Improve flags (& --help) of qfit programs #122
Merged
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
This is the crux of this PR: there's too many negatives floating around here. We fold the 'store_false' action and --no- flags together: they cancel each other out. We get a positively worded flag, and make sure to set the default to True. Finally, we assign the ToggleActionFlag type so that both options appear together in the help. Note, we lose some short flags as a result (I don't think this is a loss for clarity). What was -bb, --no-backbone Do not sample backbone using inverse kinematics. (default: True) is now: --[no-]backbone Sample backbone using inverse kinematics. (default: True) This applies to: * -ns, --no-scale → --[no-]scale * -nosub, --no-subtract → --[no-]subtract * -bb, --no-backbone → --[no-]backbone * -sa, --no-sample-angle → --[no-]sample-angle * -T, --no-threshold-selection → --[no-]threshold-selection * -Ts, --no-segment-threshold-selection → --[no-]segment-threshold-selection
… Consistency! --write_intermediate_conformers → --write-intermediate-conformers --resolution_min → --resolution-min --clash_scaling_factor → --clash-scaling-factor --external_clash → --external-clash --bulk_solvent_level → --bulk-solvent-level --rmsd_cutoff → --rmsd-cutoff Dest variables will still maintain underscores.
The logic has to change here, since the variable was a negative.
Flags that changed: * --no-waters → --no-waters-clash Loss of short flags (now-required long form): * -ns (--no-scale) * -nosub (--no-subtract) * -nw (--no-waters-clash) * -bb (--no-backbone) * -sa (--no-sample-angle) * -T (--no-threshold-selection) Now-hyphenated flags: * --resolution_min → --resolution-min * --clash_scaling_factor → --clash-scaling-factor * --external_clash → --external-clash * --bulk_solvent_level → --bulk-solvent-level * --rmsd_cutoff → --rmsd-cutoff New flags: * --write-intermediate-conformers Also: * Remove unused import 'from os import path'
Flags that changed (maintained short form): * --build-stepsize → --dofs-per-iteration (-b) * --stepsize → --dihedral-stepsize (-s) * --no-waters → --no-waters-clash Loss of short flags (now-required long form): * -ns (--no-scale) * -nosub (--no-subtract) * -nw (--no-waters-clash) * -nb (--no-build) * -nl (--no-local) * -T (--no-threshold-selection) Now-hyphenated flags: * --resolution_min → --resolution-min * --clash_scaling_factor → --clash-scaling-factor * --external_clash → --external-clash * --bulk_solvent_level → --bulk-solvent-level * --write_intermediate_conformers → --write-intermediate-conformers
|
OK, I'm pretty happy with this. |
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.
Pull Request Checklist
devbranch?Exceptions will be made for urgent bugfixes.
dev?If not, please rebase your PR onto the most recent
devtip.Explain to a new user by completing the sentence: 'This PR will: ...'
Description of the Change
Fixes #69 .
Release Notes
Command line changes
Flags that changed (maintained short form):
--build-stepsize--dofs-per-iteration(-b)--stepsize--dihedral-stepsize(-s)--no-waters--no-waters-clashRemoved short flags (now-required long form):
-ns--no-scale)-nosub--no-subtract)-nw--no-waters-clash)-nb--no-build)-nl--no-local)-bb--no-backbone)-sa--no-sample-angle)-T--no-threshold-selection)-Ts--no-segment-threshold-selection)Now-hyphenated flags:
--resolution_min--resolution-min--clash_scaling_factor--clash-scaling-factor--external_clash--external-clash--bulk_solvent_level--bulk-solvent-level--rmsd_cutoff--rmsd-cutoff--write_intermediate_conformers--write-intermediate-conformers