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With respect to the JOSS review:
These guidelines explain on a technical level how to develop the software and test it. However what seems to be missing is what type of contributions will be considered/outright rejected. What is the stance on AI-assisted additions? Do they need to be flagged? etc.
@goelakash@jonaspleyer@zachmatson: If you agree, I suggest adding the following text to what Akash has already added regarding community guidelines.
Under ## Running Tests
To confirm that STEPS runs properly using the command-line interface, one should be able to produce data that, when plotted, recreate the fitness trajectories shown in Figure 3 of the JOSS paper using the following command:
./target/release/steps simulate --seed 606 --summary-output-path BasicOutput.csv
Using a different seed will produce trajectories that are qualitatively similar, but not identical owing to the stochastic nature of the mutation and dilution processes in STEPS. Note that all other parameters (population size, mutation rates, duration, etc.) use the default values with this command. See the STEPS User Manual for additional context and options.
The same test should work with the web-based version of STEPS when using the default settings. Note that Randomization Seed is an option under the Advanced Settings menu, so one would enter 606 to obtain the identical results.
If a developer makes changes or extensions to the underlying code, the default parameters should still produce qualitatively similar results to Figure 3. However, the results will not be identical if they impact any of the stochastic events.
Under ## Submitting Changes
If the proposed changes are primarily technical in nature, you may also contact Zachary Matson via email at zacharywdmatson@gmail.com.
If the proposed changes introduce new scientific features, we suggest that you contact Richard Lenski via email at Lenski@msu.edu to discuss the proposed features.
Please also indicate whether you have used, or intend to use, AI when making changes.
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Adds community guidelines for contributing to the project.
Closes #17