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Draft Denmark YMLs #37

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a0f7a6b
Reduce the benchmarking scope, remove Daniel's commented components, …
imallona Oct 28, 2025
6c4622d
Remove old workflows, make ymls even slimmer
imallona Oct 28, 2025
14ae8f0
Update the arm recipe -for fcps, not clustbench. Untested.
imallona Oct 28, 2025
d0d6a73
Update ARM FCPS recipe as in https://github.com/btraven00/clustering_…
imallona Oct 29, 2025
74accae
Empty commit to try dev after merging https://github.com/omnibenchmar…
imallona Nov 6, 2025
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69 changes: 0 additions & 69 deletions .github/workflows/micromamba.yml.old
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78 changes: 0 additions & 78 deletions .github/workflows/miniconda_miniforge.yml.old
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60 changes: 0 additions & 60 deletions .github/workflows/oras.yml.old
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124 changes: 19 additions & 105 deletions Clustering_conda.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,15 @@ stages:
commit: 366c5a2
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
- values: ["--dataset_generator", "fcps", "--dataset_name", "chainlink"] # 2 1
# - values: ["--dataset_generator", "fcps", "--dataset_name", "engytime"] # 2 2
# - values: ["--dataset_generator", "fcps", "--dataset_name", "hepta"] # 7 1
# - values: ["--dataset_generator", "fcps", "--dataset_name", "lsun"] # 3 1
# - values: ["--dataset_generator", "fcps", "--dataset_name", "target"] # 2, 6 2
# - values: ["--dataset_generator", "fcps", "--dataset_name", "tetra"] # 4 1
# - values: ["--dataset_generator", "fcps", "--dataset_name", "twodiamonds"] # 2 1
# - values: ["--dataset_generator", "fcps", "--dataset_name", "wingnut"] # 2 1
- values: ["--dataset_generator", "graves", "--dataset_name", "dense"] # 2 1
# - values: ["--dataset_generator", "graves", "--dataset_name", "dense"] # 2 1
# - values: ["--dataset_generator", "graves", "--dataset_name", "fuzzyx"] # 2, 4, 5 6
# - values: ["--dataset_generator", "graves", "--dataset_name", "line"] # 2 1
# - values: ["--dataset_generator", "graves", "--dataset_name", "parabolic"] # 2, 4 2
Expand All @@ -64,18 +64,18 @@ stages:
# - values: ["--dataset_generator", "other", "--dataset_name", "chameleon_t4_8k"] # 6 1
# - values: ["--dataset_generator", "other", "--dataset_name", "chameleon_t5_8k"] # 6 1
# - values: ["--dataset_generator", "other", "--dataset_name", "hdbscan"] # 6 1
- values: ["--dataset_generator", "other", "--dataset_name", "iris"] # 3 1
# - values: ["--dataset_generator", "other", "--dataset_name", "iris"] # 3 1
# - values: ["--dataset_generator", "other", "--dataset_name", "iris5"] # 3 1
# - values: ["--dataset_generator", "other", "--dataset_name", "square"] # 2 1
- values: ["--dataset_generator", "sipu", "--dataset_name", "aggregation"] # 7 1
# - values: ["--dataset_generator", "sipu", "--dataset_name", "aggregation"] # 7 1
# - values: ["--dataset_generator", "sipu", "--dataset_name", "compound"] # 4, 5, 6 5
# - values: ["--dataset_generator", "sipu", "--dataset_name", "flame"] # 2 2
# - values: ["--dataset_generator", "sipu", "--dataset_name", "jain"] # 2 1
# - values: ["--dataset_generator", "sipu", "--dataset_name", "pathbased"] # 3, 4 2
# - values: ["--dataset_generator", "sipu", "--dataset_name", "r15"] # 8, 9, 15 3
# - values: ["--dataset_generator", "sipu", "--dataset_name", "spiral"] # 3 1
# - values: ["--dataset_generator", "sipu", "--dataset_name", "unbalance"] # 8 1
- values: ["--dataset_generator", "uci", "--dataset_name", "ecoli"] # 8 1
# - values: ["--dataset_generator", "uci", "--dataset_name", "ecoli"] # 8 1
# - values: ["--dataset_generator", "uci", "--dataset_name", "ionosphere"] # 2 1
# - values: ["--dataset_generator", "uci", "--dataset_name", "sonar"] # 2 1
# - values: ["--dataset_generator", "uci", "--dataset_name", "statlog"] # 7 1
Expand Down Expand Up @@ -169,16 +169,16 @@ stages:
parameters:
# - values: ["--method", "FCPS_AdaptiveDensityPeak"] # not in conda
- values: ["--method", "FCPS_Minimax", "--seed", 2]
- values: ["--method", "FCPS_MinEnergy", "--seed", 2]
- values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
- values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
- values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
- values: ["--method", "FCPS_Diana", "--seed", 2]
- values: ["--method", "FCPS_Fanny", "--seed", 2]
- values: ["--method", "FCPS_Hardcl", "--seed", 2]
- values: ["--method", "FCPS_Softcl", "--seed", 2]
- values: ["--method", "FCPS_Clara", "--seed", 2]
- values: ["--method", "FCPS_PAM", "--seed", 2]
# - values: ["--method", "FCPS_MinEnergy", "--seed", 2]
# - values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
# - values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
# - values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
# - values: ["--method", "FCPS_Diana", "--seed", 2]
# - values: ["--method", "FCPS_Fanny", "--seed", 2]
# - values: ["--method", "FCPS_Hardcl", "--seed", 2]
# - values: ["--method", "FCPS_Softcl", "--seed", 2]
# - values: ["--method", "FCPS_Clara", "--seed", 2]
# - values: ["--method", "FCPS_PAM", "--seed", 2]
inputs:
- entries:
- data.matrix
Expand All @@ -198,10 +198,10 @@ stages:
parameters:
- values: ["--metric", "normalized_clustering_accuracy"]
- values: ["--metric", "adjusted_fm_score"]
- values: ["--metric", "adjusted_mi_score"]
- values: ["--metric", "adjusted_rand_score"]
- values: ["--metric", "fm_score"]
- values: ["--metric", "mi_score"]
# - values: ["--metric", "adjusted_mi_score"]
# - 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"]
Expand All @@ -214,89 +214,3 @@ stages:
outputs:
- id: metrics.scores
path: "{input}/{stage}/{module}/{params}/{dataset}.scores.gz"

# ## daniel's data ###########################################################################

# - id: danielsdata
# modules:
# - id: iris_manual
# name: "Iris Dataset"
# software_environment: "sklearn"
# repository:
# url: https://github.com/omnibenchmark-example/iris.git
# commit: 47c63f0
# - id: penguins
# name: "Penguins Dataset"
# software_environment: "sklearn"
# repository:
# url: https://github.com/omnibenchmark-example/penguins.git
# commit: 9032478
# outputs:
# - id: data.features
# path: "{input}/{stage}/{module}/{params}/{dataset}.features.csv"
# - id: data.labels
# path: "{input}/{stage}/{module}/{params}/{dataset}.labels.csv"

# ## daniel's distances ########################################################################

# - id: distances
# modules:
# - id: D1
# software_environment: "sklearn"
# parameters:
# - values: ["--measure", "cosine"]
# - values: ["--measure", "euclidean"]
# - values: ["--measure", "manhattan"]
# - values: ["--measure", "chebyshev"]
# repository:
# url: https://github.com/omnibenchmark-example/distance.git
# commit: dd99d4f
# inputs:
# - entries:
# - data.features
# outputs:
# - id: distances
# path: "{input}/{stage}/{module}/{params}/{dataset}.distances.csv"

# ## daniel's methods ###################################################################

# - id: danielmethods
# modules:
# - id: kmeans
# software_environment: "sklearn"
# repository:
# url: https://github.com/omnibenchmark-example/kmeans.git
# commit: 049c8b1
# - id: ward
# software_environment: "R"
# repository:
# url: https://github.com/omnibenchmark-example/ward.git
# commit: 976e3f3
# inputs:
# - entries:
# - distances
# outputs:
# - id: methods.clusters
# path: "{input}/{stage}/{module}/{params}/{dataset}.clusters.csv"

# ## daniel's metrics ###################################################################

# - id: danielsmetrics
# modules:
# - id: ari
# software_environment: "R"
# repository:
# url: https://github.com/omnibenchmark-example/ari.git
# commit: 72708f0
# - id: accuracy
# software_environment: "R"
# repository:
# url: https://github.com/omnibenchmark-example/accuracy.git
# commit: e26b32f
# inputs:
# - entries:
# - methods.clusters
# - data.labels
# outputs:
# - id: metrics.mapping
# path: "{input}/{stage}/{module}/{params}/{dataset}.metrics.txt"
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