BioModStack/.gitignore at main · MolBioFreak/BioModStack · 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
# Local editor / assistant state
.vscode/
.hermes/

# Local GPU/runtime state
.gpu_*.json
.gpu_*.lock

# Local scratch/search artifacts
.protenix_cache
.protenix_anchor_root/
text_*.json
tmp_bioxp_*.py
tmp_bioxp_*.sh
platform/api/tmp_*.py
platform/api/*.log

# Python/runtime caches
__pycache__/
*.py[cod]
.pytest_cache/

# Node/build caches
node_modules/
node_modules/.tmp/
dist/
platform/frontend/.test-dist/
platform/frontend/.artifacts/
.artifacts/

# Databases, backups, and local runtime outputs
*.db
*.db-shm
*.db-wal
backups/
bms_results
molbio_toolkit.db*
biomodstack_runtime.db*
output/
rcsb/

lib/NO_*

# Nextflow/local run artifacts
.nextflow/
.nextflow.log*
.nextflow-test-artifacts/
.pytest-nextflow-*/
work/
tmp/
nxf-tmp.*
wf_test*/

# Local tool/runtime and exploratory browser-output surfaces
.ngs-tools/
dogfood-output/
/alignment_protenix.log

# Large local container images
apptainer/*.sif
apptainer/*.sif.*
ngs_runtime_fixtures/

# Private environment/configuration; retain intentionally sanitized examples.
.env
.env.*
!.env.example
!.env.sample
!.env.template
!.env.*.example
!.env.*.sample
!.env.*.template

# Local Python environments, analysis caches, and coverage output.
.venv/
venv/
.mypy_cache/
.ruff_cache/
.coverage
.coverage.*
htmlcov/

# SQLite naming variants and their runtime sidecars.
*.sqlite
*.sqlite3
*.sqlite-shm
*.sqlite-wal
*.sqlite3-shm
*.sqlite3-wal
*.db-journal
*.sqlite-journal
*.sqlite3-journal

# Local literature collection and editor metadata.
/.ngs_latest_papers/
.idea/
.DS_Store