Umami merge requestshttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests2024-03-20T13:47:39+01:00https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/751Removing `repeat_end` option from default config2024-03-20T13:47:39+01:00Alexander FrochRemoving `repeat_end` option from default config## Summary
This MR introduces the following changes
* Removing the `repeat_end` option from the default DL1 training config
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blo...## Summary
This MR introduces the following changes
* Removing the `repeat_end` option from the default DL1 training config
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/750Moving tutorial from FTAG documentation2024-03-04T10:55:52+01:00Wei Sheng LaiMoving tutorial from FTAG documentation## Summary
This MR introduces the following changes
* Moving relevant [tutorial](https://ftag-docs.docs.cern.ch/software/tutorials/tutorial-umami/) from FTAG documentation here so that they can be easily updated and stay relevant.
##...## Summary
This MR introduces the following changes
* Moving relevant [tutorial](https://ftag-docs.docs.cern.ch/software/tutorials/tutorial-umami/) from FTAG documentation here so that they can be easily updated and stay relevant.
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [ ] [Documentation](https://umami-docs.web.cern.ch)
- [ ] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [ ] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/749update link to docs in docs2024-01-18T17:32:43+01:00Ivan Oleksiyukupdate link to docs in docs## Summary
This MR introduces the following changes
* fixes a link in docs
Relates to the following issues
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/230
## Conformity
- [x] [Changelog entry](https...## Summary
This MR introduces the following changes
* fixes a link in docs
Relates to the following issues
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/230
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/740Integration of upp pre-processing package into umami framework2023-11-29T11:36:38+01:00Ivan OleksiyukIntegration of upp pre-processing package into umami framework## Summary
This MR introduces the following changes
* possibility to comfortably use upp preprocessing in umami framework,
basically one can now do all the same pre-processing steps but with using upp config file (with some tweaks)!
*...## Summary
This MR introduces the following changes
* possibility to comfortably use upp preprocessing in umami framework,
basically one can now do all the same pre-processing steps but with using upp config file (with some tweaks)!
* examples on how to utilise upp config file in preprocessing
Relates to the following issues
* https://github.com/umami-hep/umami-preprocessing/pull/30
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/240
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/233
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/234
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/231
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Rewrite PreprocessingIvan OleksiyukIvan Oleksiyukhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/748Add dark mode to mkdocs documentation2023-11-28T14:28:23+01:00Philipp GadowAdd dark mode to mkdocs documentation## Summary
This MR introduces the following changes
* adds dark mode to documentation
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Document...## Summary
This MR introduces the following changes
* adds dark mode to documentation
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/747Improved documentation + umami paper draft2023-11-22T11:23:27+01:00Philipp GadowImproved documentation + umami paper draft## Summary
This MR introduces the following changes
* improves documentation by adding a tutorial designed for non-ATLAS users and contribution guidelines
* add paper documenting umami
Relates to the following issues
* https://github...## Summary
This MR introduces the following changes
* improves documentation by adding a tutorial designed for non-ATLAS users and contribution guidelines
* add paper documenting umami
Relates to the following issues
* https://github.com/openjournals/joss-reviews/issues/5833
* https://github.com/umami-hep/umami/issues/1
* https://github.com/umami-hep/umami/issues/2
* https://github.com/umami-hep/umami/issues/3
* https://github.com/umami-hep/umami/issues/4
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/746Update paper branch2023-11-22T10:04:08+01:00Philipp GadowUpdate paper branch## Summary
This MR introduces the following changes
* adds a "how to contribute" section to the documentation
* adds a tutorial based on the JetClass dataset
Relates to the following issues
* https://github.com/umami-hep/umami/issues...## Summary
This MR introduces the following changes
* adds a "how to contribute" section to the documentation
* adds a tutorial based on the JetClass dataset
Relates to the following issues
* https://github.com/umami-hep/umami/issues/4
* https://github.com/umami-hep/umami/issues/2
* https://github.com/umami-hep/umami/issues/1
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/745Update packages to match UPP + UPP update (v0.0.5)2023-11-02T16:50:48+01:00Alexander FrochUpdate packages to match UPP + UPP update (v0.0.5)## Summary
This MR introduces the following changes
* Updating packages to match UPP needs
* Updating UPP to v0.0.5 to incorporate Scipy version changes.
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-taggin...## Summary
This MR introduces the following changes
* Updating packages to match UPP needs
* Updating UPP to v0.0.5 to incorporate Scipy version changes.
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/744Update UPP to 0042023-10-30T22:38:57+01:00Ivan OleksiyukUpdate UPP to 004## Summary
This MR introduces the following changes
* Needed for UPP integration
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation...## Summary
This MR introduces the following changes
* Needed for UPP integration
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Ivan OleksiyukIvan Oleksiyukhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/739Change truth label names2023-10-30T15:37:02+01:00Philipp GadowChange truth label names## Summary
This MR introduces the following changes
* Change truth label names to account for changes in DAODs (see salt MR here: https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/salt/-/merge_requests/142/diffs)
## Conform...## Summary
This MR introduces the following changes
* Change truth label names to account for changes in DAODs (see salt MR here: https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/salt/-/merge_requests/142/diffs)
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/741Black mismatch2023-10-16T18:55:41+02:00Ivan OleksiyukBlack mismatch## Summary
This MR introduces the following changes
* Changes to black==23.3 in CI as it is stated in dev-requirements
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/ma...## Summary
This MR introduces the following changes
* Changes to black==23.3 in CI as it is stated in dev-requirements
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Ivan OleksiyukIvan Oleksiyukhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/738Bump Version to v0.212023-09-21T18:03:36+02:00Alexander FrochBump Version to v0.21## Summary
This MR introduces the following changes
* Bump version to 0.21
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](http...## Summary
This MR introduces the following changes
* Bump version to 0.21
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/737Update UPP to 0.0.22023-09-20T14:50:02+02:00Alexander FrochUpdate UPP to 0.0.2## Summary
This MR introduces the following changes
* Update UPP to 0.0.2
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https...## Summary
This MR introduces the following changes
* Update UPP to 0.0.2
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/736Update atlas-ftag-tools and UPP2023-09-20T13:10:42+02:00Alexander FrochUpdate atlas-ftag-tools and UPP## Summary
This MR introduces the following changes
* Updating `atlas-ftag-tools` from 0.1.5 to 0.1.9
* Adding `umami-preprocessing` version 0.0.1
* Updating `Puma` to 0.2.8
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch...## Summary
This MR introduces the following changes
* Updating `atlas-ftag-tools` from 0.1.5 to 0.1.9
* Adding `umami-preprocessing` version 0.0.1
* Updating `Puma` to 0.2.8
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/735Update atlas-ftag-tools package2023-08-02T22:36:45+02:00Alexander FrochUpdate atlas-ftag-tools package## Summary
This MR introduces the following changes
* Updates the `atlas-ftag-tools` package to v0.1.5 to incorporate the changed Hbb and Hcc labels
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-too...## Summary
This MR introduces the following changes
* Updates the `atlas-ftag-tools` package to v0.1.5 to incorporate the changed Hbb and Hcc labels
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/734Update Puma version to v0.2.72023-07-19T16:23:38+02:00Alexander FrochUpdate Puma version to v0.2.7## Summary
This MR introduces the following changes
* This MR updates the Puma version to v0.2.7 which updates the labels a bit and removes some older stuff which is intended for Umami.
## Conformity
- [x] [Changelog entry](https://gi...## Summary
This MR introduces the following changes
* This MR updates the Puma version to v0.2.7 which updates the labels a bit and removes some older stuff which is intended for Umami.
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/730Add option to use tdd file format to train in umami2023-07-19T11:41:50+02:00Ivan OleksiyukAdd option to use tdd file format to train in umami## Summary
This MR introduces the following changes
* Adds a new generator base class that is able to read file from tdd format rescale variables and structure them such that they are suited for training taggers in umami
* Add all the ...## Summary
This MR introduces the following changes
* Adds a new generator base class that is able to read file from tdd format rescale variables and structure them such that they are suited for training taggers in umami
* Add all the child classes for each model
* For all models add a switch to change to this new generator
* Fixed an issue with the "writer" from the old pre-processing which was saving "weight" of a jet e.g. from sampler as one of the NN's inputs (Therefore if anyone would use the weights for training it will give one discriminative feature to the network which actually likely shouldn`t be there)
* Some simplifications with the data generator in models overall (models now get necessary parameters like data dimensions from data generator itself)
* Attempted optimising speed of the new tddgenerator but it is still lacking somewhat compared to the original generator
Solves following issues:
* #242
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Rewrite PreprocessingIvan OleksiyukIvan Oleksiyukhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/733Update Docs FAQ2023-06-20T13:46:33+02:00Alexander FrochUpdate Docs FAQ## Summary
This MR introduces the following changes
* Updating FAQ of the docs with some recent problems
* Removing doubled entry in changelog
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/alg...## Summary
This MR introduces the following changes
* Updating FAQ of the docs with some recent problems
* Removing doubled entry in changelog
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/728Boosted preprocessing: add n_jets_validation to configs to create validation ...2023-06-16T17:17:19+02:00Osama Karkouto.karkout@nikhef.nlBoosted preprocessing: add n_jets_validation to configs to create validation samples.## Summary
This MR introduces the following changes
* Add n_jets_validation to boosted preprocess config
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog....## Summary
This MR introduces the following changes
* Add n_jets_validation to boosted preprocess config
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Osama Karkouto.karkout@nikhef.nlOsama Karkouto.karkout@nikhef.nlhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/732Update PUMA and atlas-ftag-tools2023-06-14T15:46:18+02:00Alexander FrochUpdate PUMA and atlas-ftag-tools## Summary
This MR introduces the following changes
* Updating Puma (to v0.2.6)
* Updating atlas-ftag-tools (to v0.1.4)
* Updating black (to 23.3.0)
* Updating the global_config to include bc-jets correctly
Tagging @nekumari
## Con...## Summary
This MR introduces the following changes
* Updating Puma (to v0.2.6)
* Updating atlas-ftag-tools (to v0.1.4)
* Updating black (to 23.3.0)
* Updating the global_config to include bc-jets correctly
Tagging @nekumari
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Froch