Incorporate use case tutorials #665
Merged
+34
−12
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
Zethson
approved these changes
Sep 30, 2024
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #665 +/- ##
=======================================
Coverage 65.55% 65.55%
=======================================
Files 47 47
Lines 6105 6105
=======================================
Hits 4002 4002
Misses 2103 2103
|
stefanpeidli
added a commit
that referenced
this pull request
Feb 7, 2025
* 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 <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * 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 <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
stefanpeidli
added a commit
that referenced
this pull request
Feb 7, 2025
* 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 <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * 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 <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
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 <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * 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 <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * 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 <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Polish Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
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
adata.layer(doesn't exist) instead ofadata.layers, causing the code to fail whenever the layer parameter was specifiedThe Dialogue part is still missing from the Zhang tutorial, but I'll create a separate PR for that, as I'll have to run that part on the cluster.