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add logging implementation #7

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wants to merge 86 commits into from
Closed

add logging implementation #7

wants to merge 86 commits into from

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benmalef
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@benmalef benmalef commented Jul 2, 2024

Fixes #ISSUE_NUMBER

Proposed Changes

Checklist

  • CONTRIBUTING guide has been followed.
  • PR is based on the current GaNDLF master .
  • Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
  • Function/class source code documentation added/updated (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
  • Code has been blacked for style consistency and linting.
  • If applicable, version information has been updated in GANDLF/version.py.
  • If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
  • Usage documentation has been updated, if appropriate.
  • Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
  • If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].

sarthakpati and others added 30 commits June 17, 2024 16:58
@sarthakpati
enabling auroc but with guardrails
1692429
@sarthakpati
added mcc, again, with guardrails
7e82e05
@sarthakpati
updated safety logic for auroc
ef32808
@sarthakpati
change to json
7fa7fb0
@sarthakpati
lint
780bb46
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into new-apis_v0.1.0-dev__brats-pa…
f3c541f 
…th_metrics
@sarthakpati
Update classification.py
73ca696
@sarthakpati
updated to use torchmetrics, and added a generic calculators interfac…
8a5310a 
…e for metrics that do not need average. also, output dict updated to remove overwriting
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into new-apis_v0.1.0-dev__brats-pa…
f42b873 
…th_metrics
@sarthakpati
auroc fixed
1d0151d
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into new-apis_v0.1.0-dev__brats-pa…
f9eabb6 
…th_metrics
@sarthakpati
Merge pull request #15 from VukW/setup-clean
6f2a973 
Setup clean
@sarthakpati
checking if this works
ed8ce2f
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into new-apis_v0.1.0-dev__brats-pa…
20241b1 
…th_metrics
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev__brats-path_metrics' of https://git…
7a7fa1f 
…hub.com/sarthakpati/GaNDLF into new-apis_v0.1.0-dev__brats-path_metrics
@sarthakpati
updated to eval
3bf4604
@benmalef
add logging implementation
fe75f9c
@benmalef
update utils.__init__
08550d6
@benmalef
change logging_config
ea42f95
@benmalef
change logging_config
f54641c
@benmalef
change logging_config
10dee45
@benmalef
blacked gandlf_logger
e0aa707
@benmalef
add gandlf_setup in the entrypoints
d5493f1
@benmalef
blacked gandlf_logger
0d1ec65
@benmalef
blacked some files
8ee6308
@benmalef
blacked forward_pass
04fee16
@benmalef
add logging testing
b5203cf
@benmalef
update test_full
06c9d80
@benmalef
Merge pull request #8 from benmalef/add_test_logging
b29e4ef 
add logging testing
@benmalef
black test_full
abddbd7
scap3yvt and others added 29 commits July 11, 2024 09:21
@scap3yvt
fixed check for params
5853763
@scap3yvt
ensure a comma-separated file can be ingested by metrics
cf52d95
@scap3yvt
this check breaks comma-separation
126647a
@scap3yvt
tests updated
1b0ea76
@scap3yvt
tests updated
d11c769
@scap3yvt
tests updated
6d6d402
@scap3yvt
tests should pass
d32e237
@scap3yvt
fixed mask header for synthesis
22ee9bd
@scap3yvt
allow a non-required column to be checked (useful for masks)
fd2b923
@scap3yvt
corrected type
b243043
@scap3yvt
tests updated for new cli option
7e0f91c
@scap3yvt
tests updated for new cli option
20bb51b
@sarthakpati
added a missing_prediction option
1918e0c
@sarthakpati
added tests
4b2c8a2
@scap3yvt
updated missing params for test
367a55c
@scap3yvt @sarthakpati
Update GANDLF/entrypoints/generate_metrics.py
0681982 
Co-authored-by: Sarthak Pati <[email protected]>
@scap3yvt @sarthakpati
Update GANDLF/entrypoints/generate_metrics.py
7adea7b 
Co-authored-by: Sarthak Pati <[email protected]>
@scap3yvt
fixed invocation
5832c03
@sarthakpati
Merge pull request mlcommons#900 from mlcommons/new-apis_v0.1.0-dev_m…
3e02cec 
…etrics_support_separate_target-pred_files

Metrics library updated to support comma separate inputs
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into add_logging_final_version
cf740e8
@Geeks-Sid
Merge pull request mlcommons#897 from hongbozheng/patch-1
00c65bd 
Corrected forward operations order
@sarthakpati
Merge branch 'master' into new-apis_v0.1.0-dev
2c61453
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into add_logging_final_version
18921a9
@scap3yvt
fixed tests
52b2766
@scap3yvt
Merge branch 'new-apis_v0.1.0-dev' into new-apis_v0.1.0-dev_optmize-m…
79be7b6 
…odel_with_output
@sarthakpati
Merge pull request mlcommons#896 from mlcommons/new-apis_v0.1.0-dev_o…
f125e2d 
…ptmize-model_with_output

Added output path for optimize model
@sarthakpati
Merge branch 'new-apis_v0.1.0-dev' into add_logging_final_version
ba795fe
@benmalef
update gandlf_logger
935d4a3 
- Update gandlf_logging_setup
- Update logging_cofing
- Update setup.py
@benmalef
remove unnecessary imports
af46472
@benmalef benmalef closed this Jul 17, 2024
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5 participants
@benmalef @sarthakpati @scap3yvt @hongbozheng @Geeks-Sid