build: move pooch to dependencies decorator #3118
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…h for scanvae loss n_samples) (#2920) Backport PR #2867: fix(module): address shape mismatch for scanvae loss n_samples Co-authored-by: Martin Kim <[email protected]>
…on support) (#2919) Backport PR #2915: fix(model) get_normalized_expression support Co-authored-by: Can Ergen <[email protected]>
…s) (#2921) Backport PR #2362: Fixes error in get losses functions Co-authored-by: Can Ergen <[email protected]>
(cherry picked from commit ea43179)
) Addresses #2911 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Can Ergen <[email protected]> (cherry picked from commit 4722952)
…#2927) Backport PR #2926: Enable option to drop last batch. Co-authored-by: Can Ergen <[email protected]>
…uracy calculation) (#2943) Backport PR #2938: Error in scanvi_ref multiclass accuracy calculation Co-authored-by: Ori Kronfeld <[email protected]>
…t for many models functions) (#2950) Backport PR #2948: added the future annotations import for many models functions Co-authored-by: Ori Kronfeld <[email protected]>
…n celltype marker table) (#2954) Backport PR #2951: fix(model) check duplicated gene in celltype marker table Co-authored-by: Ori Kronfeld <[email protected]>
…2962) Backport PR #2961: Remove dependency anndata 0.10.8 Co-authored-by: Can Ergen <[email protected]>
…rial covariates in scArches) (#2964) Backport PR #2936: feat(train) Add support for categorial covariates in scArches Co-authored-by: Ori Kronfeld <[email protected]>
Backport PR #2970: Drop Python 3.9 Co-authored-by: Ori Kronfeld <[email protected]>
v1.2 manual merge with main before release --------- Co-authored-by: Can Ergen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Justin Hong <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: ori-kron-wis <[email protected]>
…er guide) (#2986) Backport PR #2960: docs: Counterfactual prediction user guide Co-authored-by: Justin Hong <[email protected]>
…orkflow) (#2988) Backport PR #2987: test: update the resolution test workflow Co-authored-by: Ori Kronfeld <[email protected]>
… test which was failing) (#2984) Backport PR #2982: test: Fix hugging face create repo test which was failing Co-authored-by: Ori Kronfeld <[email protected]>
Backport PR #2989: Update pyproject.toml Co-authored-by: Ori Kronfeld <[email protected]>
…r py312) (#2995) Backport PR #2991: release: updated v1.2.0 and RTD for py312 Co-authored-by: Ori Kronfeld <[email protected]>
# Conflicts: # .pre-commit-config.yaml # pyproject.toml
Backport PR #3000: Update pyproject.toml Co-authored-by: Ori Kronfeld <[email protected]>
…I) (#3001) Backport PR #2999: Fix warning for DA function in MrVI Co-authored-by: Justin Hong <[email protected]>
…to ball admissibility calculation) (#3009) Backport PR #3007: Change outlier detection for MRVI to ball admissibility calculation Co-authored-by: Justin Hong <[email protected]>
…s) (#3006) Backport PR #3005: docs: automated update of tutorials Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Ori Kronfeld <[email protected]>
…ecation warnings) (#3088) Backport PR #3085: misc: Address AnnData >= 0.11 deprecation warnings Co-authored-by: Ori Kronfeld <[email protected]>
…lse in torch.load functions) (#3096) Backport PR #3095: fix: Explicity use weights_only=False in torch.load functions Co-authored-by: Ori Kronfeld <[email protected]>
…3107) Backport PR #3038: feat: Mudata support for MultiVI Co-authored-by: Ori Kronfeld <[email protected]>
Co-authored-by: Martin Kim <[email protected]> Co-authored-by: Martin Kim <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: ori-kron-wis <[email protected]> Co-authored-by: Lumberbot (aka Jack) <[email protected]> Co-authored-by: Can Ergen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Justin Hong <[email protected]> Co-authored-by: Ethan Weinberger <[email protected]> Co-authored-by: Ethan Weinberger <[email protected]> Co-authored-by: access <[email protected]> Co-authored-by: Yishen Miao <[email protected]> Co-authored-by: Ramon Viñas <[email protected]>
Backport PR #3111: test: Fix slow tests Co-authored-by: Ori Kronfeld <[email protected]>
Re: [scverse/scvi-tools] feat: Change template for HuggingFace. (PR #3078) --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: ori-kron-wis <[email protected]> Co-authored-by: Lumberbot (aka Jack) <[email protected]> Co-authored-by: Martin Kim <[email protected]> Co-authored-by: Can Ergen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Justin Hong <[email protected]> Co-authored-by: Ethan Weinberger <[email protected]> Co-authored-by: Ethan Weinberger <[email protected]> Co-authored-by: access <[email protected]> Co-authored-by: Yishen Miao <[email protected]> Co-authored-by: Ramon Viñas <[email protected]>
# Conflicts: # CHANGELOG.md # docs/tutorials/notebooks
…ency # Conflicts: # docs/tutorials/notebooks
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3118 +/- ##
==========================================
- Coverage 89.38% 85.58% -3.80%
==========================================
Files 181 181
Lines 15424 15433 +9
==========================================
- Hits 13786 13208 -578
- Misses 1638 2225 +587
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…decorator) (#3119) Backport PR #3118: build: move pooch to dependencies decorator Co-authored-by: Ori Kronfeld <[email protected]>
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