Merge pull request #95 from umccr/dev

Push fix for #93 to pypi

src/v2_samplesheet_maker/classes/samplesheet.py

@@ -11,6 +11,7 @@
 from tempfile import NamedTemporaryFile
 
 # Relative modules
+from ..globals import HEADER_REGEX_MATCH
 from ..utils.logger import get_logger
 from ..utils import pascal_case_to_snake_case
 from .super_sections import Section, KVSection, DataFrameSection
@@ -343,10 +344,10 @@ def read_from_samplesheet_csv(cls, samplesheet_csv: Path) -> "SampleSheet":
                     continue
 
                 # Check if header
-                if line.startswith("[") and line.endswith("]"):
+                if HEADER_REGEX_MATCH.match(line):
                     if section_name is not None:
                         samplesheet_dict[section_name] = section_lines
-                    section_name = line.lstrip("[").rstrip("]")
+                    section_name = HEADER_REGEX_MATCH.match(line).group(1)
                     section_lines = []
                 else:
                     section_lines.append(line)
@@ -410,6 +411,5 @@ def read_from_samplesheet_csv(cls, samplesheet_csv: Path) -> "SampleSheet":
             cloud_settings["analysis_urns"] = cloud_analysis_urns
             samplesheet_dict_sanitised["cloud_settings"] = cloud_settings
 
-
         # Return the samplesheet object
         return cls(samplesheet_dict_sanitised)

src/v2_samplesheet_maker/globals.py

@@ -1,2 +1,8 @@
 #!/usr/bin/env python
 
+import re
+
+# https://regex101.com/r/oRfry0/1
+HEADER_REGEX_MATCH = re.compile(
+    r"\[([a-zA-Z_]+)](?:,*)?"
+)