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nb2galaxy prototype #102

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merged 35 commits into from
Feb 27, 2024
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aa8001c
nb2galaxy prototype
dsavchenko Aug 31, 2023
1e4de7d
split outputs
dsavchenko Sep 2, 2023
c5a55ad
fix regex
dsavchenko Sep 4, 2023
c55c802
run with ipython
dsavchenko Sep 4, 2023
ef496c8
fix encoding oda-annotated basic types
dsavchenko Sep 7, 2023
9704819
Merge branch 'master' into galaxy
dsavchenko Sep 20, 2023
103f05f
multiple data products
dsavchenko Sep 21, 2023
9f1f37c
either one dataproduct or several
dsavchenko Sep 22, 2023
65826b0
remove todo comment
dsavchenko Oct 5, 2023
c4bbb61
basic requrements parsing
dsavchenko Oct 24, 2023
ec36449
default tests
dsavchenko Oct 26, 2023
378a82e
combine rrequirements
dsavchenko Oct 30, 2023
9393535
Merge branch 'master' into galaxy
dsavchenko Oct 30, 2023
be14c51
no exception for unhandled requirements
dsavchenko Oct 31, 2023
4bc343d
no label duplication
dsavchenko Nov 3, 2023
1ee8706
citations and help
dsavchenko Nov 3, 2023
9e79463
remove unused md + todo
dsavchenko Nov 3, 2023
6180797
fix no dir
dsavchenko Nov 3, 2023
a3291f0
comment about galaxyxml package
dsavchenko Nov 9, 2023
7068a1c
tool id
dsavchenko Dec 20, 2023
1d234c9
xml filename
dsavchenko Dec 20, 2023
c375d94
preferably use doi in galaxy xml
dsavchenko Jan 31, 2024
840961d
optional ipython
dsavchenko Feb 7, 2024
1ae0156
script styling
dsavchenko Feb 15, 2024
749ff08
ignore get_ipython undefined with noqa
dsavchenko Feb 15, 2024
33f0030
more styling
dsavchenko Feb 15, 2024
736354b
better code injection
dsavchenko Feb 16, 2024
d920094
fix undefined outp_code
dsavchenko Feb 16, 2024
930c082
Merge branch 'master' into galaxy
dsavchenko Feb 16, 2024
2abc70f
ignore linting for now
dsavchenko Feb 16, 2024
3cc9c8c
file input
dsavchenko Feb 16, 2024
357d6cd
Merge branch 'master' into galaxy
dsavchenko Feb 19, 2024
da8eb0f
{data_style: paths} for data parameter
dsavchenko Feb 19, 2024
d6f5291
data_style in the right place
dsavchenko Feb 19, 2024
06dbdfe
Merge branch 'master' into galaxy
dsavchenko Feb 26, 2024
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -35,4 +35,5 @@ callback.json
function.xml
*_output.html
*_output.json
.nb2workflow/cache
.nb2workflow/cache
tests/testfiles/.nb2workflow
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