From 4626d95d60218ef790708aa88e03ee5cce3d79ac Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 29 Jul 2026 11:58:21 +0200 Subject: [PATCH 1/2] run check_config on methods too * Add check_config.py to comp_method.yaml's test resources * Move documentation_url/repository_url to links in the four configs that still used the old placement * Give novel and simple_mlp a nextflow resource label Control methods and metrics were checked, methods were not, which is how the deprecated info.documentation_url survived in four configs. --- CHANGELOG.md | 10 ++++++++++ src/api/comp_method.yaml | 2 ++ src/methods/guanlab_dengkw_pm/config.vsh.yaml | 5 +++-- src/methods/knnr_py/config.vsh.yaml | 5 +++-- src/methods/knnr_r/config.vsh.yaml | 5 +++-- src/methods/lm/config.vsh.yaml | 5 +++-- src/methods/novel/novel/config.vsh.yaml | 6 +++++- src/methods/simple_mlp/simple_mlp/config.vsh.yaml | 4 ++++ 8 files changed, 33 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9a8396c..06187edf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,13 @@ +# task_predict_modality 0.2.0 + +## MINOR CHANGES + +* `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`: Give the orchestrating workflow components a Nextflow resource label, which `check_config` requires (PR #37). + # task_predict_modality 0.1.1 ## NEW FUNCTIONALITY diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml index c3c56508..9414b6ea 100644 --- a/src/api/comp_method.yaml +++ b/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 diff --git a/src/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/methods/guanlab_dengkw_pm/config.vsh.yaml index e10d658c..925b5591 100644 --- a/src/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/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" diff --git a/src/methods/knnr_py/config.vsh.yaml b/src/methods/knnr_py/config.vsh.yaml index ca8df0d8..2c87c75f 100644 --- a/src/methods/knnr_py/config.vsh.yaml +++ b/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" diff --git a/src/methods/knnr_r/config.vsh.yaml b/src/methods/knnr_r/config.vsh.yaml index 0af5de3d..8a163d93 100644 --- a/src/methods/knnr_r/config.vsh.yaml +++ b/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" diff --git a/src/methods/lm/config.vsh.yaml b/src/methods/lm/config.vsh.yaml index b41977ba..6f6223b8 100644 --- a/src/methods/lm/config.vsh.yaml +++ b/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" diff --git a/src/methods/novel/novel/config.vsh.yaml b/src/methods/novel/novel/config.vsh.yaml index a30a31e4..e5e8a06a 100644 --- a/src/methods/novel/novel/config.vsh.yaml +++ b/src/methods/novel/novel/config.vsh.yaml @@ -20,4 +20,8 @@ dependencies: - name: methods/novel_train - name: methods/novel_predict runners: - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + # this component only orchestrates novel_train and novel_predict, + # which carry the resource labels that actually matter + label: [lowtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml index fe5ca358..4fa42f4e 100644 --- a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml +++ b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml @@ -25,3 +25,7 @@ dependencies: - name: methods/simple_mlp_predict runners: - type: nextflow + directives: + # this component only orchestrates simple_mlp_train and simple_mlp_predict, + # which carry the resource labels that actually matter + label: [lowtime, lowmem, lowcpu] From 3eb1e630018ee181a57c6e6e3ad5ff195945fc6b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 29 Jul 2026 14:08:37 +0200 Subject: [PATCH 2/2] mark the nextflow labels on novel and simple_mlp as placeholders * they are inert on a nextflow_script component, viash renders a workflow instead of a process * remove them once openproblems-bio/core#41 is released --- CHANGELOG.md | 2 +- src/methods/novel/novel/config.vsh.yaml | 5 ++--- src/methods/simple_mlp/simple_mlp/config.vsh.yaml | 3 +-- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 06187edf..3b0fd367 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ * `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`: Give the orchestrating workflow components a Nextflow resource label, which `check_config` requires (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). # task_predict_modality 0.1.1 diff --git a/src/methods/novel/novel/config.vsh.yaml b/src/methods/novel/novel/config.vsh.yaml index e5e8a06a..f372f394 100644 --- a/src/methods/novel/novel/config.vsh.yaml +++ b/src/methods/novel/novel/config.vsh.yaml @@ -22,6 +22,5 @@ dependencies: runners: - type: nextflow directives: - # this component only orchestrates novel_train and novel_predict, - # which carry the resource labels that actually matter - label: [lowtime, lowmem, lowcpu] \ No newline at end of file + # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41) + label: [lowtime, lowmem, lowcpu] diff --git a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml index 4fa42f4e..6b61d154 100644 --- a/src/methods/simple_mlp/simple_mlp/config.vsh.yaml +++ b/src/methods/simple_mlp/simple_mlp/config.vsh.yaml @@ -26,6 +26,5 @@ dependencies: runners: - type: nextflow directives: - # this component only orchestrates simple_mlp_train and simple_mlp_predict, - # which carry the resource labels that actually matter + # inert placeholder -- remove when check_config is updated (openproblems-bio/core#41) label: [lowtime, lowmem, lowcpu]