Add STIMULUS/CHECKTORCHMODEL

modules/nf-core/stimulus/checktorchmodel/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - conda-forge::matplotlib=3.9.2
+  - conda-forge::pandas=2.2.3
+  - conda-forge::polars=1.9.0
+  - conda-forge::python=3.12
+  - conda-forge::pytorch=2.4.1
+  - conda-forge::ray-core=2.37.0
+  - conda-forge::safetensors=0.4.5
+  - conda-forge::scikit-learn=1.5.2

modules/nf-core/stimulus/checktorchmodel/main.nf

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+process STIMULUS_CHECKTORCHMODEL {
+    tag "$experiment_config - $original_csv"
+    label 'process_medium'
+
+    // TODO freeze to Wave
+    container "docker.io/mathysgrapotte/stimulus-py:latest"
+
+    input:
+    path(original_csv)
+    path(experiment_config)
+    path(model)
+    path(ray_tune_config)
+    path(initial_weights)
+
+    output:
+    path "*_modelcheck.log", emit: log
+    path "versions.yml"    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args ?: ''
+    prefix          = task.ext.prefix ?: model.baseName.replaceFirst(/\.py/, "")
+    def weights_arg = initial_weights ? "--initial_weights ${initial_weights}" : ""
+    def gpu_arg     = task.accelerator ? "--gpus ${task.accelerator.request}" : ""
+    """
+    stimulus-check-model \
+        -d ${original_csv} \
+        -m ${model} \
+        -e ${experiment_config} \
+        -c ${ray_tune_config} \
+        ${weights_arg} \
+        ${gpu_arg} \
+        --cpus ${task.cpus} \
+        --memory "${task.memory}" \
+        $args > ${prefix}_modelcheck.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Stimulus-py: \$(pip show stimulus-py | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
+
+    stub:
+    def args         = task.ext.args ?: ''
+    prefix           = task.ext.prefix ?: model.baseName.replaceFirst(/\.py/, "")
+    def STIMULUS_VER = '0.0.9' // container not used in stub, change manually
+    """
+    touch ${prefix}_modelcheck.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Stimulus-py: ${STIMULUS_VER}
+    END_VERSIONS
+    """
+}

modules/nf-core/stimulus/checktorchmodel/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "stimulus_checktorchmodel"
+description: Sanity check a Pytorch model using raytune
+keywords:
+  - machine learning
+  - neural network
+  - unit test
+tools:
+  - "stimulus":
+      description: "Stochastic Testing and Input Manipulation for Unbiased Learning Systems"
+      homepage: "https://github.com/mathysgrapotte/stimulus-py"
+      documentation: "https://github.com/mathysgrapotte/stimulus-py"
+      tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py"
+      licence: ["MIT"]
+
+input:
+  - - original_csv:
+        type: file
+        description: A CSV file with untransformed data
+        pattern: "*.csv"
+        ontologies:
+          - edam: "http://edamontology.org/format_3752"
+  - - experiment_config:
+        type: file
+        description: A YAML file describing data transformations
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464"
+  - - model:
+        type: file
+        description: Python source file containing the model
+        pattern: "*.py"
+        ontologies:
+          - edam: "http://edamontology.org/format_3996"
+  - - ray_tune_config:
+        type: file
+        description: YAML file containing RayTune tuning parameters
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750"
+  - - initial_weights:
+        type: file
+        description: An optional SafeTensors file containing initial weights
+        pattern: "*.safetensors"
+
+output:
+  - log:
+      - "*_modelcheck.log":
+          type: file
+          description: Model check output
+          pattern: "*.log"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@mathysgrapotte"
+  - "@alessiovignoli"
+  - "@itrujnara"
+maintainers:
+  - "@itrujnara"

modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test

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+// nf-core modules test stimulus/checktorchmodel
+nextflow_process {
+
+    name "Test Process STIMULUS_CHECKTORCHMODEL"
+    script "../main.nf"
+    process "STIMULUS_CHECKTORCHMODEL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stimulus"
+    tag "stimulus/checktorchmodel"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("basic - csv - py") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true)
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { with(process.out.log) {
+                    assert path(get(1)).readLines().first().contains("Trial finishes successfully")
+                } },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("basic - csv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true)
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test.snap

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+{
+    "basic - csv - py": {
+        "content": [
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T15:30:33.424103"
+    },
+    "basic - csv - stub": {
+        "content": [
+            {
+                "0": [
+                    "dna_to_float_model_modelcheck.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,673aceb3844572cdb756ae9835f9187e"
+                ],
+                "log": [
+                    "dna_to_float_model_modelcheck.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,673aceb3844572cdb756ae9835f9187e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T16:54:27.22745"
+    }
+}