v1.0.0

Note: This changelog was automatically generated from the git log.

New functionality

• Added cell2location to the spatial_decomposition task.
• Added nearest-neighbor ranking matrix computation to _utils.
• Datasets now store nearest-neighbor ranking matrix in adata.obsm["X_ranking"].
• Added support for parsing Nextflow output and generating benchmark results for the website.
• Added max_samples parameter to qlocal, qglobal, qnn_auc, lcmc, qnn, and continuity metrics to allow for subsampling of data for faster computation.
• Added new scArches based methods: scarches_scanvi_xgb_all_genes and scarches_scanvi_xgb_hvg.
• Added prediction_method parameter to _scanvi_scarches to specify prediction method.
• Added _pred_xgb function to perform XGBoost prediction based on latent representations.
• Added obsm parameter to _xgboost function to allow specifying the embedding space for XGBoost training.

Major changes

• Updated scvi-tools to version 0.20 in both Python and R environments.
• Updated datasets to include nearest-neighbor ranking matrix.
• Modified dimensionality reduction task to include nearest-neighbor ranking matrix computation in dataset generation.
• The website update workflow was refactored to use a new workflow using json instead of markdown.
• Updated the website generation process to remove duplicate BibTex entries.
• Added a new parse_metadata.py script for generating metadata for the website.
• Added a new function to openproblems.utils.py to get the member ID of a task, dataset, method or metric.
• Removed the redundant computation and storage of the nearest-neighbor ranking matrix in datasets.

Minor changes

• Updated method names to be shorter and more consistent across tasks.
• Improved method summaries for clarity.
• Updated JAX and JAXlib versions to 0.4.6.
• Updated dependencies to support new versions of Snakemake and GitPython.
• Removed code related to "nbt2022-reproducibility" repo and merged it into the main website.
• Updated the schema for benchmark results to include submission time, code version, and resource usage metrics.
• Improved error handling and added logging to the parsing script.
• Removed the "raw.json" file from the results directory and merged all data into a single "results.json" file.
• Updated the workflow to upload the final results to the website's results directory instead of the data directory.
• Removed unnecessary code and refactored the parsing script for better readability.
• Added unit tests for the new parsing script.
• Updated the run_tests workflow to skip testing on the test_website branch.
• Updated the run_tests workflow to skip testing on the test_process branch.
• Updated the create-pull-request step to set the author for the pull request.
• Updated the run_tests workflow to skip testing on pull request reviews.
• Updated the update_website_content workflow to update the website on the main branch.
• Updated the main.bib file to fix a typo.
• Removed extraneous headings from task README files.
• Updated generate_test_matrix.py to use the new openproblems.utils.get_member_id function.
• Updated the website generation process to copy BibTex files to the correct location.
• Updated the process_requires section in setup.py to include gitpython.
• Updated git commit hash generation for openproblems functions.
• Modified _xgboost to allow for specifying tree_method.
• Modified _scanvi_scarches to consistently use unlabeled_category.
• Modified _scanvi_scarches to remove unnecessary copying of labels.
• Removed _scanvi_scarches functions that were redundant with _scanvi_scarches.
• Removed unused _scanvi functions.
• Modified _scanvi_scarches to allow for specifying prediction_method and handle unlabeled_category consistently.

Documentation

• Improved the documentation of the auprc metric.
• Improved the documentation of the cell2location methods.
• Document sub-stub task behaviour

Bug fixes

• Fixed an error in neuralee_default where the subsample_genes argument could be too small.
• Fixed an error in knn_naive where the is_baseline argument was set to False.
• Fixed calculation of ranking matrix in _utils to include ties.
• Fixed a bug in load_tenx_5k_pbmc() where a warning about non-unique variable names was being raised.
• Removed the unused _utils.py file.
• Removed the X_ranking entry from the obsm attribute of datasets.
• The _fit() function in nn_ranking.py now subsamples the data if max_samples is specified.
• The nn_ranking metrics now use subsampling in the _fit() function to improve performance.
• Fixed the git hash generation for openproblems functions
• Fixed a warning about pkg_resources being deprecated
• Removed unnecessary fetch-depth: 1 from workflow
• Fixed potential issue in _scanvi_scarches where labels_pred could be overwritten
• Fixed potential issue in _pred_xgb where num_round wasn't being used correctly
• Fixed an issue where baseline methods were not being filtered correctly from the benchmark results.
• Fixed an issue where metrics with all NaN values were not being removed from the benchmark results.
• Fixed an issue where some metrics were not being parsed correctly from the Nextflow output.
• Fixed an issue where the "mean_score" field was not being calculated correctly for each method.
• Fixed an issue where the "code_version" field was not being populated correctly for each method.
• Fixed an issue where the "submission_time" field was not being populated correctly for each method.
• Fixed an issue where the resource usage metrics were not being parsed correctly from the Nextflow output.
• Updated the run_tests workflow to skip testing on the test_website branch.
• Updated the run_tests workflow to skip testing on the test_process branch.
• Updated the create-pull-request step to set the author for the pull request.
• Updated the run_tests workflow to skip testing on pull request reviews.
• Updated the `update_website_

Full Changelog: v0.8.0...v1.0.0