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v2.2 #181

Merged
merged 87 commits into from
Jun 16, 2020
Merged

v2.2 #181

merged 87 commits into from
Jun 16, 2020

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thomasyu888
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@thomasyu888 thomasyu888 commented Jun 13, 2020 •
edited
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  • Did you run your tests locally (instructions here)?
  • Did you add a good description about your changes or additions?
  • Add archive-project and validate-project commands
  • updating submission annotations will also annotate with synapse style annotations.

thomasyu888 and others added 30 commits March 1, 2020 22:03
@thomasyu888
Use dataclass
075fc75
@thomasyu888
add uri into challenge class
acf6524
@thomasyu888
Use dataclass and dataclass json
2b79577
@thomasyu888
Add challenge service
dbecb32
@thomasyu888
Fix
2a1e5ed
@thomasyu888
Add in dataclasses req
2bac2d9
@thomasyu888
Add in requirement
e1e6a25
@thomasyu888
Use specific version
2665e04
@thomasyu888
Fix tests
c128520
@thomasyu888
Merge branch 'develop' into challenge-dataclass
e8cc34d
@thomasyu888
Remove last line
d3aa147
@thomasyu888
Revise challenge data obj + add challengeApi
6ad0de6
@thomasyu888
Add tests
746ce88
@thomasyu888
Merge branch 'develop' into challenge-dataclass
ec71d4c
@thomasyu888
Add tests for challenge service
5a7d8db
@thomasyu888
Merge branch 'challenge-dataclass' of https://github.com/Sage-Bionetw…
ab2ec0e 
…orks/challengeutils into challenge-dataclass
@thomasyu888
test rest calls
1ad71ef
@thomasyu888
Move synapse services to within challengeutils folder
ce0f77e
@thomasyu888
Fix tests
92ca97e
@thomasyu888
Fix tests
4d18021
@thomasyu888
Fix functions
8845fe9
@thomasyu888
Rename
a92218c
@thomasyu888
Switch to challenge instead of util
53c3e09
@thomasyu888
Fix tests and finish up refactor
2c0ecb9
@thomasyu888
Remove duplicate
885fe57
@thomasyu888
Remove unused var
5fe87cf
@thomasyu888
Push dev version
3fb14a1
@thomasyu888
Merge branch 'master' into develop
c2d751d
@thomasyu888
Fix
a78d3c0
@thomasyu888
Merge branch 'develop' into challenge-dataclass
06d9888
thomasyu888 and others added 14 commits May 9, 2020 09:46
@thomasyu888
Merge branch 'master' into develop
6b9d33a
@thomasyu888
Remove travis dependency (#163)
455e6a7 
* Create pythonapp.yml

* Install challengeutils

* Remove travis dependency

* Only run test on PR
@thomasyu888
Merge branch 'master' into develop
9483fae
@thomasyu888
Merge branch 'master' into develop
f407441
@thomasyu888
update version
d6b6bcd
@thomasyu888
Remove functionality to invite members to team (#167)
a9b0826
@thomasyu888
Create _copy_thread which just copies the threads, copy_thread now co…
0b21293 
…pies replies (#169)
@thomasyu888
Fix createchallenge bug (#171)
c7f0f8c 
* Make sure to not redefine 'challenge'

* Dont pass object into rest post call

* Fix tests

* Add in sage name and year
@thomasyu888
Automate code coverage (#165)
0540563 
* Add in testing of synapse service module

* Test code coverage

* Fix

* Add init

* Update

* Remove

* Add inits

* Add inits

* Remove

* Try uploading artifact

* Add in flake8

* install all dependencies

* Rename to build

* Remove duplicated test func
@thomasyu888
Refactor mirror wiki (#143)
6541710 
* Update version

* Refactor mirrowiki

* Update mirrorwiki

* Add dry run flag, fix docs

* Remove comments

* Increase update wiki pages and maps helper

* Add test mirrorwiki

* Make most functions convenience functions

* Fix indent

* add tests

* Add test

* Fix

* Add integration test

* Add integration tests

* Remove synapseclient<2 support for challenge.py

* Add -f

* Add in stdout for wiki titles that exist in destionation but not entity

* Update tests/test_mirrorwiki.py
@thomasyu888 @vpchung
Add to documentation (#175)
9227fba 
* Add in development requirements

* Add to contributing guide on how to develop

* Update documentation

* Update version and add to changelog

* Update CONTRIBUTING.md

* Add release procedure

* Add in more contributing guide

* Edit PR template

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
@thomasyu888
Merge branch 'master' into develop
9d49e10
@thomasyu888
Merge branch 'master' into develop
e88b4c0
@vpchung @thomasyu888
writeup commands (#130)
963ca72 
* validate project function

* added output param to command; added unittest plans

* bug fix; add archive_project function

* refactor writeups into smaller functions

* added tests

* adding validation status to return value of validate_project()

* updated validateproject doc; changed default "public" value to False

* added tests for overall command functionality

* added docstrings to tests

* Update docstring to follow Google standards

Co-Authored-By: Thomas Yu <thomas.yu@sagebase.org>

* update names; modularize permissions function further; update tests

* fixed and added remaining tests; update package paths

* use entity name as new archive name

* Update challengeutils/project_submission.py

Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* removed import alias and unused imports; parametrized tests

Co-authored-by: verena <vpchung@users.noreply.github.com>
Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>
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pep8speaks commented Jun 13, 2020 •
edited
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Hello @thomasyu888! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 63:80: E501 line too long (80 > 79 characters)

Comment last updated at 2020-06-15 20:48:08 UTC

thomasyu888 and others added 6 commits June 13, 2020 17:04
@thomasyu888
Updating annotations (#180)
dd88d06 
* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix
@thomasyu888
Increase version
3b21074
@thomasyu888
Increase version in conf.py
23cf4d9
@thomasyu888
Add to docs
c6bfddc
@thomasyu888
Add function
e828614
@thomasyu888
Add to docs
df612da
@thomasyu888 thomasyu888 linked an issue Jun 14, 2020 that may be closed by this pull request
Add to release contribution.md #176
Closed
@thomasyu888 thomasyu888 linked an issue Jun 15, 2020 that may be closed by this pull request
Convenience function to delete submission #179
Closed
@thomasyu888 thomasyu888 requested a review from vpchung June 15, 2020 20:51
@thomasyu888 thomasyu888 marked this pull request as ready for review June 15, 2020 20:51
vpchung
vpchung approved these changes Jun 16, 2020
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Thanks for updating the project_submissions command names too!

Looks good.

@thomasyu888 thomasyu888 merged commit 96e2e87 into master Jun 16, 2020
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Convenience function to delete submission Add to release contribution.md
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