add student_files to otter assign (#852)

CHANGELOG.md

@@ -20,6 +20,7 @@
 * Updated Otter Assign to strip type annotations from generated test code per [#796](https://github.com/ucbds-infra/otter-grader/issues/796)
 * Updated Otter Grade Docker image to create an empty `submission_metadata.json` file in the grading image to prevent plugins from erroring per [#811](https://github.com/ucbds-infra/otter-grader/issues/811)
 * Added ability to monitor grading progress to Otter Grade per [#827](https://github.com/ucbds-infra/otter-grader/issues/827)
+* Added handling of student-created files with the `student_files` configuration in Otter Assign per [#737](https://github.com/ucbds-infra/otter-grader/issues/737)
 
 **v5.6.0:**
 

otter/api.py

@@ -5,6 +5,7 @@
 import os
 
 from contextlib import nullcontext, redirect_stdout
+from typing import Optional
 
 from .export import export_notebook
 from .run import main as run_grader
@@ -17,6 +18,7 @@ def grade_submission(
     *,
     quiet: bool = False,
     debug: bool = False,
+    extra_submission_files: Optional[list[str]] = None,
 ) -> GradingResults:
     """
     Runs non-containerized grading on a single submission at ``submission_path`` using the autograder
@@ -36,6 +38,8 @@ def grade_submission(
             ``False``
         debug (``bool``): whether to run the submission in debug mode (without ignoring
             errors)
+        extra_submission_files (``list[str] | None``): extra files to copy into the submission
+            directory; this should really only be used internally by Otter, so use at your own risk
 
     Returns:
         ``otter.test_files.GradingResults``: the results object produced during the grading of the
@@ -49,7 +53,12 @@ def grade_submission(
 
     with cm:
         results = run_grader(
-            submission_path, autograder=ag_path, output_dir=None, no_logo=True, debug=debug
+            submission_path,
+            autograder=ag_path,
+            output_dir=None,
+            no_logo=True,
+            debug=debug,
+            extra_submission_files=extra_submission_files,
         )
 
     if quiet:

otter/assign/assignment.py

@@ -99,7 +99,7 @@ class ExportCellValue(fica.Config):
 
         files: list[str] = fica.Key(
             description="a list of other files to include in the student submissions' zip file",
-            default=[],
+            factory=lambda: [],
         )
 
         class RequireNoPDFAckValue(fica.Config):
@@ -157,22 +157,28 @@ class SeedValue(fica.Config):
 
     ignore_modules: list[str] = fica.Key(
         description="a list of modules to ignore variables from during environment serialization",
-        default=[],
+        factory=lambda: [],
     )
 
     files: list[str] = fica.Key(
         description="a list of other files to include in the output directories and autograder",
-        default=[],
+        factory=lambda: [],
     )
 
     autograder_files: list[str] = fica.Key(
         description="a list of other files only to include in the autograder",
-        default=[],
+        factory=lambda: [],
+    )
+
+    student_files: list[str] = fica.Key(
+        description="a list of files that will be generated by students and thus should not be included in the autograder configuration zip file",
+        factory=lambda: [],
+        type_=list,
     )
 
     plugins: list[str] = fica.Key(
         description="a list of plugin names and configurations",
-        default=[],
+        factory=lambda: [],
     )
 
     class TestsValue(fica.Config):

otter/assign/cell_factory.py

@@ -135,8 +135,9 @@ def create_export_cells(self) -> list[nbformat.NotebookNode]:
             args += ["force_save=True"]
         if self.assignment.export_cell.run_tests:
             args += ["run_tests=True"]
-        if len(self.assignment.export_cell.files) != 0:
-            args += [f"files={self.assignment.export_cell.files}"]
+        if self.assignment.export_cell.files or self.assignment.student_files:
+            l = [*self.assignment.export_cell.files, *self.assignment.student_files]
+            args += [f"files={l}"]
         source_lines.append(f"grader.export({', '.join(args)})")
         export.source = "\n".join(source_lines)
 

otter/assign/output.py

@@ -56,6 +56,21 @@ def write_output_dir(
             output_fn = "environment.yml"
             shutil.copy(assignment.environment, str(output_dir / output_fn))
 
+        if assignment.student_files:
+            for file in assignment.student_files:
+                # TODO: dedupe this logic with handling of autograder_files utils.py and logic below
+                # for assignment.files
+                if not os.path.isfile(file):
+                    raise FileNotFoundError(f"{file} is not a file")
+                if str(assignment.master.parent) not in os.path.abspath(file):
+                    raise ValueError(
+                        f"{file} is not in a subdirectory of the master notebook direcotry"
+                    )
+                file_path = pathlib.Path(file).resolve()
+                rel_path = file_path.parent.relative_to(assignment.master.parent)
+                os.makedirs(output_dir / rel_path, exist_ok=True)
+                shutil.copy(file, str(output_dir / rel_path))
+
     # write tests
     transformed_nb.write_tests(str(tests_dir), not sanitize, assignment.tests.files)
 

otter/assign/utils.py

@@ -7,6 +7,8 @@
 import pathlib
 import re
 import shutil
+import tempfile
+import zipfile
 
 from textwrap import indent
 from typing import Any, Optional, TYPE_CHECKING
@@ -224,6 +226,7 @@ def run_tests(assignment: "Assignment", debug: bool = False) -> None:
             str(assignment.ag_notebook_path),
             str(assignment.ag_zip_path),
             debug=debug,
+            extra_submission_files=assignment.student_files,
         )
 
     LOGGER.debug(f"Otter Run output:\n{run_output.getvalue()}")

otter/run/__init__.py

@@ -3,10 +3,13 @@
 import dill
 import json
 import os
+import pathlib
 import shutil
 import tempfile
 import zipfile
 
+from typing import Optional
+
 from .run_autograder import AutograderConfig, capture_run_output, main as run_autograder_main
 from ..test_files import GradingResults
 
@@ -21,6 +24,7 @@ def main(
     output_dir: str = "./",
     no_logo: bool = False,
     debug: bool = False,
+    extra_submission_files: Optional[list[str]] = None,
 ) -> GradingResults:
     """
     Grades a single submission using the autograder configuration ``autograder`` without
@@ -37,6 +41,8 @@ def main(
             the results JSON file is not copied
         no_logo (``bool``): whether to suppress the Otter logo from being printed to stdout
         debug (``bool``); whether to run in debug mode (without ignoring errors)
+        extra_submission_files (``list[str] | None``): extra files to copy into the submission
+            directory; this should really only be used internally by Otter, so use at your own risk
 
     Returns:
         ``otter.test_files.GradingResults``: the grading results object
@@ -65,6 +71,12 @@ def main(
         else:
             shutil.copy(submission, os.path.join(ag_dir, "submission"))
 
+        for file in extra_submission_files:
+            fp = pathlib.Path(os.path.join(ag_dir, file))
+            # create any intermediate directories before copying the file
+            fp.parents[0].mkdir(parents=True, exist_ok=True)
+            shutil.copy(file, os.path.join(ag_dir, "submission", file))
+
         logo = not no_logo
         run_autograder_main(ag_dir, logo=logo, debug=debug, otter_run=True)
 

test/test_api.py

@@ -23,6 +23,7 @@ def test_grade_submission(mocked_redirect, mocked_run):
         output_dir=None,
         no_logo=True,
         debug=False,
+        extra_submission_files=None,
     )
     mocked_redirect.assert_not_called()
 

test/test_assign/files/example-autograder-correct/tests/q1.py

@@ -21,7 +21,8 @@
                                        'locked': False,
                                        'points': 10,
                                        'success_message': 'Congrats you passed this test case!'},
-                                   {'code': ">>> str(print(x))\n2\n'None'", 'hidden': True, 'locked': False, 'success_message': 'Congrats you passed this test case!'}],
+                                   {'code': ">>> str(print(x))\n2\n'None'", 'hidden': True, 'locked': False, 'success_message': 'Congrats you passed this test case!'},
+                                   {'code': '>>> import student_file\n>>> assert student_file.FOO == 1\n', 'hidden': False, 'locked': False}],
                       'scored': True,
                       'setup': '',
                       'teardown': '',

test/test_assign/files/example-correct/autograder/example.ipynb

@@ -515,7 +515,7 @@
    },
    "outputs": [],
    "source": [
-    "grader.export(force_save=True, run_tests=True)"
+    "grader.export(force_save=True, run_tests=True, files=['student_file.py'])"
    ]
   },
   {
@@ -542,7 +542,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.9.19"
   },
   "otter": {
    "OK_FORMAT": true,
@@ -590,6 +590,11 @@
          "hidden": true,
          "locked": false,
          "success_message": "Congrats you passed this test case!"
+        },
+        {
+         "code": ">>> import student_file\n>>> assert student_file.FOO == 1\n",
+         "hidden": false,
+         "locked": false
         }
        ],
        "scored": true,

test/test_assign/files/example-correct/autograder/student_file.py

@@ -0,0 +1 @@
+FOO = 1

test/test_assign/files/example-correct/student/example.ipynb

@@ -406,7 +406,7 @@
    },
    "outputs": [],
    "source": [
-    "grader.export(force_save=True, run_tests=True)"
+    "grader.export(force_save=True, run_tests=True, files=['student_file.py'])"
    ]
   },
   {
@@ -433,7 +433,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.9.19"
   },
   "otter": {
    "OK_FORMAT": true,
@@ -467,6 +467,11 @@
          "locked": false,
          "points": 1,
          "success_message": "Congrats your x value is in the correct range!"
+        },
+        {
+         "code": ">>> import student_file\n>>> assert student_file.FOO == 1\n",
+         "hidden": false,
+         "locked": false
         }
        ],
        "scored": true,

test/test_assign/files/example.ipynb

@@ -16,7 +16,9 @@
     "python_version: 3.8\n",
     "exclude_conda_defaults: true\n",
     "files:\n",
-    "    - data.csv"
+    "    - data.csv\n",
+    "student_files:\n",
+    "    - student_file.py"
    ]
   },
   {
@@ -176,9 +178,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -207,6 +207,16 @@
     "str(print(x))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import student_file\n",
+    "assert student_file.FOO == 1"
+   ]
+  },
   {
    "cell_type": "raw",
    "metadata": {},
@@ -971,7 +981,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.9.19"
   },
   "varInspector": {
    "cols": {

test/test_assign/files/student_file.py

@@ -0,0 +1 @@
+FOO = 1

test/test_cli.py

@@ -546,6 +546,8 @@ def test_run(mocked_run, run_cli):
         submission="foo.ipynb",
         **run.__kwdefaults__,
     )
+    # extra_submission_files is not used by the CLI
+    std_kwargs.pop("extra_submission_files")
 
     result = run_cli([*cmd_start])
     assert_cli_result(result, expect_error=False)