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Sync with Main #10

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Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Quick tests passed locally by running ./runtest.sh.
  • In-line docstrings updated.
  • Documentation updated.

apatole and others added 30 commits July 17, 2024 12:23
This changes adds federated hierarchical stats example link in
`examples/advanced/README.md` and changes images size in
`hierarchical_stats/README.md` as the images were appearing smaller in
the web browser.

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Chester Chen <[email protected]>
…#2713)

* Fix ClientAPILauncherExecutor import path to remove torch dependency.

* Update Hello Client Controlled Workflow(CCWF) README.md (#2709)

The folder path in the command is incorrect.

* Update stats READMEs (#2711)

This changes adds federated hierarchical stats example link in
`examples/advanced/README.md` and changes images size in
`hierarchical_stats/README.md` as the images were appearing smaller in
the web browser.

Co-authored-by: Chester Chen <[email protected]>

* Fix torch ddp (#2706)

Co-authored-by: Chester Chen <[email protected]>

---------

Co-authored-by: tonywjs <[email protected]>
Co-authored-by: Arun Patole <[email protected]>
Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* Updated FOBS readme to add DatumManager, added agrpcs as secure scheme

* Merged XGB changes made in 2.4 to main

* Fixed a format error

* Undid change to histogram_based/executor.py

* Addressed comments in PR

---------

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* keep the local resources for simulator.

* fixed the local folder deploy.

---------

Co-authored-by: Chester Chen <[email protected]>
* support same app to all

* add to_server() and to_clients() routines

* comment out export

* improve input errors handling

* check for missing server components

* address comments

---------

Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* add ModelController docs

* address comments

* address comments 2

* fix code block

---------

Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
…on (#2523)

* added TIE

* add license text

* fix fstr

* support cli applet

* add tli applet

* develop flower integration

* added license text

* generate cli cmd by applet

* integrate with flower

* fix format

* fix fl ctx

* fix get_command

* run hello-flwr-pt job (#7)

* run hello-flwr-pt job

* remove print outs

* abort grpc gracefully

* fix example

* graceful shutdown of flower

* fix msg release

* fix formatting

* fix formatting

* fix formatting

* check applet stop

* update flwr server commands (#8)

* test superlink ready before starting server app

* improve log file handling

* remove unused import

* fixed _superlink_process var bug

* change namespace for flower proto; log flower msgs to file and console

* add license text

* consolidate process mgr

* improve docstrings

* address pr review issues

* address additional pr comments

* changed to use flwr proto directly

* use PyApplet for running py code

* added PyApplet

* support server app args; address pr issues

* move ccreate_channel to grpc_utils

* fix flower output formatting

* reformat

---------

Co-authored-by: Holger Roth <[email protected]>
Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
Also update its nvflare version to ~=2.5.0rc1, monai to >=1.3.1
* Update getting_started.rst

* No need to mkdir

With mkdir, the copied folder has structure simulator-example/hello-pt/jobs, while without mkdir, the copied folder has structure simulator-example/jobs

* Update getting_started.rst

* Add hello-pt to the folder structure

---------

Co-authored-by: Sean Yang <[email protected]>
* add alpha splitting

* run experiments

* add tensorboard writers; increase model size

* fedopt version

* add fedprox loss and callback

* Update ModerateTFNet to match CIFAR10 torch implementation.

* Fix multiprocessing GPU init error. Handle no alpha split case.

* Add preprocessing to match torch CIFAR10 result.

* Unify executor script for different algos.

* Remove unused codes.

* Add preprocessing steps to make TF results on par with torch examples.

* Fix script executor args.

* Add script to run all experiments.

* Add README.

* Fix graphs in README.

* Modify TF FedOpt controller.

* Update README and FedOpt result.

* Remove duplicated flare init.

* Fix result graph for centralized vs FedAvg.

* Fix README re. alpha value for centralized training.

* Improve README.

* Add workspace arg. Change min_clients to num_clients.

* Add warning on TF GPU vRAM allocation.

* Clean up TB summary logs.

* Remove FedProx which will be implemented in another PR.

* Update notebook & README, re-add missing file.

* Update license header.

* Re-include missing script.

* Remove change in torch example script.

* Fix flake8, black and isort format issues.

---------

Co-authored-by: Holger Roth <[email protected]>
Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
Add job templates arg

to avoid "Unable to handle command: config due to: job_templates_dir='None', it is not a directory" error

Use full name

Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
…#2678)

* Added id to the swarm_script_executor_cifar10 component deploy.

* codestyle fix.

* Changed to use job.as_id().

* codestyle fix.

* changed to use job.as_id(shareable_generator) for shareable_generator_id.

* removed the un-necessary job.to() calls.

---------

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Sean Yang <[email protected]>
* Updated FOBS readme to add DatumManager, added agrpcs as secure scheme

* Implemented LocalPlugin

* Refactoring plugin

* Fixed formats

* Fixed horizontal secure isses with mismatching algather-v sizes

* Added padding to the buffer so it's big enough for histograms

* Format fix

* Changed log level for tenseal exceptions

* Fixed a typo

* Added debug statements

* Fixed LocalPlugin horizontal bug

* Added #include <chrono>

* Added docstring to BasePlugin

---------

Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
NAEV95 and others added 30 commits October 4, 2024 15:05
* updated bionemo demos to v1.8

* cleaned demos outputs for clarity

* added linces and fixed naming README

* fixed license headers and readme hyperlink

* black fixing code

* isort and flake8 fixes

* addressing PR changes

* removed unrequired infer copy file

* updated other runs files/configs and fixed path in downstream notebook

* fixed fedavg max_epochs setting to 1, removed extra data in taps yamls, fixed column used for each site

* changed fedavg* and local* yamls to have site specific data for tap. for sabdab fedavg changed to original ???

* also sabdab local changed dataset.train config to ???

* tap fix configurations

* update nb, nvflare version

* use strict false

* use full data for central training of sabdab

---------

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Holger Roth <[email protected]>
Co-authored-by: Holger Roth <[email protected]>
* add flare day page

* add slides

* move link location
* use multi threading but reduce num workers

* revert nbs

* update links
…nk (#2993)

* update documentation for Dockerfile, add location of tbevents, and fix link

* add comment for Dockerfile to explain difference
Bumps [cookie](https://github.com/jshttp/cookie) to 0.7.2 and updates ancestor dependencies [cookie](https://github.com/jshttp/cookie), [@astrojs/mdx](https://github.com/withastro/astro/tree/HEAD/packages/integrations/mdx) and [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro). These dependencies need to be updated together.


Updates `cookie` from 0.5.0 to 0.7.2
- [Release notes](https://github.com/jshttp/cookie/releases)
- [Commits](jshttp/cookie@v0.5.0...v0.7.2)

Updates `@astrojs/mdx` from 1.1.5 to 3.1.7
- [Release notes](https://github.com/withastro/astro/releases)
- [Changelog](https://github.com/withastro/astro/blob/main/packages/integrations/mdx/CHANGELOG.md)
- [Commits](https://github.com/withastro/astro/commits/@astrojs/[email protected]/packages/integrations/mdx)

Updates `astro` from 3.6.5 to 4.15.12
- [Release notes](https://github.com/withastro/astro/releases)
- [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md)
- [Commits](https://github.com/withastro/astro/commits/[email protected]/packages/astro)

---
updated-dependencies:
- dependency-name: cookie
  dependency-type: indirect
- dependency-name: "@astrojs/mdx"
  dependency-type: direct:production
- dependency-name: astro
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Readme notebook polish and cleanup

* Reorganize folder structure and initial gnn

* Complete the graph generate step with edgemap output

* Format fix

* Format fix

* Add graph construction and training notebooks

* Add full gnn functionality

* Update wording for readme

---------

Co-authored-by: Chester Chen <[email protected]>
* fix cma version; upgrade nvflare version

* upgrade python to 3.12
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* 2.5 vdr enhancements

* add table

---------

Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* support multiple host names for fl server

* add connect_to check

* fix server side overseer agent

* add server identity to fed_client.json

* fix format

---------

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Isaac Yang <[email protected]>
* Readme notebook polish and cleanup

* Reorganize folder structure and initial gnn

* Complete the graph generate step with edgemap output

* Format fix

* Format fix

* Add graph construction and training notebooks

* Add full gnn functionality

* Update wording for readme

* update the GNN embedding usage

---------

Co-authored-by: Chester Chen <[email protected]>
Co-authored-by: Yuan-Ting Hsieh (謝沅廷) <[email protected]>
* Add XGB explainability output

* typo fix

* format fix
* Update README.md

* Update xgboost.ipynb
* support net bridge

* add app command handler signature

* update mock to conform to RM

* show client fqcn in check_status cmd

* change to use parent fqcn for cj2cp messages

* revert docs/quickstart.rst

* sync with main

* removed unused imports

* update docstring

* sync with main

* support old startup kits
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