Merge main into branch #706
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials
* 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
* 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>
* 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>
Signed-off-by: zethson <lukas.heumos@posteo.net>
* 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 * 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>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
* 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>
* 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>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
* 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>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Zethson
added a commit
that referenced
this pull request
Feb 20, 2025
* Implement mixture models for guide assignment Key additions: - Added a base abstract class "MixtureModel" with numpyro - Added a first mixture model "Poisson_Gauss_Mixture" - New function "assign_mixture_model" in GuideAssignment class * Merge main into branch (#705) * 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> * 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> * Refactor guide assignment logic and enhance mixture model parameters * Cleanup MixtureModel class * Enhance guide assignment validation and error handling in GuideAssignment class * Update dev nb * Add test for grna_mixture_model * Remove dev nb * Update notebook for guide assignment * Update guide assignment notebooks * Apply suggestions from code review Review comments by @Zethson Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> * Improve code to fit review suggestions - Added lots of type hints and return types - Improved naming of variables - Added and removed a few comments - Added user warnings if a guide is not expressed at all * Fix sloppy data dimensions for numpyro Previously data was (N,1) dim. Now applying ravel, and changed numpyro plates accordingly for correct batching. * Update test_grna_assignment.py We changed "Negative" to "negative" :) * Polish Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * Polish 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>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR Checklist
docsis updatedDescription of changes
Technical details
Additional context