Version 2 of PEARLTransfit algorithm

[adriazalvarez]

Description of work

As outlined in #39151, this new version tries to improve in/out handling, while making other fixes:
In version 2 of this algorithm:
- The Output Workspace and Fit Parameters Table are created as output properties and not directly extracted from the fit, this preserves workspace history.
- The Output property is a string that sets the basename for outputs in the ADS.
- There are no inputs for background parameter estimation, these can be provided in the FitParametersTable.
- There is no rebin in constant energy.
- In non-calibration fits, a debug table with information about sample temperature can be output if CreateDebugTable is set to True.

One proposed feature on #39151 was to add sequential fitting. I've discussed with Richard, and we've agreed since 6.16 is around the corner and the sequential fitting workflow is not really specified yet and would be more workflow breaking than this iteration, this will need further communication with scientist to get a better picture of what's required, or how that fits in a calibration workflow. It should be done as part of a separate issue.

Closes #39151.

To test:

• You can use the testcode example in the docs to start testing the new features. Try to test different input conditions.
• Build docs and check everything is ok.

Added release notes

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[adriazalvarez]

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📝 Walkthrough

Walkthrough

This pull request implements version 2 of the PEARLTransfit algorithm, a Mantid plugin for extracting sample temperature from neutron transmission resonance data. The implementation adds support for input calibration parameters, output workspace properties, optional debug tables, and explicit temperature calculation with uncertainty propagation via Debye/free-gas relations. Existing version 1 tests are updated with explicit version numbering. A complete test suite for version 2 is added alongside comprehensive documentation and release notes.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 2.17% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely summarizes the main change: introducing Version 2 of the PEARLTransfit algorithm with improved input/output properties.
Linked Issues check	✅ Passed	The PR successfully implements all primary coding requirements from #39151: outputs T/S_Fit as properties, makes S_Fit an input when Calibration=False, adds debug table output, removes Ediv parameter, and removes Bg0Guess properties.
Out of Scope Changes check	✅ Passed	All changes are directly aligned with #39151 requirements: algorithm implementation, tests, documentation, and release notes. No out-of-scope modifications detected.
Description check	✅ Passed	The PR description clearly relates to the changeset—it outlines Version 2 of PEARLTransfit with specific improvements to input/output handling, removal of parameters, and documentation of behavioral changes matching the added code files.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
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🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch pearltransfit_v2

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Actionable comments posted: 4

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/source/algorithms/PEARLTransfit-v2.rst`:
- Line 27: The hyperlink role currently includes a trailing period inside the
text (:ref:`PEARLTransfit-v1. <algm-PEARLTransfit-v1>`), causing the period to
render as part of the link; edit the string used in the docs so the role text
excludes the period (e.g., change :ref:`PEARLTransfit-v1.
<algm-PEARLTransfit-v1>` to :ref:`PEARLTransfit-v1 <algm-PEARLTransfit-v1>` and
place the period after the role) so the period renders outside the hyperlink.

In `@Framework/PythonInterface/plugins/algorithms/PEARLTransfit2.py`:
- Around line 355-357: The debug_params dict in PEARLTransfit2.py contains a
stray brace in the key "Eff. Temp. (K)}" causing a user-visible typo; update the
key to "Eff. Temp. (K)" in the debug_params assignment (symbol: debug_params)
and also correct the corresponding expected key in the unit test
PEARLTransfitV2Test.py (the mirrored entry around line with "Eff. Temp. (K)}")
so both the implementation and test use "Eff. Temp. (K)".
- Around line 333-339: The computation of fwhm can take sqrt of a negative value
when final_func["GaussianFWHM"]**2 < gauss_fwhm_inst**2; guard this by checking
the radicand before calling sqrt (variables: gauss_fwhm_inst,
final_func["GaussianFWHM"], fwhm, gauss_fwhm, self.gauss_fwhm_ref_temp), and if
the radicand is <= 0 either set fwhm = 0 (or a small epsilon) and log/warn about
the unphysical result, or handle it as an error path so downstream temperature
calculations don’t silently get NaN. Ensure the check is placed just before
computing fwhm and that any chosen fallback is consistently handled downstream.
- Around line 130-131: The ReferenceTemp property is declared with a string
default which makes it a text field; change the declareProperty call for
"ReferenceTemp" to use a numeric default (e.g. 290.0) so it becomes a float
property, and remove any redundant float() casts in the PyExec code that
currently convert the string to float; update references in the class where
"ReferenceTemp" is read (e.g., where PyExec casts it) to assume a float instead
of parsing a string.

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Fix all unresolved CodeRabbit comments on this PR:

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• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: dce60e99-993c-4b64-aaf6-3c759fc8330e

📥 Commits

Reviewing files that changed from the base of the PR and between c090191 and c225047.

📒 Files selected for processing (7)

• Framework/PythonInterface/plugins/CMakeLists.txt
• Framework/PythonInterface/plugins/algorithms/PEARLTransfit2.py
• Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
• Framework/PythonInterface/test/python/plugins/algorithms/PEARLTransfitTest.py
• Framework/PythonInterface/test/python/plugins/algorithms/PEARLTransfitV2Test.py
• docs/source/algorithms/PEARLTransfit-v2.rst
• docs/source/release/v6.16.0/Diffraction/Powder/New_features/39151.rst

[samtygier-stfc]

Looks good. Some nice cleanups compared to the existing code.

A few small comments:

Also, is there anything users need to know when moving to the new version? Does it need migration info?

[adriazalvarez]

Also, is there anything users need to know when moving to the new version? Does it need migration info?

Mmm, not very sure. We have a deprecated_algorithm decorator for deprecation, but for v2 there is not an equivalent that I know of. If a user tries to put a v1 keyword into the algorithm, the error message indicates that is v2 of the algorithm. Hopefully they will know how to access version 1, so other than the release notes and perhaps communicating it with the pearl scientist? I can ask Richard.
Just in case, I have added a small comment on the summary of version 2 appearing when an algorithm dialog window is created.

[samtygier-stfc]

This looks good. I have tested locally with the script and the GUI. We have had some feedback form PEARL and made some improvements.

There are some larger suggestions, so I'll write up an issue for a future improvement.