Merge pull request #13 from ESMValGroup/main

Update pre 2.9

.circleci/config.yml

@@ -127,6 +127,7 @@ jobs:
       - run:
           name: Install dependencies
           command: |
+            set -x
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
             mkdir /logs
@@ -215,7 +216,6 @@ jobs:
             esmvaltool config get_config_user
             echo "offline: false" >> ~/.esmvaltool/config-user.yml
             cat ~/.esmvaltool/config-user.yml
-            esmvaltool run examples/recipe_python.yml
             for recipe in esmvaltool/recipes/testing/recipe_*.yml; do
               esmvaltool run "$recipe"
             done

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

@@ -22,12 +22,14 @@ jobs:
         with:
           auto-update-conda: true
           activate-environment: esmvaltool-fromlock
-          python-version: "3.10"
-          miniconda-version: "latest"
-          channels: conda-forge
+          python-version: "3.11"
+          miniforge-version: "latest"
+          miniforge-variant: Mambaforge
+          use-mamba: true
       - name: Show conda config
         shell: bash -l {0}
         run: |
+          conda update -n base -c conda-forge conda
           conda info
           conda list
           conda config --show-sources
@@ -39,7 +41,10 @@ jobs:
           python --version
       - name: Install conda-lock
         shell: bash -l {0}
-        run: conda install -y conda-lock
+        run: mamba install -y conda-lock
+      - name: Check version of conda-lock
+        shell: bash -l {0}
+        run: conda-lock --version
       - name: Create conda lock file for linux-64
         shell: bash -l {0}
         run: conda-lock lock --platform linux-64 -f environment.yml --mamba --kind explicit
@@ -52,7 +57,7 @@ jobs:
       - shell: bash -l {0}
         run: conda create --name esmvaltool-fromlock --file conda-linux-64.lock
       - shell: bash -l {0}
-        run: conda install -y -c conda-forge pip
+        run: mamba install -y pip
       - shell: bash -l {0}
         run: which python
       - shell: bash -l {0}

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

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: conda-incubator/setup-miniconda@v2
@@ -55,7 +55,7 @@ jobs:
 #    runs-on: "macos-latest"
 #    strategy:
 #      matrix:
-#        python-version: ["3.8", "3.9", "3.10"]
+#        python-version: ["3.9", "3.10", "3.11"]
 #      fail-fast: false
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:

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

@@ -25,7 +25,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -73,7 +73,7 @@ jobs:
 #    runs-on: "macos-latest"
 #    strategy:
 #      matrix:
-#        python-version: ["3.8", "3.9", "3.10"]
+#        python-version: ["3.9", "3.10", "3.11"]
 #      fail-fast: false
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:

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

@@ -14,7 +14,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
@@ -58,7 +58,7 @@ jobs:
 #    runs-on: "macos-latest"
 #    strategy:
 #      matrix:
-#        python-version: ["3.8", "3.9", "3.10"]
+#        python-version: ["3.9", "3.10", "3.11"]
 #      fail-fast: false
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:

.github/workflows/pypi-build-and-deploy.yml

@@ -17,10 +17,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v1
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Install pep517
         run: >-
           python -m

.github/workflows/run-tests-monitor.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -67,7 +67,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

.github/workflows/test-development.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -36,12 +36,24 @@ jobs:
         run: |
           mamba --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
+          # this is how to export variables to the GITHUB var environment
+          echo "pver0=$(python -V)" >> $GITHUB_ENV
       - name: Install ESMValTool
         shell: bash -l {0}
         run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Install Julia dependencies
         shell: bash -l {0}
         run: esmvaltool install Julia
+      - name: Export Python minor version
+        shell: bash -l {0}
+        run: echo "pver1=$(python -V)" >> $GITHUB_ENV
+      - name: Exit if Python minor version changed
+        shell: bash -l {0}
+        if: ${{ env.pver1 != env.pver0}}
+        run: |
+          echo "Python minor version changed after Julia install"
+          python -V
+          exit 1
       - name: Run flake8
         shell: bash -l {0}
         run: flake8
@@ -59,7 +71,7 @@ jobs:
     runs-on: "macos-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ exclude: |
   ^esmvaltool/diag_scripts/cvdp/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -19,7 +19,7 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/adrienverge/yamllint
-    rev: 'v1.26.0'
+    rev: 'v1.31.0'
     hooks:
       - id: yamllint
   - repo: local  # nclcodestyle is installed alongside ESMValTool
@@ -30,34 +30,29 @@ repos:
         language: system
         files: '\.(ncl|NCL)$'
   - repo: https://github.com/lorenzwalthert/precommit/  # Checks for R
-    rev: 'v0.1.3'
+    rev: 'v0.3.2.9007'
     hooks:
       - id: style-files  # styler
       - id: lintr
   - repo: https://github.com/codespell-project/codespell
-    rev: 'v2.0.0'
+    rev: 'v2.2.4'
     hooks:
       - id: codespell
   - repo: https://github.com/PyCQA/isort
-    rev: '5.7.0'
+    rev: '5.12.0'
     hooks:
       - id: isort
   - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: 'v0.30.0'
+    rev: 'v0.32.0'
     hooks:
       - id: yapf
+        additional_dependencies:
+          - 'toml'
   - repo: https://github.com/myint/docformatter
-    rev: 'v1.4'
+    rev: 'v1.6.5'
     hooks:
       - id: docformatter
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: '3.8.4'
+  - repo: https://github.com/pycqa/flake8
+    rev: '6.0.0'
     hooks:
       - id: flake8
-  # - repo: https://github.com/PyCQA/prospector
-  #   rev: ''
-  #   hooks:
-  #     - id: prospector
-  #       additional_dependencies: [
-  #         'pyroma',
-  #       ]

.readthedocs.yaml

@@ -12,7 +12,8 @@ build:
     python: "mambaforge-4.10"
   jobs:
     post_create_environment:
-      - pip install . --no-deps
+      # use conda run executable wrapper to have all env variables
+      - conda run -n ${CONDA_DEFAULT_ENV} pip install . --no-deps
 
 # Declare the requirements required to build your docs
 conda:

README.md

@@ -2,7 +2,7 @@
 [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
 [![Documentation Status](https://readthedocs.org/projects/esmvaltool/badge/?version=latest)](https://esmvaltool.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3401363.svg)](https://doi.org/10.5281/zenodo.3401363)
-[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/ESMValGroup?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Chat on Matrix](https://matrix.to/img/matrix-badge.svg)](https://matrix.to/#/#ESMValGroup_Lobby:gitter.im)
 [![CircleCI](https://circleci.com/gh/ESMValGroup/ESMValTool/tree/main.svg?style=svg)](https://circleci.com/gh/ESMValGroup/ESMValTool/tree/main)
 [![Test in Full Development Mode](https://github.com/ESMValGroup/ESMValTool/actions/workflows/test-development.yml/badge.svg)](https://github.com/ESMValGroup/ESMValTool/actions/workflows/test-development.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/79bf6932c2e844eea15d0fb1ed7e415c)](https://www.codacy.com/gh/ESMValGroup/ESMValTool?utm_source=github.com&utm_medium=referral&utm_content=ESMValGroup/ESMValTool&utm_campaign=Badge_Coverage)
@@ -11,11 +11,11 @@
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/esmvaltool/badges/version.svg)](https://anaconda.org/conda-forge/esmvaltool)
 ![stand with Ukraine](https://badgen.net/badge/stand%20with/UKRAINE/?color=0057B8&labelColor=FFD700)
 
-![esmvaltoollogo](https://github.com/ESMValGroup/ESMValTool/blob/main/doc/sphinx/source/figures/ESMValTool-logo-2.png)
+![esmvaltoollogo](https://raw.githubusercontent.com/ESMValGroup/ESMValTool/main/doc/sphinx/source/figures/ESMValTool-logo-2.png)
 
 - [**Documentation**](https://docs.esmvaltool.org/en/latest/)
 - [**ESMValTool Website**](https://www.esmvaltool.org/)
-- [**ESMValTool Tutorial**](https://esmvalgroup.github.io/ESMValTool_Tutorial/index.html)
+- [**ESMValTool Tutorial**](https://tutorial.esmvaltool.org/index.html)
 - [**ESMValGroup Project on GitHub**](https://github.com/ESMValGroup)
 - [**Gallery**](https://docs.esmvaltool.org/en/latest/gallery.html)
 - [**`conda-forge` package feedstock**](https://github.com/conda-forge/esmvaltool-suite-feedstock)
@@ -53,7 +53,7 @@ ESMValTool can run with the following types of [data as input](https://docs.esmv
 
 # Getting started
 
-Please see [getting started](https://docs.esmvaltool.org/en/latest/quickstart/index.html) on readthedocs as well as [ESMValTool tutorial](https://esmvalgroup.github.io/ESMValTool_Tutorial/index.html). The tutorial is a set of lessons that together teach skills needed to work with ESMValTool in climate-related domains.
+Please see [getting started](https://docs.esmvaltool.org/en/latest/quickstart/index.html) on readthedocs as well as [ESMValTool tutorial](https://tutorial.esmvaltool.org/index.html). The tutorial is a set of lessons that together teach skills needed to work with ESMValTool in climate-related domains.
 
 ## Getting help