add pre-commit and instructions

SBU-BMI · Feb 22, 2024 · c26783b · c26783b
1 parent 1f35a28
commit c26783b
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,14 @@
+repos:
+  - repo: 'https://github.com/pre-commit/pre-commit-hooks'
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: 'https://github.com/astral-sh/ruff-pre-commit'
+    rev: v0.2.2
+    hooks:
+      - id: ruff
+        args:
+          - '--fix'
+      - id: ruff-format
diff --git a/README.md b/README.md
@@ -86,8 +86,11 @@ Clone this GitHub repository and install the package (in editable mode with the
 git clone https://github.com/SBU-BMI/wsinfer.git
 cd wsinfer
 python -m pip install --editable .[dev]
+pre-commit install
 ```
 
+We use `pre-commit` to automatically run various checks during `git commit`.
+
 # Citation
 
 If you find our work useful, please cite [our paper](https://doi.org/10.1038/s41698-024-00499-9)!

diff --git a/docs/installing.rst b/docs/installing.rst
@@ -84,6 +84,9 @@ Clone the GitHub repository and install the package in editable mode with the :c
     git clone https://github.com/SBU-BMI/wsinfer.git
     cd wsinfer
     python -m pip install --editable .[dev]
+    pre-commit install
+
+We use :code:`pre-commit` to automatically run various checks during :code:`git commit`.
 
 
 Supported slide backends

diff --git a/pyproject.toml b/pyproject.toml
@@ -66,6 +66,7 @@ dev = [
     "geojson",
     "mypy",
     "pandas-stubs",
+    "pre-commit",
     "pytest",
     "ruff",
     "tiffslide",