fix: force utf-8 encoding on all text file reads/writes

Several read_text()/open() calls relied on the platform's default
encoding (locale-dependent), which breaks on ASCII-locale systems
(e.g. bioconda's Linux test env, UnicodeDecodeError on texts.toml)
and mis-encodes on non-UTF-8 Windows locales (e.g. French cp1252).

Author: RalfG

ms2rescore/__main__.py

@@ -218,7 +218,7 @@ def main(tims=False):
             json.loads(
                 importlib.resources.files(package_data)
                 .joinpath("config_default_tims.json")
-                .read_text()
+                .read_text(encoding="utf-8")
             )
         )
     if cli_args.config_file:

ms2rescore/config_parser.py

@@ -130,10 +130,14 @@ def parse_configurations(configurations: list[dict | str | Path | Namespace]) ->
 
     # Initialize CascadeConfig with validation schema and defaults
     config_schema = json.loads(
-        importlib.resources.files(package_data).joinpath("config_schema.json").read_text()
+        importlib.resources.files(package_data)
+        .joinpath("config_schema.json")
+        .read_text(encoding="utf-8")
     )
     config_default = json.loads(
-        importlib.resources.files(package_data).joinpath("config_default.json").read_text()
+        importlib.resources.files(package_data)
+        .joinpath("config_default.json")
+        .read_text(encoding="utf-8")
     )
     cascade_conf = CascadeConfig(
         validation_schema=config_schema,

ms2rescore/core.py

@@ -36,7 +36,7 @@ def rescore(configuration: dict, psm_list: PSMList | None = None) -> None:
     ]  # if no intermediate, takes full name
 
     # Write full configuration including defaults to file
-    with open(output_file_root + ".full-config.json", "w") as f:
+    with open(output_file_root + ".full-config.json", "w", encoding="utf-8") as f:
         json.dump(configuration, f, indent=4)
 
     logger.debug("Using %i of %i available CPUs.", int(config["processes"]), int(cpu_count()))
@@ -273,7 +273,7 @@ def rescore(configuration: dict, psm_list: PSMList | None = None) -> None:
 
 def _write_feature_names(feature_names, output_file_root):
     """Write feature names to file."""
-    with open(output_file_root + ".feature_names.tsv", "w") as f:
+    with open(output_file_root + ".feature_names.tsv", "w", encoding="utf-8") as f:
         f.write("feature_generator\tfeature_name\n")
         for fgen, fgen_features in feature_names.items():
             f.writelines(f"{fgen}\t{feature}\n" for feature in fgen_features)

ms2rescore/report/data.py

@@ -184,7 +184,7 @@ def _read_config(path: Path) -> dict:
         logger.info("No configuration file found. Proceeding without it.")
         return {"ms2rescore": {}}
     try:
-        return json.loads(path.read_text())
+        return json.loads(path.read_text(encoding="utf-8"))
     except (json.JSONDecodeError, OSError):
         logger.warning("Could not read configuration file. Proceeding without it.")
         return {"ms2rescore": {}}

ms2rescore/report/generate.py

@@ -32,7 +32,9 @@
 # charts (DeepLC, IM2Deep, MS²PIP) reuse the same color as the feature-generator overview charts.
 FEATURE_GENERATOR_COLORS = charts.FEATURE_GENERATOR_COLORS
 
-TEXTS = tomllib.loads(importlib.resources.files(templates).joinpath("texts.toml").read_text())
+TEXTS = tomllib.loads(
+    importlib.resources.files(templates).joinpath("texts.toml").read_text(encoding="utf-8")
+)
 
 
 def generate_report(

ms2rescore/report/utils.py

@@ -28,7 +28,7 @@ def read_feature_names(feature_names_path: Path | None) -> dict:
         return feature_names
 
     try:
-        with open(feature_names_path) as f:
+        with open(feature_names_path, encoding="utf-8") as f:
             reader = DictReader(f, delimiter="\t")
             for line in reader:
                 feature_names[line["feature_generator"]].append(line["feature_name"])