.esmvaltool.org/en/latest/quickstart/installation.html#install-from-source
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
-            mamba env create
+            mamba install -c conda-forge "mamba>=2"  # mamba<2 can't solve env
+            mamba env create -n esmvaltool -f environment.yml
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
             pip install --editable .[develop]
@@ -244,7 +247,7 @@ jobs:
             mkdir /logs
             . /opt/conda/etc/profile.d/conda.sh
             # Install
-            mamba env create
+            mamba env create -n esmvaltool -f environment_python.yml
             conda activate esmvaltool
             pip install .[doc]
             # Log versions

.codacy.yml

@@ -4,7 +4,7 @@
 
 engines:
     coverage:
-        enabled: true
+        enabled: false
         exclude_paths: [
             'tests',
         ]

.dockerignore

@@ -7,4 +7,3 @@ ESMValTool.egg-info
 
 !.git
 !.zenodo.json
-

.editorconfig

@@ -27,4 +27,3 @@ indent_size = 2
 
 [*.{md,Rmd}]
 trim_trailing_whitespace = false
-

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

@@ -74,8 +74,8 @@ jobs:
         run: esmvaltool --help
       - name: Check ESMValTool help
         run: esmvaltool version
-      - name: Run flake8
-        run: flake8
+      - name: Check code quality
+        run: pre-commit run -a
       - name: Run tests
         run: pytest -n 2 -m "not installation"
       # Automated PR

.github/workflows/cron_esmvalbot_test.yml

@@ -4,9 +4,9 @@ on:
   # push:
   #   branches:
   #     - cron_esmvalbot_test
-  # scheduled once every 2 weeks
+  # scheduled twice a month (on the 1st and 16th)
   schedule:
-    - cron: '0 4 */14 * *'
+    - cron: '0 4 1,16 * *'
 
 # Required shell entrypoint to have properly configured bash shell
 defaults:

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

@@ -54,7 +54,7 @@ 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: pre-commit run -a
       - run: pytest -n 2 -m "not installation"
       - name: Upload artifacts
         if: ${{ always() }}  # upload artifacts even if fail

.github/workflows/test-development.yml

@@ -56,8 +56,8 @@ jobs:
           git clone https://github.com/ESMValGroup/ESMValCore.git
           cd ESMValCore
           pip install -e .[develop]
-      - name: Run flake8
-        run: flake8
+      - name: Check code quality
+        run: pre-commit run -a
       - name: Run tests
         run: pytest -n 2 -m "not installation" 2>&1 | tee develop_test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - name: Upload artifacts

.github/workflows/test.yml

@@ -60,8 +60,8 @@ jobs:
           exit 1
       - name: Inspect environment
         run: conda list
-      - name: Run flake8
-        run: flake8
+      - name: Check code quality
+        run: pre-commit run -a
       - name: Run tests
         run: pytest -n 2 -m "not installation" 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - name: Upload artifacts
@@ -112,8 +112,8 @@ jobs:
         run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Inspect environment
         run: conda list
-      - name: Run flake8
-        run: flake8
+      - name: Check code quality
+        run: pre-commit run -a
       - 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

.pre-commit-config.yaml

@@ -5,10 +5,11 @@ exclude: |
   (?x)
   ^doc/sphinx/source/conf.py|
   ^esmvaltool/diag_scripts/extreme_events/climdex.pcic.ncdf/|
-  ^esmvaltool/diag_scripts/cvdp/
+  ^esmvaltool/diag_scripts/cvdp/|
+  ^esmvaltool/utils/nclcodestyle/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -18,41 +19,34 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
-  - repo: https://github.com/adrienverge/yamllint
-    rev: 'v1.35.1'
-    hooks:
-      - id: yamllint
-  - repo: local  # nclcodestyle is installed alongside ESMValTool
-    hooks:
-      - id: nclcodestyle
-        name: nclcodestyle
-        entry: nclcodestyle
-        language: system
-        files: '\.(ncl|NCL)$'
-  - repo: https://github.com/lorenzwalthert/precommit/  # Checks for R
-    rev: 'v0.4.2'
-    hooks:
-      - id: style-files  # styler
-      - id: lintr
-  - repo: https://github.com/codespell-project/codespell
-    rev: 'v2.3.0'
-    hooks:
-      - id: codespell
-  - repo: https://github.com/PyCQA/isort
-    rev: '5.13.2'
-    hooks:
-      - id: isort
-  - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: 'v0.32.0'
-    hooks:
-      - id: yapf
-        additional_dependencies:
-          - 'toml'
-  - repo: https://github.com/myint/docformatter
-    rev: 'v1.7.5'
-    hooks:
-      - id: docformatter
-  - repo: https://github.com/pycqa/flake8
-    rev: '5.0.4'
-    hooks:
-      - id: flake8
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.3"
+    hooks:
+      - id: ruff
+        args:
+          - "--fix"
+          # Do not use the configuration file but configure here so we can
+          # enable more rules that are not mandatory in the configuration file.
+          - "--select=B,E,F,I,ISC001,UP,W"  # TODO: select D
+          - "--ignore=E501"
+      - id: ruff-format
+  # - repo: https://github.com/adrienverge/yamllint
+  #   rev: 'v1.35.1'
+  #   hooks:
+  #     - id: yamllint
+  # - repo: local  # nclcodestyle is installed alongside ESMValTool
+  #   hooks:
+  #     - id: nclcodestyle
+  #       name: nclcodestyle
+  #       entry: nclcodestyle
+  #       language: system
+  #       files: '\.(ncl|NCL)$'
+  # - repo: https://github.com/lorenzwalthert/precommit/  # Checks for R
+  #   rev: 'v0.4.2'
+  #   hooks:
+  #     - id: style-files  # styler
+  #     - id: lintr
+  # - repo: https://github.com/codespell-project/codespell
+  #   rev: 'v2.3.0'
+  #   hooks:
+  #     - id: codespell