deep-gw-cnv/.gitignore at master · malariagen/deep-gw-cnv · 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
# ── Python ────────────────────────────────────────────────────────────────────
__pycache__/
*.py[cod]
*.pyd
*.pyo
*.so
*.egg
*.egg-info/
dist/
build/
.eggs/
*.egg-link
pip-wheel-metadata/
.installed.cfg

# ── Virtual environments ───────────────────────────────────────────────────────
.venv/
venv/
env/
.env

# ── Sensitive / large assets (never commit) ───────────────────────────────────
assets/20260313_full_cnv_data_pf9.tsv
assets/Pf_9_samples_20260227.txt

# ── Data & weights (large binary files — never commit) ────────────────────────
data/*
weights/
# Keep the placeholder / README files and setup scripts
!data/raw/.gitkeep
!data/processed/.gitkeep
!data/README.md
!data/setup
!weights/README.md

# ── Experiment outputs (results are reproducible; only narratives are tracked) ─
experiments/*/results/
experiments/*/config.yaml
# But keep the human-written README describing each experiment
!experiments/*/README.md

# ── Jupyter ───────────────────────────────────────────────────────────────────
.ipynb_checkpoints/
*.ipynb_checkpoints

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

# ── OS noise ──────────────────────────────────────────────────────────────────
.DS_Store
Thumbs.db

# ── Testing & coverage ────────────────────────────────────────────────────────
.pytest_cache/
.mypy_cache/
.ruff_cache/
htmlcov/
.coverage
coverage.xml

*.o
*.e
*.nextflow*
*/work
*/readcounts

# ── Daemon state & generated files (never commit) ─────────────────────────────
tools/daemon.log
tools/.proposal_body.txt
tools/pending_feedback.txt
tools/.last_proposal_msgid
tools/.last_proposal_experiment
tools/.proposal_thread_msgid