Allow more path customization for feature generation/inference #493
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
had a problem deploying
to
Integrate Pull Request
GitHub Actions
Failure
bfhealy
had a problem deploying
to
Integrate Pull Request
GitHub Actions
Failure
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
temporarily deployed
to
Integrate Pull Request
GitHub Actions
Inactive
bfhealy
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
SCoPe code typically references a single
BASE_DIRthat contains the code along with input and output data. This PR adds more flexibility by allowing users to specify apath_to_featuresin the config file other than the base SCoPe directory. If this path is given, theBASE_DIRvariable will be redefined in feature generation code and results will be saved to the specified directory. This is useful for generating features on a cluster, where the code's installation directory may not be ideal for saving larger files.Additionally, this PR makes use of the existing
path_to_predsconfig entry to allow inference results to be saved in a directory other than the base code directory. Further testing will be done on Expanse to ensure the path updates work as intended.(See also #488)