Improve logging and handling of PDB writing errors. #4753
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Could this ever be used with a non-seekable output handle (e.g. stdout), and in that case is it handled gracefully? |
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I don't think so. We already assume we're dealing with a file handle (with
write and close methods) and IOBase, which all types of file and in-memory
file buffers inherit from, has both tell and truncate defined.
Unless someone is doing something very weird, they shouldn't hit this.
A segunda, 24/06/2024, 01:35, Peter Cock ***@***.***>
escreveu:
… Could this ever be used with a non-seekable output handle (e.g. stdout),
and in that case is it handled gracefully?
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…size (8, expected 4) biopython#4751 (biopython#4752) * update * fix long dtype * fix long dtype * update * update * update * update * test numpy array repr * test dtype * try printing * update * update * fix chapter_blast * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update --------- Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp> Co-authored-by: Michiel de Hoon <mdehoon@madpc2s-MacBook-Pro.local>
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Tests passed! @peterjc, if you are ok with this, go ahead and merge 💪 |
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Thank you - rebased-and-merged. |
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I hereby agree to dual licence this and any previous contributions under both
the Biopython License Agreement AND the BSD 3-Clause License.
I have read the
CONTRIBUTING.rstfile, have runpre-commitlocally, and understand that continuous integration checks will be used to
confirm the Biopython unit tests and style checks pass with these changes.
Closes #4729.
This PR improves our handling of failures in PDBIO. As is, if there is a failure, we print the full traceback, which can be hard to parse. More importantly, we write an incomplete/partial PDB file up to the point of failure. This PR adds the main error message on the last (bottom) traceback error message for easier debugging. In addition, we now delete or truncate the file if there is an exception, depending on if the user provided a string or an open file handle, respectively.