BEMIO Cleanup

[akeeste]

This scripts completes the BEMIO cleanup project board task:

• rename BEMIO variables and internal functions to camel case
• rename BEMIO scripts to camel case
• removed redundant writeh5 functions

updates after review:

• changed writeH5 to writeBEMIOH5 to prevent confusion with matlab functions
• updated H5CreateWriteAtt to writeH5Parameter since it creates a variable, writes values, and defines attributes
• removed bemio.m and replaced it with a short README.md pointing to the examples/BEMIO cases
• removed specific BEM names in normalizeBEM.m, it is general now
• removed the loadH5 function since it replicates a lot of what the built in h5read does. The only purpose it served for us was to reverse the order of the dimensions upon reading from the h5 file. I'm not sure why this is necessary, but I created a short utility function that will does this same thing after using h5read

updates building on Kelley's compareBEMIO PR into this fork:

• test plotting for different number of WEC bodies, single/double/triple, e.g. sphere, rm3, wec3
• test plotting for single, double and triple BEMIO results, e.g. WAMIT, Capytaine, AQWA
• test plotting when nested in plotBEMIO, resolve issues with nested varargin functions
• remove *.mat and AQWA files
• add examples/**/*.png to gitignore so that images of BEMIO plots are not included on the repo
• Point bodyClass to the readBEMIOH5 function
• refactor plotting scripts to remove the hydro parameter entirely. Also functions use varargin for simplicity
• create new test for the compareBEMIO functionality by running plotBEMIO for two different Sphere BEM runs

Future Task --> project board

• Compare BEM data by loading h5 data into hydro data structure. Right now, this comparison is based on a temporary hydro structure from the BEM output files

[kmruehl]

Thanks Adam, LMK if you have any questions

[akeeste]

@kmruehl I made the requested changes, namely:

• removed renaming scripts. I can't find away to attach files to a team discussion thread, but have them locally if needed
• moved the waveClass.waveNumber method to the BEMIO/waveNumber.m function so that it's accessible by both Read_NEMOH and waveClass
• removed redundant write H5 functions. These have been incorporated into writeH5.m previously

[kmruehl]

• What's the difference between h5read and loadH5? Both used in bodyClass
• Naming convention for h5write and writeH5, distinguish between built-in MATLAB and BEMIO functions
• internal functions, e.g. H5CreateWriteAtt
• What is purpose of bemio.m? Should we keep it and add description? Remove it and point to examples?
• normalizeBEM update description to include Capytaine or remove BEM names

[akeeste]

@kmruehl Thanks for discussing yesterday. I made the latest suggested changes, namely:

• changed writeH5 to writeBEMIOH5 to prevent confusion with matlab functions
• updated H5CreateWriteAtt to writeH5Parameter since it creates a variable, writes values, and defines attributes
• removed bemio.m and replaced it with a short README.md pointing to the examples/BEMIO cases
• removed specific BEM names in normalizeBEM.m, it is general now
• I removed the loadH5 function since it replicates a lot of what the built in h5read does. The only purpose it served for us was to reverse the order of the dimensions upon reading from the h5 file. I'm not sure why this is necessary, but I created a short utility function that will does this same thing after using h5read

[kmruehl]

@akeeste PR #11 should resolved bug (unchecked boxes above) with the nested varargin. Should we add/update bemio tests for this?

[akeeste]

@kmruehl I have finished the last clean up items on this PR. Everything seems to be working now and all tests pass locally. I went through all the files changed and don't see anything unintentional. I'm happy with merging this PR and then working on new tests/documentation separately.

[kmruehl]

@akeeste I'll review this again and merge it. I can work on updating the tests, if you want to work on the documentation updates. We can work off the same PR though, I'll open one and tag you in it once this is merged.

[kmruehl]

Note to self, double check the waveNumber calculation for shallow, deep and intermediate water

[kmruehl]

@akeeste thanks! I'll leave it to you to delete your own branch if you like.

[akeeste]

@akeeste I'll review this again and merge it. I can work on updating the tests, if you want to work on the documentation updates. We can work off the same PR though, I'll open one and tag you in it once this is merged.

This sounds good. Wednesday before seeing this I started on reorganizing these tests to be more efficient. Let me know when you start and we could use that branch as a jumping off point https://github.com/akeeste/WEC-Sim/tree/bemioTestDocs

[kmruehl]

@akeeste I already updated the tests in this PR. However, I did not restructure them, I just added a test for the new plot feature. If you'd like to submit your restructured tests as a PR, feel free to.

[akeeste]

@kmruehl Okay got it. I'll submit some restructuring when I update BEMIO documentation. I'm hoping to hold on to the wamit/nemoh/other hydrodata whenever it is read in to save time.