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Add inline and Tutorial documentation for internal_coords; change edr… #3898
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Codecov ReportBase: 0.00% // Head: 0.00% // No change to project coverage 👍
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Unable to work out the issue running the tutorial tests on linux. Saw same problem on MacOS and solved by wrapping some evaluations in print() statements, but my Ubuntu 18.04 linux does not show any issues for @peterjc any insights? |
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Had issues with the following doctests under linux:
The 'chain break' messages are print()ed by a subroutine a few calls down the stack. Windows and Mac see them, but Linux environment does not. The subroutine appears to work because various results are checked in the subsequent code.
On Mac and Windows the result is True as expected, but on Linux it is False. Same code in unittest (test_1a8o) passes fine in all three environments.
Same again - Linux returns False, but the same code in unittest test_1a8o passes fine. Conclusion: some math is broken in Linux doctest environment? |
@@ -18,6 +18,159 @@ | |||
description of a structure for 3D printing, and reading/writing structures as | |||
internal coordinate data files. | |||
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**Usage:** | |||
:: |
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This next block of code is just an RST literal.
Were there complications using Python syntax highlighting?
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No problems, the code is pretty much identical to what's in the Tutorial (except better annotated there). I'm just cynical and expect no one will look past the API docs so wanted the sample code there at the top of the main internal coords file.
As to the oddity with Linux from this:
That's all via https://github.com/biopython/biopython/blob/master/Tests/test_Tutorial.py which is my glorious hack combining LaTeX with doctests. Without digging into it, my guess might be some code is not using the I'm happy with the workaround (skipping that part as a doctest). |
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And fine and much valued work that (LaTeX + doctests) is! I tried working on that specific message without improvement, and now hitting the _aligners import issue raised in #3876. |
Can I leave this to you please @JoaoRodrigues since you handled #3774? |
Hi @peterjc, sure. On it. |
Thank you @JoaoRodrigues!!! You are a star and hero for making it so the rest of us can submit pull requests, well done on the investigation and solution. |
@peterjc have you noticed this problem on the ci tests?
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I think I saw that last week but haven't opened an issue yet (too busy with a sick child off school), I suspected something changed in the test environment rather than our code. Would you log this please? |
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This is not a WIP, honest -- I'm just using 'in anger' now and finding niggles. |
I do like pretty pictures for documentation :) |
…e_to_internal_coordinates
…om count for chain only rebuild test
…all atom coords for recalculation
…backbone lengths, confusion reading gly N:CA
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closes #4213 |
@JoaoRodrigues do you still want to review this pull request from Rob? If not there are a few other regular contributors to the PDB code we could ask. |
Hey Peter, I'm on it, almost done with it after this last weekend.
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I'm gonna go ahead and give this a go, since it's been a while and all tests and documentation seem in good shape. I had some comments but overall, it was nitpicking that's truly not necessary for the PR to be merged.
Great, thank you. Rob, it looks like you've deliberately tried to give a useful commit history, so shall we rebase-and-merge this then? |
Yes please, should go easily as I rebased just 2 weeks ago.
…On Tue, Jan 24, 2023 at 1:56 PM Peter Cock ***@***.***> wrote:
Great, thank you.
Rob, it looks like you've deliberately tried to give a useful commit
history, so shall we rebase-and-merge this then?
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Or are you asking me to rebase? I suspect any change from me now breaks
Joao's approval?
…On Tue, Jan 24, 2023 at 2:03 PM Rob Miller ***@***.***> wrote:
Yes please, should go easily as I rebased just 2 weeks ago.
On Tue, Jan 24, 2023 at 1:56 PM Peter Cock ***@***.***> wrote:
> Great, thank you.
>
> Rob, it looks like you've deliberately tried to give a useful commit
> history, so shall we rebase-and-merge this then?
>
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Github's rebase-and-merge button was green, it normally warns if a conflict would prevent using it. Clicked! Thank you again for your patience Rob 👍 |
Looking at this afresh, is there anything you'd like to move about in the NEWS file? |
Thank you, yes have submitted #4222 with just that part. Feel free to modify as you see fit. |
Herewith added tutorial, in-line documentation, and NEWS entry for the internal-coords module work in #3774.
I hereby agree to dual licence this and any previous contributions under both
the Biopython License Agreement AND the BSD 3-Clause License.
I have read the
CONTRIBUTING.rst
file, have runpre-commit
locally, and understand that continuous integration checks will be used to
confirm the Biopython unit tests and style checks pass with these changes.
I have added my name to the alphabetical contributors listings in the files
NEWS.rst
andCONTRIB.rst
as part of this pull request, am listedalready, or do not wish to be listed. (This acknowledgement is optional.)
The tutorial examples are mostly as doctest code. Also some IMHO minor code changes:
.aks
attribute of class edra (and thus children hedron and dihedron) to.atomkeys
as discussed in codespell blocking documentation commit on attribute name #3888. I'm going to punt here, request forgiveness later, and claim the attribute was not well documented enough / code not used enough for this to affect anyone, because it is the right thing to do and avoids tweaking the codespell parameters.ic_rebuild.structure_rebuild_test
results with the-quick
option better match the results without that flag (in particular for structures in the Tests/PDB directory).