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fix pyrfr int cast seed #1083

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wants to merge 577 commits into from
Closed

fix pyrfr int cast seed #1083

wants to merge 577 commits into from

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  • fix local search and epm-chooser issues
  • add TurBO as one of the epm_chooser
  • maint turbo with gp_mcmc
  • local bo
  • add requirement and update gpytorch model
  • update requirements and GP with Gpytorch
  • move PSGP kernel to smac/epm/kernels
  • move gpytorch to extra requirement
  • update psgp docstring
  • docstring on subspace
  • docstring on epm_chooser
  • docstring on turbo and rh2epm_boing
  • make local_bo an additional extra-requirement
  • maint
  • update docstring, only allow TS on Random Search (Ts docstring #764)
  • Fix smac-validate (Fix smac-validate #762)
  • Interrupt optimization through IncorporateRunResultCallback (Interrupt optimization through IncorporateRunResultCallback #765)
  • Fix Docstrings: runhistory2epm success_states  #662 (Fix #662 #772)
  • Create CITATION.cff
  • Update README.md
  • Do not get stuck due to adaptive capping (Do not get stuck due to adaptive capping #749)
  • Handle invalid neighbors in local search gracefully (Handle invalid neighbors in local search gracefully #773)
  • Added CITATION.cff and updated docs reference
  • removed weird rebase artifact
  • Removed repository-code as it seemed to be exported
  • Instances Documentation (Instances Documentation #777)
  • Propagate minR and maxR from scenario into intensifier (Propagate minR and maxR from scenario into intensifier #775)
  • Added SMAC theme
  • added table for later schick machen
  • renamed glossary + added entries from doc
  • first draft
  • Added minimal example
  • added index file for details
  • updates
  • Changed README
  • clsas diagram for facades
  • update
  • Fixed TOC + image path
  • Changed README
  • Added installation file
  • Changed README
  • Added minimal example
  • Added glossary+scenario
  • update
  • portet FAQ
  • portet FAQ
  • added contact/citation/license
  • added validation
  • added tae
  • Added API Reference
  • Changed API to API reference
  • added instances
  • Changed a lot of pages + style
  • Changed more pages
  • Remove sphinx_rtd_theme import
  • Changed sphinx gallery style drastically
  • Added branin examples
  • Docs example (Docs example #784)
  • Fixed branin restore
  • Stuff
  • maint
  • Documentation: Minor changes, that clarify it, including some details in the glossary
  • move spear_mf_instances under example/python
  • update gb_non_deterministic examples
  • Massive docs clean-up
  • fix tests
  • update github workflow
  • Improved doc texts
  • Fixed pre-commit bugs
  • Fixed small bugs
  • Added mypy ignore to smac theme
  • pip install bs4 for docs
  • Exclude terminal examples for now
  • Shifted terinal examples
  • Updated changelog
  • Cleaned docs directory
  • Changed README
  • Fixed some codefactor issues
  • Put index in docs root
  • changelog 1.1
  • maint
  • Fixed conf.py bug
  • Updated more doc pages
  • Added examples in workflow
  • Docs (Docs #785)
  • Added static path
  • Fixed bug in custom.css
  • Make FAQ appear again
  • Updated sphinx requirements
  • Updated sphinx requirements
  • Updated sphinx-gallery
  • test for smac_facade (Develop codecov #787)
  • update installation doc
  • remove redudant requirements
  • maint
  • fix test
  • fix conflict
  • maint turbo with gp_mcmc
  • local bo
  • solve conflict
  • update requirements and GP with Gpytorch
  • BOinG maint
  • maint
  • maint and let examples run properly
  • decouple maximizer with runhistory
  • pass global optimizer settings to local optimizer
  • correctly sampling from prior
  • test for gp gpytorch
  • Added information about CLI
  • Updated CLI warning
  • Changelog + Increased version
  • added comparison table
  • added whitespaces
  • removed comparison page
  • update
  • update
  • widths
  • Docs installation (Docs installation #794)
  • Corrected installation text
  • Removed comparison page
  • test finished
  • example to vanilla boing
  • README
  • add paper link
  • maint
  • fix cache issues
  • fix conflict
  • mypy
  • fix numerical issue in turbo
  • Update changelog.md
  • Specfiy to dask that runs shouldn't cache results (Specfiy to dask that runs shouldn't cache results #803)
  • Cleaned up workflow files, Adds PEP 561 compliance (Cleaned up workflow files, Adds PEP 561 compliance #802)
  • Let Latin Hypercube design generate configurations on constrained configuration spaces (Let Latin Hypercube design generate configurations on constrained configuration spaces #776)
  • Added name in setup
  • Multi-Objective (Multi-Objective #801)
  • Small improvements
  • Added MO feature in docs
  • Native MO
  • Updated MO docs
  • Added note on limit_resources
  • Clean up
  • Added Tim to authors
  • Multi-Objective (Multi-Objective #817)
  • Fix: Matches signature of ROAR with it's parent
  • Add Mapping type to Runhistory
  • Make flake8 happy
  • Add changelog note
  • Add changelog note
  • Update tools (Update tools #824)
  • PiBO (PiBO #813)
  • Closes [Doc] Document the callback signature better in docs #823
  • Fix codefactor issue
  • Fix codefactor issue
  • Fix codefactor issue
  • Fix codefactor issue
  • codefactor: unnecessary else after raise
  • Fix codefactor issue
  • CodeFactor fixes
  • Fix codefactor issue
  • Fix codefactor issue
  • Fix codefactor issue
  • Fix codefactor issue
  • Fix pre-commit black fail
  • Added pypi command
  • Make list
  • Increased version
  • Replaced copyright again
  • Updated changelog
  • Updated changelog
  • Changed master to main
  • rf with multi-objective
  • Added python 3.7 again
  • Increased automl-sphinx-theme version
  • Loosen package versions
  • Revert "rf with multi-objective"
  • avoid incrementing twice when computing EIPS
  • Added stale bot
  • Updated changelog
  • multi-objective surrogate model
  • Fixes version 0.0.0 bug
  • Fixed doc build
  • Make LICENSE to txt file
  • Fixing requirements path
  • Include magic flag 🦄
  • Please be generous mypy
  • Moved requirements
  • Updated changelog
  • Fix mypy
  • Corrections
  • Fixed list style
  • Added MO support for ROAR (closes ROAR Facade does not support multi-objective optimization #836)
  • References to BOHB
  • Make format (isort)
  • Fix tests?
  • Updated MO docs
  • test and examples for EIPS acquisition function
  • fix mypy
  • pre-comit
  • add docstrings
  • Delete .DS_Store
  • Ignore .DS_Store
  • Hotfix: Update cached costs for MO
  • Updated changelog
  • Updated version
  • Added entry point
  • isort+black
  • change README
  • update example
  • pre-commit
  • Revert "pre-commit"
  • Revert "avoid incrementing twice when computing EIPS"
  • fix rh2epm eips computation
  • rf with multi-objective
  • Revert "rf with multi-objective"
  • avoid incrementing twice when computing EIPS
  • multi-objective surrogate model
  • test and examples for EIPS acquisition function
  • fix mypy
  • pre-comit
  • add docstrings
  • update example
  • pre-commit
  • Revert "pre-commit"
  • Revert "avoid incrementing twice when computing EIPS"
  • fix docstring
  • Update runhistory2epm.py
  • pre_commit
  • Updated changelog
  • Fixed comment
  • Updated changelog
  • Some small improvements
  • Removed trailing space
  • Updated changelog
  • Restricted pynisher
  • Updated changelog
  • Link JMLR paper
  • Update bibtex entry
  • Fixed citation in docs
  • Fixed callback typos
  • BOinG for mixed hyperparameter search space
  • fix format
  • maint
  • maint documentation
  • maint pre-commit
  • fix workflow
  • maint
  • Add dependabot for workflow files
  • Bump actions/setup-python from 2 to 4 (Bump actions/setup-python from 2 to 4 #849)
  • Bump actions/checkout from 2 to 3 (Bump actions/checkout from 2 to 3 #850)
  • maint
  • Updated stale bot
  • Updated stale options again
  • Fixed typing
  • Increased version
  • rename check_point_in_ss to check_subspace_point
  • Make format
  • Uncomment test procedure
  • docstrings for boing facade
  • avoid typing namespace everywhere in epm_configuration_chooser
  • fix docstring in rh2epm_boing
  • Limit on dask
  • Trying to fix tests
  • Replaced typing in all files
  • docstring for boing subspace
  • Changed feature requests to feature
  • allow acq_optimizer_local_kwargs to be passed to boing subspace without acq_optimizer_local
  • fix pre-commit
  • Added any
  • Update facade
  • Add example for pSMAC
  • Removed docstring in readme's example
  • Corrected text
  • move construct_gp_kernels to smac.epm_gpytorch.boing_kernels
  • maint
  • fix wrongly imported func name in tests
  • Add reference for pSMAC Reference pSMAC correctly #609
  • Rename example file
  • Added roadmap to readme
  • Prettification
  • Add result merger
  • Reformat with black
  • Delete unnecessary import
  • Fix typing
  • Inject first trajectory entry from file from first rundir
  • Add test for ResultMerger
  • Fix docstring
  • Get runhistory and trajectory from pSMAC run
  • Get trajectory
  • Add regex to requirements
  • Fixed MO cache problem
  • Fix MO tests
  • Fixing MO in AbstractRacer
  • Accepting ints
  • Hacking in the sum cost for MO
  • Fix mypi
  • Bugfix
  • Make mypi happy
  • Fix tests
  • Make format
  • Remove num_obj in MO optimizer
  • A lot of restructuring
  • Solve importings
  • Solve importings
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Fixing, fixing, fixing, ...
  • Updated changelog
  • Still fixing :)
  • fix docstrings
  • Change directory of tests
  • Fix ambiguous variable
  • Del newlines
  • fix mypy
  • mypy and doc fix
  • Removed int type checking
  • fix tests
  • Always return List of incs
  • fix path issue in example
  • maint boing facade
  • Better docstring
  • Return values if no bounds passed
  • Removed import
  • Return only one incumbent
  • Rename n_optimizers -> n_workers
  • Update example
  • Update docstring
  • Remove legacy function
  • Update to new signature
  • Update changelog.md
  • Format black
  • Update test
  • Please pre-commit
  • Merge development
  • Fix tests
  • Fix typos
  • Format black
  • Updated text
  • Increased version
  • Improved readme
  • SMAC logo 50%
  • SMAC logo 50%
  • Removed dev-2.0
  • Added doc workflow for latest tag
  • Fixing docs latest tag
  • Fixing docs latest tag
  • First steps new intensifier
  • Make it work again
  • MOVE random weight initialization to smbo ask method
  • ADD enable parego in unittests
  • Test issues
  • FIX formatting
  • Link to old documentation
  • MOVE random weight initialization to smbo ask method
  • ADD enable parego in unittests
  • FIX formatting
  • Fix unit tests
  • Add annotation
  • corrected log prob for tophat prior
  • Removed configurations from callback
  • Fixed tests
  • Fix mypy
  • Save docs as latest version too
  • Enabled all tests again
  • Make version an env
  • Added last version to docs
  • Global variable fix
  • Added v before version number
  • New Intensifier Implementation (New Intensifier Implementation #888)
  • First benchmark steps
  • Added a warning
  • Set xi to 0.01
  • Incorporated walltime in trajectory
  • Working version of benchmark
  • Changed requirements
  • Changed xi back to 0.0 again
  • No duplicate budgets
  • Fixed bug which updated tracker wrongly
  • Bugfix: Delete correct bracket+stage
  • Fixed tests
  • Added costs to the trajectory
  • Changed initial design max ratio to 0.25
  • Make format
  • Added more details to intensifier
  • Finished benchmark
  • Added benchmark source files
  • Fixed tests because of initial design changes
  • Improved runhistory API
  • Fixed typo (fixed typo #894)
  • Merge doc fixes
  • Doc fixes (Doc fixes #893)
  • Make format
  • Satisfied mypy
  • Enabled more tests
  • Increased version
  • Mypy
  • Mypy
  • Mypy
  • Fixed critical bug when using highest budget for inc selection
  • Added SH+HB comparison
  • Stuff
  • Updated report
  • Fixed docstring
  • Fixed image path
  • Removed vscode folder
  • Bugfixes
  • Doc fixes
  • Updated changelog
  • Make isort
  • Fix typos
  • Removed new line
  • Added alpha2 to docs selection
  • update description
  • Fix 531 correctly create integers in initial design
  • Add contact paragraph to README.
  • Increase days until stale issues are closed by stalebot (Increase days until stale issues are closed by stalebot #904)
  • Edit changelog
  • Add issue number
  • Closes Continue Run w/ Successive Halving fails #907
  • Clarify origin of configurations (Clarify origin of configurations #908)
  • Random forest speed up (Random forest speed up #903)
  • Add: workflow to update pre-commit versions (Add: workflow to update pre-commit versions #874)
  • Add Git-Flow Workflow Specification
  • [DOC] acquisition function maximizers
  • Add stale reminder email action
  • Increase version number of ConfigSpace
  • Add guideline for updating copyright notice years to CONTRIBUTING.md
  • Update requirement for pyrfr (Update requirement for pyrfr #920)
  • Update pre-commit: isort,flake8 version numbers
  • Format black
  • Fix mypy
  • Ac bench (Ac bench #929)
  • [DOC] added documentation on the incumbent update
  • Feature/add version to make publish (Feature/add version to make publish #931)
  • Transform integer feature names to strings (Transform integer feature names to strings #930)
  • Update version to 2.0.0
  • Update version to 2.0.0
  • Update CHANGELOG.md
  • Add information on deepcave to the readme
  • Correct doc version
  • fix(runhistory): set id of the sampled config (fix(runhistory): set id of the sampled config #951)
  • ci: Set dependabot to target development branch (ci: set dependabot to development #963)
  • feat: Option preventing SMAC setting up logging (feat: Option preventing SMAC setting up logging #947)
  • Citation update (Citation update #961)
  • Adjust hyperband configuration distribution across brackets
  • Compute the actual differences between the isb keys. (Compute the actual differences between the isb keys. #957)
  • Adjust schedule for stale reminder
  • fix(logging): Prevent automatic logging setup at init (fix(logging): Prevent automatic logging setup at init #970)
  • Fix validate method of smbo, update docstring.
  • Allow callbacks to be added to a specific index, make callback registering public
  • Update CHANGELOG.md
  • Fix broken references (fix broken references #988)
  • Adapt developer install instructions to include pre-commit installation (Adapt developer install instructions to include pre-commit installation #994)
  • [Feature] Initial Design now supports executing the default config provided by the user by means of the configspace he generated. (and is no longer ignored)
  • Pipe dask_client through facade for exec on hpc (Pipe dask_client through facade for exec on hpc #983)
  • [Bug-fix] Pr was failing due to mutable additional configs default
  • [doc-fix] the count of initial design configs is computed slightly differently
  • Feature/metadata callback (Feature/metadata callback #999)
  • Documentation/dask client example (Documentation/dask client example #1001)
  • Documentation/dask client example (Documentation/dask client example #1001)
  • Feature/dask client (Feature/dask client #1002)
  • Update smac version (Update smac version #1003)
  • Update copyright year
  • check if config in rh when storing state (check if config in rh when storing state #997)
  • Add a workaround to be able to pass a dataset via dask.scatter (Add a workaround to be able to pass a dataset via dask.scatter #993)
  • Adding Binder links for example (Adding Binder links for example #976)
  • Remove commit message from dependabot PRs (Remove commit message from dependabot PRs #1009)
  • Bugfix/fix broken link (Bugfix/fix broken link #1012)
  • Drop torch requirements (Drop torch requirements #1015)
  • Remove leftover CLI entry points (Remove leftover CLI entry points #1014)
  • Fix incumbent selection in case of SH+MO
  • Update CHANGELOG.md
  • Feature/GitHub actions pr draft (Feature/GitHub actions pr draft #1008)
  • Update stale report to include issues with recent interactions (Update stale report to include issues with recent interactions #1025)
  • Raise error if resource limitation and parallelization is requested (Raise error if resource limitation and parallelization is requested #1023)
  • Raise an error for invalid scatter data (Raise an error for invalid scatter data #1018)
  • fix(configspace): shows all keys in print (fix(configspace): shows all keys in print #1043)
  • Fix callback order (Fix callback order #1040)
  • fix: dtypes (fix: dtypes #1044)
  • Fix(config_selector): Budget checking (Fix(config_selector): Budget checking #1039)
  • Fix: target runner with partial func (Fix: target runner with partial func #1045)
  • Feature/improve documentation (Feature/improve documentation #1028)
  • Handle configspace as dictionary in mlp example (Handle configspace as dictionary in mlp example #1057)
  • Raise version number
  • Add missing period in docs.
  • allow rf to impute OrdinalHyperparameter (allow rf to impute OrdinalHyperparameter #1065)
  • fix dask_scheduler_file path (fix dask_scheduler_file path #1055)
  • Fix config rejection for Racing: Configs worse than existing incumbent are not rejected bug #1068 (Fix config rejection for #1068 #1069)
  • fix(RandomForest): Always cast seed to int

Sarah Krebs and others added 27 commits May 17, 2023 14:15
* Remove commit message from dependabot PRs (#1010)

* rename check_point_in_ss to check_subspace_point

* Make format

* Uncomment test procedure

* docstrings for boing facade

* avoid typing namespace everywhere in epm_configuration_chooser

* fix docstring in rh2epm_boing

* Limit on dask

* Trying to fix tests

* Replaced typing in all files

* docstring for boing subspace

* Changed feature requests to feature

* allow acq_optimizer_local_kwargs to be passed to boing subspace without acq_optimizer_local

* fix pre-commit

* Added any

* Update facade

* Fix typing
* Match arguments from pSMAC with SMAC4AC signature
* Add description of pSMAC to docstring
* Add option to pass facade class to pSMAC

* Add example for pSMAC

* Removed docstring in readme's example

* Corrected text

* move construct_gp_kernels to smac.epm_gpytorch.boing_kernels

* maint

* fix wrongly imported func name in tests

* Add reference for pSMAC #609

* Rename example file

* Added roadmap to readme

* Prettification

* Add result merger

* Reformat with black

* Delete unnecessary import

* Fix typing

* Inject first trajectory entry from file from first rundir

* Add test for ResultMerger

* Fix docstring

* Get runhistory and trajectory from pSMAC run

Via the result merger. Searchers rundirs and
merges found runhistories and calculates a
new trajectory.

* Get trajectory

* Add regex to requirements

* Fixed MO cache problem

* Fix MO tests

* Fixing MO in AbstractRacer

* Accepting ints

* Hacking in the sum cost for MO

* Fix mypi

* Bugfix

* Make mypi happy

* Fix tests

* Make format

* Remove num_obj in MO optimizer

* A lot of restructuring

* Solve importings

* Solve importings

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Updated changelog

* Still fixing :)

* fix docstrings

* Change directory of tests

* Fix ambiguous variable

* Del newlines

* fix mypy

* mypy and doc fix

* Removed int type checking

* fix tests

* Always return List of incs

* fix path issue in example

* maint boing facade

* Better docstring

* Return values if no bounds passed

* Removed import

* Return only one incumbent

* Rename n_optimizers -> n_workers

* Update example

* Update docstring

* Remove legacy function

* Update to new signature

* Update changelog.md

* Format black

* Update test

* Please pre-commit

* Merge development

* Fix tests

* Fix typos

* Format black

* Updated text

* Increased version

* Improved readme

* SMAC logo 50%

* SMAC logo 50%

* Removed dev-2.0

* Added doc workflow for latest tag

* Fixing docs latest tag

* Fixing docs latest tag

* First steps new intensifier

* Make it work again

* MOVE random weight initialization to smbo ask method

* ADD enable parego in unittests

* Test issues

* FIX formatting

* Link to old documentation

* MOVE random weight initialization to smbo ask method

* ADD enable parego in unittests

* FIX formatting

* Fix unit tests

* Add annotation

* corrected log prob for tophat prior

* Removed configurations from callback

* Fixed tests

* Fix mypy

* Save docs as latest version too

* Enabled all tests again

* Make version an env

* Added last version to docs

* Global variable fix

* Added v before version number

* New Intensifier Implementation (#888)

- Completely reimplemented the intensifiers (including Successive Halving and Hyperband): All intensifiers support multi-fidelity, multi-objective and multi-threading by nature now.
- Expected behaviour for ask-and-tell interface ensured (also for Successive Halving).
- Continuing a run is now fully supported.
- Added more examples.
- Updated documentation based on new implementation.

* First benchmark steps

* Added a warning

* Set xi to 0.01

* Incorporated walltime in trajectory

* Working version of benchmark

* Changed requirements

* Changed xi back to 0.0 again

* No duplicate budgets

* Fixed bug which updated tracker wrongly

* Bugfix: Delete correct bracket+stage

* Fixed tests

* Added costs to the trajectory

* Changed initial design max ratio to 0.25

* Make format

* Added more details to intensifier

* Finished benchmark

* Added benchmark source files

* Fixed tests because of initial design changes

* Improved runhistory API

* Fixed typo (#894)

* Merge doc fixes

* Doc fixes (#893)

Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>

* Make format

* Satisfied mypy

* Enabled more tests

* Increased version

* Mypy

* Mypy

* Mypy

* Fixed critical bug when using highest budget for inc selection

* Added SH+HB comparison

* Stuff

* Updated report

* Fixed docstring

* Fixed image path

* Removed vscode folder

* Bugfixes

* Doc fixes

* Updated changelog

* Make isort

* Fix typos

* Removed new line

* Added alpha2 to docs selection

* update description

* Fix 531 correctly create integers in initial design

This PR fixes a bug in which integer hyperparameters would not
be created correctly in the initial design. This went
unnoticed, except in the case where it was part of a condition
and the function deactivate_inactive_hyperparameters was
called.

This PR fixes this bug by mapping the random float that was
sampled by, for example and LHD or Sobol sequence, to the
float representation of an integer by calling _transform and
_inverse_transform of the integer hyperparameter.

* Add contact paragraph to README.

* Increase days until stale issues are closed by stalebot (#904)

* Edit changelog

* Add issue number

* Closes #907

* Clarify origin of configurations (#908)

* Random forest speed up (#903)

Co-authored-by: René Sass <[email protected]>

* Add: workflow to update pre-commit versions (#874)

Co-authored-by: René Sass <[email protected]>

* Add Git-Flow Workflow Specification

* [DOC] acquisition function maximizers

* Add stale reminder email action

* Increase version number of ConfigSpace

* Add guideline for updating copyright notice years to CONTRIBUTING.md

* Update requirement for pyrfr (#920)

* Update pre-commit: isort,flake8 version numbers

* Format black

* Fix mypy

* Ac bench (#929)

* Add Branin AC Task

* Add ac optimization type

* Nicer plotting

* Add ac mode

* Update ac task

* Make new smac env name adjustable

* Increase python version for smac 1.4

* Update benchmark

* Update plotting

* Goodby comments

* Fix path

* Fix 1.4 wrapper

* Update benchmark results

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* [DOC] added documentation on the incumbent update

* Feature/add version to make publish (#931)

* Add version, correct package name and use bash in makefile

* Increase version

* Increase version in makefile, add places with versions to make publish

* Fix typo

* Transform integer feature names to strings (#930)

* Transform int features to str

* Fix pre-commit

* Update version to 2.0.0

* Update version to 2.0.0

* Update CHANGELOG.md

* Add information on deepcave to the readme

* Correct doc version

* fix(runhistory): set id of the sampled config (#951)

* fix: Set config_id of config in runhistory

* ci: Set dependabot to target development branch (#963)

* feat: Option preventing SMAC setting up logging (#947)

* Version 2.0.0 (#898)

* Update runhistory2epm.py

* pre_commit

* Updated changelog

* Fixed comment

* Updated changelog

* Some small improvements

* Removed trailing space

* Updated changelog

* Restricted pynisher

* Updated changelog

* Link JMLR paper

* Update bibtex entry

Before: arxiv paper, now journal article.

* Fixed citation in docs

* Fixed callback typos

* BOinG for mixed hyperparameter search space

* fix format

* maint

* maint documentation

* maint pre-commit

* fix workflow

* maint

* Add dependabot for workflow files

* Bump actions/setup-python from 2 to 4 (#849)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v2...v4)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/checkout from 2 to 3 (#850)

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* maint

* Updated stale bot

* Updated stale options again

* Fixed typing

* Increased version

* rename check_point_in_ss to check_subspace_point

* Make format

* Uncomment test procedure

* docstrings for boing facade

* avoid typing namespace everywhere in epm_configuration_chooser

* fix docstring in rh2epm_boing

* Limit on dask

* Trying to fix tests

* Replaced typing in all files

* docstring for boing subspace

* Changed feature requests to feature

* allow acq_optimizer_local_kwargs to be passed to boing subspace without acq_optimizer_local

* fix pre-commit

* Added any

* Update facade

* Fix typing
* Match arguments from pSMAC with SMAC4AC signature
* Add description of pSMAC to docstring
* Add option to pass facade class to pSMAC

* Add example for pSMAC

* Removed docstring in readme's example

* Corrected text

* move construct_gp_kernels to smac.epm_gpytorch.boing_kernels

* maint

* fix wrongly imported func name in tests

* Add reference for pSMAC #609

* Rename example file

* Added roadmap to readme

* Prettification

* Add result merger

* Reformat with black

* Delete unnecessary import

* Fix typing

* Inject first trajectory entry from file from first rundir

* Add test for ResultMerger

* Fix docstring

* Get runhistory and trajectory from pSMAC run

Via the result merger. Searchers rundirs and
merges found runhistories and calculates a
new trajectory.

* Get trajectory

* Add regex to requirements

* Fixed MO cache problem

* Fix MO tests

* Fixing MO in AbstractRacer

* Accepting ints

* Hacking in the sum cost for MO

* Fix mypi

* Bugfix

* Make mypi happy

* Fix tests

* Make format

* Remove num_obj in MO optimizer

* A lot of restructuring

* Solve importings

* Solve importings

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Fixing, fixing, fixing, ...

* Updated changelog

* Still fixing :)

* fix docstrings

* Change directory of tests

* Fix ambiguous variable

* Del newlines

* fix mypy

* mypy and doc fix

* Removed int type checking

* fix tests

* Always return List of incs

* fix path issue in example

* maint boing facade

* Better docstring

* Return values if no bounds passed

* Removed import

* Return only one incumbent

* Rename n_optimizers -> n_workers

* Update example

* Update docstring

* Remove legacy function

* Update to new signature

* Update changelog.md

* Format black

* Update test

* Please pre-commit

* Merge development

* Fix tests

* Fix typos

* Format black

* Updated text

* Increased version

* Improved readme

* SMAC logo 50%

* SMAC logo 50%

* Removed dev-2.0

* Added doc workflow for latest tag

* Fixing docs latest tag

* Fixing docs latest tag

* First steps new intensifier

* Make it work again

* MOVE random weight initialization to smbo ask method

* ADD enable parego in unittests

* Test issues

* FIX formatting

* Link to old documentation

* MOVE random weight initialization to smbo ask method

* ADD enable parego in unittests

* FIX formatting

* Fix unit tests

* Add annotation

* corrected log prob for tophat prior

* Removed configurations from callback

* Fixed tests

* Fix mypy

* Save docs as latest version too

* Enabled all tests again

* Make version an env

* Added last version to docs

* Global variable fix

* Added v before version number

* New Intensifier Implementation (#888)

- Completely reimplemented the intensifiers (including Successive Halving and Hyperband): All intensifiers support multi-fidelity, multi-objective and multi-threading by nature now.
- Expected behaviour for ask-and-tell interface ensured (also for Successive Halving).
- Continuing a run is now fully supported.
- Added more examples.
- Updated documentation based on new implementation.

* First benchmark steps

* Added a warning

* Set xi to 0.01

* Incorporated walltime in trajectory

* Working version of benchmark

* Changed requirements

* Changed xi back to 0.0 again

* No duplicate budgets

* Fixed bug which updated tracker wrongly

* Bugfix: Delete correct bracket+stage

* Fixed tests

* Added costs to the trajectory

* Changed initial design max ratio to 0.25

* Make format

* Added more details to intensifier

* Finished benchmark

* Added benchmark source files

* Fixed tests because of initial design changes

* Improved runhistory API

* Fixed typo (#894)

* Merge doc fixes

* Doc fixes (#893)

Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>

* Make format

* Satisfied mypy

* Enabled more tests

* Increased version

* Mypy

* Mypy

* Mypy

* Fixed critical bug when using highest budget for inc selection

* Added SH+HB comparison

* Stuff

* Updated report

* Fixed docstring

* Fixed image path

* Removed vscode folder

* Bugfixes

* Doc fixes

* Updated changelog

* Make isort

* Fix typos

* Removed new line

* Added alpha2 to docs selection

* update description

* Fix 531 correctly create integers in initial design

This PR fixes a bug in which integer hyperparameters would not
be created correctly in the initial design. This went
unnoticed, except in the case where it was part of a condition
and the function deactivate_inactive_hyperparameters was
called.

This PR fixes this bug by mapping the random float that was
sampled by, for example and LHD or Sobol sequence, to the
float representation of an integer by calling _transform and
_inverse_transform of the integer hyperparameter.

* Add contact paragraph to README.

* Increase days until stale issues are closed by stalebot (#904)

* Edit changelog

* Add issue number

* Closes #907

* Clarify origin of configurations (#908)

* Random forest speed up (#903)

Co-authored-by: René Sass <[email protected]>

* Add: workflow to update pre-commit versions (#874)

Co-authored-by: René Sass <[email protected]>

* Add Git-Flow Workflow Specification

* [DOC] acquisition function maximizers

* Add stale reminder email action

* Increase version number of ConfigSpace

* Add guideline for updating copyright notice years to CONTRIBUTING.md

* Update requirement for pyrfr (#920)

* Update pre-commit: isort,flake8 version numbers

* Format black

* Fix mypy

* Ac bench (#929)

* Add Branin AC Task

* Add ac optimization type

* Nicer plotting

* Add ac mode

* Update ac task

* Make new smac env name adjustable

* Increase python version for smac 1.4

* Update benchmark

* Update plotting

* Goodby comments

* Fix path

* Fix 1.4 wrapper

* Update benchmark results

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* [DOC] added documentation on the incumbent update

* Feature/add version to make publish (#931)

* Add version, correct package name and use bash in makefile

* Increase version

* Increase version in makefile, add places with versions to make publish

* Fix typo

* Transform integer feature names to strings (#930)

* Transform int features to str

* Fix pre-commit

* Update version to 2.0.0

* Update version to 2.0.0

* Update CHANGELOG.md

* Add information on deepcave to the readme

* Correct doc version

---------

Co-authored-by: dengdifan <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: Matthias Feurer <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: eddiebergman <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Katharina Eggensperger <[email protected]>
Co-authored-by: Eric Kalosa-Kenyon <[email protected]>
Co-authored-by: Pascal <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: Jeroen Rook <[email protected]>
Co-authored-by: Tim Ruhkopf <[email protected]>

* feat: Option preventing SMAC setting up logging

* fix: Run isort

* Bump peter-evans/create-pull-request from 3 to 5 (#958)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3 to 5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v3...v5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/setup-python from 2 to 4 (#945)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v2...v4)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* feat: Option preventing SMAC setting up logging

* fix: Run isort

* fix: Add to changelog

* feat: Option preventing SMAC setting up logging

* fix: Run isort

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: René Sass <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: Matthias Feurer <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Katharina Eggensperger <[email protected]>
Co-authored-by: Eric Kalosa-Kenyon <[email protected]>
Co-authored-by: Pascal <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: Jeroen Rook <[email protected]>
Co-authored-by: Tim Ruhkopf <[email protected]>

* Citation update (#961)

* update CITATION.cff

* update order in CITATION.cff

* fix citation date

* fix citation

* maint

* Adjust hyperband configuration distribution across brackets

* Compute the actual differences between the isb keys. (#957)

* Compute the actual differences between the isb keys.

* Added change to CHANGELOG.md

* Adjust schedule for stale reminder

* fix(logging): Prevent automatic logging setup at init (#970)

* fix(logging): Prevent automatic logging setup at init

* fix(logging): Rely on `setup_logging` to handle arg

* Fix validate method of smbo, update docstring.

* Allow callbacks to be added to a specific index, make callback registering public

* Update CHANGELOG.md

* Fix broken references (#988)

* Adapt developer install instructions to include pre-commit installation (#994)

* [Feature] Initial Design now supports executing the default config provided by the user by means of the configspace he generated. (and is no longer ignored)

* Pipe dask_client through facade for exec on hpc (#983)

* Pipe dask_client through facade for exec on hpc

* Handle pynisher's memory arg

Before: Could only pass int via SMAC with the default unit B, but now tuple/list is possible

* Update CHANGELOG.md

* Make format

* No printi

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* [Bug-fix] Pr was failing due to mutable additional configs default

* [doc-fix] the count of initial design configs is computed slightly differently

* Feature/metadata callback (#999)

* Add example for using a callback to log run metadata to a file

* Add issue number in changelog

* Changelog formatting

* Simplify metadata example

* Simplify metadata example

* Put callback in smac directory to allow importing it in custom repos

* Move callback files to callback directory

* Edit changelog

* Correct metadata callback argument types

* Additional metadata arguments in example

* Set metadata default values in callback

* Edit comment to fix PR

* Documentation/dask client example (#1001)

* Update requirements (dask_jobqueue)

* Fix broken link

* Ignore parallel example

* Add parallelization example

* Remove imports, add comment abt dask client

* Add E's information

* Update docs

* Add comment about n_workers

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* Documentation/dask client example (#1001)

* Update requirements (dask_jobqueue)

* Fix broken link

* Ignore parallel example

* Add parallelization example

* Remove imports, add comment abt dask client

* Add E's information

* Update docs

* Add comment about n_workers

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* Feature/dask client (#1002)

* Add info message that scenario.n_workers is ignored

When passing a dask client,
directly set n_workers in client.

* Change info to warning

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* Update smac version (#1003)

* Update smac version

* Add hint on github release in make publish

* Update copyright year

* check if config in rh when storing state (#997)

* check if config in rh when storing state

* maint

* remove unnecessary changes

* Adapt developer install instructions to include pre-commit installation (#994)

* Pipe dask_client through facade for exec on hpc (#983)

* Pipe dask_client through facade for exec on hpc

* Handle pynisher's memory arg

Before: Could only pass int via SMAC with the default unit B, but now tuple/list is possible

* Update CHANGELOG.md

* Make format

* No printi

---------

Co-authored-by: Carolin Benjamins <[email protected]>

* update changelog

* Increase tolerance for runhistory restoration test

---------

Co-authored-by: Sarah Segel <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: Helena Graf <[email protected]>

* Add a workaround to be able to pass a dataset via dask.scatter (#993)

* [feat] Support dask.scatter

* [fix] Add shared_data arg in abstract_facade

* Address the comments by Eddie

* [fix] Fix errors raised by Eddie

* [format] Apply black locally

* [fix] Get retries back to 16 as it was a mistake

* [doc] Update CHANGELOG

---------

Co-authored-by: helegraf <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>

* Adding Binder links for example (#976)

* binder

* maint

* fix dependencies

* maint docs

* Revert "maint docs"

This reverts commit 4fa1a0f.

* add requirement

---------

Co-authored-by: Difan Deng <[email protected]>

* Remove commit message from dependabot PRs (#1009)

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: René Sass <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Katharina Eggensperger <[email protected]>
Co-authored-by: Matthias Feurer <[email protected]>
Co-authored-by: Eric Kalosa-Kenyon <[email protected]>
Co-authored-by: Pascal <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: Jeroen Rook <[email protected]>
Co-authored-by: Eddie Bergman <[email protected]>
Co-authored-by: Tim Ruhkopf <[email protected]>
Co-authored-by: Difan Deng <[email protected]>
Co-authored-by: Aron Bahram <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shuhei Watanabe <[email protected]>
Co-authored-by: Difan Deng <[email protected]>

* Fix broken link

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dengdifan <[email protected]>
Co-authored-by: René Sass <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Katharina Eggensperger <[email protected]>
Co-authored-by: Matthias Feurer <[email protected]>
Co-authored-by: Eric Kalosa-Kenyon <[email protected]>
Co-authored-by: Pascal <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Alexander Tornede <[email protected]>
Co-authored-by: Sarah Krebs <[email protected]>
Co-authored-by: helegraf <[email protected]>
Co-authored-by: Jeroen Rook <[email protected]>
Co-authored-by: Eddie Bergman <[email protected]>
Co-authored-by: Tim Ruhkopf <[email protected]>
Co-authored-by: Difan Deng <[email protected]>
Co-authored-by: Aron Bahram <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shuhei Watanabe <[email protected]>
Co-authored-by: Difan Deng <[email protected]>
* Remove torch requirements

* Fix format

---------

Co-authored-by: Carolin Benjamins <[email protected]>
Fix SH get best configs in case of MO
Update the workflows only to trigger extensive tests for PRs that are not in the draft stage

---------

Co-authored-by: timruhkopf <[email protected]>
Co-authored-by: Helena Graf <[email protected]>
* Add recently updated issues to list of reminders.

* Add recently updated issues to list of reminders.

* Add recently updated issues to list of reminders.
…1023)

* Add warnings for parallelism doc

* Check for parallelization + pynisher

Does not work together, throw error.
Does not work bc Dask pickles jobs and
pynisher runs the target function in a process.

* Fix whitespaces

---------

Co-authored-by: Carolin Benjamins <[email protected]>
* [enhance] Add an error for scatter data

* Update ChangeLog

---------

Co-authored-by: C. Benjamins <[email protected]>
Co-authored-by: Carolin Benjamins <[email protected]>
* Experimental instruction for installing SMAC in windows via WSL

* More detailed documentation regarding continuing runs

* Fixes

* Fixes

* Fixes

* Update docs/10_experimental.rst

Co-authored-by: Difan Deng <[email protected]>

* Fixes from PR

* Fixes from PR

* Fixes from PR

* Fixes from PR

* Fixes from PR

---------

Co-authored-by: Difan Deng <[email protected]>
* Handle configspace as dictionary in mlp example

* Adapt sgd loss to newest scikit-learn version

* Add change to changelog

* Handle configspace as dictionary in parego example

* Correct get usage
* allow rf to impute OrdinalHyperparameter

* Add missing period in docs.

* Add issue number in changelog.

---------

Co-authored-by: Sarah Krebs <[email protected]>
* fix dask_scheduler_file path

* update change log

---------

Co-authored-by: dengdifan <[email protected]>
* racing: make sure config only deleted from rejected configs if among incumbents upon update

* test case for incumbent rejection

* update code comments

* added missing newline ahead of new test case

* update change log

---------

Co-authored-by: dengdifan <[email protected]>
Co-authored-by: Difan Deng <[email protected]>
In cases where seeds were generated from some numpy objects, sometimes
you'd get back an `np.integer`, which causes the program to crash when
communicating with `pyrfr` through `swig`. It seems that swig doesn't
know that it's an _int-like_ and so we explicitly cast it to `int`.
@eddiebergman eddiebergman deleted the fix-pyrfr-int-cast-seed branch November 16, 2023 11:25
@eddiebergman eddiebergman restored the fix-pyrfr-int-cast-seed branch November 16, 2023 11:26
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