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adding graph + tile stitching to trigger tests #2 #396

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wants to merge 154 commits into from
Closed

adding graph + tile stitching to trigger tests #2 #396

wants to merge 154 commits into from

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VarunUllanat
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jamesgwen and others added 30 commits July 12, 2023 11:17
@jamesgwen
adding platforms for build and push
921537b
@jamesgwen
updating push action version and adding platforms for mac support
092402f
@jamesgwen
changing openslide version in environ yml
a6ee903
@jamesgwen
adding adjusted openslide dependency in yml
e6bd53b
@jamesgwen
adding inference to init file
a57b7f6
@jamesgwen
add inference classes and functions
6c8cf28
@jamesgwen
add tests for inference
34237f2
@jamesgwen
fixed import statements
980c662
@jamesgwen
fixing import statements in the init and the test inference
77d5d4d
@jamesgwen
fixing init files
b3d295a
@jamesgwen
fixing comma in inference init
d144d91
@jamesgwen
getting rid of unused packages
51841aa
@jamesgwen
fixed files via black
6044024
@jamesgwen
fixed spacing and alpha order
e6002d2
@jamesgwen
added dependencies
35a3df1
@jamesgwen
re black the test inference file
c015ff8
@jamesgwen
update protobuf version in envi yml
0dd09b8
@jamesgwen
changing numpy version
5657efb
@jamesgwen
adjusting deepcel version
0b7df6b
@jamesgwen
deleted comment from yml file
4612a68
@jamesgwen
updating pytest version
4cd57a5
@jamesgwen
setting pandas version
05f19e7
@jamesgwen
adding test onnx and fixing path in test file
ddb1b07
@jamesgwen
fixing remote test
af07fb0
@jamesgwen
fixing path to onnx model in test data
7048a4e
@jamesgwen
changing numpy to latest version
f76314a
@jamesgwen
adjusting numpy to 1.24.0
69c8ce6
@jamesgwen
switching to numpy 1.22.4
a5d28ac
@jamesgwen
Merge branch 'dev-onnx' into inference
7ec4cf0
@jamesgwen
adding pandas
c84cc24
sreekarreddydfci and others added 20 commits December 4, 2023 02:12
@sreekarreddydfci
Update environment.yml
7c733b1 
Added JPype1
@sreekarreddydfci
Create testdata folder for tilestitching data
2d183db
@sreekarreddydfci
Add large .tif file with Git LFS
4413b66
@sreekarreddydfci
≈Merge branch 'dev_graphAPI' of https://github.com/sreekarreddydfci/p…
4e983de 
…athml into dev_graphAPI
@sreekarreddydfci
Remove readme file in tests
f590dd2
@sreekarreddydfci
Update tests-conda.yml
393983c 
Separately executed test cases for tilestitching functionality and other PathML modules.
@sreekarreddydfci
Added exclude marker to run tests
e4af3e4
@sreekarreddydfci
Merge branch 'dev_graphAPI' of https://github.com/sreekarreddydfci/pa…
e2bdf96 
…thml into dev_graphAPI
@sreekarreddydfci
Edited a testcase
d4e7f3f
@sreekarreddydfci
Commented testcases
9aeec4f
@VarunUllanat
Merge pull request #391 from sreekarreddydfci/dev_graphAPI
c01d6a7 
Added tilestitching code
@sreekarreddydfci
Pasted the code from graphAPI
474072a
@sreekarreddydfci
Update environment.yml
2da44a3
@sreekarreddydfci
Added testcases
71dda3d
@sreekarreddydfci
Added test cases and environment file
2e7f4f4
@sreekarreddydfci
Updated env
a6821b7
@sreekarreddydfci
Updated env
f04cb32
@sreekarreddydfci
Merge pull request #393 from sreekarreddydfci/dev-tilestitching
305f4e5 
Dev tilestitching
@VarunUllanat
Make flake8 compliant
ab59e31
@VarunUllanat
Removed tile stiching generated files
b275a04
@codecov-commenter
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codecov-commenter commented Dec 6, 2023 •
edited
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Codecov Report

Attention: 231 lines in your changes are missing coverage. Please review.

Comparison is base (dd61eea) 86.37% compared to head (44eca15) 86.69%.

Files Patch % Lines
pathml/datasets/datasets.py 71.35% 59 Missing ⚠️
pathml/datasets/utils.py 53.92% 47 Missing ⚠️
pathml/graph/preprocessing.py 89.96% 32 Missing ⚠️
pathml/ml/models/hovernet.py 92.00% 28 Missing ⚠️
pathml/ml/utils.py 39.53% 26 Missing ⚠️
pathml/preprocessing/tilestitcher.py 90.82% 21 Missing ⚠️
pathml/graph/utils.py 82.50% 14 Missing ⚠️
pathml/ml/hovernet.py 0.00% 4 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #396      +/-   ##
==========================================
+ Coverage   86.37%   86.69%   +0.31%     
==========================================
  Files          27       37      +10     
  Lines        2503     3727    +1224     
==========================================
+ Hits         2162     3231    +1069     
- Misses        341      496     +155

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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4 participants
@VarunUllanat @codecov-commenter @jamesgwen @sreekarreddydfci