Co-authored-by: Mosè Giordano <[email protected]>
Co-authored-by: Will Graham <[email protected]>

Basic class structure and some failing tests for TDD.

…se of stupid, not TDD.

With unfortunate duplication of memory into buffers. To be fixed in the
future with flattened classes.

* Trying to decipher structs

* Further towards reading a struct

* Bypass the stack-smash bug.

MATLAB saves character arrays as uint16s, and HDF5 is unable to interpret them as chars. As such, we need to do manual conversion in the test.

* Rename binary and update contents

…ility (#280)

* Reorganise hdf5 unit tests

- Move uint16 to char/str functions to the unit test utils file
- Create hdf5_and_tdms_objects subdirectory of unit/ to hold unit tests on interaction between hdf5 and tdms classes
- Move the Matrix<double> test from test_hdf5_io into the new subdirectory
- Data files needed for unit tests are defined in a unit_test_utils namespace to avoid redefinition across multiple files

* Create file to test interface and hdf5 interactions

- Add docstrings to interface.h since these are missing and I've just had to work out what they do
- Create a matlab script that can reproduce the class_data.mat file which the hdf5 unit tests will try to create tdms objects from
- Create the barebones test_hdf5_interface file

* HDF5Reader can read from .mat file and produce an InterfaceComponent

* File restructure: accounting for how many tests we are going to have with HDF5

* Prune includes

* Add .mat file for HDF5-TDMS-object unit tests to run.

- Adds scripts to reproduce this data, so in theory a new user can run a short MATLAB script to reproduce this
- Had a play with trying to get setup-matlab to run these scripts before the unit tests, but alas, no.

* Skeleton for new method

* FrequencyVectors use std::vectors instead of our custom object as members. [DOESN'T COMPILE YET]

- FrequencyVectors is now just a struct that uses std::vector datatypes
- SimualationManager is broken, along with most parts of the codebase that use FrequencyVectors
- Pending update to allow code to COMPILE

* Allow TDMS to actually be compiled again. [TESTS STILL FAIL, READER METHOD NOT READY YET]

- Move .mat data generation scripts for unit tests into benchmarking folder
- Adjust paths to unit test data accordingly
- InputMatrices stores the filename so that we can minimise disruption as we transition away from MATLAB

* IT WORKS

* Create the abstract H5Dimensions class to ease reading objects.

- Update HDF5Base::shape_of to return instances of this class
- Add unit tests for class
- Update HDF5Reader method to avoid recycled code

* Remove MATLAB pointers to InterfaceComponents in initialisation.

- simulation_manager can now instantate these members using HDF5Reader rather than still relying on the old InputMatrices object

* Add docstrings to files touched

* Produce unit test binaries on CI rather than track in repo

* - Detaches MATLAB from Cuboid class.
- Turns Cuboid class into a struct because MATLAB is now gone.
- Adds failure-case checks to HDF5Reader::read() functions.

Squashed commit of the following:

commit ce8d15e311e9dbb93bd7d7fbcd6c9cffe69657e3
Author: willGraham01 <[email protected]>
Date:   Fri May 5 15:19:51 2023 +0100

    Rename shapes.h to cuboid.h because that's all it contains

commit fe83f568c3da7491d450693574975df90a3f15e1
Author: willGraham01 <[email protected]>
Date:   Fri May 5 15:13:48 2023 +0100

    Fix faulty logic thrown up by test

commit b37a89f031519c6a356b50f91a12ad8867b78333
Author: willGraham01 <[email protected]>
Date:   Fri May 5 15:01:58 2023 +0100

    Allow tdms to actually compile

commit d7c982b9165e3ae4ccf3f42e0fb8c5cdde55b644
Author: willGraham01 <[email protected]>
Date:   Fri May 5 14:31:43 2023 +0100

    Write unit test and read method for Cuboid. Add failure test for FrequencyVectors

    - Add new .m script to produce an input file with bad object data
    - Update unit_test_utils with this new filepath
    - Write HDF5Reader(Cuboid *cube) method and unit test
    - Add failure-test check for FrequencyVectors using bad data file

commit cf61970d2052ab02ae23822f0edd28e89044734f
Author: willGraham01 <[email protected]>
Date:   Fri May 5 14:12:11 2023 +0100

    Change Cuboid to be a struct because a class is overkill

* Use one master script for setting up .mat files for unit tests.

- setup_unit_tests.m now calls all the other data-generating scripts in the folder to save updating the ci.yaml each time.

* Rework DispersiveMultiLayer class into a struct. TDMS builds.

- xyz_vector struct of 3 vector<double>s introduced
- DispersiveMultiLayer is now a struct with xyz_vector members
- Preserve method for checking if the medium is dispersive
- Temporarily disable unit tests for DispersiveMultiLayer class
- HDF5Reader::read() can now assemble a DispersiveMultiLayer
- HDF5Reader has a method for reading directly into a vector<T>
- H5Dimension can be passed a H5::DataSet as well as a H5::DataSpace

* Update paths now we need HDF5 data as well as matlab data

* TDMS builds and tests HDF5Reader::read_data_from_group (passes, no)

* Fix seg-fault in read_dataset_from_group

* Add DispersiveMultiLayer test

* Update DispersiveMultiLayer tests to not be entangled with the MATLAB jargon

* Update the CI so things actually work

* Move content of benchmark_scripts readme into doc/developers

* Update CI to produce unit test `.mat` and `.hdf5` data (#289)

* Move content of benchmark_scripts readme into doc/developers

* Update CI attempt 1

* Actually use the right syntax

* Force python version to prevent MacOS using python2.7

* Rename files to better match the data they produce

* Aplease windows syntax

* Remove pip cache due to known windows bug: actions/setup-python#436

* Apply suggestions from code review