Reorganize into a better package structure and add GHA and precommit.

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = [setup.cfg] 
+ignore-words-list = FWE, fwe

.github/workflows/test.yaml

@@ -0,0 +1,25 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev]
+    - name: Install and run pre-commit hooks
+      uses: pre-commit/action@v3.0.1
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -1,2 +1,4 @@
 dist/**
-fwe.egg-info
+fwe.egg-info
+.DS_store
+__pycache__

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [ --fix, --config, pyproject.toml ]
+      # Run the formatter
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli

README.md

@@ -4,6 +4,8 @@
 
 Implements free water elimination (FWE) models for preprocessing diffusion MRI data.
 
+This code was used in the paper: ["Free water elimination tractometry for aging brains"](https://direct.mit.edu/imag/article/doi/10.1162/IMAG.a.991/133658/Free-water-elimination-tractometry-for-aging)
+
 ---
 
 ## To install
@@ -22,7 +24,7 @@ automatically as part of the installation process specified above.
 
 ## Available Models
 
-* Free water DTI as implmented in `dipy` ([Hoy et al., 2014](https://doi.org/10.1016/j.neuroimage.2014.09.053)): Use `fwe_model="dipy_fwdti"`
+* Free water DTI as implemented in `dipy` ([Hoy et al., 2014](https://doi.org/10.1016/j.neuroimage.2014.09.053)): Use `fwe_model="dipy_fwdti"`
 * Beltrami regularized gradient descent free water DTI ([Golub et al., 2020](https://doi.org/10.1002/mrm.28599)): Use `fwe_model="golub_beltrami"`
 
 ---

pyproject.toml

@@ -6,7 +6,8 @@ build-backend = "setuptools.build_meta"
 name = "fwe"
 version = "0.0.1"
 authors = [
-  { name = "Kelly Chang", email = "kchang4@uw.edu" }
+  { name = "Kelly Chang", email = "kchang4@uw.edu" },
+  { name = "Ariel Rokem", email = "arokem@gmail.com"}
 ]
 description = "Free water elimination in diffusion MRI"
 readme = "README.md"
@@ -21,6 +22,36 @@ dependencies = [
     "dipy"
 ]
 
+[project.optional-dependencies]
+  dev = ["pre-commit",
+         "pytest"]
+
+[tool.setuptools_scm]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["fwe*"]
+
+[tool.ruff]
+target-version = "py311"
+exclude = ["src/fwe/__init__.py"]
+
+[tool.ruff.lint]
+select = [
+  "F",
+  "E",
+  "C",
+  "W",
+  "B",
+  "I",
+]
+ignore = [
+  "B905",
+  "C901",
+  "E203",
+  "F821"
+]
+
 
 [project.urls]
 Homepage = "https://github.com/nrdg/fwe"