Merge pull request #580 from mattwthompson/utf-8-xml

Ensure XML files are opened with UTF-8 encoding
mosdef-hub · Aug 30, 2024 · 469712f · 469712f
2 parents 648d714 + 2707210
commit 469712f
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -13,7 +13,7 @@ dependencies:
  - openmm
  - parmed>=3.4.3
  - ele
- - openff-toolkit >=0.11
+ - openff-toolkit-base >=0.11
  - pip
  - pre-commit
  - pytest

diff --git a/foyer/forcefield.py b/foyer/forcefield.py
@@ -66,15 +66,17 @@ def preprocess_forcefield_files(forcefield_files=None):
 
  for xml_file in forcefield_files:
  if not hasattr(xml_file, "read"):
- f = open(xml_file)
+ try:
+ f = open(xml_file, encoding="utf-8")
+ xml_contents = f.read()
+ finally:
+ f.close()
+
  _, suffix = os.path.split(xml_file)
  else:
- f = xml_file
+ xml_contents = xml_file.read()
  suffix = ""
 
- # read and preprocess
- xml_contents = f.read()
- f.close()
  xml_contents = re.sub(
  r"(def\w*=\w*[\"\'])(.*)([\"\'])",
  lambda m: m.group(1)