Remove rpy2 (#9886)

* Remove rpy2

* Add TODO comment

* Remove unused import

* Fix filename

apps/prairielearn/python/zygote.py

@@ -87,11 +87,11 @@
 prairielearn.get_unit_registry()
 
 
-# We want to conditionally allow/block importing specific modules, namely `rpy2`.
+# We want to conditionally allow/block importing specific modules.
 # This custom importer will allow us to do so, and throw a custom error message.
 #
 # While this won't prevent anything more complex than an `import` statement, it
-# will make it clear to the user that they're not allowed to use `rpy2`. If they
+# will make it clear to the user that they're not allowed to use. If they
 # try to bypass the block, it's up to them to deal with the consequences.
 class ForbidModuleMetaPathFinder(MetaPathFinder):
     def __init__(self) -> None:

apps/prairielearn/src/lib/code-caller/index.js

@@ -11,7 +11,6 @@ import * as Sentry from '@prairielearn/sentry';
 
 import * as chunks from '../chunks.js';
 import { config } from '../config.js';
-import { features } from '../features/index.js';
 import * as load from '../load.js';
 
 import { CodeCallerContainer, init as initCodeCallerDocker } from './code-caller-container.js';
@@ -197,12 +196,6 @@ export async function withCodeCaller(course, fn) {
     });
   }
 
-  // Determine if this course is allowed to use `rpy2`.
-  const allowRpy2 = await features.enabled('allow-rpy2', {
-    institution_id: course.institution_id,
-    course_id: course.id,
-  });
-
   const jobUuid = uuidv4();
   load.startJob('python_callback_waiting', jobUuid);
 
@@ -212,7 +205,7 @@ export async function withCodeCaller(course, fn) {
     const coursePath = chunks.getRuntimeDirectoryForCourse(course);
     await codeCaller.prepareForCourse({
       coursePath,
-      forbiddenModules: allowRpy2 ? [] : ['rpy2'],
+      forbiddenModules: [],
     });
   } catch (err) {
     // If we fail to prepare for a course, assume that the code caller is

apps/prairielearn/src/lib/features/index.ts

@@ -6,7 +6,6 @@ const featureNames = [
   // Can only be applied to courses/institutions.
   'process-questions-in-worker',
   'question-sharing',
-  'allow-rpy2',
   // Can only be applied to institutions.
   'lti13',
   'terms-clickthrough',

images/plbase/plbase-install.sh

@@ -45,45 +45,17 @@ echo "setting up postgres..."
 mkdir /var/postgres && chown postgres:postgres /var/postgres
 su postgres -c "initdb -D /var/postgres"
 
+# TODO: use standard OS Python installation? The only reason we switched to Conda
+# was to support R and `rpy2`, but now that we've removed those, we might not
+# get any benefit from Conda.
 echo "setting up conda..."
 cd /
 arch=`uname -m`
 curl -LO https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-${arch}.sh
 bash Miniforge3-Linux-${arch}.sh -b -p /usr/local -f
 
-# If R package installation is specifically disabled, we'll avoid installing anything R-related.
-if [[ "${SKIP_R_PACKAGES}" != "yes" ]]; then
-    echo "installing R..."
-    conda install --channel r r-base r-essentials
-
-    echo "installing Python packages..."
-    python3 -m pip install --no-cache-dir -r /python-requirements.txt
-else
-    echo "R package installation is disabled"
-    sed '/rpy2/d' /python-requirements.txt > /py_req_no_r.txt # Remove rpy2 package.
-    echo "installing Python packages..."
-    python3 -m pip install --no-cache-dir -r /py_req_no_r.txt
-fi
-
-# `pyarrow` and `rpy2` conflict in a horrible way:
-#
-# - `pyarrow` will load `/usr/lib64/libstdc++.so.6.0.29`
-# - `rpy2` will load `/usr/local/lib/libstdc++.so.6.0.32`
-#
-# `pyarrow` gets autoloaded by `pandas`, which we in turn load in the zygote.
-# If someone then tries to load `rpy2` in question code, it will fail to load
-# with the following error:
-#
-# cannot load library '/usr/local/lib/R/lib/libR.so': /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found
-#
-# This is because `rpy2` needs a version of `libstdc++` that supports libstd++ 3.4.30,
-# but `pyarrow` has already loaded a version of `libstdc++` that only supports up to 3.4.29.
-#
-# We work around that by setting up a symlink to the newer version of `libstdc++`.
-#
-# TODO: We can probably undo this change once we're removed R and `rpy2`.
-# TODO: We could also probably remove this when Amazon Linux picks up a newer version of the `gcc` suite.
-ln -sf /usr/local/lib/libstdc++.so.6 /usr/lib64/libstdc++.so.6
+echo "installing Python packages..."
+python3 -m pip install --no-cache-dir -r /python-requirements.txt
 
 # Clear various caches to minimize the final image size.
 dnf clean all

images/plbase/python-requirements.txt

@@ -24,7 +24,6 @@ pytest-repeat==0.9.3
 pytest==8.2.0
 recommonmark==0.7.1
 regex==2024.4.28
-rpy2==3.5.12
 ruff==0.4.0
 schemdraw==0.19
 scikit-learn==1.4.2