Support long argument list specified as file for all topaz commands #192
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
Using the fromfile_prefix_chars option in ArgumentParser https://docs.python.org/3/library/argparse.html#fromfile-prefix-chars
|
I like this. Was not aware argparse had this option. We need to make sure this doesn't cause any unexpected errors and is compatible with some pending unreleased updates though. |
|
This will be a welcome improvement! On several systems, I have run into the "too many command-line arguments" limitation, and there is no other solution than splitting the dataset in several batches to pick separately (pretty annoying to do, and it makes the job graph look more complicated than it really is). |
|
This would be great to have! We frequently run into this with large datasets, necessitating splitting into smaller batches. This isn't much of an issue for experienced users, but it trips up a lot of first time Topaz users in my experience. |
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Outdated suggestions cannot be applied.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.
Fixes #47
Use
fromfile_prefix_charsoption in ArgumentParser to allow specifying a long list of arguments in a file.Example invocation before (still supported):
Example invocation after:
Where
mics.txthas the following contents:This would be really beneficial to have when processing thousands of micrographs on systems that have a limit on the maximum number of allowed command-line arguments. It would also be good for debugging purposes e.g., show full command used by CryoSPARC Topaz wrapper instead of a truncated command that excludes the paths for legibility.
@tbepler please let me know if you have any feedback!