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fix: replace 5 bare excepts with except Exception in bio-research scripts #82

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fix: replace 5 bare excepts with except Exception in bio-research scripts #82

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8 changes: 4 additions & 4 deletions bio-research/skills/nextflow-development/scripts/check_environment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,15 +260,15 @@ def check_resources() -> CheckResult:
)
if result.returncode == 0:
mem_gb = int(result.stdout.strip()) / (1024**3)
except:
except Exception:
pass

# Disk space (current directory)
disk_gb = 0
try:
statvfs = os.statvfs('.')
disk_gb = (statvfs.f_frsize * statvfs.f_bavail) / (1024**3)
except:
except Exception:
pass

details = f"CPUs: {cpu_count}, Memory: {mem_gb:.1f}GB, Disk: {disk_gb:.1f}GB available"
Expand Down Expand Up @@ -319,15 +319,15 @@ def check_network() -> CheckResult:
req = urllib.request.Request("https://hub.docker.com", headers=headers)
urllib.request.urlopen(req, timeout=10)
docker_hub_ok = True
except:
except Exception:
docker_hub_ok = False

# Try nf-core (for pipeline downloads)
try:
req = urllib.request.Request("https://nf-co.re", headers=headers)
urllib.request.urlopen(req, timeout=10)
nfcore_ok = True
except:
except Exception:
nfcore_ok = False

if docker_hub_ok and nfcore_ok:
Expand Down
2 changes: 1 addition & 1 deletion bio-research/skills/nextflow-development/scripts/detect_data_type.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def scan_directory(directory: str) -> Dict:
try:
size = os.path.getsize(os.path.join(root, filename))
info['total_size_gb'] += size / (1024**3)
except:
except Exception:
pass

return info
Expand Down