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Goose-based Initialization strategies #72

Merged
merged 22 commits into from
Sep 14, 2023
Merged

Goose-based Initialization strategies #72

merged 22 commits into from
Sep 14, 2023

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GianmarcoCallegher
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@GianmarcoCallegher GianmarcoCallegher self-assigned this Jul 12, 2023
@GianmarcoCallegher GianmarcoCallegher added comp:goose This issue is related to the goose module enhancement New feature or request labels Jul 12, 2023
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@hriebl I don't know if I should use Option for _initi_startegies. If so, at some point I should get the value of the object. This can be done using the property value of the class. This works for some tests but for others I get the following error: AttributeError: 'dict' object has no attribute 'value'

hriebl
hriebl reviewed Jul 14, 2023
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Thank you for your work! I've added a few first comments. One more thought: Maybe we should not call the attribute self._init_strategies but self._jitter_fns, etc. I know I came up with the original name, but self._jitter_fns seems shorter and more descriptive.

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Ready for the second check. There are 2 warnings generated by some incompatible type with the new version of jax. See #73

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hriebl requested changes Aug 9, 2023
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Thank you for the update! I've fixed a typo and a few minor things, plus there are two more comments below.

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hriebl commented Aug 29, 2023

Is this ready for another round of review, @GianmarcoCallegher?

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Is this ready for another round of review, @GianmarcoCallegher?

Yes

@hriebl hriebl self-requested a review September 1, 2023 12:56
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hriebl approved these changes Sep 14, 2023
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Thank you for providing the additional tests, @GianmarcoCallegher! This is now ready to be merged.

@hriebl hriebl merged commit ddb6d15 into main Sep 14, 2023
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@hriebl hriebl deleted the init_strategy branch September 14, 2023 12:36
GianmarcoCallegher added a commit that referenced this pull request Feb 9, 2024
@jobrachem @hriebl
@GianmarcoCallegher @wiep @Seb-Lorek
Try to update calc on init (#92)
df53f7d 
* correct sampling for sigma_sq

* try to update calc on init

Update nodes.py

* fix test

Due to the exception being caught and re-raised in the update() method, we do not get the actual error text here.

* Add Goose-based initialization strategies / jittering (#72)

Co-authored-by: Hannes Riebl <[email protected]>

* Cap BlackJAX version (#95)

* Fix PyMC tutorial (#96)

Co-authored-by: wiep <[email protected]>

* Fix mypy errors (#97)

* Improve import name

* Fix title in plot_scatter(), closes #98

* Adapt to BlackJAX 1.0.0 (#100)

Co-authored-by: Hannes Riebl <[email protected]>

* increase timeout

* Update metadata v0.2.5

* update metadata 0.2.6-dev

* Fix Mypy errors (#102)

Co-authored-by: Gianmarco Callegher <[email protected]>

* More Efficient MVN Degenerate (#101)

* Efficient MVN Degenerate

* Fixed blackjax refactor error

* Refactor

* indent more code

* Update CHANGELOG.md

---------

Co-authored-by: Gianmarco Callegher <[email protected]>
Co-authored-by: Johannes Brachem <[email protected]>

* Fix #103 (#109)

* Update summary_m.py

* Update CHANGELOG.md

* Update deprecation message

* update deprecation messages

* Rename Param and Obs (#130)

* change names

* update usage in tests

* update usage in README

* Update CHANGELOG.md

* Make error_df public (closes #94) (#137)

* Update summary_m.py

* Update CHANGELOG.md

* Fix comparing samplers tutorial (closes #107) (#134)

* adapt to lower/case obs and param

* include rank and log?pdet in graph

* split single NUTS kernel up

* Fix group tutorial (closes #131) (#135)

* adapt to lower/case obs and param

* include rank and log?pdet in graph

* fix wrong variable names

* Update 07-groups.qmd

---------

Co-authored-by: Gianmarco Callegher <[email protected]>

* Expose sampling results (#138)

* export SamplingResults

* Update CHANGELOG.md

* Refactor goose-models to goose-interfaces (closes #110) (#136)

* Rename goose "models" to "interfaces"

* add warnings

* rename and move GooseModel -> LieselInterface

* update names in other parts of the code

* Update CHANGELOG.md

* restore goose.models module

* call super

* MVN Degenerate from smoothing param (#133)

* MVN Degenerate from smoothing param

* Added log prob test

* Fix pre commit error

* Refactor. Back to old naming

---------

Co-authored-by: Gianmarco Callegher <[email protected]>

* update revision of hooks in pre-commit-config (#139)

* fix typo

* update lsl.Node docs

* update Data docs

* update calc docs

* update dist docs

* update var docs

* Update config to avoid seaborn warnings

* Revert "Update config to avoid seaborn warnings"

This reverts commit 0bed211.

* update obs and param docs

* fix deprecation message of add_groups

* activate docs builds for PRs

* Update config to avoid seaborn warnings (#141)

Co-authored-by: Gianmarco Callegher <[email protected]>

* update graphbuilder docs

* update model docs

* update enginebuilder docs

* update interface docs

* Update README.md

* Add model and goose overview (#145)

* add overview pages to docs

* Update goose.rst

* Update index.rst

* Update nodes.py

* fix typo

* Jittering Functions documentation (#144)

* Jittering functions documentation

* Simpler example

* Simpler example

* Simpler example

* Removed set_duration and build

* Back to param

* Pre-commit happy

* Updated doc if jitter functions are not provided

---------

Co-authored-by: Gianmarco Callegher <[email protected]>

* Make GEV tutorials to work (#140)

* Make GEV tutorial to work

* Updated tutorial and jitter fn for tau2

* truncated_normal fixed for pytest

---------

Co-authored-by: Gianmarco Callegher <[email protected]>

* update linear regression tutorial

* Update 01a-transform.qmd

* Update 02-ls-reg.qmd

* remove mistakenly added lines

* add pointer to tutorials

update link

* update deprecation warning message

* Update docs.yml

* Fix some pytets warnings (#147)

* Fix some pytets warnings

* Update test_goose.py

---------

Co-authored-by: Gianmarco Callegher <[email protected]>
Co-authored-by: Johannes Brachem <[email protected]>

* Update CHANGELOG.md

* Update __version__.py

* Update __version__.py

* Different seed GEV tutorials

* Allow passing key as seed

* add

* change type to be consistent with Goose

* pin pymc version

* Implements NamedTupleInterface (#151)

* Adds NamedTupleInterface

* Format

* Add documentation

* Export NamedTupleInterface in goose.__init__.py

* Format

* Update documentation

* Update CHANGELOG.md

* Updated version

* Update CHANGELOG.md

* fix name `basis_matrix` in 07-groups.qmd (#166)

* Better data generation for location-scale regression tutorial

* Fixed deprecated warnings

* Update docs (#169)

* Update model.rst

* Update __version__.py

* Raise error if duplicate nodes are detected in GraphBuilder.transform (#167)

* Transform method handles nodes duplicates

* Refactor

* Added tests. Removed useless check

* Update CHANGELOG.md

* rename and move test

* rephrase message

* remove unnecessary code

---------

Co-authored-by: Gianmarco Callegher <[email protected]>
Co-authored-by: Johannes Brachem <[email protected]>

* try to update calc on init

Update nodes.py

* fix test

Due to the exception being caught and re-raised in the update() method, we do not get the actual error text here.

* implement init argument

* fix Calc docs

* Update CHANGELOG.md

* Removed duplicated logger in nodes module

---------

Co-authored-by: Hannes Riebl <[email protected]>
Co-authored-by: Gianmarco Callegher <[email protected]>
Co-authored-by: wiep <[email protected]>
Co-authored-by: Gianmarco Callegher <[email protected]>
Co-authored-by: Sebastian Lorek <[email protected]>
Co-authored-by: Sebastian Lorek <[email protected]>
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