diff --git a/.circleci/config.yml b/.circleci/config.yml
index 85c510efc5..c39f436453 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -7,174 +7,189 @@ orbs:
 commands:
   check_changes:
     steps:
-      - run: |
-          if (test "$CIRCLE_BRANCH" = main ||
-            git --no-pager diff --name-only origin/main... |
-            grep -q -E -f .circleci/install_triggers)
-          then
-            echo Running installation tests
-          else
-            echo Skipping installation tests
-            circleci step halt
-          fi
-
-jobs:
-  run_tests:
-    # Run Python 3 tests
-    working_directory: /test
-    docker:
-      - image: esmvalgroup/esmvaltool:development
+      - run:
+          name: Check whether or not installation tests are needed
+          command: |
+            if (test "$CIRCLE_BRANCH" = main ||
+              git --no-pager diff --name-only origin/main... |
+              grep -q -E -f .circleci/install_triggers)
+            then
+              echo Running installation tests
+            else
+              echo Skipping installation tests
+              circleci step halt
+            fi
+  test_and_report:
     steps:
-      - checkout
       - run:
-          # Update environment if needed and run tests
+          name: Run tests
           command: |
             . /opt/conda/etc/profile.d/conda.sh
-            mkdir /logs
-            conda --version > /logs/conda_version.txt
             conda activate esmvaltool
-            python --version > /logs/python_version.txt
-            conda env export > /logs/environment.yml
-            pip install .[test] > /logs/install.txt
-            # Run flake8 check with source code (it doesn't work without it)
-            pytest -n 2 -m flake8
-            # Update/install Julia dependencies
-            esmvaltool install Julia > /logs/install_Julia.txt
-            # Remove source to test installed software
-            rm -r esmvaltool
-            pytest -n 2 -m 'not flake8'
+            pytest -n 4 -m 'not flake8' --junitxml=test-reports/report.xml
+            esmvaltool version
+            esmvaltool -- --help
+            ncl -V
+            cdo --version
+      - store_test_results:
+          path: test-reports/
       - store_artifacts:
           path: /logs
+      - run:
+          name: Compress pytest artifacts
+          command: tar -cvzf pytest.tar.gz -C /tmp/pytest-of-root/ .
+          when: always
       - store_artifacts:
-          path: test-reports/
-      - store_test_results:
-          path: test-reports/
-      - coverage-reporter/send_report:
-          coverage-reports: 'test-reports/coverage.xml'
-          project-token: $CODACY_PROJECT_TOKEN
-          # Skip if token isn't defined.
-          # Useful to let forks CI pass without passing secrets
-          skip: true
-
-  test_installation_from_source_test_mode:
-    # Test Python 3 installation
-    working_directory: /test_installation
-    docker:
-      - image: condaforge/mambaforge:latest
+          path: pytest.tar.gz
+      - run:
+          name: Compress test-report artifacts
+          command: tar -cvzf test-reports.tar.gz test-reports/
+          when: always
+      - store_artifacts:
+          path: test-reports.tar.gz
+  test_installation_from_source:
+    parameters:
+      extra:
+        type: string
+      flags:
+        type: string
+        default: ""
     steps:
+      - run:
+          name: Install git+ssh
+          environment:
+            DEBIAN_FRONTEND: noninteractive  # needed to install tzdata
+          command: apt update && apt install -y git ssh
       - checkout
       - check_changes
+      - run:
+          name: Generate cache key
+          command: date '+%Y-%V' | tee cache_key.txt
       - restore_cache:
-          key: test-install-{{ .Branch }}
+          key: install-<< parameters.extra >>-{{ .Branch }}-{{ checksum "cache_key.txt" }}
       - run:
+          name: Install dependencies
           command: |
+            # Install
             . /opt/conda/etc/profile.d/conda.sh
-            set -x
             mkdir /logs
-            # Install
-            mamba create --name esmvaltool 'python=3.10' >> /logs/conda.txt 2>&1
-            mamba env update --name esmvaltool >> /logs/conda.txt 2>&1
-            set +x; conda activate esmvaltool; set -x
-            mamba install julia >> /logs/conda.txt 2>&1
-            pip install .[test] > /logs/install.txt 2>&1
-            esmvaltool install Julia
-            # Remove source to test installed software
-            rm -r esmvaltool
-            # Log versions
+            mamba env create >> /logs/conda.txt 2>&1
+            conda activate esmvaltool
+            pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
+            esmvaltool install Julia > /logs/install_julia.txt 2>&1
+            if [[ "<<parameters.flags>>" != *'--editable'* ]]
+            then
+              rm -r esmvaltool
+            fi
+      - run:
+          name: Log versions
+          command: |
+            . /opt/conda/etc/profile.d/conda.sh
+            conda activate esmvaltool
             dpkg -l > /logs/versions.txt
-            mamba env export > /logs/environment.yml
+            conda env export > /logs/environment.yml
             pip freeze > /logs/requirements.txt
-            # Test installation
-            pytest -n 2
-            esmvaltool -h
-            ncl -V
-            # cdo test, check that it supports hdf5
-            cdo --version
-            echo 0 | cdo -f nc input,r1x1 tmp.nc
-            ncdump tmp.nc | ncgen -k hdf5 -o tmp.nc
-            cdo -f nc copy tmp.nc tmp2.nc
-          no_output_timeout: 30m
+      - run:
+          name: Lint source code
+          command: |
+            . /opt/conda/etc/profile.d/conda.sh
+            conda activate esmvaltool
+            pytest -n 4 -m flake8
+      - test_and_report
       - save_cache:
-          key: test-install-{{ .Branch }}
+          key: install-<< parameters.extra >>-{{ .Branch }}-{{ checksum "cache_key.txt" }}
           paths:
-            - "/opt/conda/pkgs"
-            - ".eggs"
-      - store_artifacts:
-          path: /logs
-      - store_artifacts:
-          path: test-reports/
-      - store_test_results:
-          path: test-reports/
+            - /opt/conda/pkgs
+            - /root/.cache/pip
+            - .pytest_cache
 
-  test_installation_from_source_develop_mode:
-    # Test development installation
-    working_directory: /develop
+jobs:
+  run_tests:
+    # Run tests
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: esmvalgroup/esmvaltool:development
+    resource_class: large
     steps:
       - checkout
-      - check_changes
       - run:
+          name: Generate cache key
+          command: date '+%Y-%V' | tee cache_key.txt
+      - restore_cache:
+          key: test-{{ .Branch }}-{{ checksum "cache_key.txt" }}
+      - run:
+          name: Install dependencies
           command: |
             . /opt/conda/etc/profile.d/conda.sh
-            set -x
             mkdir /logs
-            # Install
-            mamba create --name esmvaltool 'python=3.10' >> /logs/conda.txt 2>&1
-            mamba env update --name esmvaltool >> /logs/conda.txt 2>&1
-            set +x; conda activate esmvaltool; set -x
-            mamba install julia >> /logs/conda.txt 2>&1
-            pip install -e .[develop] > /logs/install.txt 2>&1
-            esmvaltool install Julia
-            # Log versions
-            dpkg -l > /logs/versions.txt
-            mamba env export > /logs/environment.yml
-            pip freeze > /logs/requirements.txt
-            # Test installation
-            pytest -n 2
-            esmvaltool -h
-            ncl -V
-            cdo --version
-          no_output_timeout: 30m
-      - store_artifacts:
-          path: /logs
+            conda activate esmvaltool
+            pip install .[test] > /logs/install.txt 2>&1
+            # Run flake8 check with source code (it doesn't work without it)
+            pytest -n 4 -m flake8
+            # Update/install Julia dependencies
+            esmvaltool install Julia > /logs/install_julia.txt 2>&1
+            # Remove source to test installed software
+            rm -r esmvaltool
+      - test_and_report
+      - save_cache:
+          key: test-{{ .Branch }}-{{ checksum "cache_key.txt" }}
+          paths:
+            - /root/.cache/pip
+            - .pytest_cache
+      - coverage-reporter/send_report:
+          coverage-reports: 'test-reports/coverage.xml'
+          project-token: $CODACY_PROJECT_TOKEN
+          skip: true  # skip if project-token is not defined (i.e. on a fork)
+
+  test_installation_from_source_test_mode:
+    # Test installation from source
+    docker:
+      - image: condaforge/mambaforge
+    resource_class: large
+    steps:
+      - test_installation_from_source:
+          extra: test
+
+  test_installation_from_source_develop_mode:
+    # Test development installation
+    docker:
+      - image: condaforge/mambaforge
+    resource_class: large
+    steps:
+      - test_installation_from_source:
+          extra: develop
+          flags: "--editable"
 
   build_documentation:
     # Test building documentation
-    working_directory: /doc
     docker:
-      - image: condaforge/mambaforge:latest
+      - image: condaforge/mambaforge
+    resource_class: small
     steps:
       - checkout
-      - restore_cache:
-          key: documentation-{{ .Branch }}
       - run:
           command: |
             mkdir /logs
+            . /opt/conda/etc/profile.d/conda.sh
             # Install
-            pip install -r doc/sphinx/source/requirements.txt > /logs/install.txt 2>&1
-            pip install sphinx sphinx_rtd_theme >> /logs/install.txt 2>&1
+            mamba env create
+            conda activate esmvaltool
+            pip install .[doc]
             # Log versions
             dpkg -l > /logs/versions.txt
+            conda env export > /logs/environment.yml
             pip freeze > /logs/requirements.txt
             # Test building documentation
-            MPLBACKEND=Agg sphinx-build -W doc/sphinx/source/ doc/sphinx/build/
-      - save_cache:
-          key: documentation-{{ .Branch }}
-          paths:
-            - ".eggs"
+            MPLBACKEND=Agg sphinx-build -W doc/sphinx/source doc/spinx/build
       - store_artifacts:
           path: /logs
 
   test_installation_from_conda:
     # Test conda package installation
-    working_directory: /esmvaltool
     docker:
       - image: condaforge/mambaforge
+    resource_class: medium
     steps:
       - run:
-          environment:
-            R_INSTALL_N_CPUS: 2
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             set -x
@@ -184,15 +199,15 @@ jobs:
             mamba create -y --name esmvaltool -c conda-forge esmvaltool julia 'python=3.10' >> /logs/conda.txt 2>&1
             # Activate the environment
             set +x; conda activate esmvaltool; set -x
-            # install the package
-            mamba install -c conda-forge esmvaltool >> /logs/install.txt 2>&1
+            # install the Julia dependencies
+            esmvaltool install Julia > /logs/install_Julia.txt 2>&1
             # Log versions
             mamba env export > /logs/environment.yml
             # Test installation
-            esmvaltool -h
+            esmvaltool -- --help
+            esmvaltool version
             ncl -V
             cdo --version
-          no_output_timeout: 30m
       - store_artifacts:
           path: /logs
 
@@ -202,8 +217,6 @@ workflows:
       - run_tests
       - test_installation_from_source_test_mode
       - test_installation_from_source_develop_mode
-      - build_documentation
-      - test_installation_from_conda
   nightly:
     triggers:
       - schedule:
diff --git a/.dockerignore b/.dockerignore
index cfb2cc4159..7168bcfade 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -2,10 +2,9 @@
 **/__pycache__
 .*
 doc
-package
 tests
 ESMValTool.egg-info
 
-
+!.git
 !.zenodo.json
 
diff --git a/.github/workflows/citation_file_validator.yml b/.github/workflows/citation_file_validator.yml
index 0184331b65..43a4d5c444 100644
--- a/.github/workflows/citation_file_validator.yml
+++ b/.github/workflows/citation_file_validator.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0
diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
index 430b2532dc..7cd0b21d5b 100644
--- a/.github/workflows/create-condalock-file.yml
+++ b/.github/workflows/create-condalock-file.yml
@@ -3,7 +3,7 @@ name: Conda lock file creation
 on:
   # Trigger on push on main or other branch for testing
   # NOTE that push: main will create the file very often
-  # and hence lots of automated PRs 
+  # and hence lots of automated PRs
   # push:
   #   branches:
   #     - condalock-update
@@ -15,7 +15,9 @@ jobs:
     name: Create conda lock file for latest Python
     runs-on: 'ubuntu-latest'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
index 0525328ba6..c42716770f 100644
--- a/.github/workflows/install-from-conda.yml
+++ b/.github/workflows/install-from-conda.yml
@@ -18,7 +18,6 @@ jobs:
         python-version: ["3.8", "3.9", "3.10"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/install-from-condalock-file.yml b/.github/workflows/install-from-condalock-file.yml
index ca90115c51..7a82b5bd9f 100644
--- a/.github/workflows/install-from-condalock-file.yml
+++ b/.github/workflows/install-from-condalock-file.yml
@@ -29,7 +29,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool-fromlock
diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
index 5221435771..2721fc65b9 100644
--- a/.github/workflows/install-from-source.yml
+++ b/.github/workflows/install-from-source.yml
@@ -18,7 +18,9 @@ jobs:
       fail-fast: false
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
diff --git a/.github/workflows/pypi-build-and-deploy.yml b/.github/workflows/pypi-build-and-deploy.yml
index 244e7376d7..9e7ab07b88 100644
--- a/.github/workflows/pypi-build-and-deploy.yml
+++ b/.github/workflows/pypi-build-and-deploy.yml
@@ -14,7 +14,9 @@ jobs:
     name: Build and publish ESMValTool on PyPi
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
@@ -44,6 +46,7 @@ jobs:
       # Publish on PyPi
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@v1.5.0
         with:
+          user: __token__
           password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
index 2a6dd52559..26eba85855 100644
--- a/.github/workflows/run-tests-monitor.yml
+++ b/.github/workflows/run-tests-monitor.yml
@@ -21,7 +21,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
@@ -43,9 +45,6 @@ jobs:
       - name: Install ESMValTool
         shell: bash -l {0}
         run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
-      - name: Install R dependencies
-        shell: bash -l {0}
-        run: esmvaltool install R
       - name: Install Julia dependencies
         shell: bash -l {0}
         run: esmvaltool install Julia
@@ -72,7 +71,9 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
diff --git a/.github/workflows/test-development.yml b/.github/workflows/test-development.yml
index 8bef81bf0e..a5d80b290d 100644
--- a/.github/workflows/test-development.yml
+++ b/.github/workflows/test-development.yml
@@ -24,7 +24,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
@@ -43,9 +45,6 @@ jobs:
       - name: Install ESMValTool
         shell: bash -l {0}
         run: pip install -e .[develop] 2>&1 | tee develop_test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
-      - name: Install R dependencies
-        shell: bash -l {0}
-        run: esmvaltool install R
       - name: Install Julia dependencies
         shell: bash -l {0}
         run: esmvaltool install Julia
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4d9599c734..da49c08dbc 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
@@ -37,9 +39,6 @@ jobs:
       - name: Install ESMValTool
         shell: bash -l {0}
         run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
-      - name: Install R dependencies
-        shell: bash -l {0}
-        run: esmvaltool install R
       - name: Install Julia dependencies
         shell: bash -l {0}
         run: esmvaltool install Julia
@@ -61,7 +60,9 @@ jobs:
       fail-fast: false
     name: OSX Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: esmvaltool
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f8ccd23175..c481981750 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -7,19 +7,27 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "mambaforge-4.10"
 
-# Build documentation in the docs/sphinx/source directory with Sphinx
+# Declare the requirements required to build your docs
+conda:
+  environment:
+    environment.yml
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+
+# Build documentation in the doc directory with Sphinx
 sphinx:
-   configuration: doc/sphinx/source/conf.py
+  configuration: doc/sphinx/source/conf.py
+  fail_on_warning: true
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 formats:
-   - pdf
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: doc/sphinx/source/requirements.txt
+  - pdf
diff --git a/.stickler.yml b/.stickler.yml
deleted file mode 100644
index 173ac052bd..0000000000
--- a/.stickler.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# stickler-ci configuration
-
----
-
-linters:
-    flake8:
-    pep8:
-    yamllint:
-    shellcheck:
-files:
-    ignore: [
-        'doc/sphinx',
-        'esmvaltool/doc/sphinx',
-        # ignore old stuff, recent versions are in 'esmvaltool' dir
-        'backend',
-        'diag_scripts',
-        'interface_data',
-        'interface_scripts',
-        'main.py',
-        'nml',
-        'plot_scripts',
-        'reformat_scripts',
-        'variable_defs',
-    ]
diff --git a/doc/sphinx/source/api/esmvaltool.diag_scripts.mlr/custom_sklearn.rst b/doc/sphinx/source/api/esmvaltool.diag_scripts.mlr/custom_sklearn.rst
index 50f6465b80..48078b9a39 100644
--- a/doc/sphinx/source/api/esmvaltool.diag_scripts.mlr/custom_sklearn.rst
+++ b/doc/sphinx/source/api/esmvaltool.diag_scripts.mlr/custom_sklearn.rst
@@ -4,3 +4,7 @@ Custom extensions of sklearn functionalities
 ============================================
 
 .. automodule:: esmvaltool.diag_scripts.mlr.custom_sklearn
+    :no-autosummary:
+..
+    enabling autosummary with autodocsumm 0.2.8 gives a warning message:
+    WARNING: autosummary: failed to import AdvancedPipeline.steps.
diff --git a/doc/sphinx/source/community/code_documentation.rst b/doc/sphinx/source/community/code_documentation.rst
index 96f16fa2d3..555abad4f1 100644
--- a/doc/sphinx/source/community/code_documentation.rst
+++ b/doc/sphinx/source/community/code_documentation.rst
@@ -447,22 +447,11 @@ When adding or removing dependencies, please consider applying the changes in
 the following files:
 
 - ``environment.yml``
-  contains development dependencies that cannot be installed from
-  `PyPI <https://pypi.org/>`__/`CRAN <https://cran.r-project.org/>`__/`Julia package registry <https://github.com/JuliaRegistries/General>`__
+  contains dependencies that cannot be installed from
+  `PyPI <https://pypi.org/>`__/`Julia package registry <https://github.com/JuliaRegistries/General>`__
 - ``environment_osx.yml``
   contains development dependencies for MacOSX. Should be the same as ``environment.yml``,
   but currently without multi language support.
-- ``docs/sphinx/source/requirements.txt``
-  contains Python dependencies needed to build the documentation that can be
-  installed from PyPI
-- ``docs/sphinx/source/conf.py``
-  contains a list of Python dependencies needed to build the documentation that
-  cannot be installed from PyPI and need to be mocked when building the
-  documentation.
-  (We do not use conda to build the documentation because this is too time
-  consuming.)
-- ``esmvaltool/install/R/r_requirements.txt``
-  contains R dependencies that can be installed from CRAN
 - ``esmvaltool/install/Julia/Project.toml``
   contains Julia dependencies that can be installed from the default Julia
   package registry
diff --git a/doc/sphinx/source/community/release_strategy.rst b/doc/sphinx/source/community/release_strategy.rst
index 0174177f72..29752cbacf 100644
--- a/doc/sphinx/source/community/release_strategy.rst
+++ b/doc/sphinx/source/community/release_strategy.rst
@@ -325,9 +325,10 @@ All tests should pass before making a release (branch).
 2. Increase the version number
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The version number is stored in ``esmvaltool/__init__.py``, ``CITATION.cff``.
-Make sure to update both files.
-Also update the release date in ``CITATION.cff``.
+The version number is automatically generated from the information provided by
+git using [setuptools-scm](https://pypi.org/project/setuptools-scm/), but a
+static version number is stored in ``CITATION.cff``.
+Make sure to update the version number and release date in ``CITATION.cff``.
 See https://semver.org for more information on choosing a version number.
 Make a pull request and get it merged into ``main``.
 
diff --git a/doc/sphinx/source/conf.py b/doc/sphinx/source/conf.py
index 55b45ff0b3..0234dfed1f 100644
--- a/doc/sphinx/source/conf.py
+++ b/doc/sphinx/source/conf.py
@@ -32,7 +32,7 @@
 
 # This is used for linking and such so we link to the thing we're building
 rtd_version = os.environ.get("READTHEDOCS_VERSION", "latest")
-if rtd_version not in ["latest", "doc"]:  # TODO: add "stable" once we have it
+if rtd_version not in ["latest", "stable", "doc"]:
     rtd_version = "latest"
 
 # Generate gallery
@@ -70,25 +70,6 @@
     'autosummary': True,
 }
 
-autodoc_mock_imports = [
-    'cartopy',
-    'cf_units',
-    'cftime',
-    'eofs',
-    'ESMPy',
-    'esmvalcore',
-    'GDAL',
-    'iris',
-    'mapgenerator',
-    'psutil',
-    'psyplot',
-    'rasterio',
-    'scipy',
-    'sklearn',
-    'xesmf',
-    'xgboost',
-]
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
diff --git a/doc/sphinx/source/quickstart/installation.rst b/doc/sphinx/source/quickstart/installation.rst
index 7b7e8e3e65..b035ea8276 100644
--- a/doc/sphinx/source/quickstart/installation.rst
+++ b/doc/sphinx/source/quickstart/installation.rst
@@ -260,13 +260,6 @@ install the Julia dependencies:
 
     esmvaltool install Julia
 
-If you would like to run R diagnostic scripts, you will also need to install the R
-dependencies:
-
-.. code-block:: bash
-
-    esmvaltool install R
-
 .. _install_with_docker:
 
 Docker installation
@@ -551,13 +544,6 @@ install the ESMValTool Julia dependencies:
 
     esmvaltool install Julia
 
-If you would like to run R diagnostic scripts, you will also need to install the R
-dependencies. Install the R dependency packages:
-
-.. code-block:: bash
-
-    esmvaltool install R
-
 The next step is to check that the installation works properly.
 To do this, run the tool with:
 
diff --git a/doc/sphinx/source/requirements.txt b/doc/sphinx/source/requirements.txt
deleted file mode 100644
index 79a9897222..0000000000
--- a/doc/sphinx/source/requirements.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-autodocsumm>=0.2.2
-cdo
-cdsapi
-cmocean
-cython
-dask[array]
-docutils <0.17
-ecmwf-api-client
-eofs
-fiona
-jinja2
-joblib
-lime
-matplotlib
-nc-time-axis
-netCDF4
-numpy
-pandas
-pillow
-pyproj
-pyyaml
-scikit-learn
-seaborn
-seawater
-shapely
-sphinx>2
-xarray
-xgboost
-xlsxwriter
-yamale
diff --git a/docker/Dockerfile b/docker/Dockerfile
index aaccb74010..9ee3ddf0f8 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,18 +1,15 @@
 # To build this container, go to ESMValTool root folder and execute:
 # docker build -t esmvaltool:latest . -f docker/Dockerfile
-FROM continuumio/miniconda3
+FROM condaforge/mambaforge
 
-COPY ./environment.yml /src/ESMValTool/environment.yml
 WORKDIR /src/ESMValTool
-RUN conda update -y conda && conda install -y -c conda-forge mamba && mamba env create --name esmvaltool --file environment.yml && conda clean --all -y
+COPY environment.yml .
+RUN mamba update -y conda mamba pip && mamba env create --name esmvaltool --file environment.yml && conda clean --all -y
 
 # Make RUN commands use the new environment:
 SHELL ["conda", "run", "--name", "esmvaltool", "/bin/bash", "-c"]
 
-COPY ./esmvaltool/install/R /src/ESMValTool/esmvaltool/install/R
-RUN Rscript ./esmvaltool/install/R/setup.R
-
-COPY . /src/ESMValTool
-RUN pip install -e . && pip cache purge && esmvaltool install Julia
+COPY . .
+RUN pip install --no-cache . && esmvaltool install Julia
 
 ENTRYPOINT ["conda", "run", "--name", "esmvaltool", "esmvaltool"]
diff --git a/docker/Dockerfile.dev b/docker/Dockerfile.dev
index 2120e71eb6..65f1a34ea5 100644
--- a/docker/Dockerfile.dev
+++ b/docker/Dockerfile.dev
@@ -1,19 +1,14 @@
 # To build this container, go to ESMValTool root folder and execute:
 # docker build -t esmvaltool:development . -f docker/Dockerfile.dev
-FROM continuumio/miniconda3
+FROM condaforge/mambaforge
 
-COPY ./environment.yml /src/ESMValTool/environment.yml
 WORKDIR /src/ESMValTool
-RUN conda update -y conda && conda install -y -c conda-forge mamba && mamba env create --name esmvaltool --file environment.yml && conda clean --all -y
+RUN apt update && DEBIAN_FRONTEND=noninteractive apt install -y curl git ssh && apt clean
+COPY environment.yml .
+RUN mamba update -y conda mamba pip && mamba env create --name esmvaltool --file environment.yml && conda clean --all -y
 
 # Make RUN commands use the new environment:
 SHELL ["conda", "run", "--name", "esmvaltool", "/bin/bash", "-c"]
 
-COPY ./esmvaltool/install/R /src/ESMValTool/esmvaltool/install/R
-RUN Rscript ./esmvaltool/install/R/setup.R
-
-COPY . /src/ESMValTool
-RUN pip install -e .[test] && pip cache purge && esmvaltool install Julia && pip uninstall esmvaltool -y
-RUN rm -rf /src
-
-ENTRYPOINT ["conda", "run", "--name", "esmvaltool", "esmvaltool"]
+COPY . .
+RUN pip install --no-cache .[test] && esmvaltool install Julia && pip uninstall esmvaltool -y
diff --git a/docker/Dockerfile.exp b/docker/Dockerfile.exp
index e43f8863f1..a522995fc4 100644
--- a/docker/Dockerfile.exp
+++ b/docker/Dockerfile.exp
@@ -1,20 +1,18 @@
 # To build this container, go to ESMValTool root folder and execute:
 # docker build -t esmvaltool:experimental . -f docker/Dockerfile.exp
-FROM esmvalgroup/esmvalcore:latest
+FROM condaforge/mambaforge
+RUN apt update && apt install -y git && apt clean
 
-COPY ./environment.yml /src/ESMValTool/environment.yml
 WORKDIR /src/ESMValTool
-RUN conda update -n base -y conda && conda install -y -c conda-forge mamba && mamba env create --name esmvaltool --file environment.yml && conda clean --all -y
+COPY environment.yml .
+RUN    mamba update -y conda mamba pip \
+    && mamba env create --name esmvaltool --file environment.yml \
+    && conda clean --all -y
 
-# Make RUN commands use the new environment:
 SHELL ["conda", "run", "--name", "esmvaltool", "/bin/bash", "-c"]
 
-COPY . /src/ESMValTool
-RUN pip install -e .[develop]
-RUN mamba install -y -c conda-forge r-base
-RUN esmvaltool install R
-RUN mamba install -y -c conda-forge julia
-RUN esmvaltool install Julia
-RUN pip install ../ESMValCore && pip cache purge
+COPY . .
+RUN pip install --no-cache git+https://github.com/ESMValGroup/ESMValCore.git#egg=ESMValCore . \
+    && esmvaltool install Julia
 
 ENTRYPOINT ["conda", "run", "--name", "esmvaltool", "esmvaltool"]
diff --git a/environment.yml b/environment.yml
index bd170d38eb..ceb92902c8 100644
--- a/environment.yml
+++ b/environment.yml
@@ -11,35 +11,118 @@ channels:
 dependencies:
   - pip!=21.3
   - python>=3.8
-  # Python packages that cannot be installed from PyPI:
   - cartopy
-  - compilers
+  - cdo>=1.9.7
+  - cdsapi
+  - cf-units >=3.0.0,<3.1.0,!=3.0.1.post0  # see https://github.com/ESMValGroup/ESMValCore/issues/1655
+  - cftime
+  - cmocean
+  - cython
+  - dask
+  - ecmwf-api-client
+  - eofs
   - esmpy
-  - esmvalcore
+  - esmvalcore 2.5.*
+  - fiona
+  - fire
   - gdal
+  - iris>=3.1.0
+  - jinja2
+  - joblib
+  - lime
+  - mapgenerator>=1.0.5
   - matplotlib-base
-  # Non-Python dependencies
-  - cdo
-  - imagemagick
-  - julia
-  - nco
+  - natsort
+  - nc-time-axis
+  - netCDF4
+  - numpy
+  - openpyxl
+  - pandas
+  - progressbar2
+  - prov
   - psyplot
   - psy-maps
   - psy-reg
   - psy-simple
+  - pyproj>=2.1
   - python-cdo
+  - python-dateutil
+  - pyyaml
   - rasterio
+  - requests
   - ruamel.yaml
-  - scikit-learn  # may hit hw-specific issue if from pypi https://github.com/scikit-learn/scikit-learn/issues/14485
+  - scikit-image
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seawater
+  - shapely
+  - xarray>=0.12.0
+  - xesmf==0.3.0
   - xgboost
+  - xlsxwriter
+  # Python packages needed for testing
+  - pytest >=3.9,!=6.0.0rc1,!=6.0.0
+  - pytest-cov
+  - pytest-env
+  - pytest-flake8
+  - pytest-html !=2.1.0
+  - pytest-metadata >=1.5.1
+  - pytest-xdist
+  # Python packages needed for building docs
+  - autodocsumm>=0.2.2
+  - sphinx>=5
+  - sphinx_rtd_theme
+  # Python packages needed for development
+  - codespell
+  - docformatter
+  - isort
+  - pre-commit
+  - prospector
+  - pyroma
+  # - vprof not on conda-forge
+  - yamllint
+  - yapf
 
-  # Multi language support:
+  # NCL and dependencies
   - ncl
-  - r-base
-  # R packages needed for development
+  - cdo
+  - imagemagick
+  - nco
+
+  # R and dependencies
+  - cdo
+  - r-base >=3.5
+  - r-abind
+  - r-akima <=0.6-2.3  # see https://github.com/ESMValGroup/ESMValTool/issues/2695
+  - r-climdex.pcic
+  - r-climprojdiags
   - r-docopt
-  - r-git2r  # dependency of lintr
+  - r-dotcall64
+  - r-functional
+  - r-ggplot2
+  - r-gridextra
   - r-lintr
+  - r-logging
+  - r-mapproj
+  - r-maps
+  - r-multiapply
+  - r-ncdf4
+  - r-ncdf4.helpers
+  - r-pcict
+  - r-plyr
+  - r-rcolorbrewer
+  - r-rcpp
+  - r-s2dverification
+  - r-snow
+  - r-spei
   - r-styler
+  - r-udunits2
   - r-yaml
-  - r-udunits2  # needed by the docker build
+  # R packages needed for development
+  - r-git2r  # dependency of lintr
+  - r-lintr
+  - r-styler
+
+  # Julia (dependencies installed by separate script)
+  - julia
diff --git a/environment_osx.yml b/environment_osx.yml
index caf1b2a3ec..c268f6d463 100644
--- a/environment_osx.yml
+++ b/environment_osx.yml
@@ -11,25 +11,75 @@ channels:
 dependencies:
   - pip!=21.3
   - python>=3.8
-  # Python packages that cannot be installed from PyPI:
   - cartopy
-  - compilers
+  - cdo>=1.9.7
+  - cdsapi
+  - cf-units >=3.0.0,<3.1.0,!=3.0.1.post0  # see https://github.com/ESMValGroup/ESMValCore/issues/1655
+  - cftime
+  - cmocean
+  - cython
+  - dask
+  - ecmwf-api-client
+  - eofs
   - esmpy
-  - esmvalcore
+  - esmvalcore 2.5.*
+  - fiona
+  - fire
   - gdal
+  - iris>=3.1.0
+  - jinja2
+  - joblib
+  - lime
+  - mapgenerator>=1.0.5
   - matplotlib-base
-  # Non-Python dependencies
-  - cdo
-  - imagemagick
-  - nco
+  - natsort
+  - nc-time-axis
+  - netCDF4
+  - numpy
+  - openpyxl
+  - pandas
+  - progressbar2
+  - prov
+  - psyplot
   - psy-maps
   - psy-reg
   - psy-simple
-  - psyplot
+  - pyproj>=2.1
   - python-cdo
+  - python-dateutil
+  - pyyaml
   - rasterio
+  - requests
   - ruamel.yaml
-  # may hit hw-specific issue if from pypi
-  # https://github.com/scikit-learn/scikit-learn/issues/14485
+  - scikit-image
   - scikit-learn
+  - scipy
+  - seaborn
+  - seawater
+  - shapely
+  - xarray>=0.12.0
+  - xesmf==0.3.0
   - xgboost
+  - xlsxwriter
+  # Python packages needed for testing
+  - pytest >=3.9,!=6.0.0rc1,!=6.0.0
+  - pytest-cov
+  - pytest-env
+  - pytest-flake8
+  - pytest-html !=2.1.0
+  - pytest-metadata >=1.5.1
+  - pytest-xdist
+  # Python packages needed for building docs
+  - autodocsumm>=0.2.2
+  - sphinx>=5
+  - sphinx_rtd_theme
+  # Python packages needed for development
+  - codespell
+  - docformatter
+  - isort
+  - pre-commit
+  - prospector
+  - pyroma
+  # - vprof not on conda-forge
+  - yamllint
+  - yapf
diff --git a/esmvaltool/__init__.py b/esmvaltool/__init__.py
index 154d3fee24..6f3375ec51 100644
--- a/esmvaltool/__init__.py
+++ b/esmvaltool/__init__.py
@@ -1,5 +1,12 @@
 """ESMValTool diagnostics package."""
-__version__ = '2.5.0'
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("ESMValTool")
+except PackageNotFoundError as exc:
+    raise PackageNotFoundError(
+        "ESMValTool package not found, please run `pip install -e .` before "
+        "importing the package.") from exc
 
 
 class ESMValToolDeprecationWarning(UserWarning):
diff --git a/esmvaltool/install/R/r_requirements.yml b/esmvaltool/install/R/r_requirements.yml
deleted file mode 100644
index 14fa06678b..0000000000
--- a/esmvaltool/install/R/r_requirements.yml
+++ /dev/null
@@ -1,54 +0,0 @@
----
-# R packages to be installed
-# We support several installation procedures:
-
-# Latest version from CRAN:
-#  mypackage:
-
-# Specific version from CRAN (use only if last version can not be used):
-#   mypackage:
-#     origin: cran
-#     version: my_version
-
-# The next ones are NOT allowed on final code, but we support them to
-# facilitate developing and testing of recipes before merging if the CRAN
-# version is not available yet
-
-# From GitHub:
-#   mypackage:
-#     origin: github
-#     path: my_user/my_packge_repo@my_version
-
-# From a generic git:
-#   mypackage:
-#     origin: git
-#     url: my_repo_url
-#     ref: my_branch_commit_or_tag
-
-abind:
-akima:
-climdex.pcic:
-ClimProjDiags:
-docopt:
-dotCall64:
-functional:
-ggplot2:
-gridExtra:
-lintr:
-logging:
-mapproj:
-maps:
-multiApply:
-ncdf4:
-ncdf4.helpers:
-PCICt:
-plyr:
-RColorBrewer:
-Rcpp:
-s2dverification:
-snow:
-SPEI:
-styler:
-tools:
-udunits2:
-yaml:
diff --git a/esmvaltool/install/R/setup.R b/esmvaltool/install/R/setup.R
deleted file mode 100644
index e740baaf01..0000000000
--- a/esmvaltool/install/R/setup.R
+++ /dev/null
@@ -1,147 +0,0 @@
-log <- function(..., level = "INFO") {
-  cat(format(Sys.time(), "%Y-%m-%d %X"), level, ":", ..., "\n")
-}
-
-# check for present library paths
-rlibpath <- .libPaths()
-Sys.setenv(R_INSTALL_STAGED = FALSE)
-
-# check if we can write in the present R libraries paths
-if (any(file.access(rlibpath, 2) == 0)) {
-  # if possible, use the standard one for following installation
-  rlibloc <- rlibpath[which(file.access(rlibpath, 2) == 0)[1]]
-} else {
-  # if not possible, create a local library in the home directory
-  rlibloc <- Sys.getenv("R_LIBS_USER")
-  dir.create(
-    path = Sys.getenv("R_LIBS_USER"),
-    showWarnings = FALSE,
-    recursive = TRUE
-  )
-}
-
-log("Installing packages to --> ", rlibloc)
-
-# define the R mirror to download packages
-pkg_mirror <- "https://cloud.r-project.org"
-log("Using mirror: ", pkg_mirror)
-
-# install the yaml package fist to handle the yaml-file
-if (!require("yaml")) {
-  install.packages("yaml", repos = pkg_mirror)
-}
-
-# get the script path
-initial_options <- commandArgs(trailingOnly = FALSE)
-file_arg_name <- "--file="
-script_name <- sub(
-  file_arg_name, "",
-  initial_options[grep(file_arg_name, initial_options)]
-)
-script_dirname <- dirname(script_name)
-
-# read the dependencies
-dependencies <- yaml::read_yaml(
-  paste(script_dirname, "r_requirements.yml", sep = "/"),
-)
-# TODO: find a solution for script directory
-
-log(paste(unlist(names(dependencies)), collapse = ", "))
-inst_packages <- installed.packages()
-package_list <-
-  names(dependencies)[!(names(dependencies) %in% inst_packages[, "Package"])]
-
-if (length(package_list) == 0) {
-  log("All packages are already installed!")
-  quit()
-} else {
-  log("Number of packages to be installed: ", length(package_list))
-}
-
-n_cpus_override <- strtoi(Sys.getenv("R_INSTALL_N_CPUS", unset = "0"))
-if (n_cpus_override) {
-  n_cpus <- n_cpus_override
-} else {
-  n_cpus <- parallel::detectCores(all.tests = TRUE, logical = FALSE)
-  if (is.na(n_cpus)) {
-    n_cpus <- 1
-  }
-}
-log("Using", n_cpus, "threads to compile packages")
-
-# Install packages required for installation
-install_dependencies <- list("remotes", "devtools")
-install_dependencies <-
-  install_dependencies[!install_dependencies %in% inst_packages[, "Package"]]
-if (length(install_dependencies) > 0) {
-  log(
-    "Installing installation dependencies from CRAN:",
-    paste(unlist(install_dependencies), collapse = ", ")
-  )
-  install.packages(
-    unlist(install_dependencies),
-    repos = pkg_mirror,
-    Ncpus = n_cpus,
-    dependencies = c("Depends", "Imports", "LinkingTo")
-  )
-}
-
-# Special installations
-install <- function(package, info) {
-  if (!is.null(info)) {
-    if (info$origin == "github") {
-      log("Installing ", package, "from Github")
-      remotes::install_github(info$path)
-    }
-    if (info$origin == "git") {
-      log("Installing ", package, "from Git")
-      remotes::install_git(info$url, ref = info$ref)
-    }
-    if (info$origin == "cran") {
-      log("Installing version", info$version, "of", package, "from CRAN")
-      devtools::install_version(
-        package,
-        version = info$version,
-        repos = pkg_mirror
-      )
-    }
-  }
-}
-for (package_name in names(dependencies)) {
-  install(package_name, dependencies[[package_name]])
-}
-
-# Get missing packages from CRAN, last versions
-inst_packages <- installed.packages()
-package_list <-
-  names(dependencies)[!(names(dependencies) %in% inst_packages[, "Package"])]
-log(
-  "Installing packages from CRAN:",
-  paste(unlist(package_list), collapse = ", ")
-)
-if (length(package_list) != 0) {
-  install.packages(
-    package_list,
-    repos = pkg_mirror,
-    Ncpus = n_cpus,
-    dependencies = c("Depends", "Imports", "LinkingTo")
-  )
-}
-
-failed <- list()
-for (package_name in names(dependencies)) {
-  success <- library(
-    package_name,
-    character.only = TRUE,
-    logical.return = TRUE
-  )
-  if (!success) {
-    failed <- c(failed, package_name)
-  }
-}
-if (length(failed) != 0) {
-  log("Failed to install packages:", paste(failed, collapse = ", "))
-  quit(status = 1, save = "no")
-}
-
-log("Successfully installed all packages")
diff --git a/pyproject.toml b/pyproject.toml
index 121a39f5f2..8b33e256d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,5 @@
 [build-system]
-requires = ["setuptools >= 40.6.0", "wheel"]
+requires = ["setuptools >= 40.6.0", "wheel", "setuptools_scm>=6.2"]
 build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
diff --git a/setup.py b/setup.py
index 4cb9537190..15c4a22733 100755
--- a/setup.py
+++ b/setup.py
@@ -8,9 +8,6 @@
 
 from setuptools import Command, setup
 
-sys.path.insert(0, os.path.dirname(__file__))
-from esmvaltool import __version__  # noqa: E402
-
 PACKAGES = [
     'esmvaltool',
 ]
@@ -26,7 +23,9 @@
         'cartopy',
         'cdo',
         'cdsapi',
-        'cf-units',
+        # see https://github.com/SciTools/cf-units/issues/218
+        # see https://github.com/ESMValGroup/ESMValCore/issues/1655
+        'cf-units>=3.0.0,<3.1.0,!=3.0.1.post0',
         'cftime',
         'cmocean',
         'dask',
@@ -64,7 +63,7 @@
         'seawater',
         'shapely',
         'xarray',
-        'xesmf',
+        'xesmf==0.3.0',
         'xgboost',
         'xlsxwriter',
     ],
@@ -80,17 +79,20 @@
         'pytest-metadata>=1.5.1',
         'pytest-xdist',
     ],
+    # Documentation dependencies
+    'doc': [
+        'autodocsumm>=0.2.2',
+        'sphinx>=5',
+        'sphinx_rtd_theme',
+    ],
     # Development dependencies
     # Use pip install -e .[develop] to install in development mode
     'develop': [
-        'autodocsumm>=0.2.2',
         'codespell',
         'docformatter',
         'isort',
         'pre-commit',
         'prospector[with_pyroma]!=1.1.6.3,!=1.1.6.4',
-        'sphinx>2',
-        'sphinx_rtd_theme',
         'vprof',
         'yamllint',
         'yapf',
@@ -192,7 +194,6 @@ def read_description(filename):
 
 setup(
     name='ESMValTool',
-    version=__version__,
     author=read_authors('.zenodo.json'),
     description=read_description('.zenodo.json'),
     long_description=Path('README.md').read_text(),
@@ -224,8 +225,10 @@ def read_description(filename):
     install_requires=REQUIREMENTS['install'],
     tests_require=REQUIREMENTS['test'],
     extras_require={
-        'develop': (set(REQUIREMENTS['develop'] + REQUIREMENTS['test']) -
-                    {'pycodestyle'}),
+        'develop':
+        REQUIREMENTS['develop'] + REQUIREMENTS['test'] + REQUIREMENTS['doc'],
+        'doc':
+        REQUIREMENTS['doc'],
         'test':
         REQUIREMENTS['test'],
     },