Support for R / renv as a language by lorenzwalthert · Pull Request #1799 · pre-commit/pre-commit

lorenzwalthert · 2021-02-15T16:56:51Z

This PR aims to add 2nd level support for R to pre-commit via the virtual environment manager renv, motivated by isolated dependency management and (hopefully) compatibility with pre-commit.ci for 2nd level languages as outlined in lorenzwalthert/precommit#215. The implementation follows the recently contributed support for conda (#1232) for source code and tests as well as the implementation of the python virtualenv language.

Further considerations:

~~Initial tests only run on Linux. I have to add other platforms as we go if this PR is generally approved.~~
I'd appreciate feedback to the questions in the source code comments, in particular on whether or not to remove in_env() as it seems not needed or whether it should be kept for consistency with other languages. Also, let me know if you want certain comments that explain stuff to be removed. Was not sure how much.
If this gets through, we probably should add documentation for pre-commit.com.
We might want to support file types for R (https://pre-commit.com/#filtering-files-with-types).

Before this PR, I was not familiar with the pre-commit code base nor a very avid python user, hence sorry if there are obvious flaws in this PR.

lorenzwalthert · 2021-02-15T17:38:38Z

testing/get-renv.sh

+# Alternatively, we require the renv
+# package to be installed already, then we can
+# omit that.
+Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)'


This won't work if a non-root user has never installed any R package (quite unlikely at that stage but...). Maybe catch the installation error and fail (more) informatively?

asottile · 2021-02-16T00:31:27Z

pre_commit/languages/renv.py

+        # expose entry to the user for maximal control
+        return helpers.run_xargs(
+            hook, hook.cmd, file_args,
+            color=color, cwd=hook.prefix.prefix_dir,


the current expectation for hook authors is that hooks will be executed from the root of the repository, so cwd=... won't be workable here

I think that necessarily changes how the environment setup is working now -- the ~normalish way of setting this up is by pointing some set of environment variables at the ENVIRONMENT_DIR (and subdirs)

note also that things must be installed entirely inside the ENVIRONMENT_DIR or they potentially won't be persisted by caching

the current expectation for hook authors is that hooks will be executed from the root of the repository, so cwd=... won't be workable here.

of course 🤦.

the ~normalish way of setting this up is by pointing some set of environment variables at the ENVIRONMENT_DIR (and subdirs).

That's what I saw. Problem is (and that's a peculiarity of R) the most operations happen in an R session, not the terminal session. renv can only be activated properly from inside R. For that reason, my current suggestion is to place a renv::activate() call in a file, then point the R_PROFILE_USER environment variable to that file so the code will run at R startup. The idea is now to allow two versions, inline code expressions and file in entry::

Rscript -e expr # like Rscript -e "1+1" Rscript path/to/file

An inject the options --no-save, --no-restore, --no-site-file and --no-environ after Rscript (to basically have --vanilla start, but run this one renv::activate() statement) and expand the path/to/file similar to language: script since we have to run the hooks in the working directory of the repo. The files and the hook args are then passed after the above, i.e.

Rscript --no-save --no-restore --no-site-file --no-environ /abs/path/ [files] [hook args] Rscript --no-save --no-restore --no-site-file --no-environ -e expr [files] [hook args]

note also that things must be installed entirely inside the ENVIRONMENT_DIR or they potentially won't be persisted by caching.

This should be solved now. Just placing the whole env in a subdirectory now.

lorenzwalthert · 2021-02-23T18:15:34Z

testing/resources/renv_hooks_repo/DESCRIPTION

@@ -0,0 +1,18 @@
+Package: gli.clu


The DESCRIPTION file is basically the equivalent of setup.py, renv.lock is the equivalent of the conda environment.yml. Not sure if one or both should be listed in LOCAL_RESOURCES as this was introduced here:
https://github.com/pre-commit/pre-commit/pull/1232/files#diff-a52ef0cf627ce783529c259e63d4ea82b77520936a2455cbf4f90ad2fb36d27dR176

ah LOCAL_RESOURCES is to allow an additional_dependencies-only repo: local hook -- it seems like additional_dependencies is supported for R so we should probably make an empty one?

Ok, thanks for the explanation. I added a template for renv.lock in cf88089. However, there is an R version hard-coded in it which will get outdated. As far as I can tell from a quick experiment, the docs and issues in https://github.com/rstudio/renv, there is no indication that the R version recorded in the lock file will be used at renv::restore(), which we use in renv.install_environment(). Even removing seems fine (I left it there anyways). But that might still be a bit brittle.

Also, should we add a unit test for a local hook with additional dependencies to check if things work as expected? I don't think that's currently covered.

yeah it would probably be good to have one unit test demoing a local hook via additional_dependencies

lorenzwalthert · 2021-02-23T19:49:27Z

tests/repository_test.py

        test_run_a_node_hook(tempdir_factory, store)


+def _test_renv_parsing(


let me know if these are too many tests (because it slows down testing). I think we can get 100% coverage with fewer tests too (but then not cover as many combinations).

asottile

overall looks great, really happy you took this on and I'm excited to add this support!

asottile · 2021-02-27T17:22:18Z

pre_commit/languages/all.py

 from pre_commit.languages import perl
 from pre_commit.languages import pygrep
 from pre_commit.languages import python
+from pre_commit.languages import renv


I think this should maybe just be called r?

Thought about that also. The thing is that language: conda can both host R and Python hooks and renv can manage python dependencies, so I thought I go for a more specific name. On the other hand, language: python uses venv (and is still called python, not venv). Since working with virtual environments is still not as common in R compared to Python and not every R user knows renv, using r as a name might also make it easier for people to find what they are looking for. So I am happy to switch to r, please let me know what you prefer.

yeah I think r makes the most sense, conda is kinda the special case right now and I think if people google "pre-commit r" they'll be much more likely to hit this than if it were named renv

we can always add other names if new ways of installing isolated r environments happen in the future and/or shuffle them around (there used to be a python_venv language which was merged into python as virtualenv makes venv-style environments anyway nowadays)

asottile · 2021-02-27T17:23:58Z

pre_commit/languages/renv.py

+    with in_env(hook.prefix, hook.language_version):
+
+        return helpers.run_xargs(
+            hook, cmd_from_hook(hook), file_args, color=color,


I usually prefer to read a file from the bottom upwards -- also helper functions that live only in this module should be underscore-prefixed to make it more clear what is/isn't part of the api (the api specification is in the languages/all.py file)

Sure, I can adapt the order. I can also prefix the helper functions not part of the API. But why is in_env and get_env_patch not prefixed in other modules although not listed in languages/all.py?

hmmmm yeah good point, those should probably be underscore-prefixed everywhere -- probably just legacy and copy paste 😅

asottile · 2021-02-27T17:24:47Z

pre_commit/languages/renv.py

+    # TODO what if expr is x;2? not captured by shlex.split()
+    """
+    if entry[0] != 'Rscript':
+        raise SyntaxError('entry must start with `Rscript`.')


SyntaxError is for python syntax being incorrect -- these should be ValueError probably

asottile · 2021-02-27T17:25:27Z

pre_commit/languages/renv.py

+            ' '.join([
+                'The only valid syntax is `Rscript -e {expr}`',
+                'or `Rscript path/to/hook/script`',
+            ]),


this can be written as an implicitly joined string:

raise TypeError( 'first line here ' 'second line here' )

asottile · 2021-02-27T17:25:45Z

pre_commit/languages/renv.py

+            ]),
+        )
+
+    None


this line does nothing and can be removed, note that python implicitly returns None for "void" functions and doesn't support implicit-return-without-return-keyword

asottile · 2021-02-27T17:29:19Z

testing/resources/renv_hooks_repo/DESCRIPTION

@@ -0,0 +1,18 @@
+Package: gli.clu


ah LOCAL_RESOURCES is to allow an additional_dependencies-only repo: local hook -- it seems like additional_dependencies is supported for R so we should probably make an empty one?

asottile · 2021-02-27T17:30:19Z

tests/repository_test.py

 from pre_commit.languages import helpers
 from pre_commit.languages import node
 from pre_commit.languages import python
+from pre_commit.languages import renv


the tests specifically for the renv helper functions should live in tests/languages/renv_test.py (or r_test.py after renaming)

asottile · 2021-02-27T17:31:17Z

tests/repository_test.py

+
+
+def test_renv_parsing_expr_non_Rscirpt(tempdir_factory, store):
+


(throughout the review, nbd I can fix this myself later -- I don't put blank lines at the beginning or the ending of blocks)

asottile · 2021-02-27T17:32:03Z

tests/repository_test.py

+
+def test_renv_parsing_expr_non_Rscirpt(tempdir_factory, store):
+
+    with pytest.raises(SyntaxError, match='entry must start with'):


I really don't like the match= arg and prefer to test the exact error message, you can follow this pattern:

with pytest.raises(TypeHere) as excinfo: ... msg, = excinfo.value.args assert msg == ...

asottile · 2021-02-27T17:32:25Z

tests/repository_test.py



-@xfailif_windows  # pragma: win32 no cover
+@ xfailif_windows  # pragma: win32 no cover


decorators shouldn't have spaces after them -- not sure what happened here

Also wondered, but one of the pre-commit hook changed it, maybe autopep? I even rebased my PR master and tried to get rid of this. Can revert but then not sure if the pre-commit.ci passes.

ah my guess is there was a syntax error earlier in the file and then autopep8 freaked -- I've been meaning to fix that in autopep8 but it's tricky (basically sometimes it will try and rewrite a file even if it has a syntax error 😱)

asottile

asottile · 2021-03-07T23:29:13Z

added a stub for this in the docs -- pre-commit/pre-commit.com#473

lorenzwalthert marked this pull request as draft February 15, 2021 17:34

lorenzwalthert force-pushed the renv branch from 322e98a to 0816a4f Compare February 15, 2021 17:36

lorenzwalthert commented Feb 15, 2021

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lorenzwalthert force-pushed the renv branch 4 times, most recently from ca4a52b to a72bde1 Compare February 16, 2021 00:08

asottile reviewed Feb 16, 2021

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lorenzwalthert force-pushed the renv branch from 9c88fa7 to f960b87 Compare February 23, 2021 14:02

lorenzwalthert marked this pull request as ready for review February 23, 2021 18:09

lorenzwalthert commented Feb 23, 2021

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lorenzwalthert requested a review from asottile February 27, 2021 12:45

asottile reviewed Feb 27, 2021

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lorenzwalthert force-pushed the renv branch 3 times, most recently from e07dfae to 809c79e Compare March 5, 2021 10:10

lorenzwalthert mentioned this pull request Mar 5, 2021

Can 'docopt' be installed when this package is installed? lorenzwalthert/precommit#88

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asottile approved these changes Mar 7, 2021

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add support for R via renv

f150211

asottile force-pushed the renv branch from 809c79e to f150211 Compare March 7, 2021 21:59

asottile merged commit 19bffaa into pre-commit:master Mar 7, 2021

lorenzwalthert deleted the renv branch September 5, 2021 12:20

		test_run_a_node_hook(tempdir_factory, store)


		def _test_renv_parsing(

+                          ]),
+                      )
+                  None



		def test_renv_parsing_expr_non_Rscirpt(tempdir_factory, store):


		def test_renv_parsing_expr_non_Rscirpt(tempdir_factory, store):

		with pytest.raises(SyntaxError, match='entry must start with'):



		@xfailif_windows # pragma: win32 no cover
		@ xfailif_windows # pragma: win32 no cover

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