Dependency updates

.github/workflows/assign_reviewers.yml

@@ -5,4 +5,4 @@ on:
     types: [opened, ready_for_review]
 jobs:
   assign-reviewer:
-    uses: khanlab/actions/.github/workflows/[email protected].0
+    uses: khanlab/actions/.github/workflows/[email protected].4

.github/workflows/bump_version.yml

@@ -6,6 +6,6 @@ on:
 jobs:
   bump-version:
     if: github.event.pull_request.merged == true
-    uses: khanlab/actions/.github/workflows/[email protected].0
+    uses: khanlab/actions/.github/workflows/[email protected].4
     secrets:
       BP_PAT: ${{ secrets.BP_PAT_TOKEN }}

.github/workflows/deploy.yml

@@ -6,7 +6,7 @@ on:
     tags: [v*]
 jobs:
   deploy_docker:
-    uses: khanlab/actions/.github/workflows/[email protected].0
+    uses: khanlab/actions/.github/workflows/[email protected].4
     with:
       maximize_space: true
     secrets:

.github/workflows/release.yml

@@ -8,7 +8,7 @@ on:
         required: false
 jobs:
   release_package:
-    uses: khanlab/actions/.github/workflows/[email protected].0
+    uses: khanlab/actions/.github/workflows/[email protected].4
     with:
       comments: ${{ github.event.inputs.comments }}
       pipeline-description: true

.github/workflows/test.yml

@@ -2,38 +2,34 @@
 name: Lint and test workflow
 on:
   push:
-    branches: ["*", "!push-action/*"]
+    branches: ['*', '!push-action/*']
   pull_request:
-    branches: ["*", "!push-action/*"]
+    branches: ['*', '!push-action/*']
 jobs:
   quality:
     name: Lint code
     if: github.event.pull_request.merged == false
     runs-on: ubuntu-latest
     steps:
       - name: Setup Python environment
-        uses: khanlab/actions/.github/actions/[email protected].0
+        uses: khanlab/actions/.github/actions/[email protected].4
         with:
-          python-version: "3.10"
+          python-version: '3.10'
       - name: yamlfix
         run: poetry run poe yamlfix-check
-      - name: isort
-        run: poetry run poe isort-check
-      - name: black
-        run: poetry run poe black-check
       - name: ruff
-        run: poetry run poe ruff-check
+        run: poetry run poe ruff-lint-check
       - name: snakefmt
         run: poetry run poe snakefmt-check
   test:
     runs-on: ubuntu-latest
     needs: [quality]
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     steps:
       - name: Setup Python environments
-        uses: khanlab/actions/.github/actions/[email protected].0
+        uses: khanlab/actions/.github/actions/[email protected].4
         with:
           python-version: ${{ matrix.python-version }}
           install-library: true

.pre-commit-config.yaml

@@ -1,4 +1,6 @@
 ---
+default_language_version:
+  python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
@@ -8,26 +10,21 @@ repos:
       - id: trailing-whitespace
   - repo: local
     hooks:
-      - id: yamlfix
-        name: yamlfix
-        entry: bash -c "poetry run poe yamlfix"
+      - name: yamlfix
+        id: yamlfix
+        entry: poetry run poe yamlfix
+        language: system
+      - name: ruff-lint
+        id: ruff-lint
+        entry: poetry run poe ruff-lint
+        language: system
+        types_or: [cython, pyi, python]
+      - name: ruff-format
+        id: ruff-format
+        entry: poetry run poe ruff-format
+        language: system
+        types_or: [cython, pyi, python]
+      - name: snakefmt
+        id: snakefmt
+        entry: poetry run poe snakefmt
         language: system
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: [--profile=black, --multi-line=3]
-  - repo: https://github.com/psf/black
-    rev: 22.8.0
-    hooks:
-      - id: black
-        args: [--line-length=79]
-  - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
-    hooks:
-      - id: flake8
-  - repo: https://github.com/snakemake/snakefmt
-    rev: 0.6.1
-    hooks:
-      - id: snakefmt
-        args: [--include=\.smk$|^Snakefile, --line-length=79]

docs/conf.py

@@ -64,4 +64,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = ["_static"]

pyproject.toml

@@ -14,27 +14,27 @@ documentation = "https://scattr.readthedocs.io"
 packages = [{ include = "scattr" }]
 
 [tool.poetry.dependencies]
-python = ">=3.8, <3.11"
-snakebids = "^0.9.0"
+python = ">=3.8, <3.12"
+snakebids = "^0.10.2"
+labelmerge = "^0.4.7"
+matplotlib = "^3.7.1"
 nibabel = "^3.2.2"
 nilearn = "^0.10.0"
-numpy = "^1.22.3"
-scipy = "^1.8.0"
-labelmerge = "^v0.4.6"
-matplotlib = "^3.7.1"
 niworkflows = "^1.7.9"
+numpy = "^1.22.3"
 pygments = "^2.15.1"
+scipy = "^1.8.0"
+# Required constraint for compatability with snakebids
+pulp = "<2.8.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest-console-scripts = "1.2"
 pytest = "^7.0.1"
-black = "^22.1.0"
-isort = "^5.10.1"
 poethepoet = "^0.13.1"
 pre-commit = "^2.17.0"
 snakefmt = "^0.6.1"
 yamlfix = "^1.1.0"
-ruff = "^0.0.267"
+ruff = "^0.1.14"
 
 [tool.poetry.scripts]
 scattr = 'scattr.run:main'
@@ -45,22 +45,13 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poe.tasks]
 setup = "pre-commit install"
-isort = "isort scattr"
-isort-check = "isort -c scattr"
-black = "black scattr"
-black-check = "black --check scattr"
-ruff = "ruff --fix scattr"
-ruff-check = "ruff scattr"
+ruff-lint = "ruff check --fix scattr"
+ruff-lint-check = "ruff check scattr"
+ruff-format = "ruff format ."
 snakefmt = "snakefmt scattr"
 snakefmt-check = "snakefmt --check scattr"
-quality = ["yamlfix", "ruff", "isort", "black", "snakefmt"]
-quality-check = [
-    "ruff-check",
-    "yamlfix-check",
-    "isort-check",
-    "black-check",
-    "snakefmt-check",
-]
+quality = ["yamlfix", "ruff-lint", "ruff-format", "snakefmt"]
+quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"]
 test = [
     "test_base",
     "test_freesurfer",
@@ -144,15 +135,8 @@ find . -type f \\( \
 \\) -exec yamlfix --check {} \\;
 """
 
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-line_length = 79
-
-[tool.black]
-line-length = 79
-
 [tool.ruff]
+select = ["E", "W", "N", "RUF", "I", "UP"]
 line-length = 79
 builtins = ["snakemake"]
 

scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py

@@ -22,13 +22,13 @@ def create_exclude_mask(
     Path(out_dir).mkdir(parents=True, exist_ok=True)
 
     # Get number of labels
-    with open(num_labels, "r") as f:
+    with open(num_labels) as f:
         num_labels = int(f.read().strip())
 
     node_pairs = np.triu_indices(num_labels, k=1)
 
     # Zona labels (currently misisng subjects)
-    lZI = expand(  # noqa: F841 (used in shell call)
+    lZI = expand(  # (used in shell call)   # noqa: N806
         bids(
             root=base_dir,
             datatype="roi_masks",
@@ -37,7 +37,7 @@ def create_exclude_mask(
             **wildcards,
         )
     )
-    rZI = bids(  # noqa: F841 (used in shell call)
+    rZI = bids(  # (used in shell call) # noqa: N806
         root=base_dir,
         datatype="roi_masks",
         desc="22",
@@ -62,7 +62,7 @@ def create_exclude_mask(
 
     # Create masks - run sequentially due to parallelization errors
     for idx, mask in enumerate(out_mask):
-        in_roi1, in_roi2 = roi1[idx], roi2[idx]  # noqa: F841 (used in shell)
+        in_roi1, in_roi2 = roi1[idx], roi2[idx]  # (used in shell)
         shell(
             "mrcalc -nthreads {threads} "
             "{subcortical_seg} 0 -neq {in_roi1} -sub {in_roi2} -sub {lZI} "

scattr/workflow/scripts/mrtpipelines/create_roi_mask.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from snakebids import bids
-from snakemake.io import expand  # noqa: F401 (used in commented command)
+from snakemake.io import expand  # (used in commented command)
 from snakemake.shell import shell
 
 
@@ -19,12 +19,12 @@ def create_roi_mask(
     Path(out_dir).mkdir(parents=True, exist_ok=True)
 
     # Read number of labels
-    with open(num_labels, "r") as f:
+    with open(num_labels) as f:
         num_labels = int(f.read().strip())
 
     # Create masks sequentially (error with trying to do it in parallel)
     for idx in range(1, num_labels + 1):
-        roi = bids(  # noqa: F841 (used in shell call)
+        roi = bids(  # (used in shell call)
             root=base_dir,
             datatype="roi_masks",
             desc=f"{idx}",

scattr/workflow/scripts/qc/segmentation_qc.py

@@ -38,5 +38,5 @@ def segmentation_qc(
         seg_path=snakemake.input.qc_labels,
         output_path_static=snakemake.output.qc_png,
         output_path_html=snakemake.output.qc_html,
-        wildcards=snakemake.wildcards,  # noqa:F821
+        wildcards=snakemake.wildcards,
     )