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Allow RDI reader to skip junk headers #294

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merged 13 commits into from
Mar 18, 2024

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@jmcvey3 jmcvey3 commented Mar 8, 2024

Properly searches for and skips 7f79 header IDs.

Solution for lkilcher/dolfyn#128

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jmcvey3 commented Mar 8, 2024

Hi @ivicajan, see if this works for you as well.

@jmcvey3 jmcvey3 requested a review from ssolson March 12, 2024 04:13
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jmcvey3 commented Mar 12, 2024

@ssolson Hopefully this is the last new one in the dolfyn pile of PRs

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jmcvey3 commented Mar 12, 2024

Just need to add test data and this one should be good to go

@jmcvey3 jmcvey3 mentioned this pull request Mar 14, 2024
@jmcvey3 jmcvey3 added the bug Something isn't working label Mar 15, 2024
@jmcvey3 jmcvey3 self-assigned this Mar 15, 2024
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@jmcvey3 thank you for getting this PR in I only one comment on this to address before we merge.

mhkit/dolfyn/io/rdi.py Show resolved Hide resolved
@jmcvey3 jmcvey3 merged commit 7ed9d36 into MHKiT-Software:develop Mar 18, 2024
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@jmcvey3 jmcvey3 deleted the debug_7f79 branch March 18, 2024 23:24
@ssolson ssolson mentioned this pull request Apr 24, 2024
@ssolson ssolson mentioned this pull request May 6, 2024
ssolson added a commit that referenced this pull request May 8, 2024
# MHKiT v0.8.0
We're excited to announce the release of MHKiT v0.8.0, which brings a host of new features, enhancements, and bug fixes across various modules, ensuring compatibility with Python 3.10 and 3.11, and introducing full xarray support for more flexible data handling. Significant updates in the Wave and DOLfYN modules improve functionality and extend capabilities.

## Python 3.10 & 3.11 Support
MHKiT now supports python 3.10 and 3.11. Support for 3.12 will follow in the next minor update.
- #240


## Wave Module
### Enhancements:
**Automatic Threshold Calculation for Peaks-Over-Threshold**: We've introduced a new feature that automatically calculates the "best" threshold for identifying significant wave events. This method, originally developed by Neary, V. S., et al. in their 2020 study, has now been translated from Matlab to Python, enhancing our existing peaks-over-threshold functionality.

**Wave Heights Analysis**: A new function, `wave_heights`, has been added to extract the heights of individual waves from a time series. This function uses zero up-crossing analysis to accurately measure wave heights, improving upon our previous methods which only provided the maximum value between up-crossings.

**Enhanced Zero Crossing Analysis**: Building on the above, the zero crossing code previously embedded in `global_peaks` has been isolated into a helper function. This modular approach not only refines the codebase but also supports new functionalities such as calculating wave heights, zero crossing periods, and identifying crests.

### Bug Fixes:
**Contour Sampling Error in Wave Contours**: A bug identified in `mhkit.wave.contours.samples_contour` has been resolved. The issue occurred when period samples defined using the maximum period resulted in values outside the interpolation range of the contour data. This was corrected by ensuring that all sampling points are within the interpolation range and adjusting the contour data selection process accordingly.

- #268 
- #252 
- #278


## Xarray Support
MHKiT functions now fully support the use of xarray for passing and returning data.

- #279 
- #282
- #285
- #302
- #310


## DOLfYN

Thanks to the many user contributions and users of MHKiT the DOLFYN module include a significant number of enhancements and bug fixes. 

### Enhancements:
**Altimeter Support**: Enhanced the Nortek Signature Reader to add capability for reading ADCP dual profile configurations.

**Data Handling Improvements**: Introduced logic to skip messy header data that can accumulate during measurements collected via Nortek software on PCs and Macs.

**Instrument Noise Subtraction**: Added a function to subtract instrument noise from turbulence intensity estimation using RMS calculations, providing results that differ by approximately 1% from the existing standard deviation-based "I" property.

**Improved File Handling**: Updates for RDI files to handle changing "number of cells" and variable "cell sizes," which are now bin-averaged into the largest cell size.

### Bug Fixes:
**Power Spectra Calculation**: Fixed a bug where a given noise value was not being subtracted from the power spectra, and noise was inadvertently added as an input to dissipation rate calculations.

**Improved Header Handling**: Allowed RDI reader to skip junk headers effectively.

**Nortek Reader C Types Update**: Adjusted C types in the Nortek reader to handle below-zero water temperatures and to allow pitch and roll values to go negative.


- #280 
- #289
- #290
- #292
- #293
- #294
- #299


## River & Tidal: D3D
Added limits to `variable_interpolation` and added 3 array input capability to `create_points`
- #271

## Developer Experience
### Black formatting
Black formatting is now enforced on all MHKiT files. This ensures consistent formatting across the MHKiT package.
- #281

### Linting & Type Hints
MHKiT is in the process of enforcing pylint and adding type hints to all functions. Currently this has been achieved and is enforced in the Loads and Power modules.
- #288 
- #296 

### CI/CD
This release introduces significant reduction in testing time for development. This is achieved by reducing the number of tests for pulls against the develop branch and only running hindcast test when changes are made to it. A bug in the hindcast CI was fixed which only ran on changes to the hindcast tests instead of the hindcast module. Additionally the wave and wind hindcast needed to be separated in 2 jobs due to the excessive time taken to run a wind cache. This created a number of follow on PRs around solidifying the logic of these job. A special case for Python 3.8, pip, and Mac OS was added to use homebrew to install NetCDF and HDF5 to get tests to pass.
- #241
- #270
- #306
- #311
- #317
- #318
- #319
- #320
- #324

### Clean Up
MHKiT fixed an implementation error where functions used assert instead of built in errors for type and value checking. Additionally these PRs removed unused files, fixed typos, and created an argument which allows users to run CDIP API calls silently.
- #276
- #272
- #273
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