used dotenv instead of manual parsing

Author: Fabien Coelho

implementations/c-jsu/Dockerfile

@@ -11,7 +11,7 @@ WORKDIR /usr/src/myapp
 ARG JMC
 ARG JSU
 
-RUN apk add git py3-pip py3-re2 icu-data-full
+RUN apk add git py3-pip py3-re2 py3-dotenv icu-data-full
 
 # force install, otherwise it would require a virtual environment
 RUN pip install --break-system-packages jsonschema-specifications

implementations/c-jsu/bowtie_jsu_compile.py

@@ -9,6 +9,7 @@
 """
 
 from pathlib import Path
+import dotenv
 import hashlib
 import json
 import os
@@ -71,12 +72,7 @@ class Runner:
     def __init__(self, language: str = "python", options: list[str] = []):
 
         # setup environment
-        if ENV.exists():
-            with Path.open(ENV) as env:
-                for line in env:
-                    if line.startswith("export ") and "=" in line:
-                        var, val = line[7:].rstrip().split("=", 1)
-                        os.environ[var] = val
+        dotenv.load_dotenv(ENV)
 
         # setup language
         self.language: str = language.lower()