Issue 2220 #2349
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Issue 2220 #2349
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Codecov Report
@@ Coverage Diff @@
## master #2349 +/- ##
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- Coverage 84.95% 84.94% -0.02%
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Files 323 323
Lines 52690 52690
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- Hits 44764 44756 -8
- Misses 7926 7934 +8
Continue to review full report at Codecov.
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peterjc
reviewed
Nov 20, 2019
peterjc
reviewed
Nov 20, 2019
peterjc
reviewed
Nov 20, 2019
|
I didn't even know this was possible with Sphinx! Nice 👍 I have a repeated query about slashes on continued lines in the docstrings - many of which can likely be edited in multiple ways to produce nicer RST output. |
peterjc
reviewed
Nov 20, 2019
Bio/Sequencing/Applications/_bwa.py
Outdated
| @@ -431,7 +431,7 @@ def __init__(self, cmd="bwa", **kwargs): | |||
| checker_function=lambda x: isinstance(x, int), | |||
| equate=False), | |||
| _Option(["-d", "d"], | |||
| "Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between the best and the current extension score is above |i-j|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST\'s X-dropoff except that it doesn\'t penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. [100]", | |||
| r"Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between the best and the current extension score is above \|i-j\|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST\'s X-dropoff except that it doesn\'t penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. [100]", | |||
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We don't need to slash escape the apostrophes here do we?
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Still some slashes in |
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This is a big improvement, although running it locally I see something odd. e.g. Everything seems to be listed twice per class, once as attributes of the object, and again (after the methods) as properties. Visually the property list looks nicer, so I'd hide the attributes given the choice. This could just be how properties are displayed by default? Do you see the same thing (might depend on versions of Sphinx etc)? If you don't immediately see how to fix this, I am inclined to merge this as it is still an improvement. |
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The latest commit should fix this - the duplicate attributes are apparently caused by numpydoc clashing with autosummary. |
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Thank you - confirmed after testing locally. This should be live here soon: |
peterjc
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Nov 15, 2020
Original author Eric Talevich and other contributors since as tracked with version control have agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Carlos Pena (@carlosp420) biopython#898 (comment) - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Eric Talevich (@etal) biopython#898 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749
peterjc
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Nov 15, 2020
Original author Eric Talevich and contributors since tracked with version control (with one exception noted below) have all agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Eric Talevich (@etal) biopython#898 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749 - Sujan Dulal (@Dsujan) biopython#2430 We have not had explicit permission from Jingping Li (@Jingping) for the one line change applied in biopython#73 and credited to them. The change was suggested by me, but the recorded authorship was more to recognise their work in identifying the problem and testing the solution.
peterjc
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Nov 15, 2020
Original author Saket Choudhary and contributors since as tracked by version control have agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Carlos Pena (@carlosp420) biopython#898 (comment) - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Jeremy LaBarge (@biojerm) biopython#1847 (comment) - John Ma (@JohnMCMa) biopython#1790 - @morrme biopython#1172 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Saket Choudhary (@saketkc) biopython#898 (comment) - Sergei Lebedev (@superbobry) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749 - Sujan Dulal (@Dsujan) biopython#2430 - Travis Wrightsman (@twrightsman) biopython#898 (comment)
peterjc
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Nov 17, 2020
Original author Saket Choudhary and contributors since as tracked by version control have agreed: - Adhemar Zerlotini (@azneto) #1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) #2444 - Carlos Pena (@carlosp420) #898 (comment) - Chris Daley (@chebizarro) #2349 - Christian Brueffer (@cbrueffer) #898 (comment) - Jeremy LaBarge (@biojerm) #1847 (comment) - John Ma (@JohnMCMa) #1790 - @morrme #1172 (comment) - Peter Cock (@peterjc) #898 (comment) - Saket Choudhary (@saketkc) #898 (comment) - Sergei Lebedev (@superbobry) #898 (comment) - Sergio Valqui (@svalqui) #1749 - Sujan Dulal (@Dsujan) #2430 - Travis Wrightsman (@twrightsman) #898 (comment)
peterjc
added a commit
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Original author Eric Talevich and other contributors since as tracked with version control have agreed: - Adhemar Zerlotini (@azneto) #1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) #2444 - Carlos Pena (@carlosp420) #898 (comment) - Chris Daley (@chebizarro) #2349 - Christian Brueffer (@cbrueffer) #898 (comment) - Eric Talevich (@etal) #898 (comment) - Peter Cock (@peterjc) #898 (comment) - Sergio Valqui (@svalqui) #1749
peterjc
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Dec 3, 2020
Original author Eric Talevich and contributors since tracked with version control (with one exception noted below) have all agreed: - Adhemar Zerlotini (@azneto) #1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) #2444 - Chris Daley (@chebizarro) #2349 - Christian Brueffer (@cbrueffer) #898 (comment) - Eric Talevich (@etal) #898 (comment) - Peter Cock (@peterjc) #898 (comment) - Sergio Valqui (@svalqui) #1749 - Sujan Dulal (@Dsujan) #2430 We have not had explicit permission from Jingping Li (@Jingping) for the one line change applied in #73 and credited to them. The change was suggested by me, but the recorded authorship was more to recognise their work in identifying the problem and testing the solution.
JoaoRodrigues
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Jun 3, 2021
Original author Saket Choudhary and contributors since as tracked by version control have agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Carlos Pena (@carlosp420) biopython#898 (comment) - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Jeremy LaBarge (@biojerm) biopython#1847 (comment) - John Ma (@JohnMCMa) biopython#1790 - @morrme biopython#1172 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Saket Choudhary (@saketkc) biopython#898 (comment) - Sergei Lebedev (@superbobry) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749 - Sujan Dulal (@Dsujan) biopython#2430 - Travis Wrightsman (@twrightsman) biopython#898 (comment)
JoaoRodrigues
pushed a commit
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Jun 3, 2021
Original author Eric Talevich and other contributors since as tracked with version control have agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Carlos Pena (@carlosp420) biopython#898 (comment) - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Eric Talevich (@etal) biopython#898 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749
JoaoRodrigues
pushed a commit
to JoaoRodrigues/biopython
that referenced
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Jun 3, 2021
Original author Eric Talevich and contributors since tracked with version control (with one exception noted below) have all agreed: - Adhemar Zerlotini (@azneto) biopython#1412 (comment) - Andrey Raspopov (@Andrey-Raspopov) biopython#2444 - Chris Daley (@chebizarro) biopython#2349 - Christian Brueffer (@cbrueffer) biopython#898 (comment) - Eric Talevich (@etal) biopython#898 (comment) - Peter Cock (@peterjc) biopython#898 (comment) - Sergio Valqui (@svalqui) biopython#1749 - Sujan Dulal (@Dsujan) biopython#2430 We have not had explicit permission from Jingping Li (@Jingping) for the one line change applied in biopython#73 and credited to them. The change was suggested by me, but the recorded authorship was more to recognise their work in identifying the problem and testing the solution.
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This pull request addresses issue #2220
It was relatively straight-forward to create a custom documenter for the AbstractCommandLine class but many of the applications needed modifications to the formatting of the docstrings of their dynamic attributes to be compatible with rst/docutils. The resulting changes render very well in html but result in some minor artifacts (escape characters) in the command line help text.
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.rstfile, have runflake8locally, andunderstand that AppVeyor and TravisCI 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.rstandCONTRIB.rstas part of this pull request, am listedalready, or do not wish to be listed. (This acknowledgement is optional.)