Update decorator requirement from <5.0 to <6.0 #6
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Updates the requirements on [decorator](https://github.com/micheles/decorator) to permit the latest version. - [Release notes](https://github.com/micheles/decorator/releases) - [Changelog](https://github.com/micheles/decorator/blob/master/CHANGES.md) - [Commits](micheles/decorator@decorator-3.4.0...5.1.1) --- updated-dependencies: - dependency-name: decorator dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
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* init spatial * spatial decomposition * init cleanup * run precommit * README update * updated readme * api update * pre-commit * readme update * api stylefix * pre-commit * metrics update * linting * pre-commit * black * linting fix * pre-commit * cleanup * cleanup * linting * linting * task name change * Rctd (#6) Co-authored-by: almaan <[email protected]> * add stereoscope - nnls - nusvr - vanillanmf - nmfreg (#4) Co-authored-by: Hirak Sarkar <[email protected]> * Seurat (#8) Co-authored-by: almaan <[email protected]> * adding simulation (#7) Co-authored-by: giovp <[email protected]> Co-authored-by: almaan <[email protected]> * reorder requirements * Update mse.py * update R2 description * review comments, populated __init__.py files for import * update import statements * fix label dataset * Specify image * fix random * fix labels * pre-commit * add test=False * add synth data from destVI * remove logger * return spatial reference in correct format * specify cell type label * add destVI simulation to datasets * fix random * fix nusvr * fix stereoscope * added destvi * added destvi * try fix data generation * fix from previous delete * add scvitools version * Synthetic data generation (#9) * tangram first * tangram first * tangram first * tangram first * flake8 + isort _destvi_utils * tangram update; pancreas add string index * tangram update; pancreas add string index * tangram update; pancreas add string index; n_obs = 1000 in synth data * tangram update; pancreas add string index; n_obs = 1000 in synth data * new synth * add tangram-sc to docker * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * merge and split sc and st data * merged anndata in methods * merged anndata in methods * fix destvi * add code reference * shorten * Update openproblems/tasks/spatial_decomposition/_utils.py Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * comment fix * comment fix * fix pancreas dataset * update readme * fix destvi genertaion * fix sparse * minor fix * drop csr_matrix; fix double merge of anndata; update seurat v3 * updates * fix test for sparse arrays * test=False * add geos to r-extras * geos before r install * add software-properties-common * add python-software-properties * add RUN before command * rm geos from r-base * fix merging of anndata by pinning higher version * revert back anndata * fix obs_names and pin anndata * try to add swap * reduce number of spatial spots * remove swap * reduce obs * remove swap * remove step in CI * decrease dataset size * remove sparse * remove copy * remove datasets * remove datasets from init * address scott comments * skip all pancreas * fix import * remove destiv * Merge `main` into `synthetic-data-generation` (#10) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> * change test * fix from_cache * pre-commit * update data generation to remove inf * change test * check task * resolve suggestions from scott Co-authored-by: almaan <[email protected]> Co-authored-by: Giovanni Palla <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> * Remove duplicate line * Fill in baseline decorator * Check R version of seurat * pre-commit * Remove reference to __from_cache__ * Clean up proportions assert * pre-commit * set merge='unique' to retain uns * fixes from scott comments * Fix code_version for new API * Set `max_epochs` on `test` * pre-commit * Temporarily remove destvi * Add dataset metadata fields * Add task summary * Temporarily remove steroscope * pre-commit * Fix typo * Copy `uns` * fix uns_merge to include _from_cache * convert NaNs in categorical dtypes * convert string dtypes * bump tangram-sc * fix string dtypes * convert strings to categoricals inside pancreas * change api label to str * obsm cannot be pd.DataFrame * revert anndata change * fix rctd * fix R2 * fix lots of things * fix nmfreg and sample method * address scott comments * add metadata attribute decorator * Update r_requirements.txt * Handle comments in `r_requirements.txt` * Rename spacexr * Move API below metrics * Rename NNLS * Fix RCTD code URL * Set n_pcs in RCTD python call * Revert 2077c35 * Set n_pca in seuratv3.py * use `n_pcs` in seuratv3.R * Split string rather than skipping QA * Shorten line lengths * shorten line lengths * Clean up comment * Delete pbmc3k_raw.h5ad * Rename R2.py to r2.py * Fix reference to r2.py * pre-commit * Rename sc_to_sp.py to pancreas.py * Rename _sc_and_sp_utils.py to utils.py * rename _utils.py to utils.py * pre-commit * import all pancreas datasets * fix typo * fix namespace clash * need to pass test arg * fix method name (0_1 -> 0_5) * check tower auth explicitly * filter genes and cells * filter_genes_cells is in-place * remaining todos from scott * add destvi dataset * delete scvi models and dataset * fix shell string * one more syntactic fix * Add tangram to readme * Specify cell types in description * pre-commit * Better dataset descriptors * Clean up * Split don't skip * handle random_state * Fix doi URL * Move import inside * Shorten line lengths * Remove commented imports * Shorten descriptors * Fix seuratv3 URL * Remove unused projection_type arg * Remove unused toarray * Remove unused toarray * Update vanillanmf.py * Remove unused DataFrame handler * Remove unused categorical handler * Remove unused pandas import * update nmfreg * fix nmfreg * fix vanilla * fix nmf * fix alpha * rctd * pre-commit * add dataset_reference * shorten line lengths * document PYTEST_MAX_RETRIES * Allow 429 too many requests Co-authored-by: almaan <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Alma Andersson <[email protected]> Co-authored-by: Hirak Sarkar <[email protected]> Co-authored-by: Daniel Burkhardt <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
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Updates the requirements on decorator to permit the latest version.
Changelog
Sourced from decorator's changelog.
... (truncated)
Commits
ad013a2Updated changelog and bumped version to 5.1.15a20232Fixed implementation of decorator_apply9cf8151Merge pull request #137 from borishim/master5478aa3Check with inspect.routine()d5d65adMerge branch 'master' of github.com:micheles/decoratorbaf1297Fixed the ContextManagerf3daf42Merge pull request #135 from arthurzam/mastera3a8c1dsetup.cfg: Replace dashes with underscoresd37eebcMerge pull request #134 from hugovk/master7002507Add support for Python 3.10Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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