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choderalab / pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)
http://pymbar.readthedocs.io
MIT License
241 stars 92 forks source link

Move BAR to separate module #10

Closed kyleabeauchamp closed 11 years ago

kyleabeauchamp commented 11 years ago

I think code would be easier to maintain and read if BAR, MBAR, and ExpGauss were all separate python files.

jchodera commented 11 years ago

Agreed! I think this was only done the current way for two reasons:

  1. To allow "from pymbar import BAR"
  2. To share the logSum function.

On Sep 9, 2013, at 5:17 PM, kyleabeauchamp notifications@github.com wrote:

I think code would be easier to maintain and read if BAR, MBAR, and ExpGauss were all separate python files.

— Reply to this email directly or view it on GitHub.

mrshirts commented 11 years ago

Correct. These are the two reasons. I think they are reasonable reasons, but if they are outweighed by other considerations, that's fine -- one can always call logSum from another file.

On Mon, Sep 9, 2013 at 12:08 PM, John Chodera notifications@github.comwrote:

Agreed! I think this was only done the current way for two reasons:

  1. To allow "from pymbar import BAR"
  2. To share the logSum function.

On Sep 9, 2013, at 5:17 PM, kyleabeauchamp notifications@github.com wrote:

I think code would be easier to maintain and read if BAR, MBAR, and ExpGauss were all separate python files.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/choderalab/pymbar/issues/10#issuecomment-24090168 .

rmcgibbo commented 11 years ago

With the functions in separate modules, you can still import them in the init.py to bring them into the package namespace so that "from pymbar import BAR" still works.

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On Sep 9, 2013, at 12:08 PM, John Chodera notifications@github.com wrote:

Agreed! I think this was only done the current way for two reasons:

  1. To allow "from pymbar import BAR"
  2. To share the logSum function.

On Sep 9, 2013, at 5:17 PM, kyleabeauchamp notifications@github.com wrote:

I think code would be easier to maintain and read if BAR, MBAR, and ExpGauss were all separate python files.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

kyleabeauchamp commented 11 years ago

This is already done, closing.