Miscellaneous code review comments to add comments, remove redundant brackets
Also added comment to the sample environment concept page to explain where
Mantid will search for the attenuation profile file

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Runs clang-tidy pass by ref across the codebase to fix-up various
warnings we are seeing in cppcheck

Hand-fixes some cppcheck warnings, this was work prior to fixing the
cppcheck target.

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

While the primary use of the new attenuation profile file feature is expected
to be via the sample environment xml file, it also makes sense to add it into
any algorithms where the material properties can be specified. So I've added a
new attenuation profile parameter to the SetSampleMaterial and LoadSampleEnvironment
algorithms. The validations on these algorithms means they can't be called using
postional arguments so have inserted the new parameter in the logical place next
to the absorption cross section

Have updated the docs to explain how the attenuation profile file is used

Add feature where an externally generated attenuation profile can be loaded into
the material definition from a .DAT text file. This will override the normal
exp(-alpha*thickness) calculation of the attenuation. The new feature was requested
as part of the absorption calculation for the Pearl instrument where some parts
of the environment are crystalline

Found the lookup\interpolation on the loaded profile was slowing down the absorption
Monte Carlo calculation.
So improved performance of Kernel::Interpolation. Changed it to use vector of pairs
instead of two separate vectors to reduce amount of navigation around vectors

Considered adding feature into AttenuationProfile where I add any interpolated points
into the override attenuation profile to prevent interpolation next iteration of
Monte Carlo simulation. However wasn't convinced this was going to be thread-safe
during the parallel part of the absorption calculation - may revisit this. While doing
this investigation I fixed the following issues with the function Interpolation::AddPoint:

a) it doesn't add the same point twice
b) it reuses the lower_bound function rather than stepping through the vector sequentially

I removed the exception from findIndexOfNextLargerValue because the end()
iterator is a valid result if the x value supplied equals the last x value
already in the vector. Could have left check in for begin() but didn't seem
much point

Finally - the interpolation outside the range is not v good. The data at the extremes
is noisy so we end up extrapolating based on random gradient in extreme 2 points. Need
to either fit or use more points to determine gradient

Also updated class_maker.py

This commit replaces all header guards in DataHandling with #pragma once

Reuse map from NeXus file getEntries prevents creation and destruction
of std::map
addressing clang-format

This commit changes the call of workspace->x(0) to workspace->points(0) because of this I no longer need to check if the workspace is a histogram or not.

re: #27774

This commit creates an algorithm `SaveRMCProfile` to output an ascii file with the format corresponding to a file used by the RMCProfile package. the output file contains only the x and y data from a workspace with a header containing the number of y values in the file on the first line, and on the second line the type of function contained within and a title for the data.

re: #27774

The format of the sample environment xml file has been extended to support
loading a .stl file for each environment component. An example spec file
has been created in ISIS/Pearl.xml. This can be used when running the
Algorithm SetSample
Various SampleEnvironmentXXX units have been moved out the Geometry package
into the DataHandling package to facilitate this because they needed to
access the STL loading code in DataHandling
SetSample contains some features for overriding the sample geometry if the
geometry is a CSGObject. This has been sidestepped for mesh geometries.
The methods setId and setMaterial have been moved up to IObject because
it's useful to have them applicable to all objects (CSG, mesh)
Some of the repeated code in SetSample, LoadSampleEnvironment (and now
SampleEnvironmentSpecParser) has been centralised in a new class LoadStlFactory
Also changed container logic so that if there's only one container specified
in the env spec file you don't need to specify it in SetSample
Centralise code relating to scaling mesh vertices and handling of units
into the LoadShape class and rename it MeshFileIO now that SaveStl is also
descended from this class
Move repeated code to choose Ascii or binary STL reader into a factory class

This creates the framework for a saveRMCProfile algorithm that would be used for saving spectral density data in a format that can be read by RMCProfile.
TODO get propper format of metadata

re: #27774

This commit refactors the the SavePDFGui algorithm to have two seperate functions, one for metadata and one for axis data. This makes any future changes simpler and makes the algorithm easy to duplicate with different metadata for different formats

re: #27774

This commit adds a decstrings of the SavePDFGui.

re: #27774

This PR fixes a bug in SavePDFGui that caused a failure when given histogram data.

re: #27774