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Use mzdata::mz_read, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb #1

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merged 16 commits into from
Oct 24, 2024

Commits on Aug 13, 2024

  1. use mz_read to read mgfs and mzmls

    This add support for gziped files, without the need for us to implement
    it.
    paretje committed Aug 13, 2024
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  3. use infer_from_path to determine filetype

    This should add support for gzipped files, MzMLb and Thermo raw files.
    paretje committed Aug 13, 2024
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Commits on Aug 23, 2024

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  3. bump version number

    paretje committed Aug 23, 2024
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  4. use matches macro

    paretje committed Aug 23, 2024
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  5. install stable rust toolchain

    paretje committed Aug 23, 2024
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  7. update mzdata and mzpeaks

    The main issue for a fresh build (for some reason I didn't have an issue
    locally before removing my target directory) seems to be mzpeaks, but
    there is little reason not to update both.
    paretje committed Aug 23, 2024
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Commits on Aug 29, 2024

  1. drop unused function

    paretje committed Aug 29, 2024
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  2. add feature for thermo rawfile support

    Note that this feauture needs to be called thermorawfilereader. mzdata's
    feature is called thermo, but the checks, including the one in the
    `mz_read` macro tests for thermorawfilereader. The feature here needs to
    match the one tested for in the macro, otherwise rawfiles are detected
    as a file type, but the macro still wouldn't support it.
    paretje committed Aug 29, 2024
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Commits on Sep 18, 2024

  1. use git mzdata

    paretje committed Sep 18, 2024
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Commits on Sep 23, 2024

  1. use mzdata 0.30

    paretje committed Sep 23, 2024
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Commits on Oct 23, 2024

  1. update mzdata

    This leaves us with 1 test failure: in our test MGF, PEPMASS is preceded
    by CHARGE. mzdata now parses the charge, but implicitly assumes there is
    a PEPMASS first. When that isn't the case, there is no precursor ion to
    assign the charge value to, resulting in a failure of our unit test.
    paretje committed Oct 23, 2024
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  2. update test mgf

    Work around the bug in mzdata for now, but it might be interesting to,
    once we upgrade the version of mzdata, to add a test for this.
    paretje committed Oct 23, 2024
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