From fb16c52699cfa5efa9d9a66a71fe5ce9952270ed Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:24:57 +0100
Subject: [PATCH 01/20] style fixes

---
 pyproject.toml          | 22 +++++-----------------
 template/utils/_docs.py |  8 ++++----
 2 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 51b73adf..572b0672 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,10 +65,9 @@ full = [
 ]
 style = [
   'bibclean',
-  'black',
   'codespell',
   'isort',
-  'pydocstyle[toml]',
+  'mypy',
   'ruff',
   'toml-sort',
   'yamllint',
@@ -88,21 +87,6 @@ homepage = 'https://github.com/mscheltienne/template-python'
 source = 'https://github.com/mscheltienne/template-python'
 tracker = 'https://github.com/mscheltienne/template-python/issues'
 
-[tool.black]
-extend-exclude = '''
-(
-      __pycache__
-    | .github
-    | setup.py
-    | doc/
-    | examples/
-    | tutorials/
-)
-'''
-include = '\.pyi?$'
-line-length = 88
-target-version = ['py39']
-
 [tool.coverage.report]
 exclude_lines = [
   'if __name__ == .__main__.:',
@@ -152,10 +136,14 @@ extend-exclude = [
   'setup.py',
 ]
 line-length = 88
+target-version = 'py39'
 
 [tool.ruff.per-file-ignores]
 '__init__.py' = ['F401']
 
+[tool.ruff.format]
+docstring-code-format = true
+
 [tool.setuptools]
 include-package-data = false
 
diff --git a/template/utils/_docs.py b/template/utils/_docs.py
index 70caba3c..b8430c31 100644
--- a/template/utils/_docs.py
+++ b/template/utils/_docs.py
@@ -75,16 +75,16 @@ def fill_doc(f: Callable[..., Any]) -> Callable[..., Any]:
 def _indentcount_lines(lines: list[str]) -> int:
     """Minimum indent for all lines in line list.
 
-    >>> lines = [' one', '  two', '   three']
+    >>> lines = [" one", "  two", "   three"]
     >>> indentcount_lines(lines)
     1
     >>> lines = []
     >>> indentcount_lines(lines)
     0
-    >>> lines = [' one']
+    >>> lines = [" one"]
     >>> indentcount_lines(lines)
     1
-    >>> indentcount_lines(['    '])
+    >>> indentcount_lines(["    "])
     0
     """
     indent = sys.maxsize
@@ -125,7 +125,7 @@ def copy_doc(source: Callable[..., Any]) -> Callable[..., Any]:
     >>> class B(A):
     ...     @copy_doc(A.m1)
     ...     def m1():
-    ...         ''' this gets appended'''
+    ...         '''this gets appended'''
     ...         pass
     >>> print(B.m1.__doc__)
     Docstring for m1 this gets appended

From a61622059a2fd28e26b4967d1c7ec15dcc50650d Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:25:08 +0100
Subject: [PATCH 02/20] use ruff

---
 .pre-commit-config.yaml | 23 +++++++----------------
 pyproject.toml          |  1 +
 2 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 71eb6acf..1b3c515f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 ci:
-    skip: [codespell, pydocstyle, yamllint]
+    skip: [codespell, yamllint]
 
 repos:
     - repo: https://github.com/pycqa/isort
@@ -8,18 +8,16 @@ repos:
           - id: isort
             files: template
 
-    - repo: https://github.com/psf/black-pre-commit-mirror
-      rev: 23.12.0
-      hooks:
-          - id: black
-            args: [--quiet]
-            files: template
-
     - repo: https://github.com/astral-sh/ruff-pre-commit
       rev: v0.1.8
       hooks:
           - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
+            name: ruff linter
+            args: [--fix, --config=pyproject.toml]
+            files: template
+          - id: ruff-format
+            name: ruff formatter
+            args: [--config=pyproject.toml]
             files: template
 
     - repo: https://github.com/codespell-project/codespell
@@ -28,13 +26,6 @@ repos:
           - id: codespell
             args: [--check-filenames, --ignore-words=.codespellignore]
 
-    - repo: https://github.com/pycqa/pydocstyle
-      rev: 6.3.0
-      hooks:
-          - id: pydocstyle
-            files: template
-            additional_dependencies: [tomli]
-
     - repo: https://github.com/mscheltienne/bibclean
       rev: 0.8.0
       hooks:
diff --git a/pyproject.toml b/pyproject.toml
index 572b0672..98de97d8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -136,6 +136,7 @@ extend-exclude = [
   'setup.py',
 ]
 line-length = 88
+select = ["E", "F", "W"]
 target-version = 'py39'
 
 [tool.ruff.per-file-ignores]

From 207be11994680a705b5c469cde1b596b09d6d3cc Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:26:15 +0100
Subject: [PATCH 03/20] fix

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 98de97d8..f996dfe9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -139,12 +139,12 @@ line-length = 88
 select = ["E", "F", "W"]
 target-version = 'py39'
 
-[tool.ruff.per-file-ignores]
-'__init__.py' = ['F401']
-
 [tool.ruff.format]
 docstring-code-format = true
 
+[tool.ruff.per-file-ignores]
+'__init__.py' = ['F401']
+
 [tool.setuptools]
 include-package-data = false
 

From 5aabfef9585003e187e7a592e267a346a4ff9215 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 19 Dec 2023 14:27:31 +0000
Subject: [PATCH 04/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 template/utils/_docs.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/template/utils/_docs.py b/template/utils/_docs.py
index b8430c31..ca8de61f 100644
--- a/template/utils/_docs.py
+++ b/template/utils/_docs.py
@@ -16,9 +16,7 @@
 docdict: dict[str, str] = dict()
 
 # ---------------------------------- verbose ---------------------------------
-docdict[
-    "verbose"
-] = """
+docdict["verbose"] = """
 verbose : int | str | bool | None
     Sets the verbosity level. The verbosity increases gradually between ``"CRITICAL"``,
     ``"ERROR"``, ``"WARNING"``, ``"INFO"`` and ``"DEBUG"``. If None is provided, the

From 5442ed72505301dd80e82471b05eb77f45f1587b Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:31:40 +0100
Subject: [PATCH 05/20] de-duplicate code-style workflows

---
 .github/workflows/code-style.yaml | 12 ------------
 .pre-commit-config.yaml           |  9 ++++++++-
 2 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml
index 06f9d560..da53e1d0 100644
--- a/.github/workflows/code-style.yaml
+++ b/.github/workflows/code-style.yaml
@@ -24,14 +24,6 @@ jobs:
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[style]
-      - name: Run isort
-        uses: isort/isort-action@master
-      - name: Run black
-        uses: psf/black@stable
-        with:
-          options: "--check --verbose"
-      - name: Run Ruff
-        run: ruff check .
       - name: Run codespell
         uses: codespell-project/actions-codespell@master
         with:
@@ -41,9 +33,5 @@ jobs:
           ignore_words_file: ./.codespellignore
       - name: Run pydocstyle
         run: pydocstyle .
-      - name: Run bibclean
-        run: bibclean-check doc/references.bib
-      - name: Run toml-sort
-        run: toml-sort pyproject.toml --check
       - name: Run yamllint
         run: yamllint . -c .yamllint.yaml --strict
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1b3c515f..322e7871 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 ci:
-    skip: [codespell, yamllint]
+    skip: [codespell, pydocstyle, yamllint]
 
 repos:
     - repo: https://github.com/pycqa/isort
@@ -26,6 +26,13 @@ repos:
           - id: codespell
             args: [--check-filenames, --ignore-words=.codespellignore]
 
+    - repo: https://github.com/pycqa/pydocstyle
+      rev: 6.3.0
+      hooks:
+          - id: pydocstyle
+            files: template
+            additional_dependencies: [tomli]
+
     - repo: https://github.com/mscheltienne/bibclean
       rev: 0.8.0
       hooks:

From 66d888c83d55e8b08e59c3591ed25bc8d6bb9420 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:33:20 +0100
Subject: [PATCH 06/20] add back pydocstyle

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

diff --git a/pyproject.toml b/pyproject.toml
index f996dfe9..1f9f002f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -68,6 +68,7 @@ style = [
   'codespell',
   'isort',
   'mypy',
+  'pydocstyle[toml]',
   'ruff',
   'toml-sort',
   'yamllint',

From e9c056dadf1969a25dbc4c6f0d745d113c82e53b Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:36:16 +0100
Subject: [PATCH 07/20] test

---
 .pre-commit-config.yaml | 3 +--
 pyproject.toml          | 3 ---
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 322e7871..eb7a8848 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,11 +13,10 @@ repos:
       hooks:
           - id: ruff
             name: ruff linter
-            args: [--fix, --config=pyproject.toml]
+            args: [--fix]
             files: template
           - id: ruff-format
             name: ruff formatter
-            args: [--config=pyproject.toml]
             files: template
 
     - repo: https://github.com/codespell-project/codespell
diff --git a/pyproject.toml b/pyproject.toml
index 1f9f002f..09cfede6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -143,9 +143,6 @@ target-version = 'py39'
 [tool.ruff.format]
 docstring-code-format = true
 
-[tool.ruff.per-file-ignores]
-'__init__.py' = ['F401']
-
 [tool.setuptools]
 include-package-data = false
 

From fcfd9673621dea6e113848588d088cdcf3032916 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:36:23 +0100
Subject: [PATCH 08/20] ete

---
 template/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/template/__init__.py b/template/__init__.py
index 5f5bdd5f..433d7113 100644
--- a/template/__init__.py
+++ b/template/__init__.py
@@ -1,3 +1,5 @@
 from ._version import __version__  # noqa: F401
 from .utils.config import sys_info  # noqa: F401
 from .utils.logs import add_file_handler, logger, set_log_level  # noqa: F401
+
+import time

From 0aa02b38e02fa39ceb57c6c3d7223fd38a83af05 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 19 Dec 2023 14:37:10 +0000
Subject: [PATCH 09/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 template/__init__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/template/__init__.py b/template/__init__.py
index 433d7113..5f5bdd5f 100644
--- a/template/__init__.py
+++ b/template/__init__.py
@@ -1,5 +1,3 @@
 from ._version import __version__  # noqa: F401
 from .utils.config import sys_info  # noqa: F401
 from .utils.logs import add_file_handler, logger, set_log_level  # noqa: F401
-
-import time

From 790c527d02a31b4f513e947fb9fda12328565d2b Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:36:51 +0100
Subject: [PATCH 10/20] add back rule

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 09cfede6..1f9f002f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -143,6 +143,9 @@ target-version = 'py39'
 [tool.ruff.format]
 docstring-code-format = true
 
+[tool.ruff.per-file-ignores]
+'__init__.py' = ['F401']
+
 [tool.setuptools]
 include-package-data = false
 

From a804f801a88c5475f2d93ddb4cfdfb7ad58b0d79 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:40:05 +0100
Subject: [PATCH 11/20] add ruff badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 0db66652..07680413 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![codecov](https://codecov.io/gh/mscheltienne/template-python/branch/main/graph/badge.svg?token=KRYRRUXDYY)](https://codecov.io/gh/mscheltienne/template-python)
 [![tests](https://github.com/mscheltienne/template-python/actions/workflows/pytest.yaml/badge.svg?branch=main)](https://github.com/mscheltienne/template-python/actions/workflows/pytest.yaml)
 [![doc](https://github.com/mscheltienne/template-python/actions/workflows/doc.yaml/badge.svg?branch=main)](https://github.com/mscheltienne/template-python/actions/workflows/doc.yaml)

From 58f8d3ec5289123c50da253659ad743716328c69 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:40:46 +0100
Subject: [PATCH 12/20] bettre first

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 07680413..71f7f3bb 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
-[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![codecov](https://codecov.io/gh/mscheltienne/template-python/branch/main/graph/badge.svg?token=KRYRRUXDYY)](https://codecov.io/gh/mscheltienne/template-python)
 [![tests](https://github.com/mscheltienne/template-python/actions/workflows/pytest.yaml/badge.svg?branch=main)](https://github.com/mscheltienne/template-python/actions/workflows/pytest.yaml)
 [![doc](https://github.com/mscheltienne/template-python/actions/workflows/doc.yaml/badge.svg?branch=main)](https://github.com/mscheltienne/template-python/actions/workflows/doc.yaml)

From 8b331c17c0e72f8eca4e7ddac5c0a75e785bb7c1 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 15:59:03 +0100
Subject: [PATCH 13/20] try

---
 .pre-commit-config.yaml | 4 ++--
 pyproject.toml          | 8 +++++++-
 template/utils/logs.py  | 2 +-
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index eb7a8848..f94e0cc0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 ci:
-    skip: [codespell, pydocstyle, yamllint]
+    skip: [pydocstyle, yamllint]
 
 repos:
     - repo: https://github.com/pycqa/isort
@@ -23,7 +23,7 @@ repos:
       rev: v2.2.6
       hooks:
           - id: codespell
-            args: [--check-filenames, --ignore-words=.codespellignore]
+            args: [--write-changes]
 
     - repo: https://github.com/pycqa/pydocstyle
       rev: 6.3.0
diff --git a/pyproject.toml b/pyproject.toml
index 1f9f002f..bfa9d0ae 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,7 +65,7 @@ full = [
 ]
 style = [
   'bibclean',
-  'codespell',
+  'codespell[toml]>=2.2.4',
   'isort',
   'mypy',
   'pydocstyle[toml]',
@@ -88,6 +88,12 @@ homepage = 'https://github.com/mscheltienne/template-python'
 source = 'https://github.com/mscheltienne/template-python'
 tracker = 'https://github.com/mscheltienne/template-python/issues'
 
+[tool.codespell]
+check-hidden = true
+check-filenames = true
+ignore-words = '.codespellignore'
+skip = 'build,.git,.mypy_cache,.pytest_cache'
+
 [tool.coverage.report]
 exclude_lines = [
   'if __name__ == .__main__.:',
diff --git a/template/utils/logs.py b/template/utils/logs.py
index 07415453..e658ad48 100644
--- a/template/utils/logs.py
+++ b/template/utils/logs.py
@@ -82,7 +82,7 @@ def set_log_level(verbose: Optional[Union[bool, str, int]]) -> None:
 
 
 class _LoggerFormatter(logging.Formatter):
-    """Format string Syntax."""
+    """Format string snytax."""
 
     # Format string syntax for the different Log levels
     _formatters = dict()

From 07a3b0ae7e44a6245c5cb290e72672de8c435040 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 19 Dec 2023 15:00:03 +0000
Subject: [PATCH 14/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml         | 2 +-
 template/utils/logs.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index bfa9d0ae..661f216c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,8 +89,8 @@ source = 'https://github.com/mscheltienne/template-python'
 tracker = 'https://github.com/mscheltienne/template-python/issues'
 
 [tool.codespell]
-check-hidden = true
 check-filenames = true
+check-hidden = true
 ignore-words = '.codespellignore'
 skip = 'build,.git,.mypy_cache,.pytest_cache'
 
diff --git a/template/utils/logs.py b/template/utils/logs.py
index e658ad48..b3ca1307 100644
--- a/template/utils/logs.py
+++ b/template/utils/logs.py
@@ -82,7 +82,7 @@ def set_log_level(verbose: Optional[Union[bool, str, int]]) -> None:
 
 
 class _LoggerFormatter(logging.Formatter):
-    """Format string snytax."""
+    """Format string syntax."""
 
     # Format string syntax for the different Log levels
     _formatters = dict()

From fe50b39f04f3d6e674cf9c414c6c9cad1f77470d Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 16:00:52 +0100
Subject: [PATCH 15/20] remove codespell from style workflow

---
 .github/workflows/code-style.yaml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml
index da53e1d0..c4727dcd 100644
--- a/.github/workflows/code-style.yaml
+++ b/.github/workflows/code-style.yaml
@@ -24,13 +24,6 @@ jobs:
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[style]
-      - name: Run codespell
-        uses: codespell-project/actions-codespell@master
-        with:
-          check_filenames: true
-          check_hidden: true
-          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
-          ignore_words_file: ./.codespellignore
       - name: Run pydocstyle
         run: pydocstyle .
       - name: Run yamllint

From c7365fb2de2f7fd8f9b1f0de98f28e006689ca35 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 16:02:27 +0100
Subject: [PATCH 16/20] test

---
 .pre-commit-config.yaml | 89 ++++++++++++++++++++---------------------
 template/utils/logs.py  |  2 +-
 2 files changed, 44 insertions(+), 47 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f94e0cc0..e97c8b3e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,53 +1,50 @@
-ci:
-    skip: [pydocstyle, yamllint]
-
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-          - id: isort
-            files: template
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+        - id: isort
+          files: template
 
-    - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.8
-      hooks:
-          - id: ruff
-            name: ruff linter
-            args: [--fix]
-            files: template
-          - id: ruff-format
-            name: ruff formatter
-            files: template
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.8
+    hooks:
+        - id: ruff
+          name: ruff linter
+          args: [--fix]
+          files: template
+        - id: ruff-format
+          name: ruff formatter
+          files: template
 
-    - repo: https://github.com/codespell-project/codespell
-      rev: v2.2.6
-      hooks:
-          - id: codespell
-            args: [--write-changes]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+        - id: codespell
+          args: [--write-changes]
 
-    - repo: https://github.com/pycqa/pydocstyle
-      rev: 6.3.0
-      hooks:
-          - id: pydocstyle
-            files: template
-            additional_dependencies: [tomli]
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+        - id: pydocstyle
+          files: template
+          additional_dependencies: [tomli]
 
-    - repo: https://github.com/mscheltienne/bibclean
-      rev: 0.8.0
-      hooks:
-          - id: bibclean-fix
-            files: doc/references.bib
-            args: [--exit-non-zero-on-fix]
+  - repo: https://github.com/mscheltienne/bibclean
+    rev: 0.8.0
+    hooks:
+        - id: bibclean-fix
+          files: doc/references.bib
+          args: [--exit-non-zero-on-fix]
 
-    - repo: https://github.com/pappasam/toml-sort
-      rev: v0.23.1
-      hooks:
-          - id: toml-sort-fix
-            files: pyproject.toml
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+        - id: toml-sort-fix
+          files: pyproject.toml
 
-    - repo: https://github.com/adrienverge/yamllint
-      rev: v1.33.0
-      hooks:
-          - id: yamllint
-            args: [--strict, -c, .yamllint.yaml]
-            files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.yamllint.yaml)
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.33.0
+    hooks:
+        - id: yamllint
+          args: [--strict, -c, .yamllint.yaml]
+          files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.yamllint.yaml)
diff --git a/template/utils/logs.py b/template/utils/logs.py
index b3ca1307..e658ad48 100644
--- a/template/utils/logs.py
+++ b/template/utils/logs.py
@@ -82,7 +82,7 @@ def set_log_level(verbose: Optional[Union[bool, str, int]]) -> None:
 
 
 class _LoggerFormatter(logging.Formatter):
-    """Format string syntax."""
+    """Format string snytax."""
 
     # Format string syntax for the different Log levels
     _formatters = dict()

From f2290db1c9cbb2e792ba120dc989ccb6cb0bcbf5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 19 Dec 2023 15:03:15 +0000
Subject: [PATCH 17/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 template/utils/logs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/template/utils/logs.py b/template/utils/logs.py
index e658ad48..b3ca1307 100644
--- a/template/utils/logs.py
+++ b/template/utils/logs.py
@@ -82,7 +82,7 @@ def set_log_level(verbose: Optional[Union[bool, str, int]]) -> None:
 
 
 class _LoggerFormatter(logging.Formatter):
-    """Format string snytax."""
+    """Format string syntax."""
 
     # Format string syntax for the different Log levels
     _formatters = dict()

From 85b4d6575ce6cb0ca674f8d43f4f746298c60f9c Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 16:03:07 +0100
Subject: [PATCH 18/20] Revert "test"

This reverts commit c7365fb2de2f7fd8f9b1f0de98f28e006689ca35.
---
 .pre-commit-config.yaml | 89 +++++++++++++++++++++--------------------
 1 file changed, 46 insertions(+), 43 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e97c8b3e..f94e0cc0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,50 +1,53 @@
+ci:
+    skip: [pydocstyle, yamllint]
+
 repos:
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-        - id: isort
-          files: template
+    - repo: https://github.com/pycqa/isort
+      rev: 5.13.2
+      hooks:
+          - id: isort
+            files: template
 
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.8
-    hooks:
-        - id: ruff
-          name: ruff linter
-          args: [--fix]
-          files: template
-        - id: ruff-format
-          name: ruff formatter
-          files: template
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.8
+      hooks:
+          - id: ruff
+            name: ruff linter
+            args: [--fix]
+            files: template
+          - id: ruff-format
+            name: ruff formatter
+            files: template
 
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
-    hooks:
-        - id: codespell
-          args: [--write-changes]
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.2.6
+      hooks:
+          - id: codespell
+            args: [--write-changes]
 
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
-    hooks:
-        - id: pydocstyle
-          files: template
-          additional_dependencies: [tomli]
+    - repo: https://github.com/pycqa/pydocstyle
+      rev: 6.3.0
+      hooks:
+          - id: pydocstyle
+            files: template
+            additional_dependencies: [tomli]
 
-  - repo: https://github.com/mscheltienne/bibclean
-    rev: 0.8.0
-    hooks:
-        - id: bibclean-fix
-          files: doc/references.bib
-          args: [--exit-non-zero-on-fix]
+    - repo: https://github.com/mscheltienne/bibclean
+      rev: 0.8.0
+      hooks:
+          - id: bibclean-fix
+            files: doc/references.bib
+            args: [--exit-non-zero-on-fix]
 
-  - repo: https://github.com/pappasam/toml-sort
-    rev: v0.23.1
-    hooks:
-        - id: toml-sort-fix
-          files: pyproject.toml
+    - repo: https://github.com/pappasam/toml-sort
+      rev: v0.23.1
+      hooks:
+          - id: toml-sort-fix
+            files: pyproject.toml
 
-  - repo: https://github.com/adrienverge/yamllint
-    rev: v1.33.0
-    hooks:
-        - id: yamllint
-          args: [--strict, -c, .yamllint.yaml]
-          files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.yamllint.yaml)
+    - repo: https://github.com/adrienverge/yamllint
+      rev: v1.33.0
+      hooks:
+          - id: yamllint
+            args: [--strict, -c, .yamllint.yaml]
+            files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.yamllint.yaml)

From 74ad927d61358586e83ce7b416067cf8c3026e28 Mon Sep 17 00:00:00 2001
From: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch>
Date: Tue, 19 Dec 2023 16:15:21 +0100
Subject: [PATCH 19/20] rm code-style workflow entirely

---
 .github/workflows/code-style.yaml | 30 ------------------------------
 .pre-commit-config.yaml           |  3 ---
 pyproject.toml                    |  6 +++++-
 3 files changed, 5 insertions(+), 34 deletions(-)
 delete mode 100644 .github/workflows/code-style.yaml

diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml
deleted file mode 100644
index c4727dcd..00000000
--- a/.github/workflows/code-style.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: code-style
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
-  cancel-in-progress: true
-on:  # yamllint disable-line rule:truthy
-  pull_request:
-  push:
-    branches: [main]
-  workflow_dispatch:
-
-jobs:
-  style:
-    timeout-minutes: 10
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - name: Install dependencies
-        run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools
-          python -m pip install --progress-bar off .[style]
-      - name: Run pydocstyle
-        run: pydocstyle .
-      - name: Run yamllint
-        run: yamllint . -c .yamllint.yaml --strict
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f94e0cc0..2af32bc8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,3 @@
-ci:
-    skip: [pydocstyle, yamllint]
-
 repos:
     - repo: https://github.com/pycqa/isort
       rev: 5.13.2
diff --git a/pyproject.toml b/pyproject.toml
index 661f216c..66875b79 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,12 +67,16 @@ style = [
   'bibclean',
   'codespell[toml]>=2.2.4',
   'isort',
-  'mypy',
   'pydocstyle[toml]',
   'ruff',
   'toml-sort',
   'yamllint',
 ]
+stubs = [
+  'isort',
+  'mypy',
+  'ruff',
+]
 test = [
   'pytest',
   'pytest-cov',

From 042bab2b60f38a91c318a4d06d1c321a98cc8cb1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 19 Dec 2023 15:16:09 +0000
Subject: [PATCH 20/20] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 66875b79..2f461e6a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,6 +63,11 @@ doc = [
 full = [
   'template[all]',
 ]
+stubs = [
+  'isort',
+  'mypy',
+  'ruff',
+]
 style = [
   'bibclean',
   'codespell[toml]>=2.2.4',
@@ -72,11 +77,6 @@ style = [
   'toml-sort',
   'yamllint',
 ]
-stubs = [
-  'isort',
-  'mypy',
-  'ruff',
-]
 test = [
   'pytest',
   'pytest-cov',