pyXLMS v2.0.0 has been released! 🚀

[michabirklbauer]

We are happy to announce that pyXLMS v2.0.0 has been released! 🚀

Major Changes

• pyXLMS data structures for crosslink-spectrum-matches, crosslinks, and parser results have been changed from regular python dictionaries to classes inheriting from Pydantic BaseModel.
• This change provides better type checking and type validation as well as programmatically easier handling of crosslink-spectrum-matches, crosslinks, and parser results.
• Functions should also fail with better error messages now, specifically when required information is missing.
• The documentation has been majorly restructured to be more clear, this also involved majorly restructuring the code.

Important

While this is a major rewrite the changes are fully backwards compatible!

Expected Complications

The code is fully backwards compatible and crosslink-spectrum-matches, crosslinks, and parser results can still be accessed the same (dict-like) way as before. However, you might encounter the following issues if you have written code using pyXLMS previously and are upgrading to v2.0.0:

• Type annotation will most likely need correction, e.g. a function that was previously:

  def fn(crosslink: dict[str, any]):
      return

  will now have to be:

  def fn(crosslink: pyXLMS.data.Crosslink):
      return

  to pass type checking.
• Data attributes are now immutable with the exception of "additional_information". It was previously possible to do something like this:

  crosslink["alpha_proteins"] = ["PROTEIN"]

  even though this possibly introduces errors and was not intended to be used like that. With pyXLMS v2.0.0 this is no longer possible, but instead a new function has been introduced that creates a new data structure (e.g. a crosslink) with the required change. The following code would produce the desired result from above but in a safe manner:

  new_crosslink = crosslink.copy_with_update(update={"alpha_proteins": ["PROTEIN"]})

• If you have saved any documentation links they might require an update (this only affects links pointing to https://hgb-bin-proteomics.github.io/pyXLMS/ and NOT https://hgb-bin-proteomics.github.io/pyXLMS-docs or https://pyxlms.dev).

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Note

If you find any broken links in the examples or the user guide please report them to micha.birklbauer@fh-hagenberg.at or via issues.