Run check_config on methods too

CHANGELOG.md

@@ -8,6 +8,12 @@
 
 * `cellmapper_linear`: Write the unmasked variants as `mask_var: null` rather than `mask_var: None`, which YAML reads as the string `"None"` and which would resolve to `adata.var["None"]` (PR #38).
 
+* `comp_method`: Run `check_config.py` as part of the component tests, so method metadata is validated like control methods and metrics already are (PR #37).
+
+* `knnr_py`, `knnr_r`, `lm`, `guanlab_dengkw_pm`: Move `documentation_url` and `repository_url` out of `info` and into the top-level `links` (PR #37).
+
+* `novel`, `simple_mlp`: Add a placeholder Nextflow resource label. Viash renders no process for a `nextflow_script` component, so the label is inert -- it is only there because `check_config` requires one. Can be removed once openproblems-bio/core#41 is released (PR #37).
+
 ## BUG FIXES
 
 * Fix the component paths, build paths and `rename_keys` separator in the helper scripts, which prevented `scripts/create_datasets/test_resources.sh` and both `run_test.sh` scripts from running at all (PR #22).

src/api/comp_method.yaml

@@ -24,6 +24,8 @@ arguments:
     direction: output
     required: true
 test_resources:
+  - type: python_script
+    path: /common/component_tests/check_config.py
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
   - path: /resources_test/task_predict_modality/openproblems_neurips2021/bmmc_cite/swap

src/methods/guanlab_dengkw_pm/config.vsh.yaml

@@ -11,10 +11,11 @@ description: |
   singular vectors.
 references:
   doi: 10.1101/2022.04.11.487796
+links:
+  documentation: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw
+  repository: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw
 info:
   preferred_normalization: log_cp10k
-  documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw
-  repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw
   competition_submission_id: 170636
 arguments:
   - name: "--distance_method"

src/methods/knnr_py/config.vsh.yaml

@@ -5,9 +5,10 @@ summary: K-nearest neighbor regression in Python.
 description: K-nearest neighbor regression in Python.
 references:
   doi: 10.2307/1403797
+links:
+  documentation: https://scikit-learn.org/stable/modules/neighbors.html
+  repository: https://github.com/scikit-learn/scikit-learn
 info:
-  documentation_url: https://scikit-learn.org/stable/modules/neighbors.html
-  repository_url: https://github.com/scikit-learn/scikit-learn
   preferred_normalization: log_cp10k
 arguments:
   - name: "--distance_method"

src/methods/knnr_r/config.vsh.yaml

@@ -5,9 +5,10 @@ summary: K-nearest neighbor regression in R.
 description: K-nearest neighbor regression in R.
 references:
   doi: 10.2307/1403797
+links:
+  documentation: https://cran.r-project.org/package=FNN
+  repository: https://github.com/cran/FNN
 info:
-  documentation_url: https://cran.r-project.org/package=FNN
-  repository_url: https://github.com/cran/FNN
   preferred_normalization: log_cp10k
 arguments:
   - name: "--distance_method"

src/methods/lm/config.vsh.yaml

@@ -5,9 +5,10 @@ summary: Linear model regression.
 description: A linear model regression method.
 references:
   doi: 10.2307/2346786
+links:
+  documentation: https://cran.r-project.org/package=RcppArmadillo
+  repository: https://github.com/RcppCore/RcppArmadillo
 info:
-  repository_url: https://github.com/RcppCore/RcppArmadillo
-  documentation_url: https://cran.r-project.org/package=RcppArmadillo
   preferred_normalization: log_cp10k
 arguments:
   - name: "--distance_method"

src/methods/novel/novel/config.vsh.yaml

@@ -20,4 +20,7 @@ dependencies:
   - name: methods/novel_train
   - name: methods/novel_predict
 runners:
-  - type: nextflow 
+  - type: nextflow
+    directives:
+      # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41)
+      label: [lowtime, lowmem, lowcpu]

src/methods/simple_mlp/simple_mlp/config.vsh.yaml

@@ -25,3 +25,6 @@ dependencies:
   - name: methods/simple_mlp_predict
 runners:
   - type: nextflow
+    directives:
+      # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41)
+      label: [lowtime, lowmem, lowcpu]