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@KedoKudo
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add supporting functions (misc.npmath) and slits-based auto-alignment functions for tomography data from aps_1id.

@carterbox
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Hi @KedoKudo,

Thanks for proposing some new features for tomopy. It looks like your changes broke all of our tests. Check out the tests section of our development documentation to read about how to run the tests on your local machine. Please give me a shout if you run into problems.

@KedoKudo
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It seems to me that the tests failed because of the testing environment (the current testing environment cannot handle new f-string formatting, and missing package Pandas). On my local machine (python3), all tests passed without any issues (see test.log for more details).

@prjemian
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prjemian commented Nov 14, 2018

That's right, the f formatting is a py3.6+ feature. For robust code in py2.7 and py3.5+, refactor (as an example):

f"report/{reportfn}.pdf"

to

"report/{}.pdf".format(reportfn)

or (even more robust)

os.path.join("report", "{}.pdf".format(reportfn))

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The py36 build fails not for the f-string formatting but this error:

Failure: ModuleNotFoundError (No module named 'pandas') ... ERROR

@carterbox
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@KedoKudo,

Thanks in advance for you patience. As prjemian mentioned, tomopy targets python 2.7 and 3.5+ on Linux, macOS, and Windows. It may take a few days for your code to be fully reviewed. Expect that I will be asking a lot of questions and asking for more changes in order to ensure that the tomopy API doesn't break without good reason.

@carterbox carterbox self-assigned this Nov 14, 2018
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Coverage Status

Coverage decreased (-1.1%) to 48.764% when pulling 8d61858 on KedoKudo:master into a50ce62 on tomopy:master.

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coveralls commented Nov 14, 2018

Coverage Status

Coverage decreased (-0.8%) to 49.027% when pulling 25b301f on KedoKudo:master into e8911b1 on tomopy:master.

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I really like how well documented your source code is. 👍 To improve on that, some explanation should be moved/added to the docstrings of the functions. Most of our users install from conda, so they will be looking at the rendered docstrings on readthedocs instead of your beautiful comments in the source code.

@carterbox carterbox requested a review from dgursoy November 15, 2018 21:32
@carterbox carterbox removed their assignment Nov 15, 2018
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Thanks again, @KedoKudo for this pull request. It looks good to me, but I think @dgursoy had a question about something. He will ask or merge this pull request when he gets back from vacation.

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@KedoKudo Thanks for this PR and for your patience! I did a first pass and found some typos and small fixes. My main concern is that, because all aps1d functions are very specific (?), we need to better explain them in the docs. Happy to take another look once these changes are updated.

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dgursoy commented Nov 30, 2018

Thanks @KedoKudo! Could you please resolve the conversations that you fixed or edited in your final commits that doesn't need my feedback? This way I can see which ones are resolved and which ones are still open.

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@dgursoy I have resolved the conversations that do not require further feedback. A few extra docstring edits have been made to address the new comments posted today.

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dgursoy commented Dec 5, 2018

@KedoKudo Thanks! All looks good.

@dgursoy dgursoy merged commit 68875a4 into tomopy:master Dec 5, 2018
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5 participants