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feature: add proforma.modify_with #196

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9fc4b96
feature: add proforma.modify_with
mobiusklein Mar 12, 2026
229fb63
cleanup docs
mobiusklein Mar 14, 2026
473dff8
Fixes and tests
levitsky Mar 19, 2026
c7af7c8
fix previous tests
mobiusklein Mar 28, 2026
03a3cff
Add a test for proteoforms function with a dict
levitsky Mar 28, 2026
f82b8a4
Patch the failing unrelated test, Massive's PROXI server seems to be …
mobiusklein Mar 29, 2026
2e8adb4
Add expand_rules argument
mobiusklein Mar 29, 2026
c9f5f01
chore: rework USI test patch
mobiusklein Mar 29, 2026
770b2c2
Only warn if expand_rules is true and include_unmodified is explicitl…
levitsky Mar 29, 2026
a6f7f7f
Update test_from_simple_dict
levitsky Mar 29, 2026
a40f893
refactor `expand_rules`
mobiusklein Mar 30, 2026
37b0fd9
Merge branch 'feature/more_combinators' of https://github.com/mobiusk…
mobiusklein Mar 30, 2026
4736e32
Expand tests
levitsky Mar 30, 2026
cc29c34
Skip the PROXI test on timeout
levitsky Apr 14, 2026
9254a8e
Make test code slightly more descriptive
levitsky Apr 14, 2026
b4f2a6c
Add support for CoMUP with expand_rules
levitsky Apr 14, 2026
c4c0d58
Roll back unneeded value type conversions
levitsky Apr 14, 2026
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8 changes: 5 additions & 3 deletions CHANGELOG
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
5.0c0
5.0c1
-----

- Update the standard ion compositions to be more consistent with the adopted ion type notation.
Expand All @@ -14,8 +14,10 @@
- Support **ProForma 2.1** (`#183 <https://github.com/levitsky/pyteomics/pull/183>`_ by Joshua Klein).
You can calculate compositions for :py:class:`ProForma` objects using :py:meth:`pyteomics.proforma.Proforma.composition`
and get m/z with annotated or user-provided charge state using :py:meth:`pyteomics.proforma.Proforma.mz`.
You can also iterate through possible peptidoforms when a ProForma sequence is annotated with some ambiguity using
:py:meth:`pyteomics.proforma.Proforma.generate_proteoforms`.

- You can also iterate through possible peptidoforms when a ProForma sequence is annotated with some ambiguity using
:py:meth:`pyteomics.proforma.Proforma.proteoforms` and apply additional modification specifications to any ProForma sequence
using :py:func:`pyteomics.proforma.proteoforms` (`#196 <https://github.com/levitsky/pyteomics/pull/196>`_ by Joshua Klein).

- Implement **thread-based parallelism**.
Following the introduction of `official free-threading Python implementations <https://docs.python.org/3/howto/free-threading-python.html>`_
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