moved ruff.toml contents into pyproject.toml

Author: srivarra

pyproject.toml

@@ -74,3 +74,36 @@ packages = ["viscy"]
 [tool.setuptools_scm]
 write_to = "viscy/_version.py"
 
+[tool.ruff]
+line-length = 88
+src = ["viscy", "tests"]
+extend-include = ["*.ipynb"]
+target-version = "py311"
+# Exclude the following for now. Later on we should check every Python file.
+extend-exclude = ["viscy/scripts/*", "applications/*", "examples/*"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+
+[tool.ruff.lint]
+select = [
+  "D",      # pydocstyle
+  "I",      # isort
+]
+ignore = [
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107", # Missing docstring in __init__
+  # Disable one in each pair of mutually incompatible rules
+  "D203", # We don’t want a blank line before a class docstring
+  "D213", # <> We want docstrings to start immediately after the opening triple quote
+  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+  "D401", # First line should be in imperative mood; try rephrasing
+]
+per-file-ignores."*/__init__.py" = ["F401"]
+per-file-ignores."tests/*" = ["D"]
+pydocstyle.convention = "numpy"

ruff.toml

@@ -1 +0,0 @@
-"""Learning vision for cells."""

viscy/__init__.py

@@ -1,5 +1,3 @@
-"""Lightning CLI for computer vision models in VisCy."""
-
 import logging
 import os
 import sys

viscy/cli.py

@@ -1 +0,0 @@
-"""VisCy data loading and preprocessing modules."""

viscy/data/__init__.py

@@ -1,5 +1,3 @@
-"""Dataset and DataModule classes for cell classification tasks."""
-
 from collections.abc import Callable
 from pathlib import Path
 

viscy/data/cell_classification.py

@@ -1,10 +1,3 @@
-"""Combined data modules for multi-dataset ML training workflows.
-
-This module provides Lightning DataModule implementations for combining multiple
-data sources with various strategies including concatenation, batching, and
-distributed sampling optimizations for computer vision and microscopy datasets.
-"""
-
 import bisect
 import logging
 from collections import defaultdict

viscy/data/combined.py

@@ -1,5 +1,3 @@
-"""Data module for CTMCv1 autoregression dataset with HCS OME-Zarr stores."""
-
 from pathlib import Path
 
 import torch

viscy/data/ctmc_v1.py

@@ -1,5 +1,3 @@
-"""Utilities for DDP training."""
-
 from __future__ import annotations
 
 import math

viscy/data/distributed.py

@@ -1,5 +1,3 @@
-"""GPU-accelerated data augmentation modules for microscopy ML training."""
-
 from __future__ import annotations
 
 from abc import ABC, abstractmethod