Precommit

.github/actions/load-data/action.yml

@@ -31,4 +31,4 @@ runs:
       name: Download datasets from Google Drive
       shell: bash
       run: |
-        rclone copy remote:"SampleData" ./testing_data --drive-shared-with-me
+        rclone copy remote:"SampleData" ./testing_data --drive-shared-with-me

.github/workflows/all_os_versions.txt

@@ -1 +1 @@
-["ubuntu-latest", "macos-latest", "windows-2022"]
+["ubuntu-latest", "macos-latest", "windows-2022"]

.github/workflows/all_python_versions.txt

@@ -1 +1 @@
-["3.10", "3.11", "3.12", "3.13"]
+["3.10", "3.11", "3.12", "3.13"]

.github/workflows/run-tests.yml

@@ -50,7 +50,7 @@ jobs:
         run: |
           python -m pip install "."
           python -m pip install --group test
-      
+
       - name: Prepare data for tests
         uses: ./.github/actions/load-data
         with:

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+-   repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+    -   id: black
+        exclude: ^docs/
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.13.0
+  hooks:
+  - id: ruff
+    args: [ --fix ]
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+  - id: codespell
+    additional_dependencies:
+    - tomli

CHANGELOG.md

@@ -63,4 +63,4 @@
 
 # GuPPy-v1.1.1 (July 6th, 2021)
 
-It is the GuPPy's first release for people to use and give us feedbacks on it
+It is the GuPPy's first release for people to use and give us feedbacks on it

MANIFEST.in

@@ -1,2 +1,2 @@
 include *.md
-recursive-include src *.ipynb
+recursive-include src *.ipynb

README.md

@@ -14,15 +14,15 @@ To install the latest stable release of GuPPy through PyPI, simply run the follo
 pip install guppy
 ```
 
-We recommend that you install the package inside a [virtual environment](https://docs.python.org/3/tutorial/venv.html). 
-A simple way of doing this is to use a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) from the `conda` package manager ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)). 
+We recommend that you install the package inside a [virtual environment](https://docs.python.org/3/tutorial/venv.html).
+A simple way of doing this is to use a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) from the `conda` package manager ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)).
 Detailed instructions on how to use conda environments can be found in their [documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
 ### Installation from GitHub
 
-To install the latest development version of GuPPy from GitHub, you can clone the repository and install the package manually. 
-This has the advantage of allowing you to access the latest features and bug fixes that may not yet be available in the stable release. 
-To install the conversion from GitHub you will need to use `git` ([installation instructions](https://github.com/git-guides/install-git)). 
+To install the latest development version of GuPPy from GitHub, you can clone the repository and install the package manually.
+This has the advantage of allowing you to access the latest features and bug fixes that may not yet be available in the stable release.
+To install the conversion from GitHub you will need to use `git` ([installation instructions](https://github.com/git-guides/install-git)).
 From a terminal or command prompt, execute the following commands:
 
 1. Clone the repository:
@@ -88,5 +88,3 @@ This will launch the GuPPy user interface, where you can begin analyzing your fi
 - [Gabriela Lopez](https://github.com/glopez924)
 - [Talia Lerner](https://github.com/talialerner)
 - [Paul Adkisson](https://github.com/pauladkisson)
-
-

pyproject.toml

@@ -21,12 +21,12 @@ authors = [
 
 license = { file = "LICENSE" }
 keywords = [
-    "neuroscience", 
-    "fiber-photometry", 
-    "calcium-imaging", 
-    "data-analysis", 
-    "gui", 
-    "visualization", 
+    "neuroscience",
+    "fiber-photometry",
+    "calcium-imaging",
+    "data-analysis",
+    "gui",
+    "visualization",
     "signal-processing",
 ]
 classifiers = [
@@ -64,6 +64,10 @@ test = [
     "pytest-xdist"  # Runs tests on parallel
 ]
 
+dev = [
+    "pre-commit",
+]
+
 [project.scripts]
 guppy = "guppy.main:main"
 
@@ -73,3 +77,52 @@ guppy = "guppy.main:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]
+
+[tool.black]
+line-length = 120
+target-version = ['py310', 'py311', 'py312', 'py313']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  \.toml
+  |\.yml
+  |\.txt
+  |\.sh
+  |\.git
+  |\.ini
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
+
+
+[tool.ruff]
+
+[tool.ruff.lint]
+select = [
+    "F401",  # Unused import
+    "I",  # All isort rules
+    # TODO: add docstring rules after adding comprehensive docstrings to all public functions/classes
+    # "D101",  # Missing docstring in public class
+    # "D103",  # Missing docstring in public function
+    "UP006", # non-pep585 annotation (tuple, list -> tuple, list)
+    "UP007" # non-pep604 annotation (Union[x, y] -> X | Y )
+]
+fixable = ["ALL"]
+
+[tool.ruff.lint.per-file-ignores]
+"**__init__.py" = ["F401", "I"] # We are not enforcing import rules in __init__'s
+
+[tool.ruff.lint.isort]
+relative-imports-order = "closest-to-furthest"
+known-first-party = ["guppy"]
+
+
+[tool.codespell]
+skip = '.git*,*.pdf,*.css,*.svg'
+check-hidden = true
+ignore-words-list = 'assertin,sortings'