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

@@ -1,17 +1,16 @@
----
-name: Deploy packages
-on:
-  workflow_dispatch:
-  push:
-    tags: [v*]
-jobs:
-  deploy-docker:
-    uses: khanlab/actions/.github/workflows/[email protected]
-    secrets:
-      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
-      DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
-
-  deploy-pypi:
-    uses: khanlab/actions/.github/workflows/[email protected]
-    secrets:
-      PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+---
+name: Deploy packages
+on:
+  workflow_dispatch:
+  push:
+    tags: [v*]
+jobs:
+  deploy-docker:
+    uses: khanlab/actions/.github/workflows/[email protected]
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
+  deploy-pypi:
+    uses: khanlab/actions/.github/workflows/[email protected]
+    secrets:
+      PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/quality.yml

@@ -12,16 +12,12 @@ jobs:
     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"
       - name: yamlfix
         run: poetry run poe yamlfix-check
       - name: ruff
-        run: poetry run poe ruff-check
-      - name: isort
-        run: poetry run poe isort-check
-      - name: black
-        run: poetry run poe black-check
+        run: poetry run poe ruff-lint-check
       - name: snakefmt
         run: poetry run poe snakefmt-check

.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

.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-format
+        id: ruff-format
+        entry: poetry run ruff format labelmerge
+        language: system
+        types_or: [cython, pyi, python]
+      - name: ruff-lint
+        id: ruff-lint
+        entry: poetry run ruff check --fix labelmerge
+        language: system
+        types_or: [cython, pyi, python]
+      - name: snakefmt
+        id: snakefmt
+        entry: poetry run poe snakefmt
         language: system
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.290
-    hooks:
-      - id: ruff
-  - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    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/snakemake/snakefmt
-    rev: 0.6.1
-    hooks:
-      - id: snakefmt
-        args: [--include=\.smk$|^Snakefile, --line-length=79]

README.md

@@ -1,17 +1,18 @@
 ## Labelmerge
+
 ![Version](https://img.shields.io/github/v/tag/khanlab/labelmerge?label=version)
-![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10-blue.svg)
+![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11-blue.svg)
 ![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/labelmerge)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7636410.svg)](https://doi.org/10.5281/zenodo.7636410)
 
 Labelmerge: A BIDS app for merging multiple label maps and metadata into a single parcellation scheme.
 
-Examination of the brain has led to the creation and distribution of numerous parcellation schemes, studying various features or aspects including gross anatomy, cytoarchitecture, myeloarchitecture, functional connectivty, or structural connectivity. With the growing number of available schemes, there exists a need for methods to robustly merge different these different atlases from numerous sources depending on the aims of the specific study.  
+Examination of the brain has led to the creation and distribution of numerous parcellation schemes, studying various features or aspects including gross anatomy, cytoarchitecture, myeloarchitecture, functional connectivty, or structural connectivity. With the growing number of available schemes, there exists a need for methods to robustly merge different these different atlases from numerous sources depending on the aims of the specific study.
 
 Currently, combining multiple atlases requires image-processing tools to manually remove and add the regions of interest from the respective atlases. While effective, this task becomes inefficient and is prone to error when looking to combine specific labels of interest from multiple atlases or across a group of subjects. To that end we developed Labelmerge, a Brain Imaging Data Structure (BIDS) app that combines the parcellations of multiple atlases into a single parcellation scheme that can be applied towards downstream analysis.
 
-
 ### Contributing
+
 Clone the git repository. Labelmerge dependencies are managed with Poetry
 (version 1.2.x), which you'll need installed on your machine.
 You can find instructions on the Poetry
@@ -34,10 +35,8 @@ poetry run poe
 If you wish, you can also run poe [command] directly by installing poethepoet
 on your system. Follow the install instructions at the link above.
 
-Labelmerge uses pre-commit hooks (installed via the poe setup command above) to 
+Labelmerge uses pre-commit hooks (installed via the poe setup command above) to
 lint and format code (we use black, isort, flake8). By default, these hooks are
 run on every commit.
 
 Please be sure they all pass before making a PR.
-
-