fix: validate the topology before opening the output file - #181
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TopologyFileWriter.write opened the output file before any of the bonded parameters were checked, and the per-section checks for a missing bond, angle, dihedral or improper type only ran from inside the write helpers. Opening the file in overwrite mode truncates it, so a topology with a missing type raised TopologyFileError only after the destination had already been emptied, silently destroying an existing topology file. The type checks now run against the sections that are about to be written before the file is opened, so a rejected topology leaves the destination untouched. Writing itself is wrapped in a try/finally so that the file handle is closed even when a later write fails.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #181 +/- ##
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+ Coverage 93.86% 93.94% +0.07%
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Files 177 177
Lines 9215 9231 +16
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+ Hits 8650 8672 +22
+ Misses 565 559 -6
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97gamjak
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Aug 23, 2026
| "bonds": "bond", | ||
| "angles": "angle", | ||
| "dihedrals": "dihedral", | ||
| "impropers": "improper", |
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Writing a topology that fails validation destroyed the existing file.
The writer opened the file, which truncates in overwrite mode, and only then validated, so the error left an empty file behind. The handle was also not closed on that path. Validation now runs before the file is opened, and the write loop closes the file in a finally block.
Present in v1.5.0. 949 tests pass in both type checking modes.