LoadNexusLogs now extends NexusHDF5Descriptor
Allow HDF5 open to handle multiple handlers in NexusHDF5Descriptor

Expose m_fileInfo from NexusFileLoader

To do:
LoadNexusMonitors2

This means we can hide the parsing function that takes an xml string from the public interface and add a friend class to test this.
It also means that getRuns() can be called multiple times with different criteria without having to re-parse the file.

Re #26897

Giovanni Di Siena authored 4 years ago and Gigg, Martyn Anthony committed 4 years ago

In places other substitutions have been made, e.g
Clang does not yet specialize std::shared_ptr for T[]. Vector
has been used instead. The operator[] methods were incorrectly
marked const but returning a non-const reference - this has been fixed.
Refs #25842

Adds a couple of generic functions for requesting data from a journal. The main work is done by a function that takes the file contents as a string so that this can be easily tested. A wrapper function allows the file to first be fetched from a URL constructed for the instrument and cycle.

Also adds a couple of functions for requesting the list of cycles, again with one function taking the file contents and another which finds the URL for the instrument.

Re #26897

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>

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

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>

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

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 fixes garbled code resulting from a mistake during merging master
It also removes an in correctly named file that has since been replaced with a correctly spelled one.

Remove commented out code in LoadStlFactory.h
Remove redundant inline specifier from MeshFileIO and redundant clauses
in switch statements
Edits to two documentation files that are impacted by the addition of the
stl path feature to the environment definition .xml files

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