Run check_config on methods too

[rcannood]

Describe your changes

comp_control_method.yaml and comp_metric.yaml both list check_config.py in their test resources. comp_method.yaml doesn't -- so method metadata has never been validated. That's how four configs kept the deprecated placement:

info:
  documentation_url: https://cran.r-project.org/package=FNN
  repository_url: https://github.com/cran/FNN

when check_config() requires links.documentation and links.repository at the top level for type: method. Moved them in knnr_py, knnr_r, lm and guanlab_dengkw_pm.

Turning the check on also surfaced something pre-existing: novel and simple_mlp have a Nextflow runner with no directives, which trips

AssertionError: label not a field in nextflow runner directives

simple_mlp was already failing this on main -- it merges wf_method.yaml, which has always had check_config.py. It just never ran, because CI only tests components touched by a PR and nobody has touched simple_mlp in a while. Gave both wrappers a [lowtime, lowmem, lowcpu] label with a comment noting the real resources live on the train/predict sub-components.

Ran check_config() over every component after the change:

  control_methods/mean_per_gene       PASS
  control_methods/random_predict      PASS
  control_methods/solution            PASS
  control_methods/zeros               PASS
  methods/cellmapper_linear           PASS
  methods/cellmapper_scvi             PASS
  methods/guanlab_dengkw_pm           PASS
  methods/knnr_py                     PASS
  methods/knnr_r                      PASS
  methods/lm                          PASS
  methods/novel                       PASS
  methods/simple_mlp                  PASS
  metrics/correlation                 PASS
  metrics/mse                         PASS

Heads-up for the open method PRs (#16, #18, #19, #20): once this lands they'll need links.documentation and links.repository too. That's the point of the check, but worth flagging so it isn't a surprise.

Part of a series of PRs coming out of a pre-run review of the benchmark.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!