Install argparse in oras fcps, reduce benchmark scope

Author: imallona

Clustering_conda.yml

@@ -123,11 +123,11 @@ stages:
           commit: "45e43d3"
         parameters:
           - values: ["--linkage", "complete"]
-          - values: ["--linkage", "ward"]
-          - values: ["--linkage", "average"]
-          - values: ["--linkage", "weighted"]
-          - values: ["--linkage", "median"]
-          - values: ["--linkage", "centroid"]
+          # - values: ["--linkage", "ward"]
+          # - values: ["--linkage", "average"]
+          # - values: ["--linkage", "weighted"]
+          # - values: ["--linkage", "median"]
+          # - values: ["--linkage", "centroid"]
       - id: sklearn
         name: "sklearn"
         software_environment: "clustbench"
@@ -137,9 +137,9 @@ stages:
           commit: 5877378
         parameters:
           - values: ["--method", "birch"]
-          - values: ["--method", "kmeans"]
+          # - values: ["--method", "kmeans"]
           # - values: ["--method", "spectral"] ## too slow
-          - values: ["--method", "gm"]
+          # - values: ["--method", "gm"]
       - id: agglomerative
         name: "agglomerative"
         software_environment: "clustbench"
@@ -148,8 +148,8 @@ stages:
           commit: 5454368
         parameters:
           - values: ["--linkage", "average"]
-          - values: ["--linkage", "complete"]
-          - values: ["--linkage", "ward"]
+          # - values: ["--linkage", "complete"]
+          # - values: ["--linkage", "ward"]
       - id: genieclust
         name: "genieclust"
         software_environment: "clustbench"
@@ -158,8 +158,8 @@ stages:
           commit: 6090043
         parameters:
           - values: ["--method", "genie", "--gini_threshold", 0.5]
-          - values: ["--method", "gic"]
-          - values: ["--method", "ica"]
+          - # values: ["--method", "gic"]
+          # - values: ["--method", "ica"]
       - id: fcps
         name: "fcps"
         software_environment: "fcps"
@@ -202,11 +202,11 @@ stages:
           - values: ["--metric", "adjusted_rand_score"]
           - values: ["--metric", "fm_score"]
           - values: ["--metric", "mi_score"]
-          - values: ["--metric", "normalized_clustering_accuracy"]
-          - values: ["--metric", "normalized_mi_score"]
-          - values: ["--metric", "normalized_pivoted_accuracy"]
-          - values: ["--metric", "pair_sets_index"]
-          - values: ["--metric", "rand_score"]
+          # - values: ["--metric", "normalized_clustering_accuracy"]
+          # - values: ["--metric", "normalized_mi_score"]
+          # - values: ["--metric", "normalized_pivoted_accuracy"]
+          # - values: ["--metric", "pair_sets_index"]
+          # - values: ["--metric", "rand_score"]
     inputs:
       - entries:
           - clustering.predicted_ks_range

Clustering_oras.yml

@@ -123,11 +123,11 @@ stages:
           commit: "45e43d3"
         parameters:
           - values: ["--linkage", "complete"]
-          - values: ["--linkage", "ward"]
-          - values: ["--linkage", "average"]
-          - values: ["--linkage", "weighted"]
-          - values: ["--linkage", "median"]
-          - values: ["--linkage", "centroid"]
+          # - values: ["--linkage", "ward"]
+          # - values: ["--linkage", "average"]
+          # - values: ["--linkage", "weighted"]
+          # - values: ["--linkage", "median"]
+          # - values: ["--linkage", "centroid"]
       - id: sklearn
         name: "sklearn"
         software_environment: "clustbench"
@@ -137,9 +137,9 @@ stages:
           commit: 5877378
         parameters:
           - values: ["--method", "birch"]
-          - values: ["--method", "kmeans"]
+          # - values: ["--method", "kmeans"]
           # - values: ["--method", "spectral"] ## too slow
-          - values: ["--method", "gm"]
+          # - values: ["--method", "gm"]
       - id: agglomerative
         name: "agglomerative"
         software_environment: "clustbench"
@@ -148,8 +148,8 @@ stages:
           commit: 5454368
         parameters:
           - values: ["--linkage", "average"]
-          - values: ["--linkage", "complete"]
-          - values: ["--linkage", "ward"]
+          # - values: ["--linkage", "complete"]
+          # - values: ["--linkage", "ward"]
       - id: genieclust
         name: "genieclust"
         software_environment: "clustbench"
@@ -158,8 +158,8 @@ stages:
           commit: 6090043
         parameters:
           - values: ["--method", "genie", "--gini_threshold", 0.5]
-          - values: ["--method", "gic"]
-          - values: ["--method", "ica"]
+          # - values: ["--method", "gic"]
+          # - values: ["--method", "ica"]
       - id: fcps
         name: "fcps"
         software_environment: "fcps"
@@ -202,11 +202,11 @@ stages:
           - values: ["--metric", "adjusted_rand_score"]
           - values: ["--metric", "fm_score"]
           - values: ["--metric", "mi_score"]
-          - values: ["--metric", "normalized_clustering_accuracy"]
-          - values: ["--metric", "normalized_mi_score"]
-          - values: ["--metric", "normalized_pivoted_accuracy"]
-          - values: ["--metric", "pair_sets_index"]
-          - values: ["--metric", "rand_score"]
+          # - values: ["--metric", "normalized_clustering_accuracy"]
+          # - values: ["--metric", "normalized_mi_score"]
+          # - values: ["--metric", "normalized_pivoted_accuracy"]
+          # - values: ["--metric", "pair_sets_index"]
+          # - values: ["--metric", "rand_score"]
     inputs:
       - entries:
           - clustering.predicted_ks_range

envs/fcps_singularity.def

@@ -31,7 +31,7 @@ From: rocker/tidyverse:4.3.3
     Rscript -e 'BiocManager::install(c("kernlab", "cclust", "dbscan", "kohonen", "MCL", "ADPclust", "cluster", "DatabionicSwarm", "orclus", "subspace", "flexclust", "ABCanalysis", "apcluster", "pracma", "EMCluster", "pdfCluster", "parallelDist", "plotly", "ProjectionBasedClustering", "GeneralizedUmatrix", "mstknnclust", "densityClust", "parallel", "energy", "R.utils", "tclust", "Spectrum", "genie", "protoclust", "fastcluster", "clusterability", "signal", "reshape2", "PPCI", "clustrd", "smacof", "rgl", "prclust", "dendextend", "moments", "prabclus", "VarSelLCM", "sparcl", "mixtools", "HDclassif", "clustvarsel", "knitr", "rmarkdown", "FCPS"))' 
 
     ## no versioning here -- plotting deps
-    Rscript -e 'BiocManager::install(c("rmarkdown", "svglite", "ggplot2", "tidyr", "ComplexHeatmap"))' 
+    Rscript -e 'BiocManager::install(c("rmarkdown", "svglite", "ggplot2", "tidyr", "ComplexHeatmap", "argparse"))' 
 
     echo '. /opt/default/bin/activate' >> $SINGULARITY_ENVIRONMENT