Update to Python3 #154

itsJiaqi · 2019-12-03T19:10:10Z

New Features

Python 3 🎉

Breaking Changes

Python 3 Support (not expected to be backwards compatible)

Dependency updates

bumped dependencies to python3 compatible versions
also bumped Jinja2 and urllib3 for security compliance

lgtm-com · 2019-12-03T19:19:42Z

This pull request introduces 5 alerts and fixes 5 when merging 4e19db7 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for Unused import
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

4 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-03T20:07:02Z

This pull request introduces 4 alerts and fixes 6 when merging 2b65b02 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-04T21:25:50Z

This pull request introduces 4 alerts and fixes 6 when merging 427b9ed into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-04T23:03:28Z

This pull request introduces 4 alerts and fixes 6 when merging c2b2814 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-05T18:53:20Z

This pull request introduces 4 alerts and fixes 6 when merging b62e778 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-05T19:40:00Z

This pull request introduces 4 alerts and fixes 6 when merging 94e5cb9 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-06T04:23:39Z

This pull request introduces 4 alerts and fixes 6 when merging d57fb1f into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-06T17:31:32Z

This pull request introduces 4 alerts and fixes 6 when merging 9beb33f into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-09T20:09:38Z

This pull request introduces 4 alerts and fixes 6 when merging b47e4eb into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import
1 for 'import *' may pollute namespace

lgtm-com · 2019-12-09T22:08:17Z

This pull request introduces 4 alerts and fixes 5 when merging 92c6cf1 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import

github-actions · 2019-12-09T22:13:13Z

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

lgtm-com · 2019-12-09T22:26:36Z

This pull request introduces 4 alerts and fixes 5 when merging 2a53c43 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2019-12-10T21:38:10Z

This pull request introduces 4 alerts and fixes 5 when merging df4904f into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2019-12-10T21:58:43Z

This pull request introduces 4 alerts and fixes 5 when merging 7a1cf20 into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2019-12-13T04:12:00Z

This pull request introduces 4 alerts and fixes 5 when merging 0eea9aa into 25956da - view on LGTM.com

new alerts:

2 for Module is imported with 'import' and 'import from'
1 for 'import *' may pollute namespace
1 for 'input' function used

fixed alerts:

5 for Unused import

peregrine/resources/submission/graphql/node.py

peregrine/utils/json2csv.py

tests/graphql/test_graphql.py

Dockerfile

peregrine/utils/request.py

bin/setup_psqlgraph.py

tests/graphql/test_graphql.py

TestDockerfile

peregrine/resources/submission/__init__.py

peregrine/resources/submission/graphql/__init__.py

paulineribeyre · 2019-12-30T21:36:44Z

requirements.txt

-six==1.10.0
-urllib3==1.24.1
-wsgiref==0.1.2
+six==1.12.0


what do we need six for?

we don't, deleting

removing it caused travis to fail so I added it back. It's weird because psqlgraph does use six but it also specifies in setup.py so not sure why it's not being properly installed on travis.

requirements.txt

dev-requirements.txt

tests/graphql/conftest.py

lgtm-com · 2020-01-02T18:56:48Z

This pull request introduces 1 alert and fixes 5 when merging 21719a8 into 25956da - view on LGTM.com

new alerts:

1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2020-01-02T19:23:50Z

This pull request introduces 1 alert and fixes 5 when merging 816a1f0 into 25956da - view on LGTM.com

new alerts:

1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2020-01-02T19:44:56Z

This pull request introduces 1 alert and fixes 5 when merging 99d79d3 into 25956da - view on LGTM.com

new alerts:

1 for 'input' function used

fixed alerts:

5 for Unused import

lgtm-com · 2020-01-03T17:52:57Z

This pull request introduces 1 alert and fixes 5 when merging 8b58566 into feece74 - view on LGTM.com

new alerts:

1 for 'input' function used

fixed alerts:

5 for Unused import

paulineribeyre

lgtm

vpsx

!!

itsJiaqi requested review from paulineribeyre and vpsx December 13, 2019 17:03

vpsx reviewed Dec 26, 2019

View reviewed changes

paulineribeyre reviewed Dec 30, 2019

View reviewed changes

Jiaqi Liu added 7 commits January 3, 2020 11:36

chore(py3): run 2to3 and fix sorting

51487ec

use uc-cdis psqlgraph

65f01af

bump travis py3

7544333

chore(py3): fix dependencies

8faa2c7

chore(py3): bump versions

2a4f8ed

chore(py3): update dockerfile

b94ecb1

chore(py3): remove unused imports

2aeda10

Jiaqi Liu added 17 commits January 3, 2020 11:36

fix dependencies

d5a9cd1

fix dockerfile

4d7c302

edit uswgi file to use nginx

02b8697

dictionaryutils

3f5bf8b

update uwsgi.ini

7660131

python path

b94093b

update dockerfile

2b7f8be

ran black

5a9e7d0

change docker cmd

8e4f439

fix chown

4c8f92e

Remove editable vcs

c53e30b

use pypi dependencies

cba2b52

fix cdispyutils

8ada8ab

feedback py3

e75b3af

TestDockerfile builds py3

020a8ae

fix tests

4cb77e8

ran black

8b58566

itsJiaqi force-pushed the chore/py3 branch from 99d79d3 to 8b58566 Compare January 3, 2020 17:46

paulineribeyre approved these changes Jan 3, 2020

View reviewed changes

vpsx approved these changes Jan 3, 2020

View reviewed changes

itsJiaqi merged commit e74f55f into master Jan 6, 2020

PlanXCyborg mentioned this pull request Oct 21, 2022

Gen3 Monthly Release 2022.10 dcf-interop.kidsfirstdrc.org 1666320713 uc-cdis/cdis-manifest#5281

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update to Python3 #154

Update to Python3 #154

itsJiaqi commented Dec 3, 2019

lgtm-com bot commented Dec 3, 2019

lgtm-com bot commented Dec 3, 2019

lgtm-com bot commented Dec 4, 2019

lgtm-com bot commented Dec 4, 2019

lgtm-com bot commented Dec 5, 2019

lgtm-com bot commented Dec 5, 2019

lgtm-com bot commented Dec 6, 2019

lgtm-com bot commented Dec 6, 2019

lgtm-com bot commented Dec 9, 2019

lgtm-com bot commented Dec 9, 2019

github-actions bot commented Dec 9, 2019

lgtm-com bot commented Dec 9, 2019

lgtm-com bot commented Dec 10, 2019

lgtm-com bot commented Dec 10, 2019

lgtm-com bot commented Dec 13, 2019

paulineribeyre Dec 30, 2019

itsJiaqi Jan 2, 2020

itsJiaqi Jan 2, 2020

paulineribeyre Jan 3, 2020

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 3, 2020

paulineribeyre left a comment

vpsx left a comment

Update to Python3 #154

Update to Python3 #154

Conversation

itsJiaqi commented Dec 3, 2019

New Features

Breaking Changes

Dependency updates

lgtm-com bot commented Dec 3, 2019

lgtm-com bot commented Dec 3, 2019

lgtm-com bot commented Dec 4, 2019

lgtm-com bot commented Dec 4, 2019

lgtm-com bot commented Dec 5, 2019

lgtm-com bot commented Dec 5, 2019

lgtm-com bot commented Dec 6, 2019

lgtm-com bot commented Dec 6, 2019

lgtm-com bot commented Dec 9, 2019

lgtm-com bot commented Dec 9, 2019

github-actions bot commented Dec 9, 2019

lgtm-com bot commented Dec 9, 2019

lgtm-com bot commented Dec 10, 2019

lgtm-com bot commented Dec 10, 2019

lgtm-com bot commented Dec 13, 2019

paulineribeyre Dec 30, 2019

Choose a reason for hiding this comment

itsJiaqi Jan 2, 2020

Choose a reason for hiding this comment

itsJiaqi Jan 2, 2020

Choose a reason for hiding this comment

paulineribeyre Jan 3, 2020

Choose a reason for hiding this comment

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 2, 2020

lgtm-com bot commented Jan 3, 2020

paulineribeyre left a comment

Choose a reason for hiding this comment

vpsx left a comment

Choose a reason for hiding this comment