Modern arguments #1216
Open
Modern arguments #1216
Conversation
This file contains hidden or 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
# Conflicts: # src/dr/app/tools/oldtreeannotator/TreeAnnotator.java # src/dr/app/tools/treeannotator/TreeAnnotator.java
# Conflicts: # src/dr/app/tools/treeannotator/TreeAnnotator.java
# Conflicts: # src/dr/app/tools/treeannotator/TreeAnnotator.java
There was a problem hiding this comment.
Copilot reviewed 47 out of 47 changed files in this pull request and generated 1 comment.
Comments suppressed due to low confidence (2)
src/dr/app/tools/Branch2dRateToGrid.java:1479
- The description for the 'TRAIT_NOISE' option includes an extra closing parenthesis. Consider removing the extra ')' to maintain consistency.
new Arguments.StringOption(TRAIT_NOISE, null, falseTrue, false, "add true noise to 2D traits [default = true])")
src/dr/app/beast/BeastMain.java:397
- The shorthand 'bi' is reused for both 'beagle_info' and 'beagle_instances', which could lead to ambiguity. Consider using a unique shorthand flag for 'beagle_instances'.
new Arguments.IntegerOption("beagle_instances", "bi", "BEAGLE: divide site patterns amongst instances"),
There was a problem hiding this comment.
Copilot reviewed 47 out of 47 changed files in this pull request and generated 1 comment.
Comments suppressed due to low confidence (3)
src/dr/app/phylogeography/tools/DiscreteTreeToKML.java:277
- The help message for the TEMP option appears to be missing a closing bracket (']') in its default value description.
new Arguments.StringOption(TEMP, null, falseTrue, false, "display branches only temporary [default=false")
src/dr/app/beast/BeastMain.java:370
- The short flag 's' for the 'strict' option conflicts with another option; consider assigning a unique short flag to avoid ambiguity.
new Arguments.Option("strict", "s", "Fail on non-conforming BEAST XML file")
src/dr/app/beast/BeastMain.java:374
- The short flag 's' for the 'seed' option conflicts with the 'strict' option; a unique short flag should be used here to prevent conflicts.
new Arguments.LongOption("seed", "s", "Specify a random number generator seed")
| new Arguments.StringOption(CLADESTEM, null, falseTrue, false, "include clade stem [default=false]"), | ||
| new Arguments.StringOption(EXCLUDECLADESTEM, null, falseTrue, true, "include clade stem in the exclusion [default=true]"), | ||
| new Arguments.StringOption(BACKBONETAXA,null, "Backbone taxa file", "specifies a file with taxa that define the backbone"), | ||
| new Arguments.StringOption(ZEROBRANCHES,null, falseTrue, true, "include branches with 0 N and S subtitutions [default=included]"), |
There was a problem hiding this comment.
The help text for ZEROBRANCHES contains a typo ('subtitutions'); it should be 'substitutions'.
Suggested change
| new Arguments.StringOption(ZEROBRANCHES,null, falseTrue, true, "include branches with 0 N and S subtitutions [default=included]"), | |
| new Arguments.StringOption(ZEROBRANCHES,null, falseTrue, true, "include branches with 0 N and S substitutions [default=included]"), |
Copilot uses AI. Check for mistakes.
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.
This pull request updates all the command line options to use the 'modern' convention of using
--for a long form command line option and-for a shortened equivalent. Note that the original options using a single-with the long form also work for backwards compatibility.This could wait until after the BEAST X 10.5.1 release.