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BSD dual license Bio.Nexus #2250

Merged
merged 8 commits into from Nov 4, 2019
Merged

BSD dual license Bio.Nexus #2250

merged 8 commits into from Nov 4, 2019

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peterjc
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@peterjc peterjc commented Sep 2, 2019

This pull request addresses issue #2246

  • 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 run flake8 locally, and
    understand 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.rst and CONTRIB.rst as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

Perhaps @frankkl or @cymon would like to review this in case I've overlooked any named contributor?

Original authors Frank Kauff and Cymon J. Cox and other contributors
as tracked with version control have all agreed:

 - Brian Osborne (@bosborne)
   biopython#898 (comment)
 - Cymon J. Cox (@cymon)
   biopython#898 (comment)
 - Frank Kauff (CVS username fkauff, on GitHub as @frankkl)
   biopython#2246 (comment)
 - Iddo Friedberg (@idoerg)
   biopython#898 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
Original authors Frank Kauff and Cymon J. Cox and all the contributors
since as tracked with version control have agreed:

 - Adhemar Zerlotini (@azneto)
   biopython#1412 (comment)
 - @Amrithasuresh
   biopython#1575
 - @biojerm
   biopython#1847 (comment)
 - Carlos Pena (@carlosp420)
   biopython#898 (comment)
 - Chris Rands (@chris-rands)
   biopython#1301
 - Chris Warth (@cswarth)
   biopython#898 (comment)
 - Christian Brueffer (@cbrueffer)
   biopython#898 (comment)
 - Connor McCoy (@cmccoy)
   biopython#898 (comment)
 - Cymon J. Cox (@cymon)
   biopython#898 (comment)
 - Eric Talevich (@etal)
   biopython#898 (comment)
 - Francesco Gastaldello (@Gasta88)
   biopython#1063
 - Frank Kauff (CVS username fkauff, on GitHub as @frankkl)
   biopython#2246 (comment)
 - Iddo Friedberg (@idoerg)
   biopython#898 (comment)
 - Joe Cora (@JoeCora)
   biopython#898 (comment)
 - Kamil Slowikowski (@slowkow)
   biopython#30 (comment)
 - Lenna Peterson (@lennax)
   biopython#898 (comment)
 - Michiel de Hoon (@mdehoon)
   biopython#898 (comment)
 - @morrme
   biopython#1172 (comment)
 - Nick Negretti (@nimne)
   biopython#1768 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
 - Sergei Lebedev (@superbobry)
   biopython#898 (comment)
 - Sergio Valqui (@svalqui)
   biopython#1749
 - Sourav Singh (@souravsingh)
   biopython#957
 - Tiago Antao (@tiagoantao)
   biopython#898 (comment)
 - Travis Wrightsman (@twrightsman)
   biopython#898 (comment)
 - @unify
   N/A
 - Vincent Davis (@vincentdavis)
   biopython#898 (comment)
 - Wayne Decatur (@fomightez)
   biopython#898 (comment)
 - Wibowo Arindrarto (@bow)
   biopython#898 (comment)
Also standardise GitHub profile URLs without trailing slash.
Original authors Frank Kauff and Cymon J. Cox and all the contributors
since as tracked with version control have agreed:

 - Adhemar Zerlotini (@azneto)
   biopython#1412 (comment)
 - Brad Chapman (@chapmanb)
   http://mailman.open-bio.org/pipermail/biopython-dev/2013-July/019903.html
 - Brian Osborne (@bosborne)
   biopython#898 (comment)
 - Carlos Pena (@carlosp420)
   biopython#898 (comment)
 - Chris Rands (@chris-rands)
   biopython#1301
 - Chris Warth (@cswarth)
   biopython#898 (comment)
 - Christian Brueffer (@cbrueffer)
   biopython#898 (comment)
 - Connor McCoy (@cmccoy)
   biopython#898 (comment)
 - Cymon J. Cox (@cymon)
   biopython#898 (comment)
 - Francesco Gastaldello (@Gasta88)
   biopython#1063
 - Frank Kauff (@frankkl)
   biopython#2246 (comment)
 - Iddo Friedberg (@idoerg)
   biopython#898 (comment)
 - @morrme
   biopython#1172 (comment)
 - Nick Negretti (@nimne)
   biopython#1768 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
 - Sergei Lebedev (@superbobry)
   biopython#898 (comment)
 - Sergio Valqui (@svalqui)
   biopython#1749
 - Suresh Panneerselvam (@Amrithasuresh)
   biopython#1575
Original authors Frank Kauff and Cymon J. Cox and all the contributors
since as tracked with version control have agreed:

 - Brian Osborne (@bosborne)
   biopython#898 (comment)
 - Carlos Pena (@carlosp420)
   biopython#898 (comment)
 - Christian Brueffer (@cbrueffer)
   biopython#898 (comment)
 - Connor McCoy (@cmccoy)
   biopython#898 (comment)
 - Cymon J. Cox (@cymon)
   biopython#898 (comment)
 - Francesco Gastaldello (@Gasta88)
   biopython#1063
 - Frank Kauff (@frankkl)
   biopython#2246 (comment)
 - Iddo Friedberg (@idoerg)
   biopython#898 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
 - Sergio Valqui (@svalqui)
   biopython#1749
 - Suresh Panneerselvam (@Amrithasuresh)
   biopython#1575
Original author Joe Cora and all the contributors since as tracked
with version control have agreed:

 - Adhemar Zerlotini (@azneto)
   biopython#1412 (comment)
 - Francesco Gastaldello (@Gasta88)
   biopython#1063
 - Joe Cora (@JoeCora)
   biopython#898 (comment)
 - @morrme
   biopython#1172 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
 - Sergio Valqui (@svalqui)
   biopython#1749
Named copyright holders and other contributors tracked with version
control have all agreed:

 - Benjamin Rowell (@benjaminr)
   biopython#2023
 - Brad Chapman (@chapmanb)
   http://mailman.open-bio.org/pipermail/biopython-dev/2013-July/019903.html
 - Chris Warth (@cswarth)
   biopython#898 (comment)
 - Christian Brueffer (@cbrueffer)
   biopython#898 (comment)
 - Eric Talevich (@etal)
   biopython#898 (comment)
 - Francesco Gastaldello (@Gasta88)
   biopython#1063
 - Frank Kauff (@frankkl)
   biopython#2246 (comment)
 - Iddo Friedberg (@idoerg)
   biopython#898 (comment)
 - Joe Cora (@JoeCora)
   biopython#898 (comment)
 - Michiel de Hoon (@mdehoon)
   biopython#898 (comment)
 - Milind Luthra (@milindl)
   biopython#1020
 - Nick Negretti (@nimne)
   biopython#1768 (comment)
 - Peter Cock (@peterjc)
   biopython#898 (comment)
 - Sourav Singh (@souravsingh)
   biopython#957
 - Steve Bond (@biologyguy)
   biopython#898 (comment)
 - Tiago Antao (@tiagoantao)
   biopython#898 (comment)
 - Vincent Davis (@vincentdavis)
   biopython#898 (comment)
@codecov
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codecov bot commented Sep 2, 2019

Codecov Report

Merging #2250 into master will increase coverage by 1.38%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2250      +/-   ##
==========================================
+ Coverage    83.5%   84.89%   +1.38%     
==========================================
  Files         319      321       +2     
  Lines       51610    51942     +332     
==========================================
+ Hits        43099    44095     +996     
+ Misses       8511     7847     -664
Impacted Files Coverage Δ
Bio/Nexus/Nexus.py 72.33% <ø> (ø) ⬆️
Bio/Nexus/StandardData.py 71.64% <ø> (ø) ⬆️
Bio/Nexus/Nodes.py 87.37% <ø> (ø) ⬆️
Bio/Nexus/__init__.py 100% <ø> (ø) ⬆️
Bio/Nexus/Trees.py 80.28% <ø> (ø) ⬆️
Bio/SearchIO/_model/query.py 91.5% <0%> (-0.93%) ⬇️
Bio/PDB/mmtf/mmtfio.py 95.04% <0%> (ø)
Bio/PDB/mmtf/DefaultParser.py 100% <0%> (ø)
Bio/SearchIO/HHsuiteIO/hhsuite2_text.py 97.03% <0%> (+0.02%) ⬆️
Bio/Align/__init__.py 87.43% <0%> (+0.03%) ⬆️
... and 43 more

Continue to review full report at Codecov.

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@peterjc
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peterjc commented Sep 5, 2019

As the original authors @frankkl & @cymon, would either of you be willing to review this to check if I omitted someone? The most likely route is anyone acknowledged in the code comments and/or commit messages.

@peterjc
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peterjc commented Sep 25, 2019

Anyone else want to volunteer to review this? @JoeCora or @cbrueffer maybe?

@peterjc peterjc merged commit 4a527a0 into biopython:master Nov 4, 2019
@peterjc peterjc deleted the dual_nexus branch November 4, 2019 17:24
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