Tidying up YAML configs to run full benchmark and adding Zenodo DOI

README.md

@@ -9,6 +9,7 @@
 [![Google Colab](https://img.shields.io/badge/Google-Colab-orange?logo=googlecolab&style=flat-square)](https://colab.research.google.com/drive/1J-yNXu_FcSnhrCwTDQKjWCBSHsmdbohJ?usp=sharing)
 [![Install](https://github.com/li-lab-mcgill/scTimeBench/actions/workflows/ci-install.yml/badge.svg)](https://github.com/li-lab-mcgill/scTimeBench/actions/workflows/ci-install.yml)
 [![Pypi](https://img.shields.io/badge/pypi-0.1.0-orange?logo=pypi&style=flat-square)](https://pypi.org/project/scTimeBench/)
+[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.19196641.svg)](https://doi.org/10.5281/zenodo.19196641)
 <!-- TODO: --> <!-- [![Documentation](https://img.shields.io/badge/Documentation-Online-green.svg?style=flat-square)]() -->
 
 

configs/CellMNN.yaml

@@ -19,5 +19,6 @@ method:
     auto_device: true
 
 metrics:
-  - name: OTLossMetric
-  #- name: GraphSimMetric
+ - name: OTLossMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/MIOFlow.yaml

@@ -22,5 +22,6 @@ method:
     t_max: 5
 
 metrics:
-  - name: OTLossMetric
- # - name: GraphSimMetric
+ - name: OTLossMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/PISDE.yaml

@@ -1,15 +1,3 @@
-datasets:
-  - tag: EasyDrosophila
-  - tag: MediumDrosophila
-  - tag: HardDrosophila
-  - tag: EasyMEF
-  - tag: MediumMEF
-  - tag: HardMEF
-  - tag: EasyZebrafish
-  - tag: MediumZebrafish
-  - tag: HardZebrafish
-
-
 method:
   name: PISDE
   train_and_test_script: ./methods/PISDE/train_and_test.sh
@@ -34,5 +22,6 @@ method:
     leaveouts: null
 
 metrics:
-  - name: OTLossMetric
-  #- name: MMDLoss
+ - name: OTLossMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/PRESCIENT/PRESCIENT.yaml → configs/PRESCIENT.yaml

@@ -26,6 +26,6 @@ method:
     epoch: best
 
 metrics:
-  #- name: MMDLoss
-  #- name: GraphSimMetric
-  - name: OTLossMetric
+ - name: OTLossMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/Squidiff.yaml

@@ -26,3 +26,5 @@ method:
 
 metrics:
  - name: OTLossMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/WOT.yaml

@@ -1,12 +1,7 @@
-datasets:
-  - tag: defaultGarciaAlonso
-  - tag: defaultGarciaAlonsoPseudotimeEvenCells
-  - tag: defaultMa
-  - tag: defaultMaPseudotimeEvenCells
-
 method:
   name: WOT
   train_and_test_script: ./methods/WOT/train_and_test.sh
 
 metrics:
  - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/moscot.yaml

@@ -3,4 +3,5 @@ method:
   train_and_test_script: ./methods/moscot/train_and_test.sh
 
 metrics:
-  - name: GraphSimMetric
+ - name: GraphSimMetric
+ - name: EmbeddingMetrics

configs/scIMF.yaml

@@ -1,10 +1,3 @@
-##TODO
-# 2026-02-04 16:26:28,575 | DEBUG | root | [warn] Ignoring unknown scIMF config parameter: auto_device
-# 2026-02-04 16:26:28,575 | DEBUG | root | [warn] Ignoring unknown scIMF config parameter: cache_n_cells
-# 2026-02-04 16:26:28,575 | DEBUG | root | [warn] Ignoring unknown scIMF config parameter: cuda_device
-# 2026-02-04 16:26:28,575 | DEBUG | root | [warn] Ignoring unknown scIMF config parameter: leaveouts
-# 2026-02-04 16:26:28,575 | DEBUG | root | [warn] Ignoring unknown scIMF config parameter: use_cuda
-
 method:
   name: scIMF
   train_and_test_script: ./methods/scIMF/train_and_test.sh
@@ -29,5 +22,6 @@ method:
 
 
 metrics:
-  # - name: OTLossMetric
+ - name: OTLossMetric
  - name: GraphSimMetric
+ - name: EmbeddingMetrics

docs/source/base_run.rst

@@ -12,6 +12,8 @@ metrics, and let the benchmark resolve the default datasets for those metrics.
 The dataset definitions, preprocessing steps, and metric-group defaults are then
 pulled from the shared dataset registry.
 
+The datasets, configuration files and scripts for methods implemented in the scTimeBench paper can be downloaded from `Zenodo <https://doi.org/10.5281/zenodo.19196641>`_.
+
 Start from a config file
 ------------------------
 

docs/source/index.rst

@@ -27,6 +27,10 @@ scTimeBench Documentation
       <a href="https://pypi.org/project/scTimeBench/">
          <img src="https://img.shields.io/badge/pypi-0.1.0-orange?logo=pypi&style=flat-square" alt="Pypi" />
       </a>
+      </a>
+      <a href="https://doi.org/10.5281/zenodo.19196641">
+         <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19196641.svg" alt="DOI" />
+      </a>
    </p>
 
 Welcome to the scTimeBench documentation!