Remove R development dependencies (#4306)

Co-authored-by: Bouwe Andela <b.andela@esciencecenter.nl>

Author: valeriupredoi

doc/sphinx/source/community/code_documentation.rst

@@ -274,12 +274,30 @@ R
 ~
 
 Best practices for R code are described in `The tidyverse style
-guide <https://style.tidyverse.org/>`__. We check adherence to this
-style guide by using
-`lintr <https://cran.r-project.org/web/packages/lintr/index.html>`__ on
-CircleCI. Please use `styler <https://styler.r-lib.org/>`__ to
-automatically format your code according to this style guide. In the
-future we would also like to make use of
+guide <https://style.tidyverse.org/>`__. We currently don't check adherence
+to this, but we strongly encourage any new R diagnostic to be checked against the
+style guide by using `lintr <https://cran.r-project.org/web/packages/lintr/index.html>`__.
+Please use `styler <https://styler.r-lib.org/>`__ to automatically format your code according
+to this style guide. To run these tools, uncomment these lines:
+
+.. literalinclude:: ../../../../.pre-commit-config.yaml
+    :language: yaml
+    :start-at: # - repo: https://github.com/lorenzwalthert/precommit/  # Checks for R
+    :end-at: - id: lintr
+    :caption: R configuration in ``.pre-commit-config.yaml``.
+
+and run the commands:
+
+.. code-block:: bash
+
+    pre-commit run style-files --files esmvaltool/diag_scripts/your_script.R
+    pre-commit run lintr --files esmvaltool/diag_scripts/your_script.R
+
+These pre-commit hooks have been disabled by default because over the past few
+years all diagnostics that have been contributed were written in Python.
+However, if R contributions pick up again, we would be happy to enable these
+pre-commit hooks again.
+In the future we would also like to make use of
 `goodpractice <https://cran.r-project.org/web/packages/goodpractice/index.html>`__
 to assess the quality of R code.
 

environment.yml

@@ -96,7 +96,7 @@ dependencies:
 
   # R and dependencies
   - cdo
-  - r-base >=3.5
+  - r-base >=4.4
   - r-abind
   - r-akima
   - r-climdex.pcic
@@ -121,7 +121,3 @@ dependencies:
   - r-spei
   - r-udunits2
   - r-yaml
-  # R packages needed for development
-  - r-git2r  # dependency of lintr
-  - r-lintr ==3.1.2
-  - r-styler ==1.10.3

tests/unit/test_lint.py

@@ -1,13 +1,8 @@
 """Lint tests."""
 
-import os
-import subprocess
-import sys
 import textwrap
 from pathlib import Path
 
-import pytest
-
 import esmvaltool
 from esmvaltool.utils.nclcodestyle import nclcodestyle
 
@@ -47,34 +42,3 @@ def test_nclcodestyle():
         )
 
     assert success, "Your NCL code does not follow our formatting standards."
-
-
-@pytest.mark.installation
-@pytest.mark.skipif(
-    sys.platform == "darwin",
-    reason="ESMValTool R not supported on OSX",
-)
-def test_r_lint(monkeypatch):
-    """Test R lint."""
-    monkeypatch.setenv("LINTR_COMMENT_BOT", "FALSE")
-    package_root = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
-    checker = os.path.join(package_root, "tests", "unit", "check_r_code.R")
-    try:
-        output = subprocess.check_output(
-            ("Rscript", checker, package_root),
-            stderr=subprocess.STDOUT,
-            universal_newlines=True,
-        )
-        print(output)
-        return
-    except subprocess.CalledProcessError as ex:
-        print(
-            textwrap.dedent("""
-            Your R code does not follow our formatting standards.
-
-            Please fix the following issues:
-        """),
-        )
-        print(ex.output)
-
-    assert False, "Your R code does not follow our formatting standards."