MEMORIES/.gitignore at main · HolobiomicsLab/MEMORIES · 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
# =============================================================================
# NMR Quantification Project - Git Ignore
# =============================================================================

# -----------------------------------------------------------------------------
# Raw Data Files (Large, shouldn't be version controlled)
# -----------------------------------------------------------------------------
# JCAMP-DX NMR data files (raw spectra)
*.dx
raw_data/

# -----------------------------------------------------------------------------
# Generated Output Files (Reproducible from scripts)
# -----------------------------------------------------------------------------
# Quantification results
quantification_results/
integration_results/
tsp_corrected_spectra/

# CSV output files
*.csv

# Archive files
*.tar.gz
*.zip

# -----------------------------------------------------------------------------
# Analysis Figures (Generated by scripts, can be reproduced)
# -----------------------------------------------------------------------------
# All PNG files (generated plots)
*.png

# Individual analysis plots
*_quantification.png
*_analysis.png
*_comparison.png
*_check.png
*_region.png
*_example.png

# Specific named output figures
alanine_*.png
arginine_*.png
asparagine_*.png
aspartate_*.png
glucose_*.png
glutamate_*.png
glutamine_*.png
isoleucine_*.png
lactate_*.png
leucine_*.png
methionine_*.png
phenylalanine_*.png
tyrosine_*.png
valine_*.png

# Other generated figures
figure*.png
lmfit_*.png
lineshape_*.png
nmr_*.png
peak_*.png
tsp_*.png
water_*.png

# -----------------------------------------------------------------------------
# Large Documentation Files
# -----------------------------------------------------------------------------
# Excel files (raw data, too large for git)
*.xlsx
*.xls

# PDF files (SI, papers, etc. - too large for git)
*.pdf

# -----------------------------------------------------------------------------
# Python Cache
# -----------------------------------------------------------------------------
__pycache__/
*.py[cod]
*$py.class
*.so
.Python

# -----------------------------------------------------------------------------
# IDE and Editor Files
# -----------------------------------------------------------------------------
# VS Code
.vscode/
*.code-workspace

# PyCharm/IntelliJ
.idea/
*.iml

# Jupyter Notebook
.ipynb_checkpoints/
*.ipynb

# -----------------------------------------------------------------------------
# OS Generated Files
# -----------------------------------------------------------------------------
# macOS
.DS_Store
.AppleDouble
.LSOverride

# Windows
Thumbs.db
ehthumbs.db
Desktop.ini
*$RECYCLE.BIN/

# Linux
*~
.nfs*

# Windows Zone.Identifier files (downloaded from internet)
*:Zone.Identifier
*.Zone.Identifier

# -----------------------------------------------------------------------------
# Temporary Files
# -----------------------------------------------------------------------------
*.tmp
*.temp
*.bak
*.swp
*.swo
*~

# -----------------------------------------------------------------------------
# Logs
# -----------------------------------------------------------------------------
*.log
logs/

# Allow latest quantification results in results/quantification/
!results/quantification/quantification_summary_v3.csv
!results/quantification/*_v3_ref20_quantification.png