Included Licensing Decision Processes

code_strategy.md

@@ -22,6 +22,9 @@ We are cautious in using these examples, validating that they work specifically
 Most of the time, it is safe to assume that all code you can view publicly can be used freely.
 However, we are also aware that certain licenses might exist that prevent us from repurposing other people’s code.
 We must look out for these exceptions, and steer clear from using code with restrictive licenses.
+However, if you must include code from a repository under a restrictive license you can either change the license or modify adapted code substantially to avoid conflicts.
+The following flowchart demonstrates the decision process if the adapted code is licensed under a GPL-3 license:
+![Process for adapting code under a restrictive license.](images/using_code.png)
 
 ## 2. Writing code
 

github_strategy.md

@@ -57,6 +57,12 @@ We also include code for generating all publication quality figures as the last
 
 We use software libraries in these analyses, and we save specific versions in conda environment files or docker containers.
 We also must specify the license, present a clear README with reproducibility/usage instructions, a brief summary of the results, and citation instructions.
+We suggest following the flowchart below to choose a license when creating a repository:
+![Process for choosing a repository license.](images/selecting_a_license.png)
+According to the [CU Innovations office](https://www.cuanschutz.edu/cu-innovations) when creating or modifying a license you must include the following line (with the appropriate year):
+`Copyright (c) <year> the Regents of the University of Colorado`
+For further questions about licensing requirements contact the [CU Innovations Office](https://www.cuanschutz.edu/cu-innovations).
+To generate a license from a template in github follow [this github docs guide](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository)
 
 Analysis repositories must be included in our publications, and we consider them to be the ground truth methods section. The analyses must be fully reproducible (we aim for [Gold Reproducibility](https://www.nature.com/articles/s41592-021-01256-7#Sec4)) and open source.
 For each submission and subsequent resubmission, we generate specific “github releases”.