Skip to content

Update submodule and changelog #939

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
rcannood wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update submodule and changelog #939

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 25 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# openproblems v2.1.0
# openproblems v3.0.0

## Breaking changes

Expand All @@ -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).
Expand Down
2 changes: 1 addition & 1 deletion common
Open in desktop
Submodule common updated 3 files
+7 −160 component_tests/check_config.py
+8 −255 component_tests/run_and_check_output.py
+0 −17 component_tests/run_tests.py
Loading