From 19fb1a885b98bab0b826dbfe5a683612cc44b0e0 Mon Sep 17 00:00:00 2001
From: Austin Gregg-Smith <blooop@gmail.com>
Date: Thu, 14 Nov 2024 10:46:29 +0000
Subject: [PATCH] Feature/pre commit (#64)

* add pre-commit for ruff

* add pre commit

* add precommit github workflow

* update pre-commit version

* add pre-commit task

* run pre-commit

* enable more pre-commit checks

* remove black

* update pixi.lock

* add typo

* add precommit to docker

* remove black settings

* extract ruff settings into ruff.toml

* extract ruff settings into ruff.toml

* update pre-commit hooks
---
 .devcontainer/Dockerfile          |   2 +-
 .gitattributes                    |   2 +-
 .github/workflows/ci.yml          |   2 +-
 .github/workflows/pre-commit.yaml |  10 +
 .github/workflows/publish.yml     |   2 +-
 .pre-commit-config.yaml           |  44 +++
 .vscode/extensions.json           |   2 +-
 .vscode/settings.json             |   2 +-
 CHANGELOG.md                      |   2 -
 README.md                         |   3 -
 docs/requirements.txt             |   2 +-
 pixi.lock                         | 627 ++++++++++++++++--------------
 pyproject.toml                    |  26 +-
 python_template.deps.yaml         |   1 +
 ruff.toml                         |  16 +
 scripts/setup_host.sh             |   2 +-
 16 files changed, 411 insertions(+), 334 deletions(-)
 create mode 100644 .github/workflows/pre-commit.yaml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 ruff.toml

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 66ae0524..8d9fb5e7 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -10,4 +10,4 @@ RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix
 USER vscode
 WORKDIR /home/vscode
 
-RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc
\ No newline at end of file
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc
diff --git a/.gitattributes b/.gitattributes
index da2f70b8..e5075801 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -43,4 +43,4 @@
 # numpy file format
 *.npy filter=lfs diff=lfs merge=lfs -text
 # GitHub syntax highlighting
-pixi.lock linguist-language=YAML merge=ourslock
\ No newline at end of file
+pixi.lock linguist-language=YAML merge=ourslock
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d7f24833..a69819e5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,4 +29,4 @@ jobs:
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
\ No newline at end of file
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
new file mode 100644
index 00000000..667659d7
--- /dev/null
+++ b/.github/workflows/pre-commit.yaml
@@ -0,0 +1,10 @@
+name: pre-commit
+
+on: [pull_request]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: pre-commit/action@v3.0.0
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 6e745b75..ce03a161 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -15,4 +15,4 @@ jobs:
       with:
         pypi-token: ${{ secrets.PYPI_API_TOKEN }}
         gh-token: ${{ secrets.GITHUB_TOKEN }}
-        parse-changelog: true
\ No newline at end of file
+        parse-changelog: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..9183eb04
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,44 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://github.com/pre-commit/pre-commit
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+        args: ['--unsafe']  # Fixes errors parsing custom jinja templates
+      # - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      # - id: trailing-whitespace
+      - id: fix-byte-order-marker
+
+  # Formatter for python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi ]
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
index 4cf65aad..c31655f3 100644
--- a/.vscode/extensions.json
+++ b/.vscode/extensions.json
@@ -14,4 +14,4 @@
         "ryanluker.vscode-coverage-gutters",
         "jjjermiah.pixi-vscode"       
     ]
-}
\ No newline at end of file
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
index b1772fe6..bda5af73 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -11,4 +11,4 @@
 		"/home/vscode/.local/lib/python3.10/site-packages/python_template/**": true
 	},
 	"python.analysis.autoImportCompletions": false //vscode gets it wrong more than right and mostly gets in the way
-}
\ No newline at end of file
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5d9734ad..99f9c7a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,5 +3,3 @@
 ## python_template
 
 ## [0.0.0]
-
-
diff --git a/README.md b/README.md
index 6f11f2c6..344afaed 100644
--- a/README.md
+++ b/README.md
@@ -94,6 +94,3 @@ There are two core tasks.
 2. run \<cfg\>
 
     This runs python with the file set in \<cfg\>
-
-
-
diff --git a/docs/requirements.txt b/docs/requirements.txt
index d43dc9d2..4f180895 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,3 +1,3 @@
 sphinxcontrib-napoleon
 sphinx-rtd-theme
-sphinx-autoapi
\ No newline at end of file
+sphinx-autoapi
diff --git a/pixi.lock b/pixi.lock
index 4d14f9f2..4a95c74d 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -11,18 +11,18 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda
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-  version: 14.1.0
+  version: 14.2.0
   build: h77fa898_1
   build_number: 1
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda
-  sha256: c96724c8ae4ee61af7674c5d9e5a3fbcf6cd887a40ad5a52c99aa36f1d4f9680
-  md5: 23c255b008c4f2ae008f81edcabaca89
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda
+  sha256: 1911c29975ec99b6b906904040c855772ccb265a1c79d5d75c8ceec4ed89cd63
+  md5: cc3573974587f12dda90d96e3e55a702
   depends:
   - _libgcc_mutex 0.1 conda_forge
   license: GPL-3.0-only WITH GCC-exception-3.1
   license_family: GPL
   purls: []
-  size: 460218
-  timestamp: 1724801743478
+  size: 460992
+  timestamp: 1729027639220
 - kind: conda
   name: libmpdec
   version: 4.0.0
@@ -708,20 +676,21 @@ packages:
   timestamp: 1697359010159
 - kind: conda
   name: libsqlite
-  version: 3.46.1
-  build: hadc24fc_0
+  version: 3.47.0
+  build: hadc24fc_1
+  build_number: 1
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.1-hadc24fc_0.conda
-  sha256: 9851c049abafed3ee329d6c7c2033407e2fc269d33a75c071110ab52300002b0
-  md5: 36f79405ab16bf271edb55b213836dac
+  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda
+  sha256: 8a9aadf996a2399f65b679c6e7f29139d5059f699c63e6d7b50e20db10c00508
+  md5: b6f02b52a174e612e89548f4663ce56a
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=13
   - libzlib >=1.3.1,<2.0a0
   license: Unlicense
   purls: []
-  size: 865214
-  timestamp: 1725353659783
+  size: 875349
+  timestamp: 1730208050020
 - kind: conda
   name: libuuid
   version: 2.38.1
@@ -777,12 +746,6 @@ packages:
   url: https://files.pythonhosted.org/packages/27/1a/1f68f9ba0c207934b35b86a8ca3aad8395a3d6dd7921c0686e23853ff5a9/mccabe-0.7.0-py2.py3-none-any.whl
   sha256: 6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e
   requires_python: '>=3.6'
-- kind: pypi
-  name: mypy-extensions
-  version: 1.0.0
-  url: https://files.pythonhosted.org/packages/2a/e2/5d3f6ada4297caebe1a2add3b126fe800c96f56dbe5d1988a2cbe0b267aa/mypy_extensions-1.0.0-py3-none-any.whl
-  sha256: 4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d
-  requires_python: '>=3.5'
 - kind: conda
   name: ncurses
   version: '6.5'
@@ -799,14 +762,20 @@ packages:
   purls: []
   size: 889086
   timestamp: 1724658547447
+- kind: pypi
+  name: nodeenv
+  version: 1.9.1
+  url: https://files.pythonhosted.org/packages/d2/1d/1b658dbd2b9fa9c4c9f32accbfc0205d532c8c6194dc0f2a4c0428e7128a/nodeenv-1.9.1-py2.py3-none-any.whl
+  sha256: ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9
+  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*'
 - kind: conda
   name: openssl
-  version: 3.3.2
+  version: 3.4.0
   build: hb9d3cd8_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda
-  sha256: cee91036686419f6dd6086902acf7142b4916e1c4ba042e9ca23e151da012b6d
-  md5: 4d638782050ab6faa27275bed57e9b4e
+  url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda
+  sha256: 814b9dff1847b132c676ee6cc1a8cb2d427320779b93e1b6d76552275c128705
+  md5: 23cc74f77eb99315c0360ec3533147a9
   depends:
   - __glibc >=2.17,<3.0.a0
   - ca-certificates
@@ -814,19 +783,13 @@ packages:
   license: Apache-2.0
   license_family: Apache
   purls: []
-  size: 2891789
-  timestamp: 1725410790053
+  size: 2947466
+  timestamp: 1731377666602
 - kind: pypi
   name: packaging
-  version: '24.1'
-  url: https://files.pythonhosted.org/packages/08/aa/cc0199a5f0ad350994d660967a8efb233fe0416e4639146c089643407ce6/packaging-24.1-py3-none-any.whl
-  sha256: 5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124
-  requires_python: '>=3.8'
-- kind: pypi
-  name: pathspec
-  version: 0.12.1
-  url: https://files.pythonhosted.org/packages/cc/20/ff623b09d963f88bfde16306a54e12ee5ea43e9b597108672ff3a408aad6/pathspec-0.12.1-py3-none-any.whl
-  sha256: a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08
+  version: '24.2'
+  url: https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl
+  sha256: 09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759
   requires_python: '>=3.8'
 - kind: pypi
   name: platformdirs
@@ -856,6 +819,18 @@ packages:
   - pytest ; extra == 'testing'
   - pytest-benchmark ; extra == 'testing'
   requires_python: '>=3.8'
+- kind: pypi
+  name: pre-commit
+  version: 4.0.1
+  url: https://files.pythonhosted.org/packages/16/8f/496e10d51edd6671ebe0432e33ff800aa86775d2d147ce7d43389324a525/pre_commit-4.0.1-py2.py3-none-any.whl
+  sha256: efde913840816312445dc98787724647c65473daefe420785f885e8ed9a06878
+  requires_dist:
+  - cfgv>=2.0.0
+  - identify>=1.0.0
+  - nodeenv>=0.11.1
+  - pyyaml>=5.1
+  - virtualenv>=20.10.0
+  requires_python: '>=3.9'
 - kind: pypi
   name: pylint
   version: 3.3.1
@@ -863,9 +838,9 @@ packages:
   sha256: 2f846a466dd023513240bc140ad2dd73bfc080a5d85a710afdb728c420a5a2b9
   requires_dist:
   - platformdirs>=2.2.0
-  - astroid<=3.4.0.dev0,>=3.3.4
-  - isort!=5.13.0,<6,>=4.2.5
-  - mccabe<0.8,>=0.6
+  - astroid>=3.3.4,<=3.4.0.dev0
+  - isort>=4.2.5,!=5.13.0,<6
+  - mccabe>=0.6,<0.8
   - tomlkit>=0.10.1
   - typing-extensions>=3.10.0 ; python_full_version < '3.10'
   - dill>=0.2 ; python_full_version < '3.11'
@@ -884,7 +859,7 @@ packages:
   requires_dist:
   - iniconfig
   - packaging
-  - pluggy<2,>=1.5
+  - pluggy>=1.5,<2
   - exceptiongroup>=1.0.0rc8 ; python_full_version < '3.11'
   - tomli>=1 ; python_full_version < '3.11'
   - colorama ; sys_platform == 'win32'
@@ -899,27 +874,27 @@ packages:
   requires_python: '>=3.8'
 - kind: pypi
   name: pytest-cov
-  version: 5.0.0
-  url: https://files.pythonhosted.org/packages/78/3a/af5b4fa5961d9a1e6237b530eb87dd04aea6eb83da09d2a4073d81b54ccf/pytest_cov-5.0.0-py3-none-any.whl
-  sha256: 4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652
+  version: 6.0.0
+  url: https://files.pythonhosted.org/packages/36/3b/48e79f2cd6a61dbbd4807b4ed46cb564b4fd50a76166b1c4ea5c1d9e2371/pytest_cov-6.0.0-py3-none-any.whl
+  sha256: eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35
   requires_dist:
   - pytest>=4.6
-  - coverage[toml]>=5.2.1
+  - coverage[toml]>=7.5
   - fields ; extra == 'testing'
   - hunter ; extra == 'testing'
   - process-tests ; extra == 'testing'
   - pytest-xdist ; extra == 'testing'
   - virtualenv ; extra == 'testing'
-  requires_python: '>=3.8'
+  requires_python: '>=3.9'
 - kind: conda
   name: python
   version: 3.10.15
-  build: h4a871b0_1_cpython
-  build_number: 1
+  build: h4a871b0_2_cpython
+  build_number: 2
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.15-h4a871b0_1_cpython.conda
-  sha256: 7611846de94e1b7c41b308dc6788e65227e8c65bd2f1575e1753acc9a3129fd9
-  md5: 9e1b028075ff7348a194d524b6910f12
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.15-h4a871b0_2_cpython.conda
+  sha256: c1e5e93b887d8cd1aa31d24b9620cb7eb6645c08c97b15ffc844fd6c29051420
+  md5: 98059097f62e97be9aed7ec904055825
   depends:
   - __glibc >=2.17,<3.0.a0
   - bzip2 >=1.0.8,<2.0a0
@@ -941,17 +916,17 @@ packages:
   - python_abi 3.10.* *_cp310
   license: Python-2.0
   purls: []
-  size: 25198492
-  timestamp: 1727719762520
+  size: 25321141
+  timestamp: 1729042931665
 - kind: conda
   name: python
   version: 3.11.10
-  build: hc5c86c4_2_cpython
-  build_number: 2
+  build: hc5c86c4_3_cpython
+  build_number: 3
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.10-hc5c86c4_2_cpython.conda
-  sha256: 06aef8aee7d379851df48e78eec81820817aaf7e4788dde1b945d903cd4af7ea
-  md5: 2a07cf98fe8c2f039a1ccfea22eaaad4
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.10-hc5c86c4_3_cpython.conda
+  sha256: b7fa3bd48e3a3d30f65608e07759cefd27885c6388b3f612af85ce40282e6936
+  md5: 9e1ad55c87368e662177661a998feed5
   depends:
   - __glibc >=2.17,<3.0.a0
   - bzip2 >=1.0.8,<2.0a0
@@ -974,8 +949,8 @@ packages:
   - python_abi 3.11.* *_cp311
   license: Python-2.0
   purls: []
-  size: 30574701
-  timestamp: 1727721739918
+  size: 30543977
+  timestamp: 1729043512711
 - kind: conda
   name: python
   version: 3.12.7
@@ -1043,15 +1018,15 @@ packages:
   name: python-template
   version: 0.2.0
   path: .
-  sha256: f9abf99440c550543b52a036e8128cc8772af1bae9d252a7ba14e2ae1854f4d3
+  sha256: e40291388966efb5015d3a9758e2c4e00bec48ced6ad6db8b00a05422b242d0d
   requires_dist:
-  - black>=23,<=24.8.0 ; extra == 'test'
   - pylint>=3.2.5,<=3.3.1 ; extra == 'test'
-  - pytest-cov>=4.1,<=5.0.0 ; extra == 'test'
+  - pytest-cov>=4.1,<=6.0.0 ; extra == 'test'
   - pytest>=7.4,<=8.3.3 ; extra == 'test'
-  - hypothesis>=6.104.2,<=6.112.2 ; extra == 'test'
-  - ruff>=0.5.0,<=0.6.8 ; extra == 'test'
-  - coverage>=7.5.4,<=7.6.1 ; extra == 'test'
+  - hypothesis>=6.104.2,<=6.116.0 ; extra == 'test'
+  - ruff>=0.5.0,<=0.7.2 ; extra == 'test'
+  - coverage>=7.5.4,<=7.6.4 ; extra == 'test'
+  - pre-commit<=4.0.1 ; extra == 'test'
   editable: true
 - kind: conda
   name: python_abi
@@ -1069,6 +1044,30 @@ packages:
   purls: []
   size: 6217
   timestamp: 1723823393322
+- kind: pypi
+  name: pyyaml
+  version: 6.0.2
+  url: https://files.pythonhosted.org/packages/04/24/b7721e4845c2f162d26f50521b825fb061bc0a5afcf9a386840f23ea19fa/PyYAML-6.0.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 70b189594dbe54f75ab3a1acec5f1e3faa7e8cf2f1e08d9b561cb41b845f69d5
+  requires_python: '>=3.8'
+- kind: pypi
+  name: pyyaml
+  version: 6.0.2
+  url: https://files.pythonhosted.org/packages/6b/4e/1523cb902fd98355e2e9ea5e5eb237cbc5f3ad5f3075fa65087aa0ecb669/PyYAML-6.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: ec031d5d2feb36d1d1a24380e4db6d43695f3748343d99434e6f5f9156aaa2ed
+  requires_python: '>=3.8'
+- kind: pypi
+  name: pyyaml
+  version: 6.0.2
+  url: https://files.pythonhosted.org/packages/75/e4/2c27590dfc9992f73aabbeb9241ae20220bd9452df27483b6e56d3975cc5/PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 3ad2a3decf9aaba3d29c8f537ac4b243e36bef957511b4766cb0057d32b0be85
+  requires_python: '>=3.8'
+- kind: pypi
+  name: pyyaml
+  version: 6.0.2
+  url: https://files.pythonhosted.org/packages/b9/2b/614b4752f2e127db5cc206abc23a8c19678e92b23c3db30fc86ab731d3bd/PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 80bab7bfc629882493af4aa31a4cfa43a4c57c83813253626916b8c7ada83476
+  requires_python: '>=3.8'
 - kind: conda
   name: readline
   version: '8.2'
@@ -1088,9 +1087,9 @@ packages:
   timestamp: 1679532220005
 - kind: pypi
   name: ruff
-  version: 0.6.8
-  url: https://files.pythonhosted.org/packages/48/44/7caa223af7d4ea0f0b2bd34acca65a7694a58317714675a2478815ab3f45/ruff-0.6.8-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-  sha256: 6ef0411eccfc3909269fed47c61ffebdcb84a04504bafa6b6df9b85c27e813b0
+  version: 0.7.2
+  url: https://files.pythonhosted.org/packages/a0/57/4642e57484d80d274750dcc872ea66655bbd7e66e986fede31e1865b463d/ruff-0.7.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: dba53ed84ac19ae4bfb4ea4bf0172550a2285fa27fbb13e3746f04c80f7fa088
   requires_python: '>=3.7'
 - kind: pypi
   name: sortedcontainers
@@ -1116,9 +1115,9 @@ packages:
   timestamp: 1699202167581
 - kind: pypi
   name: tomli
-  version: 2.0.2
-  url: https://files.pythonhosted.org/packages/cf/db/ce8eda256fa131af12e0a76d481711abe4681b6923c27efb9a255c9e4594/tomli-2.0.2-py3-none-any.whl
-  sha256: 2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38
+  version: 2.1.0
+  url: https://files.pythonhosted.org/packages/de/f7/4da0ffe1892122c9ea096c57f64c2753ae5dd3ce85488802d11b0992cc6d/tomli-2.1.0-py3-none-any.whl
+  sha256: a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391
   requires_python: '>=3.8'
 - kind: pypi
   name: tomlkit
@@ -1145,6 +1144,36 @@ packages:
   purls: []
   size: 122354
   timestamp: 1728047496079
+- kind: pypi
+  name: virtualenv
+  version: 20.27.1
+  url: https://files.pythonhosted.org/packages/ae/92/78324ff89391e00c8f4cf6b8526c41c6ef36b4ea2d2c132250b1a6fc2b8d/virtualenv-20.27.1-py3-none-any.whl
+  sha256: f11f1b8a29525562925f745563bfd48b189450f61fb34c4f9cc79dd5aa32a1f4
+  requires_dist:
+  - distlib>=0.3.7,<1
+  - filelock>=3.12.2,<4
+  - importlib-metadata>=6.6 ; python_full_version < '3.8'
+  - platformdirs>=3.9.1,<5
+  - furo>=2023.7.26 ; extra == 'docs'
+  - proselint>=0.13 ; extra == 'docs'
+  - sphinx>=7.1.2,!=7.3 ; extra == 'docs'
+  - sphinx-argparse>=0.4 ; extra == 'docs'
+  - sphinxcontrib-towncrier>=0.2.1a0 ; extra == 'docs'
+  - towncrier>=23.6 ; extra == 'docs'
+  - covdefaults>=2.3 ; extra == 'test'
+  - coverage-enable-subprocess>=1 ; extra == 'test'
+  - coverage>=7.2.7 ; extra == 'test'
+  - flaky>=3.7 ; extra == 'test'
+  - packaging>=23.1 ; extra == 'test'
+  - pytest-env>=0.8.2 ; extra == 'test'
+  - pytest-freezer>=0.4.8 ; (python_full_version >= '3.13' and platform_python_implementation == 'CPython' and sys_platform == 'win32' and extra == 'test') or (platform_python_implementation == 'PyPy' and extra == 'test')
+  - pytest-mock>=3.11.1 ; extra == 'test'
+  - pytest-randomly>=3.12 ; extra == 'test'
+  - pytest-timeout>=2.1 ; extra == 'test'
+  - pytest>=7.4 ; extra == 'test'
+  - setuptools>=68 ; extra == 'test'
+  - time-machine>=2.10 ; platform_python_implementation == 'CPython' and extra == 'test'
+  requires_python: '>=3.8'
 - kind: conda
   name: xz
   version: 5.2.6
diff --git a/pyproject.toml b/pyproject.toml
index 8b164303..2c97e0ef 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,13 +34,13 @@ python_template = { path = ".", editable = true }
 
 [project.optional-dependencies]
 test = [
-  "black>=23,<=24.10.0",
   "pylint>=3.2.5,<=3.3.1",
   "pytest-cov>=4.1,<=6.0.0",
   "pytest>=7.4,<=8.3.3",
   "hypothesis>=6.104.2,<=6.116.0",
   "ruff>=0.5.0,<=0.7.2",
   "coverage>=7.5.4,<=7.6.4",
+  "pre-commit<=4.0.1"
 ]
 
 [build-system]
@@ -60,7 +60,9 @@ py313 = ["py313","test"]
 
 
 [tool.pixi.tasks]
-format = "black ."
+pre-commit = "pre-commit run -a"
+pre-commit-update = "pre-commit autoupdate"
+format = "ruff format ."
 check-clean-workspace = "git diff --exit-code"
 ruff-lint = "ruff check . --fix"
 pylint = "pylint --version && echo 'running pylint...' && pylint $(git ls-files '*.py')"
@@ -90,26 +92,6 @@ jobs = 16                           #detect number of cores
 disable = "C,logging-fstring-interpolation,line-too-long,fixme,broad-exception-caught,missing-module-docstring,too-many-instance-attributes,too-few-public-methods,too-many-arguments,too-many-locals,too-many-branches,too-many-statements,use-dict-literal,cyclic-import,duplicate-code,too-many-public-methods"
 enable = "no-else-return,consider-using-in"
 
-[tool.black]
-line-length = 100
-
-[tool.ruff]
-line-length = 100 # Same as Black.
-
-target-version = "py310"
-
-[tool.ruff.lint]
-# Never enforce `E501` (line length violations).
-#"F841" will auto remove unused variables which is annoying during development, pylint catches this anyway
-ignore = ["E501", "E902", "F841"]
-# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
-
-# Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
-
-
 [tool.coverage.run]
 omit = ["*/test/*", "__init__.py"]
 
diff --git a/python_template.deps.yaml b/python_template.deps.yaml
index 548d0fd7..63e6e6bf 100644
--- a/python_template.deps.yaml
+++ b/python_template.deps.yaml
@@ -7,3 +7,4 @@ apt_tools:
 pip_language-toolchain:
   - uv #use uv instead of pip
   - pip #update to the latest pip
+  - pre-commit
diff --git a/ruff.toml b/ruff.toml
new file mode 100644
index 00000000..6aacb0e6
--- /dev/null
+++ b/ruff.toml
@@ -0,0 +1,16 @@
+line-length = 100
+
+[lint]
+# E501: Lines too long (maximum of 79 characters).
+ignore = [
+    "E501", # Long line that exceeds maximum allowed length.
+    "F841", # Local variable referenced before assignment, this is annoying during development.
+]
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+[lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+"**/{tests,docs,tools}/*" = ["E402"]
diff --git a/scripts/setup_host.sh b/scripts/setup_host.sh
index 246ae2d1..833c2615 100755
--- a/scripts/setup_host.sh
+++ b/scripts/setup_host.sh
@@ -56,4 +56,4 @@ echo 'eval "$(pixi completion --shell bash)"' >> ~/.bashrc
 
 sudo groupadd docker
 sudo usermod -aG docker $USER
-newgrp docker || true
\ No newline at end of file
+newgrp docker || true