isolib: strip terminal polarity markers from formulas before isotopic parsing

[Copilot]

isolib failed on formulas containing polarity/charge suffixes (+/- forms), even though polarity does not affect isotopic pattern generation. This change normalizes formula strings before enviPat parsing so charged input representations are handled consistently.

• Formula preprocessing (R runtime)

  • Normalize compound_table$formula in parse_args() by removing only terminal sign-led charge/polarity suffixes.
  • Supported stripped suffixes include: +, -, +2, -2 (with optional trailing whitespace context at end of string).

• Regression coverage (Galaxy tool tests)

  • Added tools/isolib/test-data/markers_no_rt_polarity.tsv with formulas carrying polarity suffixes.
  • Added a new test case in tools/isolib/isolib.xml that runs this input and asserts equivalence with existing expected output (test1.msp), confirming polarity markers are ignored for isotopic pattern computation.

compound_table$formula <- stringr::str_remove(
    compound_table$formula,
    "\\s*[+-]\\d*$"
)

[hechth]

@copilot limit the strip to only +X or -X, because otherwise you might not be sure whether the previous digit refers to the number of atoms of the last type or so ... normally there should only be + and - without any digits. The test case looks good and can stay like this.

[Copilot]

@copilot limit the strip to only +X or -X, because otherwise you might not be sure whether the previous digit refers to the number of atoms of the last type or so ... normally there should only be + a...

Updated in commit 2148512. The regex now strips only sign-led terminal suffixes (+, -, +N, -N) and no longer strips digit-led forms.