Merge branch 'main' into 3873_use_site_directories

* main: (43 commits)
  use python-only environment file for Circle build documentation (#3981)
  Added option to plot horizontal lines in monitoring line plots (#3977)
  [Condalock] Update Linux condalock file (#3974)
  Run esmvalbot test PR twice a month (#3976)
  unpin upper limit `r-base` (#3971)
  [Condalock] Update Linux condalock file (#3968)
  Update CMORizer for OSI-450 aka OSISAF/CCI (sea ice concentration) (#3963)
  Add recipe for seasonal cycle and time series of Arctic/Antarctic sea ice area (REF) (#3891)
  use Python-only environment for ReadTheDocs builds (#3955)
  [Condalock] Update Linux condalock file (#3961)
  Create scatterplots for the REF (#3923)
  [Condalock] Update Linux condalock file (#3957)
  Unsafe and manual fixes
  Automatic fixes
  Replace flake8, yapf, and isort with ruff
  Add recipe and diagnostic for ZEC (Zero Emissions Commitment) (#3897)
  Update ESACCI-OZONE CMORizer(formatter and downloader) for REF (#3899)
  Update citation and changelog for version 2.12 (#3945)
  use mamba>=2 for Circle CI upstream development test (#3949)
  Force install mamba2 in CircleCI and add ipython and pin it to <9.0 (#3947)
  ...

Author: ehogan

.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/check-rtw.yml

@@ -28,6 +28,7 @@ jobs:
   check-rtw:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
+    if: github.event_name != 'schedule' || github.repository == 'ESMValGroup/ESMValTool' # avoid scheduled GHAs in forks
 
     # Steps represent a sequence of tasks that will be executed as part
     # of the job

.github/workflows/citation_file_validator.yml

@@ -14,6 +14,7 @@ jobs:
   validate:
     name: "validate"
     runs-on: ubuntu-latest
+    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

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

@@ -19,6 +19,7 @@ jobs:
   create-lock-file:
     name: Create conda lock file for latest Python
     runs-on: 'ubuntu-latest'
+    if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     steps:
       - uses: actions/checkout@v4
         with:
@@ -73,8 +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:
@@ -16,6 +16,7 @@ defaults:
 jobs:
   run-esmvalbot:
     runs-on: 'ubuntu-latest'
+    if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     steps:
       - uses: actions/checkout@v4
         with:

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

@@ -17,6 +17,7 @@ defaults:
 jobs:
   linux:
     runs-on: "ubuntu-latest"
+    if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     strategy:
       fail-fast: false
       matrix:
@@ -53,6 +54,7 @@ jobs:
 #
 #  osx:
 #    runs-on: "macos-latest"
+#    if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
 #    strategy:
 #      matrix:
 #        python-version: ["3.10", "3.11"]

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

@@ -28,6 +28,7 @@ defaults:
 jobs:
   linux:
     runs-on: "ubuntu-latest"
+    if: github.repository == 'ESMValGroup/ESMValTool'  # avoid GAs in forks
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
@@ -53,7 +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