Remove template boilerplate comments from spearman_corr config

Author: luisabender

src/metrics/spearman_corr/config.vsh.yaml

@@ -1,88 +1,48 @@
-# The API specifies which type of component this is.
-# It contains specifications for:
-#   - The input/output files
-#   - Common parameters
-#   - A unit test
 __merge__: ../../api/comp_metric.yaml
 
-# A unique identifier for your component (required).
-# Can contain only lowercase letters or underscores.
 name: spearman_corr
 
-
-
-# Metadata for your component
 info:
   metrics:
-      # A unique identifier for your metric (required).
-      # Can contain only lowercase letters or underscores.
     - name: spearman_corr
-      # A relatively short label, used when rendering visualisarions (required)
       label: Spearman's Corr
-      # A one sentence summary of how this metric works (required). Used when 
-      # rendering summary tables.
       summary: "Computes the Spearman rank correlation coefficient between inferred and ground-truth pseudotime."
-      # A multi-line description of how this component works (required). Used
-      # when rendering reference documentation.
       description: |
         Calculates the Spearman rank correlation coefficient (rho) between predicted cell pseudotime
         values and the true ground-truth pseudotime. Measures monotonic relationships regardless of linearity.
-      
       references:
-        doi: 
+        doi:
           - 10.1038/s41592-020-0772-5
         bibtex: |
-           @article{Virtanen_2020,
-            author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Jarrod Millman, K. and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C. J. and Polat, {\dot{I}}lhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
-            title   = {Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python},
-            journal = {Nature Methods},
-            volume  = {17},
-            number  = {3},
-            pages   = {352},
-            year    = {2020},
-            doi     = {10.1038/s41592-020-0772-5}
-            }
-             
+          @article{Virtanen_2020,
+           author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Jarrod Millman, K. and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C. J. and Polat, {\dot{I}}lhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
+           title   = {Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python},
+           journal = {Nature Methods},
+           volume  = {17},
+           number  = {3},
+           pages   = {352},
+           year    = {2020},
+           doi     = {10.1038/s41592-020-0772-5}
+           }
       links:
-        # URL to the documentation for this metric (required).
         documentation: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html
-        # URL to the code repository for this metric (required).
         repository: https://github.com/scipy/scipy
-      # The minimum possible value for this metric (required)
       min: -1
-      # The maximum possible value for this metric (required)
       max: 1
-      # Whether a higher value represents a 'better' solution (required)
       maximize: true
 
-# Component-specific parameters (optional)
-# arguments:
-  #- name: "--true_col"
-   # type: string
-    #default: "pseudotime_true"
-    #description: "obs column name for ground-truth pseudotime"
-#  - name: "--inferred_col"
- #   type: string
- #   default: "pseudotime"
- #   description: "obs column name for inferred pseudotime"
-
-# Resources required to run the component
 resources:
-  # The script of your component (required)
   - type: python_script
     path: script.py
-  # Additional resources your script needs (optional)
-  # - type: file
-  #   path: weights.pt
 
 engines:
   - type: docker
     image: python:3.11-slim
     setup:
       - type: apt
         packages:
-          - procps
-          - git
+          - procps              # required by Nextflow
+          - git                 # pip needs it to install openproblems core from git+https
       - type: python
         packages:
           - anndata~=0.10.0
@@ -96,9 +56,7 @@ engines:
           - "openproblems-bio/core#subdirectory=packages/python/openproblems"
 
 runners:
-  # This platform allows running the component natively
   - type: executable
-  # Allows turning the component into a Nextflow module / pipeline.
   - type: nextflow
     directives:
       label: [midtime,midmem,midcpu]