v3.0.0

Breaking changes

• Moved src/tasks/batch_integration to task_batch_integration (PR #910).

• Moved src/tasks/denoising to task_denoising (PR #910).

• Moved src/tasks/dimensionality_reduction to task_dimensionality_reduction (PR #910).

• Moved src/tasks/label_projection to task_label_projection (PR #910).

• Moved src/tasks/match_modalities to task_match_modalities (PR #910).

• Moved src/tasks/predict_modality to task_predict_modality (PR #910).

• Moved src/tasks/spatial_decomposition to task_spatial_decomposition (PR #910).

• Moved src/tasks/spatially_variable_genes to task_spatially_variable_genes (PR #910).

• Moved src/datasets to datasets (PR #933).

Major changes

• Update results processing workflow for the new website, including new JSON schema (v4), new combine_output and filter_results components, and updated get_dataset_info, get_method_info, get_metric_info, get_results, get_task_info reporting scripts (PR #919).

• Update paper reference from preprint to published article (PR #919).

• Update Viash to 0.9.0 (PR #911).

• Update Viash to 0.9.4 (PR #925).

• Update Viash to 0.9.7 (PR #938).

Minor changes

• Add openproblems_op3 (Open Problems Perturbation Prediction) scRNA-seq dataset loader from GEO GSE279945 (PR #926, PR #930).

• Add --output_compression argument to dataset loader, normalization, and processor components (PR #930).

• Add contact email address to Code of Conduct (PR #923).

• Update Docker image tags from :1.0.0 to :1 for openproblems/base_python and openproblems/base_r images (PR #928).

• Add filter_results component and dataset/method/metric filtering arguments to the process_task_results workflow (PR #935).

• Update common submodule (PR #934).

• Add the CELLxGENE immune cell atlas dataset as a common test resource (PR #907).

• Update dataset_id for tenx_visium, zenodo_spatial, zenodo_spatial_slidetags datasets and use mouse_brain_coronal as a test resource in the spatially_variable_genes task (PR #908).

• Update get_task_info, get_method_info and get_metrics_info reporting components with more info and extend output (PR #915).

• Use new functionality in Python openproblems package to generate a project's README (PR #938).

Bug fixes

• Fix metric direction (maximize/minimize) handling in generate_qc and render_report components of the process_task_results workflow (PR #936).

• Fix bug in metric maximize handling and add raw scores table to the benchmark report (PR #937).

• Fix extracting metadata from anndata files in the extract_metadata component (PR #914).

• Fix path in touch cmd in reporting/process_task_results/run_test.sh (PR #915).