From f9d91a8f6e08848a5e69f0e2d6d59585c95e9fd5 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Mon, 8 Apr 2024 20:02:25 -0500
Subject: [PATCH 01/12] add ruff, remove black/flake8/isort/pyupgrade

---
 .flake8                     | 31 -------------
 .github/workflows/style.yml | 90 ++-----------------------------------
 pyproject.toml              | 58 +++++++++++++++++-------
 requirements/style.txt      |  5 +--
 4 files changed, 48 insertions(+), 136 deletions(-)
 delete mode 100644 .flake8

diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 9c96dfa8..00000000
--- a/.flake8
+++ /dev/null
@@ -1,31 +0,0 @@
-[flake8]
-max-line-length = 88
-extend-ignore =
-    # See https://github.com/PyCQA/pycodestyle/issues/373
-    E203,
-exclude =
-    # Extra files
-    data/,
-    images/,
-    logo/,
-    logs/,
-    output/,
-
-    # Docs
-    docs/src/,
-
-    # Spack
-    .spack-env/,
-
-    # Python
-    build/,
-    dist/,
-    .cache/,
-    .mypy_cache/,
-    .pytest_cache/,
-    __pycache__/,
-    *.egg-info/,
-
-    # Git
-    .git/,
-    .github/,
\ No newline at end of file
diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 61278910..be1e0da4 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -9,8 +9,8 @@ on:
     - main
     - release**
 jobs:
-  black:
-    name: black
+  ruff:
+    name: ruff
     runs-on: ubuntu-latest
     steps:
     - name: Clone repo
@@ -19,96 +19,14 @@ jobs:
       uses: actions/setup-python@v5.0.0
       with:
         python-version: '3.11'
-    - name: Cache dependencies
-      uses: actions/cache@v4.0.0
-      id: cache
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/style.txt') }}
-    - name: Install pip dependencies
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        pip install -r requirements/style.txt
-        pip cache purge
-    - name: List pip dependencies
-      run: pip list
-    - name: Run black checks
-      run: black . --check --diff
-  flake8:
-    name: flake8
-    runs-on: ubuntu-latest
-    steps:
-    - name: Clone repo
-      uses: actions/checkout@v4.1.1
-    - name: Set up python
-      uses: actions/setup-python@v5.0.0
-      with:
-        python-version: '3.11'
-    - name: Cache dependencies
-      uses: actions/cache@v4.0.0
-      id: cache
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/style.txt') }}
-    - name: Install pip dependencies
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        pip install -r requirements/style.txt
-        pip cache purge
-    - name: List pip dependencies
-      run: pip list
-    - name: Run flake8 checks
-      run: flake8
-  isort:
-    name: isort
-    runs-on: ubuntu-latest
-    steps:
-    - name: Clone repo
-      uses: actions/checkout@v4.1.1
-    - name: Set up python
-      uses: actions/setup-python@v5.0.0
-      with:
-        python-version: '3.11'
-    - name: Cache dependencies
-      uses: actions/cache@v4.0.0
-      id: cache
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/style.txt') }}
-    - name: Install pip dependencies
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        pip install -r requirements/style.txt
-        pip cache purge
-    - name: List pip dependencies
-      run: pip list
-    - name: Run isort checks
-      run: isort . --check --diff
-  pyupgrade:
-    name: pyupgrade
-    runs-on: ubuntu-latest
-    steps:
-    - name: Clone repo
-      uses: actions/checkout@v4.1.1
-    - name: Set up python
-      uses: actions/setup-python@v5.0.0
-      with:
-        python-version: '3.11'
-    - name: Cache dependencies
-      uses: actions/cache@v4.0.0
-      id: cache
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/style.txt') }}
     - name: Install pip dependencies
-      if: steps.cache.outputs.cache-hit != 'true'
       run: |
         pip install -r requirements/style.txt
         pip cache purge
     - name: List pip dependencies
       run: pip list
-    - name: Run pyupgrade checks
-      run: pyupgrade --py39-plus
+    - name: Run ruff checks
+      run: ruff format --check -v
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 7dd46c4c..b4ae4df2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,10 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 style = [
-    "black[jupyter]>=21.8",
-    "flake8>=3.8",
-    "isort[colors]>=5.8",
-    "pyupgrade>=2.8",
+    "ruff>=0.3.0"
 ]
 tests = [
     "pytest>=7.3",
@@ -56,11 +53,6 @@ all = [
 [project.urls]
 Homepage = "https://github.com/isaaccorley/torchseg"
 
-[tool.black]
-target-version = ["py39", "py310"]
-color = true
-skip_magic_trailing_comma = true
-
 [tool.coverage.report]
 # Ignore warnings for overloads
 # https://github.com/nedbat/coveragepy/issues/970#issuecomment-612602180
@@ -69,12 +61,6 @@ exclude_lines = [
     "@overload",
 ]
 
-[tool.isort]
-profile = "black"
-known_first_party = ["tests", "torchseg", "train"]
-skip_gitignore = true
-color_output = true
-
 [tool.pytest.ini_options]
 norecursedirs = [
     ".ipynb_checkpoints",
@@ -95,3 +81,45 @@ torchseg = ["py.typed"]
 
 [tool.setuptools.packages.find]
 include = ["torchseg*"]
+
+[tool.ruff]
+exclude = [
+    # Extra files
+    "data/",
+    "images/",
+    "logo/",
+    "logs/",
+    "output/",
+
+    # Docs
+    "docs/src/",
+
+    # Spack
+    ".spack-env/",
+
+    # Python
+    "build/",
+    "dist/",
+    ".cache/",
+    ".mypy_cache/",
+    ".pytest_cache/",
+    "__pycache__/",
+    "*.egg-info/",
+
+    # Git
+    ".git/",
+    ".github/",
+]
+
+line-length = 88
+indent-width = 4
+target-version = "py311"
+
+[tool.ruff.format]
+skip-magic-trailing-comma = true
+
+[tool.ruff.lint]
+ignore = ["E203"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["tests", "torchseg"]
\ No newline at end of file
diff --git a/requirements/style.txt b/requirements/style.txt
index 5080345a..efb6ec75 100644
--- a/requirements/style.txt
+++ b/requirements/style.txt
@@ -1,5 +1,2 @@
 # style
-black[jupyter]==24.3.0
-flake8==7.0.0
-isort[colors]==5.13.2
-pyupgrade==3.15.2
\ No newline at end of file
+ruff==0.3.5
\ No newline at end of file

From e3d05dcb5a06e7d47afb03e8adeef41cbe571b5c Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 12:28:24 -0500
Subject: [PATCH 02/12] update ruff commands and settings

---
 .github/workflows/style.yml | 24 +++++++++++++++++++---
 .gitignore                  |  6 ++++++
 README.md                   | 22 +++++++++++++++++++-
 pyproject.toml              | 40 +++++++++----------------------------
 4 files changed, 57 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index be1e0da4..70d4b8aa 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -9,8 +9,8 @@ on:
     - main
     - release**
 jobs:
-  ruff:
-    name: ruff
+  ruff-formatting:
+    name: ruff-formatting
     runs-on: ubuntu-latest
     steps:
     - name: Clone repo
@@ -26,7 +26,25 @@ jobs:
     - name: List pip dependencies
       run: pip list
     - name: Run ruff checks
-      run: ruff format --check -v
+      run: ruff format --check
+  ruff-linting:
+    name: ruff-linting
+    runs-on: ubuntu-latest
+    steps:
+    - name: Clone repo
+      uses: actions/checkout@v4.1.1
+    - name: Set up python
+      uses: actions/setup-python@v5.0.0
+      with:
+        python-version: '3.11'
+    - name: Install pip dependencies
+      run: |
+        pip install -r requirements/style.txt
+        pip cache purge
+    - name: List pip dependencies
+      run: pip list
+    - name: Run ruff checks
+      run: ruff check
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index b0990628..21cb8ecb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,9 @@
+data/
+images/
+logo/
+logs/
+output/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/README.md b/README.md
index d3cf3009..15c3fa3d 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ The goal of this fork is to 1) provide maintenance support for the original libr
 Additionally we have performed the following for improved software standards:
 
 - More thorough testing and CI
-- Formatting using `black`, `isort`, `flake8`, `mypy`
+- Formatting using `ruff` and `mypy`
 - Reduction of dependence on unmaintained libraries (now depends only on `torch`, `timm`, and `einops`)
 - Reduce lines of code to maintain (removed custom utils, metrics, encoders) in favor of newer libraries such as `torchmetrics` and `timm`
 
@@ -227,3 +227,23 @@ Note that some models like `ConvNext` and `Swin` only have 4 intermediate featur
 ```python
 model = torchseg.Unet('resnet50', encoder_depth=4)
 ```
+
+## Contribute
+
+We welcome new contributions for modern semantic segmentation models, losses, and methods!
+
+#### Install dev dependencies
+
+For development you can install the required dependencies using `pip install '.[all]'.
+
+#### Code Formatting
+
+To format files `ruff format --fix` and `ruff check --fix`
+
+#### Code Linting
+
+To check for linting errors run `ruff check`
+
+#### Tests
+
+To run tests use `pytest -ra`
diff --git a/pyproject.toml b/pyproject.toml
index b4ae4df2..4d851ba2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -83,43 +83,21 @@ torchseg = ["py.typed"]
 include = ["torchseg*"]
 
 [tool.ruff]
-exclude = [
-    # Extra files
-    "data/",
-    "images/",
-    "logo/",
-    "logs/",
-    "output/",
-
-    # Docs
-    "docs/src/",
-
-    # Spack
-    ".spack-env/",
-
-    # Python
-    "build/",
-    "dist/",
-    ".cache/",
-    ".mypy_cache/",
-    ".pytest_cache/",
-    "__pycache__/",
-    "*.egg-info/",
-
-    # Git
-    ".git/",
-    ".github/",
-]
-
 line-length = 88
-indent-width = 4
-target-version = "py311"
+src = ["torchseg", "tests", "scripts"]
+show-fixes = true
 
 [tool.ruff.format]
 skip-magic-trailing-comma = true
+docstring-code-format = true
 
 [tool.ruff.lint]
 ignore = ["E203"]
+extend-select = ["UP", "I"]
 
 [tool.ruff.lint.isort]
-known-first-party = ["tests", "torchseg"]
\ No newline at end of file
+known-first-party = ["tests", "torchseg"]
+split-on-trailing-comma=false
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
\ No newline at end of file

From 1118d1778e65efb7c352dfbab09d7c98afe76c89 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 12:33:20 -0500
Subject: [PATCH 03/12] fix import sorting

---
 pyproject.toml       | 2 --
 tests/test_losses.py | 1 -
 tests/test_models.py | 1 -
 3 files changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4d851ba2..c1fbf9fb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -83,7 +83,6 @@ torchseg = ["py.typed"]
 include = ["torchseg*"]
 
 [tool.ruff]
-line-length = 88
 src = ["torchseg", "tests", "scripts"]
 show-fixes = true
 
@@ -96,7 +95,6 @@ ignore = ["E203"]
 extend-select = ["UP", "I"]
 
 [tool.ruff.lint.isort]
-known-first-party = ["tests", "torchseg"]
 split-on-trailing-comma=false
 
 [tool.ruff.lint.pydocstyle]
diff --git a/tests/test_losses.py b/tests/test_losses.py
index 74d07b3b..ba84607f 100644
--- a/tests/test_losses.py
+++ b/tests/test_losses.py
@@ -1,6 +1,5 @@
 import pytest
 import torch
-
 import torchseg
 import torchseg.losses._functional as F
 from torchseg.losses import (
diff --git a/tests/test_models.py b/tests/test_models.py
index 106ec4c1..4524792c 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -1,6 +1,5 @@
 import pytest
 import torch
-
 import torchseg
 from torchseg.encoders import mix_transformer_encoders
 

From 658eeaa23aa644059ee85047f791c5cf9e25bd1d Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 12:51:53 -0500
Subject: [PATCH 04/12] update to auto fix when running ruff check

---
 .github/workflows/style.yml | 2 +-
 pyproject.toml              | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 70d4b8aa..4324c957 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -44,7 +44,7 @@ jobs:
     - name: List pip dependencies
       run: pip list
     - name: Run ruff checks
-      run: ruff check
+      run: ruff check --output-format=github --exit-non-zero-on-fix
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index c1fbf9fb..3d058d88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -85,6 +85,8 @@ include = ["torchseg*"]
 [tool.ruff]
 src = ["torchseg", "tests", "scripts"]
 show-fixes = true
+fix = true
+unsafe-fixes = true
 
 [tool.ruff.format]
 skip-magic-trailing-comma = true
@@ -98,4 +100,8 @@ extend-select = ["UP", "I"]
 split-on-trailing-comma=false
 
 [tool.ruff.lint.pydocstyle]
-convention = "google"
\ No newline at end of file
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"docs/**" = ["D"]
+"tests/**" = ["D"]
\ No newline at end of file

From 874468a797ff6188180146ead4d99db60cf503e1 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 12:52:07 -0500
Subject: [PATCH 05/12] test that CI throws an error

---
 torchseg/decoders/fpn/decoder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/torchseg/decoders/fpn/decoder.py b/torchseg/decoders/fpn/decoder.py
index 7f78d727..9ffd3061 100644
--- a/torchseg/decoders/fpn/decoder.py
+++ b/torchseg/decoders/fpn/decoder.py
@@ -1,6 +1,6 @@
-import torch
 import torch.nn as nn
 import torch.nn.functional as F
+import torch
 
 
 class Conv3x3GNReLU(nn.Module):

From 2d29c9bb716ccc95f1122114bbab35c3c9b81524 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 12:59:22 -0500
Subject: [PATCH 06/12] try again

---
 .github/workflows/style.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 4324c957..698741c8 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -44,7 +44,7 @@ jobs:
     - name: List pip dependencies
       run: pip list
     - name: Run ruff checks
-      run: ruff check --output-format=github --exit-non-zero-on-fix
+      run: ruff check --output-format=github
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file

From 85a702e6b95c4ba6b26f749fb8f4c841ae6540f3 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 13:01:46 -0500
Subject: [PATCH 07/12] try without output format

---
 .github/workflows/style.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 698741c8..8692bfb2 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -44,7 +44,7 @@ jobs:
     - name: List pip dependencies
       run: pip list
     - name: Run ruff checks
-      run: ruff check --output-format=github
+      run: ruff check --exit-non-zero-on-fix
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file

From 27827e4397baf0bb0d5ef4d8f43ad7347ed62e7f Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 13:19:16 -0500
Subject: [PATCH 08/12] fix

---
 torchseg/decoders/fpn/decoder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/torchseg/decoders/fpn/decoder.py b/torchseg/decoders/fpn/decoder.py
index 9ffd3061..7f78d727 100644
--- a/torchseg/decoders/fpn/decoder.py
+++ b/torchseg/decoders/fpn/decoder.py
@@ -1,6 +1,6 @@
+import torch
 import torch.nn as nn
 import torch.nn.functional as F
-import torch
 
 
 class Conv3x3GNReLU(nn.Module):

From 1dcaa360ad599a357865427a604ae0318feafeda Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 13:21:40 -0500
Subject: [PATCH 09/12] update min version of ruff

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3d058d88..d9b1c855 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 style = [
-    "ruff>=0.3.0"
+    "ruff>=0.2.0"
 ]
 tests = [
     "pytest>=7.3",

From 75eb401e4941aa9d428801204e959db0e7350e6f Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sat, 13 Apr 2024 15:07:46 -0500
Subject: [PATCH 10/12] update

---
 .github/workflows/style.yml | 37 ++++++++++++++-----------------------
 pyproject.toml              | 14 ++++----------
 requirements/style.txt      |  2 +-
 tests/test_losses.py        |  1 +
 tests/test_models.py        |  1 +
 5 files changed, 21 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index 8692bfb2..e64e8dc6 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -9,42 +9,33 @@ on:
     - main
     - release**
 jobs:
-  ruff-formatting:
-    name: ruff-formatting
+  ruff:
+    name: ruff
     runs-on: ubuntu-latest
     steps:
     - name: Clone repo
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.2
     - name: Set up python
-      uses: actions/setup-python@v5.0.0
+      uses: actions/setup-python@v5.1.0
       with:
-        python-version: '3.11'
-    - name: Install pip dependencies
-      run: |
-        pip install -r requirements/style.txt
-        pip cache purge
-    - name: List pip dependencies
-      run: pip list
-    - name: Run ruff checks
-      run: ruff format --check
-  ruff-linting:
-    name: ruff-linting
-    runs-on: ubuntu-latest
-    steps:
-    - name: Clone repo
-      uses: actions/checkout@v4.1.1
-    - name: Set up python
-      uses: actions/setup-python@v5.0.0
+        python-version: '3.12'
+    - name: Cache dependencies
+      uses: actions/cache@v4.0.2
+      id: cache
       with:
-        python-version: '3.11'
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/style.txt') }}
     - name: Install pip dependencies
+      if: steps.cache.outputs.cache-hit != 'true'
       run: |
         pip install -r requirements/style.txt
         pip cache purge
     - name: List pip dependencies
       run: pip list
     - name: Run ruff checks
-      run: ruff check --exit-non-zero-on-fix
+      run: |
+        ruff check --no-fix
+        ruff format --diff
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}
   cancel-in-progress: true
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index d9b1c855..cb5da30f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,6 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 style = [
+    # ruff 0.2+ required for [ruff.lint]
     "ruff>=0.2.0"
 ]
 tests = [
@@ -83,25 +84,18 @@ torchseg = ["py.typed"]
 include = ["torchseg*"]
 
 [tool.ruff]
-src = ["torchseg", "tests", "scripts"]
-show-fixes = true
+extend-include = ["*.ipynb"]
 fix = true
-unsafe-fixes = true
+show-fixes = true
 
 [tool.ruff.format]
 skip-magic-trailing-comma = true
-docstring-code-format = true
 
 [tool.ruff.lint]
-ignore = ["E203"]
-extend-select = ["UP", "I"]
+extend-select = ["I", "UP"]
 
 [tool.ruff.lint.isort]
 split-on-trailing-comma=false
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
-
-[tool.ruff.lint.per-file-ignores]
-"docs/**" = ["D"]
-"tests/**" = ["D"]
\ No newline at end of file
diff --git a/requirements/style.txt b/requirements/style.txt
index efb6ec75..038caa5a 100644
--- a/requirements/style.txt
+++ b/requirements/style.txt
@@ -1,2 +1,2 @@
 # style
-ruff==0.3.5
\ No newline at end of file
+ruff==0.3.7
\ No newline at end of file
diff --git a/tests/test_losses.py b/tests/test_losses.py
index ba84607f..74d07b3b 100644
--- a/tests/test_losses.py
+++ b/tests/test_losses.py
@@ -1,5 +1,6 @@
 import pytest
 import torch
+
 import torchseg
 import torchseg.losses._functional as F
 from torchseg.losses import (
diff --git a/tests/test_models.py b/tests/test_models.py
index 4524792c..106ec4c1 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -1,5 +1,6 @@
 import pytest
 import torch
+
 import torchseg
 from torchseg.encoders import mix_transformer_encoders
 

From 6930106c52c5edf6d451274989c4fb4c6d3cd81b Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Sun, 14 Apr 2024 10:51:44 -0500
Subject: [PATCH 11/12] add output-format=github

---
 .github/workflows/style.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
index e64e8dc6..d688e81f 100644
--- a/.github/workflows/style.yml
+++ b/.github/workflows/style.yml
@@ -34,7 +34,7 @@ jobs:
       run: pip list
     - name: Run ruff checks
       run: |
-        ruff check --no-fix
+        ruff check --output-format=github --no-fix .
         ruff format --diff
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}

From 07caa22f2b1193a979852b99d03b0a1a3dd0e854 Mon Sep 17 00:00:00 2001
From: isaaccorley <22203655+isaaccorley@users.noreply.github.com>
Date: Tue, 16 Apr 2024 20:56:34 -0500
Subject: [PATCH 12/12] fixes per suggestions

---
 README.md      | 8 ++------
 pyproject.toml | 3 +--
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 15c3fa3d..b68f91c0 100644
--- a/README.md
+++ b/README.md
@@ -236,13 +236,9 @@ We welcome new contributions for modern semantic segmentation models, losses, an
 
 For development you can install the required dependencies using `pip install '.[all]'.
 
-#### Code Formatting
+#### Code Formatting/Linting
 
-To format files `ruff format --fix` and `ruff check --fix`
-
-#### Code Linting
-
-To check for linting errors run `ruff check`
+To format files run `ruff format`. To check for linting errors run `ruff check`.
 
 #### Tests
 
diff --git a/pyproject.toml b/pyproject.toml
index cb5da30f..4f7e5eb0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,7 +84,6 @@ torchseg = ["py.typed"]
 include = ["torchseg*"]
 
 [tool.ruff]
-extend-include = ["*.ipynb"]
 fix = true
 show-fixes = true
 
@@ -95,7 +94,7 @@ skip-magic-trailing-comma = true
 extend-select = ["I", "UP"]
 
 [tool.ruff.lint.isort]
-split-on-trailing-comma=false
+split-on-trailing-comma = false
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"