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

Bare `except:` clauses catch `KeyboardInterrupt` and `SystemExit`, which
can mask real errors and make debugging harder. Replace with
`except Exception:` to preserve the intended error-suppression behavior
while allowing system-level exceptions to propagate normally.

Files changed:
- bio-research/skills/nextflow-development/scripts/check_environment.py (4 sites)
- bio-research/skills/nextflow-development/scripts/detect_data_type.py (1 site)

Co-authored-by: haosenwang1018 <haosenwang1018@users.noreply.github.com>

Author: haosenwang1018

bio-research/skills/nextflow-development/scripts/check_environment.py

@@ -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"
@@ -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:

bio-research/skills/nextflow-development/scripts/detect_data_type.py

@@ -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