Remove support for deprecated --output flag, now --output-node-data #529
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
Updates augur commands that previously included `--output` as an option for node data outputs to only support the `--output-node-data` flag. However, a side effect of how argparse infers arguments will actually prevent most users who currently rely on `--output` from having to change most of their commands. The augur ancestral command is the only exception. This commit also updates end-to-end tests based on builds and documentation to refer to the `--output-node-data` flag.
Codecov Report
@@ Coverage Diff @@
## master #529 +/- ##
==========================================
+ Coverage 18.65% 18.68% +0.02%
==========================================
Files 31 31
Lines 5061 5053 -8
Branches 1282 1281 -1
==========================================
Hits 944 944
+ Misses 4090 4082 -8
Partials 27 27
Continue to review full report at Codecov.
|
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Outdated suggestions cannot be applied.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.
Description of proposed changes
Updates augur commands that previously included
--outputas an option for nodedata outputs to only support the
--output-node-dataflag. However, a sideeffect of how argparse infers arguments will actually prevent most users who
currently rely on
--outputfrom having to change most of their commands. Theaugur ancestral command is the only exception.
This commit also updates end-to-end tests based on builds and documentation to
refer to the
--output-node-dataflag.Related issue(s)
Related to #518
Testing
All tests pass after updating the output flags.