remove rmarkdown dedicated singularity image

Author: btraven00

Clustering.yaml

@@ -56,7 +56,8 @@ stages:
         software_environment: "clustbench"
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters: # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] # 2 1
           # - values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] #  2 1

Clustering_apptainer_optimized.yml

@@ -25,7 +25,7 @@ software_environments:
     description: "R with some plotting dependencies"
     conda: envs/rmarkdown.yml # not used
     envmodule: na
-    apptainer: envs/rmarkdown.sif
+    apptainer: envs/fcps.sif  # we reuse fcps env
 
 
 metric_collectors:
@@ -50,7 +50,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters:  # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
           - values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] #	2	1

Clustering_apptainer_vanilla.yml

@@ -25,7 +25,7 @@ software_environments:
     description: "R with some plotting dependencies"
     conda: envs/rmarkdown.yml # not used
     envmodule: na
-    apptainer: envs/rmarkdown.sif
+    apptainer: envs/fcps.sif  # we reuse fcps env
 
 
 metric_collectors:
@@ -50,7 +50,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters:  # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
           - values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] #	2	1

Clustering_apptainer_vanilla_smoketest.yml

@@ -47,7 +47,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters: # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
     outputs:

Clustering_conda.yml

@@ -50,7 +50,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters:  # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
           - values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] #	2	1

Clustering_conda_smoketest.yml

@@ -47,7 +47,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters: # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
     outputs:

Clustering_envmodules.yml

@@ -50,7 +50,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters: # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
           - values: [

Clustering_envmodules_smoketest.yml

@@ -47,7 +47,8 @@ stages:
         software_environment: clustbench
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters: # comments depict the possible cardinalities and the number of curated labelsets
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
     outputs:

Clustering_oras.yml

@@ -40,7 +40,8 @@ stages:
         software_environment: "clustbench"
         repository:
           url: https://github.com/imallona/clustbench_data
-          commit: 366c5a2
+          commit: 31ac323
+
         parameters:
           - values: ["--dataset_generator", "fcps", "--dataset_name", "atom"] #	2	1
           - values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] #	2	1

envs/build_singularity.sh

@@ -4,5 +4,5 @@ BUILD='build --fakeroot'
 $CMD ${BUILD} clustbench-vanilla.sif clustbench_apptainer_vanillapy.def
 # enable this if you want to compare with the custom python compilation
 # $CMD ${BUILD} clustbench-optimized.sif clustbench_apptainer_optimized.def
-$CMD ${BUILD} fcps.sif fcps.def
-$CMD ${BUILD} rmarkdown.sif rmarkdown.def  # this one is very similar to fcps, remove
+#$CMD ${BUILD} fcps.sif fcps.def
+#$CMD ${BUILD} rmarkdown.sif rmarkdown.def  # this one is very similar to fcps, remove