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CHANGELOG.md

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Changelog

v6.1.0:

  • Update Otter Assign to handle notebooks with an invalid kernelspec by assuming the language is Python per #895
  • Fixed assignment summary in Otter Assign so that manual questions are included per #886
  • Wrap ModuleNotFoundError for otter in grading image to include debugging instructions per #907
  • Updated Otter Assign to disallow metadata tests for Colab notebooks per #901
  • Updated Otter Assign to leave solution cell tags in student notebooks per #893
  • Updated Notebook.export zip validation to emit a RuntimeWarning instead of a RuntimeError when anything is written to stderr per #915

v6.0.5:

  • Added liblzma-devel, zlib-devel-amzn2-aarch64, and zlib to R grading environment

v6.0.4:

  • Added jupyter_server to grading environment to allow for installation of nb_conda_kernels

v6.0.3:

  • Fixed TypeError thrown by Otter Run

v6.0.2:

  • Fixed dependency issues when installing on JupyterLite per #875

v6.0.1:

  • Updated dependency specifications to support any new minor version within the matching major version
  • Fixed SyntaxError thrown by gmail_oauth2 binary

v6.0.0:

  • Switched to poetry for packaging
  • Removed compatibility patches for nbconvert < 6 per #777
  • Updated Otter Export to throw an error if nbconvert<6.0.0 is found
  • Converted Otter Export's PDF via HTML exporter to use nbconvert's WebPDF exporter per #781
  • Removed pdfkit from dependencies
  • Added ability to export PDFs via HTML in grading containers per #782
  • Set default Python version for grading images to 3.12
  • Remove support for Python versions < 3.9 per #668
  • Removed setuptools and pkg_resources dependencies
  • Remove dependencies not strictly required by Otter in the grading environment per #739
  • Handle empty assignment configs in Otter Assign per #795
  • Removed Notebook colab and jupyterlite arguments, switching to always determining the interpreter automatically
  • Made dill a required dependency
  • Removed variables key of assignment config in favor of generate.serialized_variables in Otter Assign per #628
  • Update Otter Assign to add cell metadata so that questions with no check cell have their tests run after the last solution cell per #798
  • Updated Otter Assign to strip type annotations from generated test code per #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
  • Added ability to monitor grading progress to Otter Grade per #827
  • Added handling of student-created files with the student_files configuration in Otter Assign per #737
  • Updated Otter Assign to add a cell to install Otter at the top of Colab notebooks per #861
  • Added the ability to ignore the .OTTER_LOG file to Notebook.export and Otter Assign per #857
  • Fixed OK-test support for the all_or_nothing config per #751
  • Added exception-based test support for the all_or_nothing config per #751
  • Added Otter Assign support for the all_or_nothing config per #751
  • Updated Otter Assign to only allow a function definition and statement to call the test function in exception-based test cells and automatically ignore the latter statement instead of requiring an explicit # IGNORE comment per #516
  • Added additional package versions to the output of otter --version per #843
  • Fixed bug in converting test cells containing indented functions to doctests in Otter Assign per #840

v5.7.1:

  • Removed testing code unintentioanlly committed in v5.7.0 per #849

v5.7.0:

v5.6.0:

  • Updated Otter Grade to write grading summary for each notebook per #814
  • Updated Otter Grade CSV to indicate which notebooks timeout per #813
  • Updated Otter Grade CSV to include the number of points per question in the first row
  • Updated Otter Grade CSV to include total points column
  • Updated Otter Grade CSV to round percentages to four decimal places
  • Updated Otter Grade CSV output switched from labeling submissions by file path to notebook name and is now sorted by notebook name per #738
  • Added backwards compatibility to Otter Grade for autograder configuration zip files generated in previous major versions of Otter-Grader
  • Add gcc_linux-64 and gxx_linux-64 to R grading image dependencies per #819
  • Fixed a bug where the loop variable used in Otter's generated grading code overwrote variables defined by the notebook per #817
  • Add --pickle-results option to Otter Run to output the results pickle file per #818
  • Added setuptools to Otter's required dependencies per #823

v5.5.0:

  • Suppress all warnings when running otter.check.validate_export as a module per #735
  • Updated default version of ottr to v1.5.0
  • Added a way to exclude Conda's defaults channel from autograder environment.yml files in Otter Assign and Otter Generate per #778

v5.4.1:

  • Fixed import of the LatexFailed error for nbconvert 7

v5.4.0:

  • Updated submission runners to export and submit the PDF and then remove all copies of the API token before executing the submission to ensure that student code can't gain access to the token
  • Updated Otter Run to skip PDF export and upload in debug mode

v5.3.0:

  • Updated Otter Assign to throw a ValueError when invalid Python code is encountered in test cells per #756
  • Fixed an error causing intercell seeding code to be added to cells using cell magic commands which caused syntax errors per #754
  • Add support for submitting the PDF uploaded in a submission for manual grading instead of generating a new one per #764
  • Validate that a course ID and assignment ID were provided before attempting PDF upload
  • Upgrade and pin pandoc to v3.1.11.1 in grading images per #709

v5.2.3:

  • Fixed the no PDF acknowledgement feature to handle when PDF exports throw an error instead of failing silently

v5.2.2:

  • Fixed an AttributeError when using Notebook.check_all per #746

v5.2.1:

  • Fixed an AttributeError when using OK tests from notebook metadata per #743

v5.2.0:

  • Migrate installation of ottr from setup.sh to environment.yml with the r-ottr conda-forge recipe
  • Updated Otter Assign to allow multiline statements in test cases for Python 3.9+ per #590
  • Added otter_include tag to allow inclusion of tagged markdown cells within the solution block into the student notebook per #730
  • Removed dependency on nbconvert during import so that Otter can be imported on Jupyterlite per #736

v5.1.4:

  • Prevented the Notebook class from attempting to resolve the notebook path when in grading mode
  • Gracefully handle a failure in reading the results pickle file by returning results indicating that such a failure has occurred per #723
  • Use tempfile.mkstemp instead of tempfile.NamedTemporaryFile for the results pickle file used during notebook execution per #723#issuecomment-1710689536

v5.1.3:

  • Fixed bug in submission zip download link per #719

v5.1.2:

  • Enabled the use of custom Jupyter kernels by enforcing the use of the python3 kernel inside Otter grading containers per #706
  • Fixed a bug that was preventing Otter from exiting when an error was thrown during notebook execution caused by the log capturing solution per #707
  • Updated PDF upload logic to surface error statuses returned by the Gradescope API

v5.1.1:

  • Fixed a bug in attempting to read the users from the submission metadata when validating the autograder notebook in Otter Assign per #695
  • Added __getstate__ to test_case to fix pickling bug for exception style tests per #696
  • Added back remove cell ID patch to Otter Assign for notebooks with nbformat version < 4.5 per #701

v5.1.0:

  • Removed patch that strips cell IDs from notebooks in Otter Assign per #677
  • Added notebook force-save to R notebook assignments per #474
  • Updated default version of ottr to v1.4.0
  • Added a configuration to require students to acknowledge when a PDF of their notebook cannot be generated when using Notebook.export before exporting the zip file per #599
  • Added a simple TCP socket server for receiving Otter's logs from the executed notebook to re-enable question logging during Otter Assign per #589
  • Fixed recursive inclusion of files when a directory is in the list passed to the files argument of Notebook.export per #620
  • Fixed the grader export cell failing due to warnings about frozen modules per #686

v5.0.2:

  • Fixed local submission zip checking with otter.Notebook per #678

v5.0.1:

  • Added nbconvert as a required dependency for non-WASM environments

v5.0.0:

  • Converted all dependency management in the autograder configuration zip file to Conda per #501
  • Removed deprecated Otter Assign format v0
  • Disabled editing for question prompt cells in the notebooks generated by Otter Assign per #431
  • Removed ucbdsinfra/otter-grader Docker image and made default image for Otter Grade ubuntu:22.04 per #534
  • Make xeCJK opt-in behavior for exporting notebooks via LaTeX per #548
  • Convert from use of deprecated PyPDF2 package to pypdf
  • Add configuration to submit blank PDF to manual-grading Gradescope assignment if PDF generation fails per #551
  • Removed the after_execution event from the plugin lifecycle
  • Updated execution internals to use nbconvert.preprocessors.ExecutePreprocessor instead of the exec function to execute submissions per #604
  • Deprecated the variables key of the assignment config in favor of generate.serialized_variables
  • Enabled Otter Generate for all assignments created with Otter Assign
  • Updated Otter Assign to use Otter Run to validate that all tests in the assignment pass, allowing tests to be run for R assignments as well as Python, per #427
  • Allow Markdown cells to be used instead of raw cells for Otter Assign per #592
  • Use Otter Grade CLI flags to update otter_config.json values in the grading container per #395
  • Removed linux/amd64 platform specification for Docker images in Otter Grade
  • Updated Otter Assign to normalize notebooks before writing them with nbformat.validator.normalize per #658
  • Added summary of assignment questions to Otter Assign logging per #564
  • Converted to Mamba from Conda for package management in grading containers per #660
  • Upgraded default Python version in grading containers from 3.7 to 3.9

v4.4.1:

  • Update Otter Grade to close file handles before copying files out of Docker containers to fix bug on Windows

v4.4.0:

  • Moved google-api-python-client, google-auth-oauthlib, and six from required installation dependencies to test dependencies to allow installation of Otter with Mamba per #633
  • Added question name to point value validation error messages per #586
  • Fixed bug in copying plugin configurations from assignment config to otter_config.json in Otter Assign

v4.3.4:

  • Set tests directory path when calling ottr::run_autograder from Otter Run

v.4.3.3:

  • Fix Otter Assign slowdown due to poor-performance regex per #634

v4.3.2:

  • Fix bug in determining whether the active interpreter is Jupyterlite in otter.Notebook per #511
  • Fix bug in verifying scores against logs that caused all verifications to throw an error if hidden tests were ignored

v4.3.1:

  • Change sklearn to scikit-learn in requirements files generated by Otter Generate

4.3.0:

  • Support dictionary and tuple assignments in solution substitution in Otter Assign per #587
  • Add the pdf argument to ottr::export in R assignments created with Otter Assign per #440

v4.2.1:

  • Update Otter Grade image tag when the base image changes per #583
  • Make gspread an optional dependency per #577

v4.2.0:

  • Added configuration files for Otter Assign per #565
  • Fixed log execution bug from Slack as described in #571

v4.1.2:

  • Added ipython to install_requires

v4.1.1:

  • Added MANIFEST.in

v4.1.0:

  • Display emojis with test results to more clearly show which tests pass and which fail, as per #533.
  • Allow users to specify a Python version in Otter Generate and Otter Assign
  • Round results.json point values to 5 decimal places per #538
  • Optionally display PDF generation/submission failures to students via results.json per #494
  • Added the force_public_test_summary key to the autograder config per #539
  • Made the "Public Tests" section on Gradescope appear as failing when not all public tests passed per #539

v4.0.2:

  • Close temporary file handle before removal when checking tests in otter.Notebook.export
  • Fixed bug caused by unspecified encoding in Windows JSON loads per #524
  • Updated autograder zip setup.sh file and r-base version per #514
  • Fix point value filtering for student tests in Otter Assign per #503

v4.0.1:

  • Fix Otter Grade Dockerfile per #517
  • Fix display of Public Tests output on Gradescope due to new output format
  • Updated Otter Export to only import the HTML exporter and its dependencies when an HTML export is indicated per #520

v4.0.0:

  • Added a new test file format based on raising exceptions per #95
  • Refactored execution internals to remove mocks and AST parsing
  • Added use of tempfile to store the executed source for compilation per #229
  • Added use of wrapt for otter.Notebook method decorators
  • Set export_cell: run_tests: true and check_all_cell: false as new defaults for Otter Assign per #378
  • Made the v1 format of Otter Assign the default and added the --v0 flag to the CLI
  • Converted logging in some of Otter's tooling from print statements to the logging library, and added verbosity flags to each command
  • Updated containerized grading to better handle grading single files
  • Made Otter compatible with Jupyterlite per #458
  • Added Otter Assign R Markdown format v1 per #491
  • Refactored Otter Assign internals per #491
  • Converted user-supplied configuration management and documentation to fica per #485
  • Added assignment names to Otter Assign and Otter Generate that can be verified by Otter Run to prevent students from submitting to the wrong autograder per #497
  • Set the default version of ottr to v1.2.0

v3.3.0:

  • Made otter.check.utils.save_notebook compatible with JupyterLab and RetroLab per #448
  • Add libmagick++-dev to Gradescope R autograding image

v3.2.1:

  • Display instructor-specified messages ahead of doctest messages per #441
  • Round point values for display to 5 decimal places in Otter Assign per #457

v3.2.0:

  • Changed Otter Generate to accept the path to the zip file to write as the output argument rather than a directory in which to write a file called autograder.zip
  • Changed the file name of the zip file generated by Otter Assign to include the master notebook basename and a timestamp per #401
  • Made xeCJK in Otter Export's LaTeX templates optional per #411
  • Removed concise error messages and debug mode from Otter Export, instead opting to always display the full error message, per #407
  • Upgraded to Ottr v1.1.3
  • Set the default for the --ext option for Otter Grade to ipynb per #418
  • Fixed the display of success messages when all tests cases pass per #425
  • Added an error when the expected notebook file does not exist in otter.Notebook per #433
  • Allow unset conda channel_priority in R setup.sh files per #430
  • Reset all cell execution counts in Assign student notebook per #422

v3.1.4:

  • Added the question name to the otter.assign.utils.AssignNotebookFormatException per #398
  • Switched from manual install of the fandol font in grading images to installing the texlive-lang-chinese package
  • Allowed submission zip to be exported even when PDF generation fails per #403
  • Fixed bug in Otter Assign that fails when a notebook has no tests

v3.1.3:

  • Fixed #389 by closing file handles in Otter Grade before removing them
  • Fixed R image builds by setting Conda channel_priority to strict in R setup.sh files per #386
  • Fix loading docker images after building
  • Added the --ext option to Otter Grade per #386

v3.1.2:

  • Specify UTF-8 encoding in all open calls used for reading JSON for Windows compatibility per #380
  • Fixed incorrect prompt substitution in R notebooks and Rmd assignments

v3.1.1:

  • Added libgomp to R environment.yml

v3.1.0:

  • Added a tool to convert Assign v0-formatted notebooks to v1 format
  • Added xeCJK to the LaTeX exporter template and Docker images
  • Added PDF generation and submission in R per #302
  • Updated intercell seeding in R per #302
  • Fixed bug in test case point values for Assign R assignments per #360
  • Enabled solutions_pdf and template_pdf in Assign R assignments per #364
  • Added options to limit execution time of grading and permit network access
  • Refactored R submission reformatting per #369
  • Added export cells for R notebooks in Otter Assign per #369
  • Updated the default version of Ottr to v1.1.1
  • Changed prompts in R notebooks to match Rmd documents
  • Added filtering of notebook cells with syntax errors during R notebook execution
  • Enured that "empty" tokens are ignored in Otter Generate per #361
  • Prevented save text when export_cell: force_save: true is specified in Otter Assign assignment metadata per #332

v3.0.6: re-release of v3.0.5

v3.0.5:

  • Refactored Otter's execution internals
  • Added intercell seeding via seed variables per #346
  • Made Otter Run compatible with ZIP submissions
  • Fixed argument bug in Otter Run per #349

v3.0.4:

  • Fixed bug in Otter Assign format v1 for closing exports when the last question is manually-graded
  • Removed cell IDs in Otter Assign output notebooks per #340
  • Changed submission zip download link to use the HTML download attribute per #339

v3.0.3:

  • Fix some minor bugs using docker for grading
  • Added support for test config blocks in R assignments
  • Fixed use of autograder_files in Otter Assign
  • Removed the generate: pdfs key from Otter Assign assignment configurations
  • Converted from Docker-py to Python on Whales for containerized grading

v3.0.2:

  • Made otter.Notebook.check_all compatible with metadata tests
  • Refactored logging in otter.Notebook
  • Fixed parsing of Windows newlines in Otter Assign

v3.0.1:

  • Updated the default version of Ottr to v1.0.0
  • Ensured that metadata tests for R notebooks are disabled

v3.0.0:

  • Added Colab support to otter.Notebook by disabling methods that require a notebook path and ensuring that a tests directory is present
  • Added Otter Assign format v1
  • Added FutureWarning for Otter Assign format v0
  • Default-disabled separate test files in Otter Assign v1 format
  • Fixed bug in Otter Assign for R causing point values in test files not to render
  • Added the check_cell key to question metadata in Otter Assign
  • Fixed installation of stringi in Gradescope R build per #259
  • Added support for Ottr v1.0.0.b0
  • Converted CLI to click from argparse
  • Converted documentation source from Markdown to RST, removing use of recommonmark
  • Added token argument to Otter Generate and Otter Assign
  • Implemented submission zip validation against local test cases in otter.Notebook
  • Removed metadata files for Otter Grade
  • Added flags for disabling file auto-inclusion in Otter Generate

v2.2.7:

  • Added student-visible error reporting in Gradescope results

v2.2.6:

  • Updated Otter Grade Dockerfile to simplify build process
  • Updated Otter Grade container management workflow
  • Updated setup.sh templates to reflect the new Dockerfile changes
  • Changed the display of failed test results in Otter Assign validation
  • Made rpy2 an optional depenency

v2.2.5:

  • Upgraded to Miniconda 4.10.3 in grading images
  • Fixed #272

v2.2.4:

  • Fixed total score printout for the use of the points_possible configuration

v2.2.3:

  • Added NotebookMetadataTestFile for reading tests from Jupyter Notebook metadata

  • Added optional storage of tests in notebook metadata for Otter Assign (default-off until v3)

  • Removed deprecated tool Otter Service

  • Added printout of total score to autograder output

v2.2.2:

  • Added show_all_public configuration for grading

v2.2.1:

  • Added metadata for each test case to Otter Assign format
  • Added success and failure messages for test cases
  • Added Gmail notifications plugin
  • Added timestamps to otter.Notebook.export filenames

v2.2.0:

  • Changed grouping of results to be per-question rather than per-test case

v2.1.8:

  • Fixed bug in total score calculation when the grade override plugin is used

v2.1.7:

  • Swapped IPython.core.inputsplitter.IPythonInputSplitter for IPython.core.inputtransformer2.TransformerManager in otter.execute.execute_notebook

v2.1.6:

  • Fixed try/except statements in tests per #228
  • Added error handling in GoogleSheetsGradeOverride plugin for when the Google API hits a rate-limit error

v2.1.5:

  • Added custom environment.yml files in autograder per #103
  • Set display.max_rows to None for pandas to print all rows in summary per #224

v2.1.4:

  • Added otter.utils.nullcontext to be compatible with Python<3.7

v2.1.3:

  • Added the notebook_export plugin event
  • Fixed plugin bug resulting from running tests in Otter Assign
  • Added creation of plugin collection resulting from Otter Generate for running tests in Otter Assign

v2.1.2:

  • Added otter.Notebook.export format support for Otter Grade
  • Fixed tutorial in documentation
  • Added force_save argument to otter.Notebook.export to make notebook force-save optional

v2.1.1:

  • Fixed UnboundLocalError with log in otter.run.run_autograder.run_autograder

v2.1.0:

  • Added nb_conda_kernels to template environment.yml
  • Fixed duplicate token calls when using Otter Assign to call Otter Generate
  • Updated grading image to Miniconda 4.9.2 with Python 3.8
  • Changed Otter conda environment name to otter-env
  • Added warnings import to otter.check.notebook

v2.0.8:

  • Passed plugin collection while running tests in Otter Assign
  • Fixed adding directories in files with Otter Generate

v2.0.7:

  • Changed scripts to entry_points in setup.py for Windows compatibility and removed bin/otter
  • Added otter.check.utils.save_notebook for autosaving notebooks on export calls
  • Updated OK format to allow points key to be a list of length equal to the number of test cases

v2.0.6:

  • Fixed requirements not found error for R notebooks in Otter Assign
  • Removed use of re in overriding Notebook test directory override in otter.execute.execute_notebook by adding otter.Notebook._test_dir_override

v2.0.5:

  • Fixed NoneType issue in PluginCollection.generate_report

v2.0.4:

  • Added ignoreable lines in Otter Assign
  • Added error handling for log deserialization per #190
  • Added plugin data storage per #191

v2.0.3:

  • Fixed positional arg count in otter.plugins.builtin.GoogleSheetsGradeOverride
  • Fixed working directory in otter.plugins.builtin.GoogleSheetsGradeOverride during Otter Assign

v2.0.2:

v2.0.1:

  • Added the each key to points in question metadata for Otter Assign

v2.0.0:

  • Changed granularity of results to be test case-by-test case rather than by file
  • Added ability to list requirements directly in assignment metadata w/out requirements.txt file
  • Unified assignment grading workflow and converted local grading to container-per-submission
  • Exposed grading internals for non-containerized grading via otter run and otter.api
  • Added plugins for altering grades and execution, incl. built-in plugins
  • Added ignorable cells to Otter Assign
  • Added autograder_files configuration for Otter Assign
  • Added passdown of assignment configurations to Otter Generate from Otter Assign
  • Fixed whitespace bug in Assign solution parsing
  • Resolved conflicts with nbconvert>=6.0.0, removed version pin
  • Added otter.assign.utils.patch_copytree as a patch for shutil.copytee on WSL
  • Refactored Otter Generate to use zipfile to generate zips
  • Refactored CLI to allow creation of programmatic API
  • Changed otter generate autograder to otter generate
  • Removed otter generate token as all interaction with otter.generate.token.APIClient can be handled elsewhere
  • Added intercell seeding for R Jupyter Notebooks
  • Added ValueError on unexpected config in otter.assign.assignment.Assignment
  • Added --username, --password flags to Otter Assign and Otter Generate
  • Added support for Python files
  • Removed FutureWarning for deprecated global hidden key of OK tests
  • Add missing file specifier in environment template

v1.1.6:

  • Fixed ZeroDivisionError when an assignment has 0 points total

v1.1.5:

  • Fixed error in parsing requirements when using Otter Grade

v1.1.4:

  • Fixed KeyError when kernelspec unparsable from notebook in Otter Assign

v1.1.3:

  • Changed Rmd code prompt to NULL # YOUR CODE HERE for assignment statements and # YOUR CODE HERE for whole-line and block removal

v1.1.2:

  • Made requirements specification always throw an error if a user-specified path is not found
  • Pinned nbconvert<6.0.0 as a temporary measure due to new templating issues in that release

v1.1.1:

  • Fixed handling variable name collisions with already-tested test files
  • Added --no-pdfs flag to Otter Assign

v1.1.0:

  • Moved Gradescope grading to inside conda env within container due to change in Gradescope's grading image
  • Added ability to specify additional tests to be run in cell metadata without need of explicit Notebook.check cells

v1.0.1:

  • Fixed bug with specification of overwriting requirements in Otter Generate

v1.0.0:

  • Changed structure of CLI into six main commands: otter assign, otter check, otter export, otter generate, otter grade, and otter service
  • Added R autograding integrations with autograding package ottr
  • Added Otter Assign, a forked version of jassign that works with Otter
  • Added Otter Export, a forked version of nb2pdf and gsExport for generating PDFs of notebooks
  • Added Otter Service, a deployable grading service that students can POST their submissions to
  • Added logging to otter.Notebook and Otter Check, incl. environment serialization for grading
  • Changed filenames inside the package so that names match commands (e.g. otter/cli.py is now otter/grade.py)
  • Added intercell seeding
  • Moved all argparse calls into otter.argparser and the logic for routing Otter commands to otter.run
  • Made several fixes to otter check, incl. ability to grade notebooks with it
  • otter generate and otter grade now remove tmp directories on failure
  • Fixed otter.ok_parser.CheckCallWrapper finding and patching instances of otter.Notebook
  • Changed behavior of hidden test cases to use individual case "hidden" key instead of global "hidden" key
  • Made use of metadata files in otter grade optional
  • Added otter_ignore cell tag to flag a cell to be ignored during notebook execution

v0.4.8:

  • added import of IPython.display.display to otter/grade.py
  • patched Gradescope metadata parser for group submissions

v0.4.7:

  • fix relative import issue on Gradescope (again, sigh)

v0.4.6: re-release of v0.4.5

v0.4.5:

  • added missing patch of otter.Notebook.export in otter/grade.py
  • added __version__ global in otter/__init__.py
  • fixed relative import issue when running on Gradescope
  • fixed not finding/rerunning tests on Gradescope with otter.Notebook.check

v0.4.4:

  • fixed template escape bug in otter/gs_generator.py

v0.4.3:

  • fixed dead link in docs/gradescope.md
  • updated to Python 3.7 in setup.sh for Gradescope
  • made otter and otter gen CLIs find ./requirements.txt automatically if it exists
  • fix bug where GS generator fails if no -r flag specified