Fix the blockers for the next denbi run (#115)

* fix liger build by dropping the github RcppPlanc install

* register the missing methods and metrics in run_benchmark

* add metric_type to cilisi and method_types to drvi

* let scimilarity use the gpu

* update changelog

Author: rcannood

CHANGELOG.md

@@ -60,6 +60,13 @@
 * Fix `methods/pyliger` failing to build: louvain has no python 3.12 wheel and needs cmake to build igraph from source.
 * Bump `methods/cellplm`, `methods/condo`, `methods/drvi` and `metrics/bras` from base image `:1.0.0` to `:1`, so their
     `openproblems` is new enough for the component tests in `common`.
+* Fix `methods/liger` failing to build: drop the GitHub install of RcppPlanc, which no longer configures; rliger already
+    pulls it in from CRAN.
+* Register `methods/condo`, `methods/drvi`, `methods/limma_removebatcheffect`, `methods/seurat_cca`, `methods/seurat_rpca`,
+    `methods/stacas`, `metrics/bras` and `metrics/cilisi` in the `run_benchmark` workflow; they were never run.
+* Add the missing `metric_type` to `metrics/cilisi` and `method_types` to `methods/drvi`, without which the workflow
+    never schedules them.
+* Give `methods/scimilarity` a `gpu` label and let it use the GPU when one is available; it was running CPU-only.
 * Fix `methods/scanorama` scrambling its output: scanorama returns one object per batch with the genes sorted by
     name, so both axes ended up permuted with respect to the `obs` and `var` they were labelled with. This affected
     every metric, not just `hvg_overlap`.

src/methods/drvi/config.vsh.yaml

@@ -14,6 +14,7 @@ links:
   documentation: https://drvi.readthedocs.io/latest/index.html
   repository: https://github.com/theislab/DRVI?tab=readme-ov-file
 info:
+  method_types: [embedding]
   preferred_normalization: counts
 arguments:
   - name: --n_hvg

src/methods/liger/config.vsh.yaml

@@ -26,7 +26,6 @@ engines:
         packages: cmake
       - type: r
         cran: rliger
-        github: welch-lab/RcppPlanc
 runners:
   - type: executable
   - type: nextflow

src/methods/scimilarity/config.vsh.yaml

@@ -32,4 +32,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [hightime, midmem, lowcpu]
+      label: [hightime, midmem, lowcpu, gpu]

src/methods/scimilarity/script.py

@@ -6,6 +6,7 @@
 
 import anndata as ad
 import scimilarity
+import torch
 
 ## VIASH START
 par = {
@@ -52,8 +53,12 @@
             f"The 'model' argument should be a directory a .zip file or a .tar.gz file"
         )
 
-print("Load SCimilarity model", flush=True)
-scimilarity_embedding = scimilarity.cell_embedding.CellEmbedding(model_path=model_dir)
+use_gpu = torch.cuda.is_available()
+print(f"Load SCimilarity model (use_gpu={use_gpu})", flush=True)
+scimilarity_embedding = scimilarity.cell_embedding.CellEmbedding(
+    model_path=model_dir,
+    use_gpu=use_gpu,
+)
 print("SCimilarity version:", scimilarity.__version__)
 
 print("Create input data", flush=True)

src/metrics/cilisi/config.vsh.yaml

@@ -1,6 +1,7 @@
 __merge__: ../../api/comp_metric.yaml
 name: cilisi
 info:
+  metric_type: embedding
   metrics:
     - name: cilisi
       label: CiLISI

src/workflows/run_benchmark/config.vsh.yaml

@@ -94,12 +94,15 @@ dependencies:
   - name: methods/cellplm
   - name: methods/combat
   - name: methods/combat_seq
+  - name: methods/condo
   - name: methods/density_adaptive
+  - name: methods/drvi
   - name: methods/fadvi
   - name: methods/geneformer
   - name: methods/harmony
   - name: methods/harmonypy
   - name: methods/liger
+  - name: methods/limma_removebatcheffect
   - name: methods/mnnpy
   - name: methods/pyliger
   - name: methods/sca
@@ -112,12 +115,17 @@ dependencies:
   - name: methods/scimilarity
   - name: methods/scprint
   - name: methods/scvi
+  - name: methods/seurat_cca
+  - name: methods/seurat_rpca
   - name: methods/ss_stacas
+  - name: methods/stacas
   - name: methods/uce
   # metrics
   - name: metrics/asw_batch
   - name: metrics/asw_label
+  - name: metrics/bras
   - name: metrics/cell_cycle_conservation
+  - name: metrics/cilisi
   - name: metrics/clustering_overlap
   - name: metrics/graph_connectivity
   - name: metrics/hvg_overlap

src/workflows/run_benchmark/main.nf

@@ -24,12 +24,15 @@ methods = [
   ),
   combat,
   combat_seq,
+  condo,
   density_adaptive,
+  drvi,
   fadvi,
   geneformer,
   harmony,
   harmonypy,
   liger,
+  limma_removebatcheffect,
   mnnpy,
   pyliger,
   sca,
@@ -48,7 +51,10 @@ methods = [
   ),
   scprint,
   scvi,
+  seurat_cca,
+  seurat_rpca,
   ss_stacas,
+  stacas,
   uce.run(
     args: [model: file("s3://openproblems-work/cache/uce-model-v5.zip")]
   )
@@ -58,7 +64,9 @@ methods = [
 metrics = [
   asw_batch,
   asw_label,
+  bras,
   cell_cycle_conservation,
+  cilisi,
   clustering_overlap,
   graph_connectivity,
   hvg_overlap,