Merge branch 'main' into fix/atlasbundleseg

scilus · Dec 18, 2024 · 760c0cd · 760c0cd
2 parents 8d206a8 + 3429ec3
commit 760c0cd
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Showing 26 changed files with 493 additions and 93 deletions.
diff --git a/.devcontainer/devops/devcontainer.json b/.devcontainer/devops/devcontainer.json
@@ -4,7 +4,9 @@
         "dockerfile": "Dockerfile",
         "args": {
             "NFTEST_VERSION": "0.9.0",
-            "POETRY_VERSION": "1.8.*"
+            "POETRY_VERSION": "1.8.*",
+            "NFT_DIFF": "pdiff",
+            "NFT_DIFF_ARGS": "--line-numbers --width 120 --expand-tabs=2"
         }
     },
     "forwardPorts": [3000],

diff --git a/.github/workflows/manual_checks.yml b/.github/workflows/manual_checks.yml
@@ -0,0 +1,16 @@
+name: Trigger checks manually
+on:
+  issue_comment:
+    types:
+      - created
+      - edited
+
+jobs:
+  checks:
+    if: github.event.issue.pull_request && contains(github.event.comment.body, '@rerun-checks')
+    # Cancel if a newer run is started
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    uses: ./.github/workflows/run_checks_suite.yml
+    secrets: inherit
diff --git a/.github/workflows/update_pr.yml b/.github/workflows/update_pr.yml
@@ -6,7 +6,8 @@ on:
   merge_group:
     types:
       - checks_requested
-    branches: -main
+    branches:
+      - main
 
 # Cancel if a newer run is started
 concurrency:

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -19,5 +19,24 @@
     "testDataExplorer.dataserver": "scil.usherbrooke.ca",
     "testDataExplorer.serverdatalocation": "scil_test_data/dvc-store/files/md5",
     "testDataExplorer.localListingLocation": "tests/test_data.json",
-    "testDataExplorer.remoteListingLocation": "tests/test_data.json"
+    "testDataExplorer.remoteListingLocation": "tests/test_data.json",
+    "nextflow.files.exclude": [
+        ".git",
+        ".nf-test",
+        "work",
+        ".venv",
+        ".nextflow",
+        "node_modules",
+        ".tests/runs"
+    ],
+    "cSpell.ignorePaths": [
+        "package-lock.json",
+        "node_modules",
+        "vscode-extension",
+        ".git/",
+        ".vscode",
+        ".vscode-insiders",
+        ".venv",
+        "tests/.runs"
+    ]
 }
diff --git a/cspell.json b/cspell.json
@@ -0,0 +1,24 @@
+{
+    "version": "0.2",
+    "dictionaryDefinitions": [
+        {
+            "name": "neuroscience",
+            "path": "docs/cspell/neuroscience.txt",
+            "addWords": true
+        }
+    ],
+    "dictionaries": [
+        "typescript",
+        "node",
+        "python",
+        "latex",
+        "bash",
+        "companies",
+        "softwareTerms",
+        "misc",
+        "en_US",
+        "en-gb",
+        "filetypes",
+        "neuroscience"
+    ]
+}
diff --git a/docs/cspell/neuroscience.txt b/docs/cspell/neuroscience.txt
@@ -0,0 +1,104 @@
+*anat*
+*anthony
+*apply*
+*b0*
+*bet*
+*bore
+*bundle*
+*bval*
+*bvec*
+*coeff
+*coeffs
+*container
+*containers
+*core
+*crop*
+*denoise*
+*dwi*
+*easy*
+*extract*
+*fast*
+*field*
+*fodf*
+*frf*
+*image
+*local*
+*mask
+*mean*
+*means*
+*metrics
+*morph*
+*mov*
+*neuro*
+*normalise
+*pack
+*par
+*pft*
+*reg*
+*registration*
+*rev*
+*seg*
+*synth*
+*test*
+*to*
+*tracking*
+*transforms
+*volume*
+ants*
+aparc
+arnaud*
+aseg
+connectomics
+denoised
+denoising
+descoteaux
+dev*
+dipy
+dti*
+dtype
+etienne
+evals
+evecs
+extension*
+freesurfer*
+fsl*
+gagnon*
+interp
+medde
+mkdirs
+mppca
+mrdegibbs
+mrtrix
+msmt
+nextflow
+nf*
+nifti
+nl*
+nufo
+onge
+parcellation
+parcellations
+preproc
+reconst
+rheault
+robsyme
+sbref
+scilpy
+scilus
+seed*
+ssst
+stanislas
+subworkflow
+subworkflows
+thoumyre
+topup
+track*
+tractoflow
+tractogram
+tractograms
+tractography
+transfo
+uchar
+unbias
+wmparc
+zenodo
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/main.nf b/modules/nf-neuro/betcrop/fslbetcrop/main.nf
@@ -69,16 +69,9 @@ process BETCROP_FSLBETCROP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    scil_dwi_extract_b0.py -h
-    bet -h
-    scil_volume_math.py -h
-    mrcalc -h
-    scil_volume_crop.py -h
-
     touch ${prefix}__image_bet.nii.gz
     touch ${prefix}__image_bet_mask.nii.gz
     touch ${prefix}__image_boundingBox.pkl
@@ -89,5 +82,18 @@ process BETCROP_FSLBETCROP {
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    bet
+    scil_dwi_extract_b0.py -h
+    scil_volume_math.py -h
+    mrcalc -h
+    scil_volume_crop.py -h
     """
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test
@@ -108,4 +108,32 @@ nextflow_process {
 
     }
 
+    test("betcrop - fslbetcrop - stub-run") {
+
+        options "-stub-run"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/dwi/dwi.nii.gz"),
+                        file("\${test_data_directory}/dwi/dwi.bval"),
+                        file("\${test_data_directory}/dwi/dwi.bvec")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
@@ -1,4 +1,16 @@
 {
+    "betcrop - fslbetcrop - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,cc45ab23921525536874337c1c88e5cf"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T10:33:04.50811"
+    },
     "betcrop - fslbetcrop - dwi": {
         "content": [
             {

diff --git a/modules/nf-neuro/denoising/mppca/main.nf b/modules/nf-neuro/denoising/mppca/main.nf
@@ -3,9 +3,7 @@ process DENOISING_MPPCA {
     tag "$meta.id"
     label 'process_medium'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
     tuple val(meta), path(dwi), path(mask)
@@ -30,13 +28,12 @@ process DENOISING_MPPCA {
     export MRTRIX_RNG_SEED=112524
 
     dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")}
-    scil_volume_math.py lower_clip ${prefix}_dwi_denoised.nii.gz 0 \
-        ${prefix}_dwi_denoised.nii.gz -f
+    mrcalc ${prefix}_dwi_denoised.nii.gz 0 -gt ${prefix}_dwi_denoised.nii.gz 0 \
+        -if ${prefix}_dwi_denoised.nii.gz -force
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -46,14 +43,13 @@ process DENOISING_MPPCA {
 
     """
     dwidenoise -h
-    scil_volume_math.py -h
+    mrcalc -h
 
     touch ${prefix}_dwi_denoised.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/denoising/mppca/meta.yml b/modules/nf-neuro/denoising/mppca/meta.yml
@@ -12,9 +12,6 @@ tools:
   - "MRtrix3":
       description: "Toolbox for image processing, analysis and visualisation of dMRI."
       homepage: "https://mrtrix.readthedocs.io/en/latest/"
-  - "scilpy":
-      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
-      homepage: "https://github.com/scilus/scilpy.git"
 
 input:
   - meta:

diff --git a/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ],
                 "image": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-05T15:17:51.718413"
+        "timestamp": "2024-12-12T18:27:14.057961679"
     }
 }
diff --git a/modules/nf-neuro/image/applymask/main.nf b/modules/nf-neuro/image/applymask/main.nf
@@ -2,9 +2,7 @@ process IMAGE_APPLYMASK {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
         tuple val(meta), path(image), path(mask)