Fix 26aug (#139)

* adapted anndata version. issue #137

* removed old implementations (bras and n_peaks_inconsistency)

* remove shuffle integration by batch/cell type as they are not used anymore

* Removed shuffle_by_batch/cell_type mentions in other files

* Updated changelog

Author: LuLeom

CHANGELOG.md

@@ -193,6 +193,7 @@
 * `run_benchmark`: write the commit the workflow ran from and the launch time into
   `task_info.yaml`, instead of publishing `_viash.yaml` verbatim (PR #136).
 
+* Remove `metrics/bras` , `metrics/n_inconsitent_peaks` and `control_methods/shuffle_by_cell_type` and `control_methods/batch`
 
 ## BUG FIXES
 
@@ -260,3 +261,5 @@
 
 
 * Fix check cell_type_in_both to > 0 (instead of 1) and some spelling mistakes in print.
+
+* Updated anndata version to 0.12 in lisi metric to support NULL writing (PR #139)

scripts/run_benchmark/wehi_hpc/images.txt

@@ -2,8 +2,6 @@ docker://ghcr.io/openproblems-bio/openproblems/utils/extract_uns_metadata:build_
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/no_integration:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/perfect_integration:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_globally:build_setup_run_hpc
-docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_within_batch:build_setup_run_hpc
-docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_within_cell_type:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/batchadjust_all_controls:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/batchadjust_one_control:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/combat:build_setup_run_hpc

src/control_methods/shuffle_integration_within_batch/config.vsh.yaml

@@ -110,7 +110,7 @@ engines:
         packages:
           - jax~=0.6.2
           - jaxlib~=0.6.2
-          - anndata~=0.11.0
+          - anndata~=0.12.0
           - scanpy~=1.11.0
           - scib-metrics~=0.5.7
           - pyyaml