AutoGS Template

Quickstart Guide

Install this in an environment using your chosen package manager. In this example we are using virtualenv

Install:

• python (3.8 or greater): https://www.python.org/downloads/
• virtualenv: https://virtualenv.pypa.io/en/latest/installation.html

Create a new virtual environment:

virtualenv venv

Note: You want to ensure that the python version matches that of autora. If necessary you can specify the respective python version directly, e.g., virtualenv venv --python=python3.9

Activate it:

source venv/bin/activate

Use pip install to install the current project (".") in editable mode (-e) with dev-dependencies ([dev]):

pip install -e ".[dev]"

Note: You may install new dependencies via pip install packagename inside your virtual environment. If those dependencies are vital to your package, you will have to add them to the pyproject.toml (see Step 6 of the Contribution Guide).

Contribution Guide

Step 1: Choose Feature Category

First you have to choose which type of feature you would like to add to AutoRA. There are four categories of contributions:

(1) Theorist: An sklearn regressor that returns an interpretable model relating experiment conditions $X$ to observations $Y$.
Example: The Bayesian Machine Scientist (Guimerà et al., 2020, in Science Advances) returns an equation governing the relationship between $X$ and $Y$.

(2) Experimentalist: A method that identifies novel experiment conditions $X'$ that yield scientific merit. Experiment conditions may be determined based on an existing pool of candidate conditions, based on the most recent model or other factors.
Example: The Novelty Sampler selects novel experiment conditions $X'$ with respect to a pairwise distance metric applied to existing experiment conditions $X$.

(3) Experiment Runners: A method that orchestrates the collecting of observations for a given set of experiment conditions, which may include the recruitment of participants.
Example: The Firebase-Prolific Runner enables the collection of behavioral data from human participants via web-based experiments hosted on Firebase, using a pool of participants registered through Prolific.
(3a) Recruitment Manager: A method (or collection of methods) to recruit participants.
Example: The Prolific Recruitment Manager enables the recruitment of participants via Prolific.
(3b) Experimentation Manager: A method (or collection of methods) to handle the requisite experimentation processes.
Example: The Firebase Experimentation Manager enables the hosting of a web-based experiment on Firebase and the storage of conditions and observations via Firestore.

(4) Synthetic Data: A ground-truth model that implements a hypothesized relationship between experimental conditions $X$ and observations $Y$. Synthetic models may act as objects of study for which the underlying mechanisms are known, and be used for benchmarking theorists and experimentalists in AutoRA in terms of their ability to recover the underlying model from synthetic data, e.g., by acting as "synthetic participants". Example: The basic Synthetic Data Package implements simple models of economic choice and psychophysics.

Step 2: Delete Irrelevant Files

Depending on which feature you want to contribute, you can remove initialization files from all irrelevant features. You may delete the following initialization files from the template:

• Theorist: src/autora/theorist/example_theorist/__init__.py
• Experimentalist: src/autora/experimentalist/example_experimentalist/__init__.py
• Experiment Runner: src/autora/experiment_runner/example_runner/__init__.py
• Recruitment Manager: src/autora/experiment_runner/example_runner/recruitment_manager/__init__.py
• Experimentation Manager: src/autora/experiment_runner/example_runner/experimentation_manager/__init__.py
• Synthetic Data: src/autora/synthetic/example_data/__init__.py

In addition, you may delete the following test files from the template:

• Theorist: tests/test_example_theorist.py
• Experimentalist: tests/test_example_experimentalist.py

For instance, if you would like to implement an experimentalist, then you may remove all files listed above except for

• src/autora/experimentalist/example_experimentalist/__init__.py and
• tests/test_example_experimentalist.py.

Step 3: Implement Your Code

You may now add a folder in the respective feature category. For instance, if you would like to implement and an experimentalist, then you may rename the subfolder example_experimentalist in src/autora/experimentalist/ and add your implementation of the sampler in the __init__.py file. You may also add additional files in this folder. Just make sure to import the core function or class of your feature in the ``init.py''' if it is implemented elswhere.

Note: You can create folders for new categories if none of the existing feature categories seems fitting.

Step 4 (Optional): Add Tests

It is highly encouraged to add unit tests to ensure your code is working as intended. These can be doctests or as test cases in tests/test_your_contribution_name.py. For example, if you are implementing an experiment sampler, you may rename and modify the tests/test_experimentalist_sampler_example.py.

Note: Tests are required if you wish that your feature becomes part of the main autora package. However, regardless of whether you choose to implement tests, you will still be able to install your package separately, in addition to autora.

Step 5 (Optional): Add Documentation

It is highly encouraged that you add documentation of your package in your docs/index.md. You can also add new pages in the docs folder. Update the mkdocs.yml file to reflect structure of the documentation. For example, you can add new pages or delete pages that you deleted from the docs folder.

Note: Docmentation is required if you wish that your feature becomes part of the main autora package. However, regardless of whether you choose to write documentation, you will still be able to install your package separately, in addition to autora.

Step 6: Add Dependencies

In pyproject.toml add the new dependencies under dependencies

Install the added dependencies

pip install -e ".[dev]"

Step 7: Publish Your Package

Once your project is implemented, you may publish it as subpackage of AutoRA. If you have not thoroughly vetted your project or would otherwise like to refine it further, you may nervous about the state of your package–you will be able to publish it as a pre-release, indicating to users that the package is still in progress.

Step 7.1: Update Metadata

To begin publishing your package, update the metadata under project in the pyproject.toml file to include

• name,
• description,
• author-name,
• author-email, and
• version.

Also, update the URL for the repository under project.urls.

There are at least two options for publishing the package. For beginners, we recommend Option 1 (via Github Actions) as it is easier to follow.

Step 7.2 (Option 1): Publish via GitHub Actions

To automate the publishing process for your package, you can use a GitHub action instead of Twine:

• Add the GitHub action to the .github/workflows directory: For example, you can use the default publishing action:
  • Navigate to the actions on the GitHub website of your repository.
  • Search for the Publish Python Package action and add it to your project
• Create a new release: Click on create new release on the GitHub website of your repository.
• Choose a tag (this is the version number of the release. If you didn't set up dynamic versioning it should match the version in the pyproject.toml file)
• Generate release notes automatically by clicking generate release, which adds the markdown of the merged pull requests and the contributors.
• If this is a pre-release check the box set as pre-release
• Click on publish release

Step 7.2 (Option 2): Publish via Twine

You can follow the guide here: https://packaging.python.org/en/latest/tutorials/packaging-projects/

Then, build the package using:

python -m build

Publish the package to PyPI using twine:

twine upload dist/*

Step 7.3 (Optional): Dynamic Versioning

To automatically generate the version number for each release, you can use dynamic versioning instead of updating the version number manually. To set this up, you need to alter the pyproject.toml file:

• Replace version = "..." with dynamic = ["version"] under project
• Replace the build-system section with the following:

[build-system]
requires = ["setuptools", "setuptools_scm"]
build-backend = "setuptools.build_meta"

• Add a new section to the pyproject.toml file:

[tool.setuptools_scm]

Dynamic Versioning: Publishing via GitHub Actions

You can use dynamic versioning with the GitHub action described in the previous section. The workflow remains the same, but you don't have to update the version in the pyproject.toml file.

Dynamic Versioning: Publishing Using twine

If you are using dynamic versioning with Twine, follow these steps to publish your package:

• Commit all of your changes.
• Tag the commit: Create an annotated Git tag at the commit you want to release. This is typically the most recent commit on your main branch. For example, you can run git tag -a 1.0.0a to create a tag named "1.0.0a" at the current commit.
• Build and release the package using Twine as described in the above section.

Questions & Help

If you have any questions or require any help, please add your question in the Contributer Q&A of AutoRA Discussions. We look forward to hearing from you!