Merge main into branch (#706)

* Set legend anchor as parameter (#660)

* Fix missing space

* Remove explicit anndata in dependencies (#666)

* Incorporate use case tutorials (#665)

* Fixed DEG layer retrieval

* Use-case tutorial icons

* Restructure tutorial page

* Subgroup tutorials

* Improve KNN label_transfer in PerturbationSpace (#658)

* Add uncertainty score in KNN label_transfer in PerturbationSpace
Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors.

* Update pre-commit-config.yaml
Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/

* Improve label imputation in PerturbationSpace class
Key changes:
- Now uses KNN graph in adata: saves cost and increases consistency
- Vectorized operations instead of expensive for loop
- Distance weighting for KNN imputation
- Quantifies uncertainty as local KNN label entropy

* Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667)

* Augur scsim warnings (#670)

* Augur scsim warnings

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Submodules

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Add PerturbationDataValidator (#672)

* Augur scsim warnings

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Submodules

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Add super draft of pertpy validator

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Polish

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Polish

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Nested try

Signed-off-by: zethson <lukas.heumos@posteo.net>

* validator in test

Signed-off-by: zethson <lukas.heumos@posteo.net>

* try uv for rtd

Signed-off-by: zethson <lukas.heumos@posteo.net>

* rtd uv

Signed-off-by: zethson <lukas.heumos@posteo.net>

* rtd uv

Signed-off-by: zethson <lukas.heumos@posteo.net>

* rtd uv fix

Signed-off-by: zethson <lukas.heumos@posteo.net>

* mb sphinx fix for validator

Signed-off-by: zethson <lukas.heumos@posteo.net>

* docs

Signed-off-by: zethson <lukas.heumos@posteo.net>

* remove PerturbationValidator from docs

Signed-off-by: zethson <lukas.heumos@posteo.net>

* remove PerturbationValidator from docs

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Latest OS for RTD

* Remove curator again

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Fix jax random array (#686)

* Fix jax random array

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Fix further jax warnings

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Fix edger

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Fix choice

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Switch to formulaic-contrasts (#682)

* Switch to formulaic-contrasts

* Cleanup

* removing design matrix workaround (#691)

Co-authored-by: Emma Dann <emmadann@comino.stanford.edu>

* Fix PyDESeq2

* Update tests

* fix typo in gitignore

* Remove contrast dataclass, which isnt used anywhere

* Fix edgeR rpy2 tests (#692)

* fix broken rpy2 edger tests

* updated edger tests

* Fix tests (scipy)

Signed-off-by: zethson <lukas.heumos@posteo.net>

* submodule

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Remove unused code

Signed-off-by: zethson <lukas.heumos@posteo.net>

* type hints

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
Co-authored-by: Emma Dann <32264060+emdann@users.noreply.github.com>
Co-authored-by: Emma Dann <emmadann@comino.stanford.edu>
Co-authored-by: zethson <lukas.heumos@posteo.net>

* Release 0.9.5

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Prepare 0.10.0

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Added Mixscape seeds and test (#683)

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

* Fix probability data type (#696)

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Optimize MeanVarDistributionDistance (#697)

* Fix probability data type

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Optimize mean_var distance

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

---------

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Optimize test speed (#699)

* Try buildjet

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Try buildjet large

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* speed up predict_differential_prioritization

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* speed up tests

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

---------

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Lower bound for scikit-learn (#701)

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Fix type annotation

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* Fix empty figure returns when show=True in plotting functions (#703)

* Removed show parameter

* Adapt plotting API for Augur, Coda, Dialogue

* Adapted plotting API for Milo, Mixscape, scgen

* Add joblib

* Remove joblib

---------

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

* Fix scikit-learn intendation

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Co-authored-by: Lilly May <93096564+Lilly-May@users.noreply.github.com>
Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Emma Dann <32264060+emdann@users.noreply.github.com>
Co-authored-by: Emma Dann <emmadann@comino.stanford.edu>