Use @rmcgibbo's commandline class to rework command-line app about yank HOT 15 CLOSED

One of the key benefits is allowing us to split up various "groups" of inputs into separate classes for re-use in multiple apps.

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Can you point me to the source files that have the command-line code?

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The mixtape/commands directory are the apps
On Mar 9, 2014 11:17 AM, "John Chodera" [email protected] wrote:

Can you point me to the source files that have the command-line code?

Reply to this email directly or view it on GitHubhttps://github.com//issues/30#issuecomment-37129188
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So you mean we should use mixtape.cmdline?

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Yes Its one possibility.

There's also ipython cmdline.

Just good to think about options.
On Mar 9, 2014 11:29 AM, "John Chodera" [email protected] wrote:

So you mean we should use mixtape.cmdline?

Reply to this email directly or view it on GitHubhttps://github.com//issues/30#issuecomment-37129526
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We could certainly do that, but I don't think I understand what the shortcomings of optparse are that cmdline fixes? Can you elaborate a bit?

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It would be easiest to give examples of what kinds of command-line specifications you're thinking about...

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Optparse is inflexible.
On Mar 9, 2014 11:37 AM, "John Chodera" [email protected] wrote:

We could certainly do that, but I don't think I understand what the
shortcomings of optparse are that cmdline fixes? Can you elaborate a bit?

Reply to this email directly or view it on GitHubhttps://github.com//issues/30#issuecomment-37129712
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Sure, but so is mixtape.cmdline, compared to some more flexible counterpart.

I'm just missing a description of what kind of flexibility you think we should include that optparse lacks. Like, a few example command-lines for yank that would make use simpler than optparse permits.

I'm totally not opposed to this---I'm just not understanding the suggestion!

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The problem I wanted to solve with mixtape was really that I have many different subcommands that I want to structure under the same command line call. (In the way git clone/fetch/merge are all "subcommands" of the root git command.) And I'd like to be able to do the equivalent of git -h to get a full listing of all my commands and a short description. The structure of the mixtape commands was mostly to enable this, and make it so new commands can get "registered" seamlessly without a having some single master block of argparse/optparse code that sets up all the parsers in one place.

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@kyleabeauchamp: I worked a lot with trying to "pull out" the command line infrastructure from IPython and adapt it to a standalone thing. I did that for the openmm command line executable actually. But IMO it is more complex than necessary. Traitlets are kind of nice and clever, but very magical and tricky to debug when things aren't hooked up correctly.

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Thanks for the insight, that was my thinking but I wasn't quite sure.

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Thanks for the detailed explanation, @rmcgibbo! I agree that this makes a lot of sense for yank.

For example, we food have yank analyze be separate from yank run or yank progress.

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I think we will definitely add this feature.

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I think we've settled on a command-line interface, as such I'm going to close this. If anyone disagrees, feel free to reopen.

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