Quality (actions, pre-commit) and tests

.github/auto_assign.yml

@@ -1,3 +1,4 @@
+---
 # Set to true to add reviewers to pull requests
 addReviewers: true
 
@@ -26,4 +27,4 @@ numberOfReviewers: 0
 
 # A list of keywords to be skipped the process that add reviewers if pull requests include it
 # skipKeywords:
-#   - wip
+#   - wip

.github/release-drafter.yml

@@ -1,44 +1,45 @@
-name-template: '$RESOLVED_VERSION'
-tag-template: 'v$RESOLVED_VERSION'
+---
+name-template: $RESOLVED_VERSION
+tag-template: v$RESOLVED_VERSION
 filter-by-commitish: true
 
 template: |
   ## Changes
   $CHANGES
 categories:
-  - title: '🚀 Features'
+  - title: 🚀 Features
     labels:
-      - 'breaking'
-      - 'enhancement'
-  - title: '🐛 Bug Fixes'
+      - breaking
+      - enhancement
+  - title: 🐛 Bug Fixes
     labels:
-      - 'bug'
-  - title: '🧰 Maintenance'
+      - bug
+  - title: 🧰 Maintenance
     labels:
-      - 'maintenance'
-      - 'test'
-  - title: '📝 Documentation'
+      - maintenance
+      - test
+  - title: 📝 Documentation
     labels:
-      - 'documentation'
+      - documentation
 
 exclude-labels:
   - skip_changelog
 
 change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
-change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+change-title-escapes: \<*_&    # You can add  # and @ to disable mentions, and add ` to disable code blocks.
 
 version-resolver:
   # major:
   #   labels:
   #     - 'breaking'
   minor:
     labels:
-      - 'breaking'
-      - 'enhancement'
+      - breaking
+      - enhancement
   patch:
     labels:
-      - 'maintenance'
-      - 'bug'
-      - 'test'
-      - 'documentation'
-  default: patch
+      - maintenance
+      - bug
+      - test
+      - documentation
+  default: patch

.github/workflows/assign_reviewers.yml

@@ -1,9 +1,11 @@
-name: Assign reviewer 
+---
+name: Assign reviewer
 
 on:
-  pull_request_target: 
+  pull_request_target:
+    types: [opened, ready_for_review]
 
-jobs: 
+jobs:
   assign:
     runs-on: ubuntu-latest
     if: github.event.pull_request.assignee == null
@@ -12,4 +14,4 @@ jobs:
       - name: Assign reviewer
         uses: kentaro-m/auto-assign-action@v1.1.2
         with:
-          repo-token: "${{ secrets.GITHUB_TOKEN }}" 
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/bump_version.yml

@@ -1,3 +1,4 @@
+---
 name: Bump version
 on:
   pull_request_target:
@@ -49,9 +50,9 @@ jobs:
       - name: Update version in pyproject.toml
         uses: jacobtomlinson/gha-find-replace@master
         with:
-          include: 'pyproject.toml'
-          find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
-          replace: 'version = "${{ env.NEW_RELEASE }}-pre.${{ env.NEW_BUMP }}"'
+          include: pyproject.toml
+          find: version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"
+          replace: version = "${{ env.NEW_RELEASE }}-pre.${{ env.NEW_BUMP }}"
 
       - name: Commit updates
         env:
@@ -60,10 +61,10 @@ jobs:
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"
           git diff-index --quiet HEAD || git commit -m "Bump version to $SNAKEBIDS_VERSION" -a
-          
+
       - name: Push changes
         uses: CasperWA/push-protected@v2
         with:
           branch: ${{ github.event.pull_request.base.ref }}
           token: ${{ secrets.BP_PAT_TOKEN }}
-          unprotect_reviews: True
+          unprotect_reviews: true

.github/workflows/test.yml

@@ -0,0 +1,118 @@
+---
+name: Lint and test workflow
+
+on:
+  push:
+    branches:
+      - '*'
+      - '!push-action/*'
+  pull_request:
+    branches:
+      - '*'
+      - '!push-action/*'
+
+jobs:
+  quality:
+    name: Lint code
+    if: github.event.pull_request.merged == false
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Clone repo
+        uses: actions/checkout@master
+
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-3.10
+          restore-keys: ${{ runner.os }}-pip-3.10
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.2.0
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-3.10
+
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root --with dev
+
+      - name: yamlfix
+        run: poetry run poe yamlfix
+
+      - name: isort
+        run: poetry run poe isort
+
+      - name: black
+        run: poetry run poe black
+
+      - name: flake8
+        run: poetry run poe flake8
+
+      - name: snakefmt
+        run: poetry run poe snakefmt
+
+  test:
+    runs-on: ubuntu-latest
+    needs: [quality]
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10']
+    steps:
+      - name: Clone repo
+        uses: actions/checkout@master
+
+      - name: Select Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}
+          restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.2.0
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-${{ matrix.python-version
+            }}
+
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root --with dev
+
+      - name: Test minimum inputs
+        run: poetry run poe test_base
+
+      - name: Test freesurfer input
+        run: poetry run poe test_freesurfer
+
+      - name: Test responsemean input
+        run: poetry run poe test_responsemean
+
+      - name: Test dwi input
+        run: poetry run poe test_dwi

.gitignore

@@ -0,0 +1,12 @@
+# Add testing folders to ignore
+test/data/derivatives/.snakemake/
+test/data/derivatives/config/
+test/data/derivatives/.snakebids
+
+# Tar files
+*.tar
+
+# Ignore files that are available in tar
+**/zona_bb_subcortex/MNI152
+**/zona_bb_subcortex/MNI2009b
+**/zona_bb_subcortex/transforms

.pre-commit-config.yaml

@@ -1,27 +1,39 @@
+---
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
 
--   repo: https://github.com/pycqa/isort
+  - repo: local
+    hooks:
+      - id: yamlfix
+        name: yamlfix
+        entry: bash -c "poetry run poe yamlfix"
+        language: system
+
+  - repo: https://github.com/pycqa/isort
     rev: 5.10.1
     hooks:
-    -   id: isort
+      - id: isort
+        args: [--profile=black, --multi-line=3]
 
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 22.8.0
     hooks:
-    -   id: black
+      - id: black
+        args: [--line-length=79]
 
--   repo: https://github.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 5.0.4
     hooks:
-    -   id: flake8
+      - id: flake8
+        args: [--ignore=E501]
 
--   repo: https://github.com/snakemake/snakefmt
+  - repo: https://github.com/snakemake/snakefmt
     rev: 0.6.1
     hooks:
-    -   id: snakefmt
+      - id: snakefmt
+        args: [--include=\.smk$|^Snakefile, --line-length=79]

dbsc/config/snakebids.yml

@@ -86,11 +86,22 @@ parse_args:
   --freesurfer_dir:
     help: The path to the freesurfer directory. If not provided, workflow
           assumes the directory exists at <output_dir>/freesurfer.
+    nargs: "?"
+    type: Path
+
+  --dwi_dir:
+    help: The path to the directory containing pre-processed dwi data
+          transformed to subject T1w space. If not provided, workflow assumes
+          this data exists in <bids_dir>/<subject>/dwi.
+    nargs: "?"
+    type: Path
 
   --responsemean_dir:
     help: 'Provide directory containing average response functions. If not
           provided, one will be computed from the subjects in the input
           directory.'
+    nargs: "?"
+    type: Path
 
   --shells:
     help: '(Mrtrix3) specify one or more b-values to use during processing, as
@@ -142,29 +153,28 @@ parse_args:
 
 # Workflow specific config
 # Spaces available (MNI152, MNINlin2009bAsym)
-Space: MNI152
+Space: MNI152NLin6Asym
 
 zona_bb_subcortex:
-  MNI152:
-    dir: 'resources/MNI152'
-    T1w: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_T1w.nii.gz'
-    seg: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_ZonaBBSubCorSeg.nii.gz'
-    exclude: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_desc-exclude_ROI.nii.gz'
-  MNI2009:
-    dir: 'resources/MNI2009b'
-    T1w: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNI152_T1w.nii.gz'
-    seg: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_ZonaBBSubCorSeg.nii.gz'
-    exclude: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_desc-exclude_ROI.nii.gz'
+  tsv: 'resources/zona_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv'
+  MNI152NLin6Asym:
+    dir: 'resources/zona_bb_subcortex/MNI152NLin6Asym/'
+    T1w: 'tpl-MNI152NLin6Asym_res-04_desc-brain_T1w.nii.gz'
+    seg:  'sub-SNSX32NLin2020Asym_space-MNI152NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz'
+  MNI152NLin2009bAsym:
+    dir: 'resources/zona_bb_subcortex/MNI152NLin2009bAsym/'
+    seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz'
 
 # NOTE: This may not be needed with labelmerge
 freesurfer:
-  labels: 'resources/freesurfer/fs_labels.csv'
+  tsv: 'resources/freesurfer/desc-FreesurferThal_dseg.tsv'
 
 # Containers
 # NOTE: Update from latest to use specific tags
 singularity:
   freesurfer: "docker://pwighton/freesurfer:7.2.0"
   neuroglia-core: "docker://khanlab/neuroglia-core:latest"
   mrtrix: "docker://brainlife/mrtrix:3.0.3"
+  labelmerge: "docker://kaitj/labelmerge:v0.1.0"
 
 fs_license: /path/to/fs/license