Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Rename Param and Obs #130

Merged
merged 4 commits into from
Nov 1, 2023
Merged

Rename Param and Obs #130

merged 4 commits into from
Nov 1, 2023

Conversation

jobrachem
Copy link
Contributor

@jobrachem jobrachem commented Nov 1, 2023 •
edited
Loading

Closes #53

Notes:

  • Getting the documentation right was a little tricky, because Sphinx does not work well with two objects of the same name (except for case differences) in the same module.
  • To deal with this, I moved Param and Obs to the liesel.model.legacy module.
  • The import paths for users are not affected. I made sure that Param and Obs are imported to liesel.model.__init__.py, so they can still be used as lsl.Param and lsl.Obs
  • The two functions are marked as deprecated, issue FutureWarnings and are marked to be removed in v0.4.0, see Remove deprecations for v0.4.0 #129

@jobrachem jobrachem requested a review from wiep November 1, 2023 11:10
@jobrachem jobrachem self-assigned this Nov 1, 2023
@jobrachem
Copy link
Contributor Author

Hi @wiep, would you do the review on this one?

wiep
wiep approved these changes Nov 1, 2023
View reviewed changes
Copy link
Contributor

@wiep wiep left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

looks good to me. do you want me to build the documentation locally?

@jobrachem
Copy link
Contributor Author

jobrachem commented Nov 1, 2023 •
edited
Loading

Thanks! I think that's not necessary.

I just added a changelog entry. If you approve, feel free to merge and delete the branch.

@wiep
Copy link
Contributor

wiep commented Nov 1, 2023

great. Just a note: We need to publish a new version when we update the manuscript on arxiv so that the manuscript and software are in sync.

@wiep wiep merged commit f833af4 into main Nov 1, 2023
@jobrachem jobrachem deleted the rename-Param-Obs branch November 2, 2023 13:02
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 <hriebl@uni-goettingen.de>

* Cap BlackJAX version (#95)

* Fix PyMC tutorial (#96)

Co-authored-by: wiep <wiep@users.noreply.github.com>

* 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 <hriebl@uni-goettingen.de>

* increase timeout

* Update metadata v0.2.5

* update metadata 0.2.6-dev

* Fix Mypy errors (#102)

Co-authored-by: Gianmarco Callegher <gianmarco.callegher@uni-goettinge.de>

* More Efficient MVN Degenerate (#101)

* Efficient MVN Degenerate

* Fixed blackjax refactor error

* Refactor

* indent more code

* Update CHANGELOG.md

---------

Co-authored-by: Gianmarco Callegher <gianmarco.callegher@uni-goettinge.de>
Co-authored-by: Johannes Brachem <37882800+jobrachem@users.noreply.github.com>

* 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 <gianmarco.callegher@uni-goettingen.de>

* 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 <gianmarco.callegher@uni-goettinge.de>

* 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 <gianmarco.callegher@uni-goettinge.de>

* 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 <gianmarco.callegher@uni-goettinge.de>

* 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 <gianmarco.callegher@uni-goettinge.de>

* 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 <gianmarco.callegher@uni-goettinge.de>
Co-authored-by: Johannes Brachem <37882800+jobrachem@users.noreply.github.com>

* 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 <gianmarco.callegher@uni-goettinge.de>
Co-authored-by: Johannes Brachem <37882800+jobrachem@users.noreply.github.com>

* 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 <hriebl@uni-goettingen.de>
Co-authored-by: Gianmarco Callegher <gianmarco.callegher@uni-goettingen.de>
Co-authored-by: wiep <wiep@users.noreply.github.com>
Co-authored-by: Gianmarco Callegher <gianmarco.callegher@uni-goettinge.de>
Co-authored-by: Sebastian Lorek <sebastian.lorek@gmx.de>
Co-authored-by: Sebastian Lorek <76441080+Seb-Lorek@users.noreply.github.com>
@jobrachem jobrachem mentioned this pull request Aug 17, 2024
Merged
3 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@wiep wiep wiep approved these changes

Assignees

@jobrachem jobrachem

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Rename helper functions: Param -> param
2 participants
@jobrachem @wiep