openproblems-bio · KaiWaldrant · Mar 5, 2024 · Mar 5, 2024 · Mar 5, 2024 · Mar 18, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## MAJOR CHANGES
 
+* Update Denoising task to OpenProblems v2 results (PR #325).
+
 * Migrated the result scaling from R to JavaScript to allow dynamically updating the results (PR #332).
 
 ## MINOR CHANGES

diff --git a/_core b/_core
diff --git a/_openproblems b/_openproblems
diff --git a/_task_template b/_task_template
diff --git a/results/denoising/data/dataset_info.json b/results/denoising/data/dataset_info.json
diff --git a/results/denoising/data/method_info.json b/results/denoising/data/method_info.json
diff --git a/results/denoising/data/metric_info.json b/results/denoising/data/metric_info.json
+2 −0		packages/r/openproblems.docs/NAMESPACE
+2 −2		packages/r/openproblems.docs/R/openproblems.docs-package.R
+3 −14		packages/r/openproblems.docs/R/read_task_metadata.R
+44 −3		packages/r/openproblems.docs/R/render_task_readme_qmd.R
+1 −0		schemas/api_file_format.yaml
+136 −28		schemas/schema_openproblems_definitions.yaml
+0 −2		schemas/task_control_method.yaml
+0 −2		schemas/task_method.yaml
+1 −9		schemas/task_metric.yaml
+5 −0		viash/core/src/h5ad/extract_uns_metadata/config.vsh.yaml
+2 −2		viash/core/src/h5ad/extract_uns_metadata/script.py
+37 −30		CHANGELOG.md
+1 −1		src/datasets/loaders/tenx_visium/script.py
+1 −1		src/datasets/loaders/tenx_visium/test.py
+134 −147		src/datasets/resource_scripts/tenx_visium.sh
+123 −123		src/datasets/resource_scripts/zenodo_spatial.sh
+4 −4		src/datasets/resource_scripts/zenodo_spatial_slidetags.sh
+48 −0		src/datasets/resource_test_scripts/cxg_immune_cell_atlas.sh
+2 −2		src/datasets/resource_test_scripts/mouse_brain_coronal.sh
+5 −5		src/tasks/spatially_variable_genes/README.md
+2 −2		src/tasks/spatially_variable_genes/api/comp_control_method.yaml
+2 −2		src/tasks/spatially_variable_genes/api/comp_method.yaml
+2 −2		src/tasks/spatially_variable_genes/api/comp_metric.yaml
+2 −2		src/tasks/spatially_variable_genes/api/comp_process_dataset.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_common_dataset.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_dataset.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_output.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_score.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_simulated_dataset.yaml
+1 −1		src/tasks/spatially_variable_genes/api/file_solution.yaml
+2 −2		src/tasks/spatially_variable_genes/control_methods/random_ranking/script.py
+2 −2		src/tasks/spatially_variable_genes/control_methods/true_ranking/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/boostgp/script.R
+1 −1		src/tasks/spatially_variable_genes/methods/gpcounts/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/moran_i/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/nnsvg/script.R
+1 −1		src/tasks/spatially_variable_genes/methods/scgco/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/sepal/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/somde/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/spagcn/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/spagft/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/spanve/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/spark/script.R
+1 −1		src/tasks/spatially_variable_genes/methods/spark_x/script.R
+1 −1		src/tasks/spatially_variable_genes/methods/spatialde/script.py
+1 −1		src/tasks/spatially_variable_genes/methods/spatialde2/script.py
+2 −2		src/tasks/spatially_variable_genes/metrics/correlation/script.py
+2 −2		src/tasks/spatially_variable_genes/process_dataset/select_reference/config.vsh.yaml
+1 −1		src/tasks/spatially_variable_genes/process_dataset/select_reference/script.py
+2 −2		src/tasks/spatially_variable_genes/process_dataset/simulate_svg/config.vsh.yaml
+1 −1		src/tasks/spatially_variable_genes/process_dataset/simulate_svg/script.R
+2 −2		src/tasks/spatially_variable_genes/process_dataset/split_dataset/config.vsh.yaml
+1 −1		src/tasks/spatially_variable_genes/process_dataset/split_dataset/script.py
+23 −19		src/tasks/spatially_variable_genes/resources_scripts/process_datasets.sh
+15 −17		src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh
+9 −9		src/tasks/spatially_variable_genes/resources_test_scripts/mouse_brain_coronal_section1.sh
+3 −3		src/tasks/spatially_variable_genes/workflows/process_datasets/run_test.sh