gently/.gitignore at main · pskeshu/gently · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Virtual environments
venv/
env/
ENV/
.venv/

# IDE
.vscode/
.idea/
*.swp
*.swo
*~

# OS
.DS_Store
Thumbs.db

# Logs
*.log

# Environment variables
.env
.env.local
.env.*.local

# Jupyter Notebook
.ipynb_checkpoints

# pytest
.pytest_cache/
.coverage
htmlcov/

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Napari/Qt
*.qss

# Node.js / TUI
gently/tui/node_modules/
gently/tui/dist/

# Database
*.db
*.sqlite
*.sqlite3

# Test scripts (one-off tests in repo root, not tests/ directory)
/test_*.py
/check_*.py

# SAM model weights
*.pth

# Binary data
*.tif
!docs/*.tif
*.npz
*.gif

# Test images
*_centering_*.png
*_marked_*.png
analysis_*.png
embryo_*.png
initial_view_*.png
comparison_*.png
sam_*.png
spim_*.png
*_montage.png
*_analysis.png
bottom_camera_*.png

# HuggingFace benchmark data (large volumes)
benchmarks/data/hf-benchmark/

# Output directories (experiment data, calibration artifacts)
experiment_data/
dispim_data/
lightsheet_captures/

# Temporary JSON data
dispim_baseline_state_*.json
dispim_parameters_*.json

# Windows artifacts
nul
*.bak

# Local settings
.claude/settings.local.json
*.local.json

# Backup files
*_backup.py
*_backup/

# Mesh networking runtime artifacts (generated at startup, NEVER commit keys)
config/mesh_*.pem
config/mesh_key.pem
config/mesh_cert.pem
config/mesh_instance_id
config/mesh_audit.jsonl
config/mesh_trusted_peers.json

# LaTeX build artifacts
*.aux
*.out
*.toc
paper/*.log
paper/*.pdf
paper/*.synctex.gz

# Dead Electron app
electron/

# Root-level one-off documents
/stage_definitions_for_review.pdf
/stage_definitions_for_review.txt
gently/ui/tui/node_modules/
gently/ui/tui/dist/