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Upgrade input/output methods #57

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sobolevnrm opened this issue May 30, 2020 · 4 comments
Open
2 tasks

Upgrade input/output methods #57

sobolevnrm opened this issue May 30, 2020 · 4 comments
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API enhancement I/O file parsing and writing

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@sobolevnrm
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sobolevnrm commented May 30, 2020 •
edited by orbeckst
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  • Convert read/write file manipulation to context managers
  • Allow for StringIO and related file-like classes
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Excellent idea.

Some of this already works. We use run.single() https://github.com/jensengroup/propka-3.1/blob/0cb470fbdbc9e57c4487e421b9110975d21799ce/propka/run.py#L28 with a StreamIO in propkatraj namely https://github.com/Becksteinlab/propkatraj/blob/2abd91fca33a5e980a2b8d8c6e18a2d192fda2c3/propkatraj/propkatraj.py#L73-L96

@orbeckst orbeckst added I/O file parsing and writing API enhancement labels Jun 18, 2020
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Excellent; thank you!

@IAlibay IAlibay mentioned this issue Jul 14, 2020
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@orbeckst
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As @IAlibay found out and noted in #83: StringIO does not work any longer so my #57 (comment) is not true anymore.

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orbeckst commented Jul 17, 2020 •
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With #83 and #82 fixed, StreamIO (EDIT: for a single input PDB) should be working again (with a cleaner API, too, mainly thanks to @speleo3 's suggestions in PR #84 ).

@sobolevnrm sobolevnrm self-assigned this Aug 30, 2020
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