diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d8b095b3..16d6e18e7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# openproblems v2.1.0 +# openproblems v3.0.0 ## Breaking changes @@ -22,20 +22,44 @@ ## 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). diff --git a/common b/common index c5fba7efc..92cb9feaa 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit c5fba7efceb5b6dfc49a53a11cabbe8356e5d32e +Subproject commit 92cb9feaa0deb86ee267105d155be984a3f66e64