From 35255ccd0c3837e65c6d566754dcaf82dc420c46 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 17 Dec 2024 19:44:37 +0000
Subject: [PATCH 1/3] neuroscience dictionary for cspell

---
 .vscode/settings.json        |  21 ++++++-
 cspell.json                  |  24 ++++++++
 docs/cspell/neuroscience.txt | 103 +++++++++++++++++++++++++++++++++++
 3 files changed, 147 insertions(+), 1 deletion(-)
 create mode 100644 cspell.json
 create mode 100644 docs/cspell/neuroscience.txt

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 0d7d8836..7270868c 100755
--- 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
new file mode 100644
index 00000000..c886734e
--- /dev/null
+++ 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
new file mode 100644
index 00000000..3008e2f8
--- /dev/null
+++ b/docs/cspell/neuroscience.txt
@@ -0,0 +1,103 @@
+*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*
+*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
+mppca
+mrdegibbs
+mrtrix
+msmt
+neuro*
+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

From 3a9742ea4b69ba400b4b44485a8ce88fa2a99e22 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 17 Dec 2024 20:06:35 +0000
Subject: [PATCH 2/3] add comment trigger for checks

---
 .github/workflows/manual_checks.yml | 17 +++++++++++++++++
 .github/workflows/update_pr.yml     |  3 ++-
 2 files changed, 19 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/manual_checks.yml

diff --git a/.github/workflows/manual_checks.yml b/.github/workflows/manual_checks.yml
new file mode 100644
index 00000000..68f78b72
--- /dev/null
+++ b/.github/workflows/manual_checks.yml
@@ -0,0 +1,17 @@
+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
index cd600206..4cb09366 100644
--- 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:

From fb1ab8cde62331911cfa83efb6d2ed1c18b1a5b0 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 17 Dec 2024 20:09:49 +0000
Subject: [PATCH 3/3] prettier

---
 .github/workflows/manual_checks.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/manual_checks.yml b/.github/workflows/manual_checks.yml
index 68f78b72..2b51e6b0 100644
--- a/.github/workflows/manual_checks.yml
+++ b/.github/workflows/manual_checks.yml
@@ -5,7 +5,6 @@ on:
       - created
       - edited
 
-
 jobs:
   checks:
     if: github.event.issue.pull_request && contains(github.event.comment.body, '@rerun-checks')