Fix up some cases where open was not done with a context manager, etc. - #644
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Codecov Report
@@ Coverage Diff @@
## main #644 +/- ##
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Coverage 95.11% 95.11%
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Files 27 27
Lines 3089 3093 +4
=======================================
+ Hits 2938 2942 +4
Misses 151 151
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Closes #641.