fixed encoding in binary

Author: matthiaskoenig

_docs/development.qmd

@@ -21,7 +21,7 @@ Testing is performed with pytest and tox:
 
 Run single tox target:
 ```bash
-tox r -e py314
+tox -e py314
 ```
 Run all tests in parallel:
 ```bash

src/sbmlsim/sensitivity/analysis.py

@@ -365,7 +365,7 @@ def read_cache(self, cache_filename: str, cache: bool) -> Optional[Any]:
 
         # retrieve from cache
         if cache and cache_path.exists():
-            with open(cache_path, "rb", encoding="utf-8") as f:
+            with open(cache_path, "rb") as f:
                 data = dill.load(f)
                 console.print(f"Simulated samples loaded from cache: '{cache_path}'")
                 return data
@@ -377,7 +377,7 @@ def write_cache(self, data: Any, cache_filename: str, cache: bool) -> Optional[A
             self.results_path / cache_filename if cache_filename else None
         )
         if cache_path:
-            with open(cache_path, "wb", encoding="utf-8") as f:
+            with open(cache_path, "wb") as f:
                 console.print(f"Simulated samples written to cache: '{cache_path}'")
                 dill.dump(data, f)
 

src/sbmlsim/utils.py

@@ -16,7 +16,7 @@ def md5_for_path(path):
     """Calculate MD5 of file content."""
 
     # Open,close, read file and calculate MD5 on its contents
-    with open(path, "rb", encoding="utf-8") as f_check:
+    with open(path, "rb") as f_check:
         # read contents of the file
         data = f_check.read()
         # pipe contents of the file through

tests/data/combine/omex/jws/download_omex.py

@@ -58,7 +58,7 @@ def download_omex(url, omex_path):
     """
     r = requests.get(url, stream=True)
     if r.status_code == 200:
-        with open(omex_path, "wb") as f:
+        with open(omex_path, "wb", encoding="utf-8") as f:
             r.raw.decode_content = True
             shutil.copyfileobj(r.raw, f)
 

tests/data/diff/simulate_examples.py

@@ -64,7 +64,7 @@ def run_comparisons(create_files=True):
             plt.show()
 
             report_path = diff_path / f"{simulation_key}_diff.tsv"
-            with open(report_path, "w") as f_report:
+            with open(report_path, "w", encoding="utf-8") as f_report:
                 f_report.write(dsc.report_str())