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WIP Don't merge yet #614

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WIP Don't merge yet #614

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Commits on Feb 28, 2024

  1. fl support code

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    hasan7n committed Feb 28, 2024
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  2. adapt mock_tokens folder

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    hasan7n committed Feb 28, 2024
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Commits on Feb 29, 2024

  1. fix passing port and collaborator env variable

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    hasan7n committed Feb 29, 2024
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  2. fixes related to cube.download refactoring

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    hasan7n committed Feb 29, 2024
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  3. remove TODOs from version control

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    hasan7n committed Feb 29, 2024
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  4. update code according storage related changes

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    hasan7n committed Feb 29, 2024
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Commits on Mar 2, 2024

  1. minor server fixes

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    hasan7n committed Mar 2, 2024
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  2. fix config storage

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    hasan7n committed Mar 2, 2024
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Commits on Mar 5, 2024

  1. fix typo

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    hasan7n committed Mar 5, 2024
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  2. Merge remote-tracking branch 'upstream/main' into fl-poc

    @hasan7n
    hasan7n committed Mar 5, 2024
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  3. tmp fix mlcube issue

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    hasan7n committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. add FL integration test

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    hasan7n committed Mar 6, 2024
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  2. debug

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  3. debug

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  4. debug

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  5. debug

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    hasan7n committed Mar 6, 2024
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Commits on Mar 12, 2024

  1. add prep cube for FL tests

    @hasan7n
    hasan7n committed Mar 12, 2024
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  2. update and restructure fl example

    @hasan7n
    hasan7n committed Mar 12, 2024
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  3. update cli training tests

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    hasan7n committed Mar 12, 2024
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  4. fix bugs

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    hasan7n committed Mar 12, 2024
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Commits on Mar 21, 2024

  1. TMP TO BE REVERTED

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    hasan7n committed Mar 21, 2024
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Commits on Mar 25, 2024

  1. multiple datasets per collaborator cert

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    hasan7n committed Mar 25, 2024
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Commits on Mar 26, 2024

  1. fix training tests

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    hasan7n committed Mar 26, 2024
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  2. empty

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    hasan7n committed Mar 26, 2024
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  3. Merge remote-tracking branch 'upstream/main' into fl-poc

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    hasan7n committed Mar 26, 2024
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  4. post-merging-main fixes

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    hasan7n committed Mar 26, 2024
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  5. debug

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    hasan7n committed Mar 26, 2024
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Commits on Apr 1, 2024

  1. Merge remote-tracking branch 'upstream/main' into fl-poc

    @hasan7n
    hasan7n committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. fix testing util

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    hasan7n committed Apr 2, 2024
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  2. fix training tests

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    hasan7n committed Apr 2, 2024
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  3. use ip address for aggregtor

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    hasan7n committed Apr 2, 2024
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Commits on Apr 18, 2024

  1. aggregator changes

    @hasan7n
    hasan7n committed Apr 18, 2024
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  2. add ca server entity

    @hasan7n
    hasan7n committed Apr 18, 2024
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  3. associations refactoring

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    hasan7n committed Apr 18, 2024
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  4. remove signing code

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    hasan7n committed Apr 18, 2024
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Commits on Apr 22, 2024

  1. add training event object

    @hasan7n
    hasan7n committed Apr 22, 2024
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  2. modify training event

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    hasan7n committed Apr 22, 2024
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  3. modify training event

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    hasan7n committed Apr 22, 2024
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  4. changes to training entity

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    hasan7n committed Apr 22, 2024
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  5. traindataset association updates

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    hasan7n committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. add aggregator_association

    @hasan7n
    hasan7n committed Apr 23, 2024
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  2. add ca_association

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    hasan7n committed Apr 23, 2024
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  3. update state logic in benchmarks for consistency

    @hasan7n
    hasan7n committed Apr 23, 2024
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  4. create migrations and admin views

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    hasan7n committed Apr 23, 2024
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Commits on Apr 26, 2024

  1. update fl mlcube interface

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    hasan7n committed Apr 26, 2024
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Commits on Apr 27, 2024

  1. Merge remote-tracking branch 'upstream/main' into fl-tmp

    @hasan7n
    hasan7n committed Apr 27, 2024
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  2. refactor entities

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    hasan7n committed Apr 27, 2024
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Commits on Apr 29, 2024

  1. client updates

    @hasan7n
    hasan7n committed Apr 29, 2024
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  2. update FL example

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    hasan7n committed Apr 29, 2024
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  3. update/create missing APIs

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    hasan7n committed Apr 29, 2024
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  4. update new migration files

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    hasan7n committed Apr 29, 2024
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  5. add mock crt mlcube

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  6. update test env

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Commits on Apr 30, 2024

  1. bug fixes

    @hasan7n
    hasan7n committed Apr 30, 2024
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  2. use event's report within a subfolder

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    hasan7n committed Apr 30, 2024
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  3. use IP address instead of hostname in integration tests

    @hasan7n
    hasan7n committed Apr 30, 2024
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  4. fix tests

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    hasan7n committed Apr 30, 2024
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  5. remove comment

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    hasan7n committed Apr 30, 2024
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Commits on May 1, 2024

  1. add --overwrite flag for an easier life

    @hasan7n
    hasan7n committed May 1, 2024
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  2. use abs path for training config

    @hasan7n
    hasan7n committed May 1, 2024
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  3. add missing call

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    hasan7n committed May 1, 2024
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  4. REVERT ME

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  5. remove trailing equals

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    hasan7n committed May 1, 2024
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  6. fix mock certs issue

    @hasan7n
    hasan7n committed May 1, 2024
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  7. add download run files

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    hasan7n committed May 1, 2024
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  8. Revert "REVERT ME" 

    This reverts commit 5b7da41.
    @hasan7n
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  9. use ip address in integration tests

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    hasan7n committed May 1, 2024
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Commits on May 6, 2024

  1. add option to choose interface for publishing port

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    hasan7n committed May 6, 2024
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Commits on May 17, 2024

  1. remove some TODOs from the code

    @hasan7n
    hasan7n committed May 17, 2024
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  2. add ca server and client code

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    hasan7n committed May 17, 2024
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Commits on May 20, 2024

  1. Merge remote-tracking branch 'upstream/main' into fl-tmp

    @hasan7n
    hasan7n committed May 20, 2024
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Commits on May 21, 2024

  1. temporary measures for minimum UI friction

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    hasan7n committed May 21, 2024
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  2. empty

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    hasan7n committed May 21, 2024
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  3. Merge remote-tracking branch 'upstream/main' into fl-tmp

    @hasan7n
    hasan7n committed May 21, 2024
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  4. post-merge main

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    hasan7n committed May 21, 2024
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  5. skip approval in tests

    @hasan7n
    hasan7n committed May 21, 2024
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  6. bug fix for association ls

    @hasan7n
    hasan7n committed May 21, 2024
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  7. better UI for data owners

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    hasan7n committed May 21, 2024
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Commits on May 22, 2024

  1. config storage migration

    @hasan7n
    hasan7n committed May 22, 2024
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  2. update medperf version

    @hasan7n
    hasan7n committed May 22, 2024
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  3. use check update again

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    hasan7n committed May 22, 2024
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Commits on Jun 11, 2024

  1. Draft example of NNUNet Integration with OpenFL and MedPerf

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    msheller committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. Merge branch 'main' into fl-poc

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  2. Merge remote-tracking branch 'origin/fl-poc' into fl-poc-nnunet-draft

    @hasan7n
    hasan7n committed Jun 12, 2024
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  3. use same setup files as fl/fl

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Commits on Jun 13, 2024

  1. Added missing utils file and changed import path to read from the src… 

    … folder
    @msheller
    msheller committed Jun 13, 2024
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  2. Merge branch 'fl-poc-nnunet-draft' of https://github.com/hasan7n/medperf 

     into fl-poc-nnunet-draft
    @msheller
    msheller committed Jun 13, 2024
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  3. remove buggy unused imports

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    hasan7n committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. modify build script

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    hasan7n committed Jun 14, 2024
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  2. Merge remote-tracking branch 'origin/fl-dev' into fl-poc-nnunet-draft

    @hasan7n
    hasan7n committed Jun 14, 2024
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Commits on Jul 2, 2024

  1. sync fl examples

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    hasan7n committed Jul 2, 2024
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Commits on Jul 10, 2024

  1. draft update for the shape mismatch fix

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    hasan7n committed Jul 10, 2024
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  2. rename imports

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    hasan7n committed Jul 10, 2024
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Commits on Jul 18, 2024

  1. bugfixes, add init_model task

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    hasan7n committed Jul 18, 2024
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  2. change tests config scripts

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    hasan7n committed Jul 18, 2024
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  3. modify test setup script

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    hasan7n committed Jul 18, 2024
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Commits on Jul 28, 2024

  1. WIP. About to merge openfl PR 996

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Commits on Jul 29, 2024

  1. add fl-admin mlcube

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  2. allow passing col list when starting an event

    @hasan7n
    hasan7n committed Jul 29, 2024
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  3. add fl admin mlcube to training exp object

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  4. some setup/tests changes

    @hasan7n
    hasan7n committed Jul 29, 2024
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  5. bugfix in tests

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    hasan7n committed Jul 29, 2024
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  6. tests bugfixes

    @hasan7n
    hasan7n committed Jul 29, 2024
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  7. Added admin config to test plan

    @msheller
    msheller committed Jul 29, 2024
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  8. Merge branch 'fl-poc-nnunet-draft' of https://github.com/hasan7n/medperf 

     into fl-poc-nnunet-draft
    @msheller
    msheller committed Jul 29, 2024
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  9. Added admin endpoints to list of functions that can use the network. … 

    …Added fix for files in nnunet data directories.
    @msheller
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  10. add cutofftime task in cube.py

    @hasan7n
    hasan7n committed Jul 29, 2024
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  11. Successfully tested with admin endpoint to set straggler handler timeout

    @msheller
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  12. Merge branch 'fl-poc-nnunet-draft' of https://github.com/hasan7n/medperf 

     into fl-poc-nnunet-draft
    @msheller
    msheller committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. update numpy version in requirements

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    hasan7n committed Jul 30, 2024
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  2. update testing scripts

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Commits on Aug 1, 2024

  1. support gpu drivers v470

    @hasan7n
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  2. aggregator copy files bugfix

    @hasan7n
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  3. singularity option for fl tests

    @hasan7n
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  4. add test option for admin fl

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Commits on Aug 16, 2024

  1. enabled specification of batches per epoch for training and validation 

    in both the core NNUnet train function and the runner. Still need to
compute these using the desired partial_epoch rate and feed to runner instantiation, as well as have the dummy loader correspondingly modify the collaborator weight (via loader 'length') according to the partial epoch value
    @brandon-edwards
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  2. dummy loader now also uses the per collaborator partial_epoch param

    @brandon-edwards
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Commits on Aug 18, 2024

  1. admin commands in medperf

    @hasan7n
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Commits on Aug 22, 2024

  1. typo

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  2. refactor steps in fl mlcube 

    connectivity check, setup certs, now happen before nnunet preprocessing
    @hasan7n
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  3. modify tests scripts

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Commits on Aug 27, 2024

  1. add error checking in step-ca client

    @hasan7n
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Commits on Aug 28, 2024

  1. some clean up, as well as backing off to only pass partial_epoch to 

    runner and train method, inferring number of batches from data size and
batch size via the trainer object
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Commits on Sep 2, 2024

  1. update commit hash for fl admin mlcube

    @hasan7n
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  2. update step-ca client dockerfile

    @hasan7n
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  1. bugfix argument name in training.submit

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  2. store status in a temporary file to avoid read-only problem

    @hasan7n
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  3. update cli integration tests

    @hasan7n
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  4. update mock tokens

    @hasan7n
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  5. update fl testing scripts

    @hasan7n
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  6. update fl integration test mlcube example

    @hasan7n
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Commits on Sep 4, 2024

  1. recent changes

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Commits on Sep 9, 2024

  1. initial changes to support timeouts rather than partial_epoch values

    @brandon-edwards
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Commits on Sep 14, 2024

  1. now tracking time in train and val loop directly

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  2. moving new param change to the nnunet train function

    @brandon-edwards
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  3. had a typo in param and also unsued args check

    @brandon-edwards
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Commits on Sep 16, 2024

  1. some clean up

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Commits on Sep 19, 2024

  1. corrected percent completed calculation

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Commits on Sep 25, 2024

  1. supporting max_num_epochs as nnunet runner init parameter

    @brandon-edwards
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  2. changing previous commit using max_num_epochs to TOTAL_max_num_epochs

    @brandon-edwards
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Commits on Sep 26, 2024

  1. putting timeout check at beginning of train and val loops so that we can 

    perform train or val independently using the timouts
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  2. first pass at accounting for separate train and val tasks into config

    @brandon-edwards
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Commits on Sep 30, 2024

  1. allowing val_cutoff to pass through to nnunet training function

    @brandon-edwards
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  2. Revert "allowing val_cutoff to pass through to nnunet training function" 

    This reverts commit b7970cf.
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  3. implementing separate train and val tasks

    @brandon-edwards
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  4. correcting timeouts for train and val tasks

    @brandon-edwards
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  5. five collaborators

    @brandon-edwards
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  6. changing fl plan file to indicate which model to apply for local vs 

    global validation
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  7. more of my local files,and changing be_setup.. script to copy over 

    changes from hasan_medperf code
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  8. correcting training config

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Commits on Oct 1, 2024

  1. some more test infrastructure

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  2. need to pass epochs value of 1 to nnunet train function used for 

    validation task
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  3. now copying over whole repo into raid homedir

    @brandon-edwards
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  4. another testing change

    @brandon-edwards
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  5. now using validation_only parameter

    @brandon-edwards
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  6. allowing at most 1 second over one batch of val (during training) to 

    avoid NNUnet code throwing exception due to empty val results
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  7. need to account for loaders being different when validate_only is used

    @brandon-edwards
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Commits on Oct 2, 2024

  1. typo 'validate_only'

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  2. local setup script changes

    @brandon-edwards
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  3. moving back to not using validation_only in order that we still have 

    access to training data for calibrating data size
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Commits on Oct 3, 2024

  1. preping to move all local stuff over the files named with be_...

    @brandon-edwards
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  2. putting back fl-poc versions of some files

    @brandon-edwards
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  3. changes to make sure validate method in nnunet runner does not save a 

    new checkpoint with epoch one greater
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Commits on Oct 4, 2024

  1. some debug statements

    @brandon-edwards
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  2. some debug statements

    @brandon-edwards
    brandon-edwards committed Oct 4, 2024
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  3. some more debug statements

    @brandon-edwards
    brandon-edwards committed Oct 4, 2024
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  4. New handling of epoch in checkpoint and new handling of lr scheduling, 

    both using the param val_epoch
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Commits on Oct 7, 2024

  1. passing self.TOTAL_max_num_epochs to lr scheduler computation

    @brandon-edwards
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  2. will try absolutely no train/val in val/train cases respectively

    @brandon-edwards
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  3. new changes to keep global results out of checkpoints, returning metrics 

    directly from nnunet train call, should help to keep checkpoints cleaner
and nnunet code from throwing exceptions
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    brandon-edwards committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. fixing syntax error

    @brandon-edwards
    brandon-edwards committed Oct 8, 2024
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  2. syntax

    @brandon-edwards
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  3. function for local val now only grabs metrics from checkpoint

    @brandon-edwards
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  4. having now to designate both val_epoch and train_epoch booleans at the 

    nnunet train function level
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  5. removing variable no longer used

    @brandon-edwards
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  6. removing check for no val work done during train call, no longer the 

    case
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  7. moving validation from checkpoint and not both under function 'validate'

    @brandon-edwards
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  8. adding single val funciton to training config

    @brandon-edwards
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  9. syntax

    @brandon-edwards
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  10. replaced np.sum for torch.sum, and preparing for per_task data size 

    using amount of work completed
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  11. was using np on tensors

    @brandon-edwards
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  12. casting to numpy (some are already, and some are torch tensors)

    @brandon-edwards
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  13. typo

    @brandon-edwards
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  14. setting checkpoint delta error to 0.1 for now as well as verbose 

    printing of delta
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  15. correcting metric that had train loss instead of val metric

    @brandon-edwards
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Commits on Oct 10, 2024

  1. removing some testing output

    @brandon-edwards
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  2. enabling task dependent data size

    @brandon-edwards
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  3. commenting out debug print

    @brandon-edwards
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  4. adding recent changes to intel_build for local openfl changes

    @brandon-edwards
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  5. ensuring get_data_size returns an int so as to satisfy proto schema

    @brandon-edwards
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Commits on Oct 11, 2024

  1. changing test setting

    @brandon-edwards
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  2. only including model in task results in train task (not local or global 

    val)
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  3. inconsistency in new variable name

    @brandon-edwards
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  4. now including per label DICE for global and local val

    @brandon-edwards
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  5. correcting syntax

    @brandon-edwards
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Commits on Oct 12, 2024

  1. nnunet training function should return more

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Commits on Oct 13, 2024

  1. syntax

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  2. corrected return to be train and val completed as opposed to batches 

    trained and validated
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  3. typo

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Commits on Oct 14, 2024

  1. small cleanup

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Commits on Oct 16, 2024

  1. setting train and val cutoff in plan, and setting defaults to infinity

    @brandon-edwards
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  2. Merge branch 'fl-poc' of https://github.com/hasan7n/medperf into be_e… 

    …nable_partial_epochs
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Commits on Oct 17, 2024

  1. post review with Micah

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Commits on Oct 18, 2024

  1. inserting old debug stuff as info (stdout) to have going forward

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  2. now inserting info to stdout

    @brandon-edwards
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  3. changing to 300 rounds for testing

    @brandon-edwards
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  4. was not printing at the time info was properly populated

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Commits on Oct 19, 2024

  1. now using round and not saving any checkpoints

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Commits on Oct 21, 2024

  1. I want to be explicit about where we are writing checkpoints now

    @brandon-edwards
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  2. round instead of current_epoch

    @brandon-edwards
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  3. some clean up

    @brandon-edwards
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  4. default argument at end

    @brandon-edwards
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  5. provide checkpoint path

    @brandon-edwards
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  6. Nowing using fl_round rather than round to avoid collision with internal 

    function
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  7. missed another spot where checkpoint path was needed

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    brandon-edwards committed Oct 21, 2024
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Commits on Oct 22, 2024

  1. setting of epoch pre nnunet train/val corresponds to previous epoch 

    trained
    @brandon-edwards
    brandon-edwards committed Oct 22, 2024
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  2. inserting some debug prints

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    brandon-edwards committed Oct 22, 2024
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  3. indentation issues

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    brandon-edwards committed Oct 22, 2024
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  4. removing some debug prints

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    brandon-edwards committed Oct 22, 2024
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  5. removing a print

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    brandon-edwards committed Oct 22, 2024
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  6. changes due to new signature for nnunet train function

    @brandon-edwards
    brandon-edwards committed Oct 22, 2024
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  7. preparing to test on brain threshold data

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    brandon-edwards committed Oct 22, 2024
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  8. changes to training config for testing

    @brandon-edwards
    brandon-edwards committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. another iteration of data creation (so changing data file names)

    @brandon-edwards
    brandon-edwards committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. changes new config and parameter definitions

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    brandon-edwards committed Oct 24, 2024
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Commits on Oct 26, 2024

  1. enabling dampening of the train_completion with admin control

    @brandon-edwards
    brandon-edwards committed Oct 26, 2024
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  2. left a stray idea in the training config that does not belong

    @brandon-edwards
    brandon-edwards committed Oct 26, 2024
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Commits on Oct 27, 2024

  1. setting min train_completion_dampener to -1 to allow multiplication 

    instead of division by amount of training completed when modifying data
size for update weighting, also allowing col1 to be admin for testing
admin control of dampener as well as train and val cutoff time for
train (training and local model validation)
    @brandon-edwards
    brandon-edwards committed Oct 27, 2024
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Commits on Oct 28, 2024

  1. removing be scripts from branch

    @brandon-edwards
    brandon-edwards committed Oct 28, 2024
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  2. removing be_Dockerfile

    @brandon-edwards
    brandon-edwards committed Oct 28, 2024
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  3. doc string

    @brandon-edwards
    brandon-edwards committed Oct 28, 2024
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  4. doc changes and removing validation_only param as we control that 

    another way
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    brandon-edwards committed Oct 28, 2024
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  5. remiving epochs variable since nnunet trainer run_training is hard coded 

    to train one epoch
    @brandon-edwards
    brandon-edwards committed Oct 28, 2024
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  6. docstring

    @brandon-edwards
    brandon-edwards committed Oct 28, 2024
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  7. dockstring and fl plan fixing rounds to train for both agg and task 

    runner blocks
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    brandon-edwards committed Oct 28, 2024
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  8. dockstring

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    brandon-edwards committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. removing comment and test piece in config

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    brandon-edwards committed Oct 29, 2024
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  2. removing unused function and providing default args

    @brandon-edwards
    brandon-edwards committed Oct 29, 2024
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  3. removing a line of print output

    @brandon-edwards
    brandon-edwards committed Oct 29, 2024
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