Use PQAnalysis for shared parsing - #46
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## main #46 +/- ##
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- Coverage 93.78% 93.61% -0.17%
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Files 21 21
Lines 1190 1191 +1
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- Hits 1116 1115 -1
- Misses 74 76 +2
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Follow-up to #46 (shared parsing via PQAnalysis). Verifying that refactor surfaced one critical regression plus a couple of lower-severity issues, fixed here with regression coverage. ## Critical: Hessian reading was broken on real DFTB+ output DFTB+ writes `hessian.out` as a flat stream of second derivatives wrapped at a fixed number of values per line (with a ragged final line per matrix row), not as a square grid. The refactor routed it through a reader that requires an already-square `numpy.loadtxt` result, so it raised on every real file: - uniform-width output loaded as `(n, 4)` and failed the square check; - ragged output made `numpy.loadtxt` itself fail. This is invisible to CI because the integration tests need the `dftb+`/`modes` binaries and are skipped, while the unit test fed a synthetic square grid DFTB+ never emits. Restored flat-token parsing that reads every value and reshapes to `(3N, 3N)`, keeping the explicit size validation. Verified bit-for-bit against real 72x72 and 78x78 Hessians. ## xyz coordinate precision `read_xyz` routed coordinates through `XYZFrameReader`, which stores positions as float32, perturbing every value by ~1e-7 relative to the source and to `read_gen` (float64). Now reads the coordinate columns in float64 while keeping `XYZFrameReader` for validation, atom count, symbols and cell detection. ## Smaller fixes - `read_xyz` no longer masks a missing file as "Invalid XYZ coordinate file."; it raises `FileNotFoundError` again. - `Modes.read` stops at a trailing tag section (e.g. `saved_modes :integer:..`) instead of casting the section header to float and crashing. ## Test coverage - Regression test for the Hessian reader using the authentic ragged wrapped layout (asserts `numpy.loadtxt` cannot parse it, so the fixture can't be reduced to a square grid). - Small fixtures (`tests/data/calculator/modes/`) plus an integration test that drives `Hessian.read` -> `Modes` -> wave numbers end to end with only the `modes` binary mocked, closing the no-binary gap. - float64-precision and missing-file tests for `read_xyz`; a trailing-section test for `Modes.read`. 134 passed, 5 skipped (the 5 still need the DFTB+ binaries); pylint 7.94/10.
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Summary
Validation