Test generator for GitHub Classroom autograding

classroom-generator builds template repositories for GitHub Classroom assignments.

Homework tests are generated from templates and a generate.yml file that contains the individual tests with points. The generate_tests.py script then creates

• the appropriate tests themselves
• the autograding.json configuration for the .github/workflows/classroom/autograding.json (The py4phy/autograding@v1 workflow is used; this is a fork of stevenbitner/autograding, @stevenbitner 's updated version of the original GitHub education/autograding workflow)

The generate.yml file contains data for problems with their individual tests. For each problem, a subdirectory is made under tests/. Each test gets its own test file, point value, and entry in autograding.yml.

At the moment the following is supported:

• template tests for checking fixed variables
• template tests for running a script with input() from stdin that sets variables
• template test for comparing output against regular expression
• template test for checking existence of an image file
• template test for checking existence of a file
• template test for checking existence of at least one file matching a regular expression
• template test for multiline regular expression match for file content
• template test for function evaluation (parametrized, always provide args/kwargs/references as a list of lists or list of dicts)
• custom test files

A hacky BUILD_all.sh script is provided to bundle the generated tests, assets, and GitHub workflow into a repository that can be immediately pushed to an empty template repository on GitHub.

All code and files are made available under the terms of the GNU General Public License v3.

Tutorial

In this mini-tutorial we will create a Classroom assignment for simple in-class exercises with NumPy and matplotlib. All materials are publicly available at https://github.com/Py4Phy .

We will use Py4Phy/activity_04_source as input (normally, students would likely not see this repository because I am including the solutions there). The generated template repository with the files for the GitHub actions autograding workflow is Py4Phy/Activity_04_numpy_and_matplotlib.

Get classroom-generator

You need a Python environment with the pyyaml package included.

Currently, no real installation is provided. Just clone the repo:

git clone https://github.com/Py4Phy/classroom-generator.git

Then use the scripts in the classroom-generator/bin directory.

Get the example sources

Clone the Py4Phy/activity_04_source repository:

git clone https://github.com/Py4Phy/activity_04_source.git

Create the template repository for GitHub Classroom

We first build the template locally in a directory templates:

mkdir templates

Run classroom-generator's BUILD_all.sh script:

./classroom-generator/bin/BUILD_all.sh -B templates activity_04_source/generate.yml

The new template repo is created as templates/Activity_04_numpy_and_matplotlib. During this process, files are copied and new tests are created. An input file for the autograding workflow is generated and moved to the right place. Finally, everything is turned into a local git repository and checked in. Note that running the process again will add commits to the repo (if anything changed).

Push template repo to GitHub

Now create a new repository on GitHub named Activity_04_numpy_and_matplotlib under YOURORG or YOURNAME.

Push changes from the local Activity_04_numpy_and_matplotlib.git repo to the remote:

git remote add origin [email protected]:YOURORG/Activity_04_numpy_and_matplotlib.git
git branch -M main
git push -u origin main

Set the remote to be a template under the Settings. (IMPORTANT: Otherwise GitHub Classroom cannot use it!)

Your remote template repository should look like Py4Phy/Activity_04_numpy_and_matplotlib.

Set up an assignment in Classroom

In GitHub Classroom create a New Assignment with the following settings:

• Assignment basics
  • Assignment Title: activity-04 (or whatever you want to call it)
  • Deadline: (choose one if you like)
  • Individual or group assignment: Individual assignment
  • Repository visibility: Private
  • Grant students admin access to their repository: no (recommended, but your choice)
• Starter code and environment
  • Add a template repository to give students starter code: YOURORG/Activity_04_numpy_and_matplotlib
  • Add a supported editor: (your choice)
• Grading and feedback
  • Add autograding tests: leave empty (do NOT add tests here as this will overwrite your generated configuration!)
  • Enable feedback pull requests: (your choice)

Then Create assignment.

Distribute the magic link to your students.

Usage

Primitive at the moment...

./classroom-generator/bin/BUILD_all.sh -B ./template_assignments hw02/generate.yml

where hw02/ contains the configuration, starter code, and problem description. A template repository is then created under ./template_assignments/HW_02.

Example

Example layout for hw02:

hw02/
├── README.md                        <----- documentation
├── Solution                         <----- solution files
│   ├── hello.py                            (not distributed)
│   └── planets
│       └── iceplanets
│           └── hoth.txt
├── assignment.md                     <----- problem description
├── generate.yml                      <----- configuration file
├── hello.py                          <----- starter code
└── tests                             <----- custom tests
    ├── test_files_and_directories.py
    └── test_helloworld.py

The generate.yml file contains

problemset:
  name: HW 02
  assets: ["README.md", "assignment.md"]
  problems:
  - problem: 1
    title: Hello World
    filename: "hello.py"
    assets: ["hello.py"]
    items:
    - name: print_output
      points: 3
      output: 'Hello World!'
      pytest_args: '--tb=short'
    - name: run_program
      points: 2
      test: test_helloworld.py
  - problem: 2
    title: Directories and Files
    setup: "sudo -H pip3 install pytest"
    filename: "planets/"
    items:
    - name: tree_structure
      points: 5
      test: test_files_and_directories.py

Example layout of the generated HW_02 template directory (it's named HW_02 because the key problemset.name: HW 02 was made filepath-safe and used as a name):

HW_02/
├── .github                         <--- GitHub autograding workflow
│   ├── classroom
│   │   └── autograding.json
│   └── workflows
│       └── classroom.yml
├── .gitignore
├── README.md                       <--- documentation
├── assignment.md                   <--- problem description
├── hello.py                        <--- starter code
└── tests                           <--- tests for pytest
    ├── __init__.py
    ├── problem_1
    │   ├── __init__.py
    │   ├── test_print_output.py    <--- generated "output" test
    │   └── test_run_program.py     <--- custom test (test_helloworld.py)
    ├── problem_2
    │   ├── __init__.py
    │   └── test_tree_structure.py  <--- custom test (test_files_and_directories.py)
    └── tst.py                      <--- test framework asset

Documentation

• Include README.md with points banner and generic instructions. (Can be nearly identical between assignments.)
• Create the assignment.md or assignment.pdf with instructions for students. If in markdown or restructured text, also include the points banner.

Configuration

Include any docs into assets in the generate.yml file (namely, in the problemset.assets key at the top) so that they get copied.

Example:

assets: ["README.md", "assignment_00.md"]

Points banner

Make sure to include the points banner that updates with the currently achieved points and the status of the tests:

[![GitHub Classroom Workflow](../../workflows/GitHub%20Classroom%20Workflow/badge.svg?branch=main)](../../actions/workflows/classroom.yml) ![Points badge](../../blob/badges/.github/badges/points.svg)

The banner is the same for all assignments. Clicking the GitHub Classroom Workflow status badge links to the Action so that students can read the test feedback from the autograding step.

Starter code

Create any starter code that students need. Files are copied verbatim. Whole directories can also be copied.

Configuration

Include any starter code filenames or directory names in the problem.assets.

For example:

  - problem: 2
    title: Hello World
    assets: ["hello.py"]

Note that assets is always a list, even if you only have one file. Directory names can be terminated with a slash but that is not necessary.

Building the template repository

Simple usage

Run the BUILD_all.sh script as

BUILD_all.sh -B /tmp/BUILD hw00/generate.yml

where -B is the path to where you want the final repository with tests to show up under and the argument is the path to the configuration yml file.

The shell script

1. calls generate_tests.py -B $BUILD generate.yml
2. copies static files to the final destination directory
3. creates the specific workflow for GitHub
4. initializes a git repo there and/or commits changes

You can then push the repo to a remote repository that can be used as a template for GitHub Classroom.

Only generating tests

The generate_tests.py script can be also run separately, e.g., for testing.

Tests are generated in the BUILD_DIR directory, typically BUILD/<name> where <name> is generated from the assignment title in problemset.name in the generate.yml file (after making the name "shell"-safe); we will refer to it as $BUILD.

generate_tests.py -B BUILD_DIR  path/to/hw00/generate.yml

See below for notes on generate.yml

All necessary files are copied into the $BUILD directory.

Notes on BUILD_all

The BUILD_all.sh script does the following:

• runs generate_tests.py -B BUILD_DIR generate.yml

• mkdir $BUILD/.github/{workflows,classroom}

• copy classroom.json (static): cp $ASSETS/workflows/classroom.yml $BUILD/.github/workflows (does not change)

• copy autograding.json (created): cp autograding.json $BUILD/.github/classroom (is specific for this assignment)

• create .gitignore

• create a template repository for the HWxx (which is updated on further runs of BUILD_all.sh)

  (Manually push the repo to a bare GitHub repo to create an assignment template that can be used with GitHub Classroom.)

Configuration file

The configuration file is in YAML format and is conventionally called generate.yml (but can in principle be called anything).

Example with common usage (the keys are explained below):

problemset:
  name: HW example
  test_assets: ["conftest.py", "base.py"]
  assets: ["README.md", "assignment.pdf"]
  used_templates: True
  setup: 'sudo -H pip3 install pytest numpy matplotlib'
  problems:
  - problem: 1
    title: Copy, rename, delete
    filename: "PHY494/"
    assets: ["PHY494/"]
    setup: 'sudo -H pip3 install pytest numpy'
    items:
    - name: top_dir
      points: 1
      test: test_top_dir.py
    - name: top_all_dirs
      points: 4
      test: test_all_dirs.py
  - problem: 2
    title: Hello World
    filename: "hello.py"
    items:
    - name: print_output
      points: 3
      output: 'Hello World!'
      pytest_args: '--tb=short'
  - problem: 3
    title: Data types
    filename: datatypes.py
    assets: ["datatypes.py", "xmodule.py"]
    items:
    - name: string
      points: 1
      variable: a
      reference: "'42'"
      check_type: True
    - name: list
      points: 1
      variable: g
      reference: [3, 2, 1, 0, "lift off"]
      check_type: True
  - problem: 4
    title: Kinetic energy calculator
    filename: KEcalc.py
    items:
    - name: KEcalc
      points: 5
      variable: KE_kJ
      input_values: [8.2, 10]
      reference: 0.41
  - problem: 5
    title: Indexing lists
    filename: list_slicing.py
    items:
    - name: slice_3d
      points: 2
      variable: ['d0', 'd1', 'd2start' ,'d2stop']
      reference: [0, 1, 2, 4]
  - problem: 1
    title: Create functions
    filename: myfuncs.py
    setup: 'sudo -H pip3 install pytest numpy'
    items:
    - name: heaviside
      points: 4
      function: heaviside
      args:  [[0], [-1.e+100], [42.1], [1.2e-24], [10], [-10]]
      reference: [0.5, 0, 1., 1., 1., 0]
    - name: area_kwargs
      points: 4
      function: area
      args:  [[2, 4], [2, 4], [1, 1]]
      kwargs: [{}, {'scale': 2}, {'scale': 0.5}] 
      reference: [8, 16, 0.5]      
  - problem: 4
    title: Plot functions
    filename: myfuncs.py
    items:
    - name: heaviside
      points: 4
      function: heaviside
      args:  [[0], [-1.e+100], [42.1], [1.2e-24], [10], [-10]]
      reference: [0.5, 0, 1., 1., 1., 0]
      relative_tolerance: 1.e-6
      absolute_tolerance: 1.e-12
    - name: plot
      points: 1
      imagefilename: "heaviside.png"
    - name: discussion of plot
      points: 1
      file: "discussion.txt"
  - problem: 4b
    title: discussion
    filename: discussion.txt
    assets: ["graph.png", "data.csv"]
    - name: mention energy conservation
      points: 1
      content: |
         \s*energy\s*conservation
  - problem: 5
    title: data analysis (BONUS)
    extra: True
    - name: produce numbered data files
      points: 3
      fileregex: "datafiles/data_\d+\.(dat|csv)"

General notes

• Starter code *.py, assignment sheet (*.{pdf,md}) etc are copied to the top of the template directory; if you want directory trees, put them in a directory and list the directory in assets because trees are copied as-is.

• Be careful about how yaml interprets data; for instance, scientific/engineering notation is only understood when a decimal point is included an a sign after 'e': 1.e+1 (good), 1e+1 (bad), 1.e1 (bad) --- the bad cases are interpreted as strings. See the pyyaml documentation.

Keys in generate.yml

General

Keys at the top level (problemset)

• name : will be rewritten to a Python/filename-safe form (spaces to underscores, most weird characters stripped); will be used to name tests and the $BUILD directory

• test_assets: list of files in the local tests/ that should be copied; by default, only tests that are named in a test: key are copied. This is useful to copy additional files such as conftest.py for global fixtures.

• used_templates: Normally omitted; explicitly indicate with True that the testing infrastructure files (e.g., tst.py) should be copied even though no autogenerated tests are included. If any autogenerated tests are part of this assignment then a False will be automatically overriden. This flag is useful when custom tests import testing framework, e.g.

  from ..tst import get_attribute, import_module

  Note that the testing infrastructure module (tst.py) requires the numpy package so installation of numpy should normally be included in a custom setup keyword.

• setup: Complete command to install the environment; setup at the top level is the default for individual problem instances. setup inside a problem overrides the global default.

  If setup is not provided, it defaults to "sudo -H pip3 install pytest numpy".

Problem

Each problem contains one or more tests.

• problem : will be used to generate directory names

• title : name of the problem

• filename : this filename will be used for all autogenerated tests in the test items list that require a filename as input. Custom tests (test) can test another filename.

• assets : list of files and/or directories that will be copied to the assignment (e.g., starter code, data, ...). Only list top level files/directories. Sub-paths such as "problem_1/data.csv" would just copy "data.csv" to the top level. Instead copy "problem_1/" (trailing slash is ignored by shutil.copytree). The assets can be listed at the problemset (top) level and the problem level (q.v.).

• setup: Complete command to install the environment for this problem only. (Packages are only downloaded once so installing a new environment is fast.)

• items: each entry in this list is an independent test run, which runs in a fresh environment, and counts as a separate test for the autograder.

• extra: Set to True if this problem counts as extra credit (or bonus). The default is False. Points for extra credit are accrued but the total is listed as the sum of points without any extra credit. Note that failing extra tests still lead to a failing workflow banner, which can be confusing for students.

  Using this flag requires the special py4phy/[email protected] workflow.

Individual tests

The philosophy is to have one test per property that is to be tested.

• name: name of the test (will be made Python-safe and used for naming the generated test file)

• points: Each test has a points value. A failed test is 0 points, a passed test accrues the points value.

  Test that are part of problems with extra: True can fail/pass as usual but the points are not included in the point total for the full problem set.

• extra: Set to True if this test counts as extra credit (or bonus). The default is False. See the notes on extra for the whole problem.

  The values of extra at the problem and the test level are combined with logical or so that if any of them are set to True then the test will count as extra credit.

Available tests

Each test item should contain exactly one of the follwing keys that determines how code is being tested. Many tests are generated from templates and do not need to be explicitly included (see variable, output, function, ...). A custom test can be selected with the test keyword.

The behavior of some of the generated tests can be modified with additional keys as described in the documentation below.

• test : Indicates a custom test file. Custom tests must be stored in the assignment directory under tests/.

• variable : Check the value of the variable in filename after running (actually: importing) the file.

  With check_type: True can also check the type (default: False).

• output : Run the code as python3 filename and match the string in the standard output. By default, this is a regular expression.

  Can be turned into a bare string with regular_expression: False.

  Be aware of how to structure blocks in yml (e.g., > for folded, | for indented blocks, and |3 for indented with 3 whitspace (e.g., when first line is indented compared to following lines).

• file: name of a file that should have been submitted; the test only checks that the file exists.

  A path relative to the repository root directory can be used.

fileregex: Python regular expression for one or more filenames. If the expression matches at least one filename then the test passes.

Directory names do not count as matches.

The fileregex can be a path including directory names relative to the repository root directory. However, regular expressions may only be used for the filename part as directory parts of the path are never matched but used literally.

• imagefilename: name of a file that should have been submitted; the test only checks that the file exists and that it can be loaded as an image with matplotlib.image.imread().

• content: multiline regular expression (like output) but matches the content of filename.

• function: : functions are always tested with parametrized fixtures, i.e., arguments args/kwargs must always be present in a list in the yaml generate file.

  Entries in args and kwargs are paired (like zip(args, kwargs)).

  Functions are always called with func(*args, **kwargs) for each parameter set.

  The list of reference values must have the same length as the args and kwargs lists, with one reference for each input.

  Only one of args or kwargs need to be provided; the other is generated with empty content if necessary.

Test parameters

• input_values : input to be read from standard input. Each element of the list is turned into a string and supplied with a newline.

• args: arguments for a function test as a list of lists

• kwargs: keyword arguments for a function test as a list of dictionaries

• reference: reference values to compare the output of a function test against. The list of reference values must have the same length as the args and kwargs lists, with one reference for each input.

  If a tested value is a numpy array or a tuple of numpy arrays then the reference is converted to a numpy array or tuple of numpy arrays for the test with numpy.testing.assert_allclose(). Otherwise, numbers are tested with pytest.approx or with ==. The absolute_tolerance and relative_tolerance values are used for either the numpy or the pytest comparison.

• relative_tolerance and absolute_tolerance: set the tolerance values rel and/or abs for pytest.approx() for any test that checks for floating point numbers (variable and function). By default they are set to None so that the pytest defaults of rel=1e-6 and abs=1e-12 are used. Note that only setting either relative_tolerance or absolute_tolerance leads to different behavior of pytest.approx(), as described in the docs. Leaving these values unset should be fine in most cases.

  If an array comparison with assert_allclose() is performed, the tolerances behave like np.allclose(actual, desired, rtol, atol) where the difference between actual and desired to atol + rtol * abs(desired) is compared.

• check_type: True or False (default): also check the type for a variable test

• regular_expression: True (default) or False: select if the reference value for output is treated as Python regular expression (True) or matched as a bare string (False).

Directory layout

classroom-generator

The class-room generator needs the following fixed directory structure to find assets (relative to the bin directory):

.
├── README.md
├── assets
│   ├── testing
│   │   ├── templates
│   │   │   ├── ...
│   │   │   ├── _test_multi_variables.template.py
│   │   │   ├── _test_variable.template.py
│   │   │   └── _test_variable_with_input.template.py
│   │   └── tst.py
│   └── workflows
│       └── classroom.yml
└── bin
    ├── BUILD_all.sh
    └── generate_tests.py

Assignments

Assignments are stored separately but also need to have a fixed layout:

hw02/
├── README.md
├── Solution
│   ├── hello.py
│   └── planets
│       └── iceplanets
│           └── hoth.txt
├── assignment_00.md
├── generate.yml
├── hello.py
└── tests
    ├── test_files_and_directories.py
    └── test_helloworld.py

• The generate.yml file is the config file and drives the classroom-generator script generate_tests.py.

  It defines the top level directory for an assignment.

• The tests directory must be in the top directory. It contains custom tests that will be copied into the full problem directory.

• Starter code such as hello.py is put in the top directory.

• Add a README.md file that will be displayed when browsing the repository. It should contain the badges that show points:

  [![GitHub Classroom Workflow](../../workflows/GitHub%20Classroom%20Workflow/badge.svg?branch=main)](../../actions/workflows/classroom.yml) ![Points badge](../../blob/badges/.github/badges/points.svg)

• Add additional documents (as .md or .pdf files) to describe the task.

• Keep solutions in a Solution directory for reference. They are not used anywhere. The generate.yml file needs to either contain the correct reference values or the custom tests need to contain the code to check for correctness.

  Keep assignment template repositories private if they contain solutions.