Add pre-commit hooks

.editorconfig

@@ -0,0 +1,12 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true

.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on:
+    push:
+        branches: main
+    pull_request:
+        branches: main
+
+jobs:
+    linting:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+            - name: Setup Python 3.12
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.12"
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install pre-commit
+            - name: Check pre-commit compatibility
+              run: pre-commit run --all-files --show-diff-on-failure

.gitignore

@@ -182,9 +182,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
 #  you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 
@@ -205,4 +205,4 @@ __marimo__/
 # Custom
 .dev
 .dev/*
-*.pyc
+*.pyc

.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - pre-commit
+    - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/psf/black
+      rev: "23.1.0"
+      hooks:
+          - id: black
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.4
+      hooks:
+          - id: prettier
+            # Newer versions of node don't work on systems that have an older version of GLIBC
+            # (in particular Ubuntu 18.04 and Centos 7)
+            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+            # https://github.com/jupyterlab/jupyterlab/issues/12675
+            language_version: "17.9.1"
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.253
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'

README.md

@@ -2,15 +2,16 @@
 
 ## pip
 
-Before installing **segger**, please install GPU-accelerated versions of PyTorch, RAPIDS, and related packages compatible with your system. *Please ensure all CUDA-enabled packages are compiled for the same CUDA version.*
+Before installing **segger**, please install GPU-accelerated versions of PyTorch, RAPIDS, and related packages compatible with your system. _Please ensure all CUDA-enabled packages are compiled for the same CUDA version._
 
-- **PyTorch & torchvision:** [Installation guide](https://pytorch.org/get-started/locally/)
-- **torch_scatter:** [Installation guide](https://github.com/rusty1s/pytorch_scatter#installation)
-- **RAPIDS (cuDF, cuML, cuGraph):** [Installation guide](https://docs.rapids.ai/install)
-- **CuPy:** [Installation guide](https://docs.cupy.dev/en/stable/install.html)
-- **cuSpatial:** [Installation guide](https://docs.rapids.ai/api/cuspatial/stable/user_guide/cuspatial_api_examples/#Installing-cuSpatial)
+-   **PyTorch & torchvision:** [Installation guide](https://pytorch.org/get-started/locally/)
+-   **torch_scatter:** [Installation guide](https://github.com/rusty1s/pytorch_scatter#installation)
+-   **RAPIDS (cuDF, cuML, cuGraph):** [Installation guide](https://docs.rapids.ai/install)
+-   **CuPy:** [Installation guide](https://docs.cupy.dev/en/stable/install.html)
+-   **cuSpatial:** [Installation guide](https://docs.rapids.ai/api/cuspatial/stable/user_guide/cuspatial_api_examples/#Installing-cuSpatial)
 
 For example, on Linux with CUDA 12.1 and PyTorch 2.5.0:
+
 ```bash
 # Install PyTorch and torchvision for CUDA 12.1
 pip install torch==2.5.0 torchvision==0.20.0 --index-url https://download.pytorch.org/whl/cu121
@@ -24,6 +25,7 @@ pip install --extra-index-url=https://pypi.nvidia.com cuspatial-cu12 cudf-cu12 c
 # Install CuPy for CUDA 12.x
 pip install cupy-cuda12x
 ```
+
 **December 2025:** To stay up-to-date with new developments, we recommend installing the latest version directly from GitHub:
 
 ```bash
@@ -35,11 +37,13 @@ pip install -e .
 # Usage
 
 You can run **segger** from the command line with:
+
 ```bash
 segger segment -i /path/to/your/ist/data/ -o /path/to/save/outputs/
 ```
 
 To see all available parameter options:
+
 ```bash
 segger segment --help
-```
+```

pyproject.toml

@@ -31,6 +31,11 @@ dependencies = [
     "torch_geometric",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "pre-commit",
+]
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
@@ -39,4 +44,89 @@ build-backend = "hatchling.build"
 packages = ["src/segger"]
 
 [project.scripts]
-segger = "segger.cli.main:app"
+segger = "segger.cli.main:app"
+
+[tool.black]
+line-length = 120
+include = '\.pyi?$|\.ipynb?$'
+exclude = '''
+(
+  /(
+      \.eggs
+    | \.git
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | buck-out
+    | build
+    | dist
+  )/
+)
+'''
+
+[tool.isort]
+profile = "black"
+use_parentheses = true
+known_num = "geopandas,lightning,networkx,numba,numpy,opencv-python,pandas,polars,scipy,scikit-image,scikit-learn,shapely,sklearn,statmodels,torch_geometric"
+known_bio = "anndata,scanpy"
+sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
+no_lines_before = "LOCALFOLDER"
+balanced_wrapping = true
+length_sort = "0"
+indent = "    "
+float_to_top = true
+order_by_type = false
+
+[tool.ruff]
+src = ["."]
+line-length = 119
+target-version = "py38"
+select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+    "TID",  # flake8-tidy-imports
+    "C4",  # flake8-comprehensions
+    "BLE",  # flake8-blind-except
+    "UP",  # pyupgrade
+    "RUF100",  # Report unused noqa directives
+]
+ignore = [
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix
+    "E741",
+    # Missing docstring in public package
+    "D104",
+    # Missing docstring in public module
+    "D100",
+    # Missing docstring in __init__
+    "D107",
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
+    "B008",
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    "D400",
+    # First line should be in imperative mood; try rephrasing
+    "D401",
+    ## Disable one in each pair of mutually incompatible rules
+    # We don’t want a blank line before a class docstring
+    "D203",
+    # We want docstrings to start immediately after the opening triple quote
+    "D213",
+    # Missing argument description in the docstring TODO: enable
+    "D417",
+    # Unable to detect undefined names
+    "F403",
+    # Underfined, or defined from star imports: module
+    "F405",
+    # Within an except clause, raise exceptions with `raise ... from err`
+    "B904",
+]

src/segger/cli/config.yaml

@@ -39,4 +39,4 @@ transcripts_loss_weight_end: 1.
 cells_loss_weight_start: 1.
 cells_loss_weight_start: 1.
 segmentation_loss_weight_start: 0.
-segmentation_loss_weight_end: 0.1
+segmentation_loss_weight_end: 0.1