fix: Open Snakefile for reading with explicit encoding specified (#1146)

* fix: Open Snakefile for reading with explicit encoding specified

* fix merge

* fmt

* only apply encoding if not using binary mode

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

snakemake/sourcecache.py

@@ -352,7 +352,9 @@ def runtime_cache_path(self):
 
     def open(self, source_file, mode="r"):
         cache_entry = self._cache(source_file)
-        return self._open_local_or_remote(LocalSourceFile(cache_entry), mode)
+        return self._open_local_or_remote(
+            LocalSourceFile(cache_entry), mode, encoding="utf-8"
+        )
 
     def exists(self, source_file):
         try:
@@ -403,21 +405,21 @@ def _do_cache(self, source_file, cache_entry):
             # as mtime.
             os.utime(cache_entry, times=(mtime, mtime))
 
-    def _open_local_or_remote(self, source_file, mode):
+    def _open_local_or_remote(self, source_file, mode, encoding=None):
         from retry.api import retry_call
 
         if source_file.is_local:
-            return self._open(source_file, mode)
+            return self._open(source_file, mode, encoding=encoding)
         else:
             return retry_call(
                 self._open,
-                [source_file, mode],
+                [source_file, mode, encoding],
                 tries=3,
                 delay=3,
                 backoff=2,
             )
 
-    def _open(self, source_file, mode):
+    def _open(self, source_file, mode, encoding=None):
         from smart_open import open
 
         if isinstance(source_file, LocalGitFile):
@@ -432,6 +434,6 @@ def _open(self, source_file, mode):
         path_or_uri = source_file.get_path_or_uri()
 
         try:
-            return open(path_or_uri, mode)
+            return open(path_or_uri, mode, encoding=None if "b" in mode else encoding)
         except Exception as e:
             raise WorkflowError("Failed to open source file {}".format(path_or_uri), e)