merge: Omit generated source columns by default #1632
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Removes default naming template and requires users to explicitly provide their own template to include source columns. This makes the output from an `augur merge` invocation more self-documenting without columns "magically" appearing. In the expected context of usage within a workflow, the burden of the extra option is negligible. See also discussion on a prior PR.¹ ¹ <#1625 (comment)>
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Once this is merged, I'd like to cut a new (major) Augur release and get it published everywhere so I can then merge nextstrain/measles#52. |
victorlin
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| output_group.add_argument('--no-source-columns', dest="source_columns", action="store_const", const=None, help=f"Suppress generated columns (described above) identifying the source of each row's data. This is the default behaviour, but it may be made explicit or used to override a previous --source-columns." + SKIP_AUTO_DEFAULT_IN_HELP) | ||
| output_group.add_argument('--quiet', action="store_true", default=False, help="Suppress informational and warning messages normally written to stderr. (default: disabled)" + SKIP_AUTO_DEFAULT_IN_HELP) |
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Why keep --no-source-columns around when it is already the default behavior? It seems unnecessary, with the equivalent being options such as --not-quiet or --no-output-metadata.
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It's a bit arbitrary/preference, but in general --x / --no-x is a nice (and very common) pattern to allow disabling previously-set options. This allows more flexibility in command invocation construction (e.g. a fixed list of options including --x can be changed by tacking on --no-x instead of finding and removing --x). It also provides a way for invocations to opt-into usages which aren't broken by changes to the defaults. We haven't generally done this as a matter of course in Augur, but I don't think it'd be a bad idea to start and it was easy to keep this pattern here.
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See also click's implementation of this pattern.
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Thanks for the explanation, makes sense!
If you end up doing this while I'm gone on lab retreat, could you also merge other breaking changes #1613 and #1629? Those have been approved and I just haven't gotten around to doing the actual release. The only thing is there will be changelog merge conflicts. |
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Looks good, I'll defer to you for #1632 (comment) so consider that non-blocking.
Removes default naming template and requires users to explicitly provide their own template to include source columns. This makes the output from an
augur mergeinvocation more self-documenting without columns "magically" appearing. In the expected context of usage within a workflow, the burden of the extra option is negligible. See also discussion on a prior PR.¹¹ #1625 (comment)
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