Black Formatting #281
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Black Formatting #281
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Sync `develop` & `master`
…ntours (MHKiT-Software#278)" This reverts commit 2387a25.
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@akeeste this is ready for review |
akeeste
approved these changes
Feb 1, 2024
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Thanks @ssolson. This looks like a lot of good work to get this up and running, especially adding all those error handling tests.
As we've discussed, the large number of files makes this difficult to review. So my review involved:
- reviewing readme instructions on using black
- installing and testing black myself on new python files
- reviewing how formatting has generally been changed in a few sample files
- skimming changes to test files to identify where new tests have been added
- non-test python files ignored
A couple notes here:
- with my current MHKiT environment I had some dependency conflicts (jupyter-server and pywinpty) when installing pre-commit. I tried upgrading a those specific packages which broke others (jupyterlab, jupyterlab-server). I have not tried reinstalling everything at once yet. Did you get pre-commit installed okay with the rest of your MHKiT environment?
- See note about commented tests in wave.test_contours
mhkit/tests/wave/test_contours.py
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| # def test_nonparametric_copulas(self): | ||
| # methods = [ | ||
| # "nonparametric_gaussian", | ||
| # "nonparametric_clayton", | ||
| # "nonparametric_gumbel", | ||
| # ] | ||
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| # np_copulas = wave.contours.environmental_contours( | ||
| # self.wdrt_Hm0, self.wdrt_Te, self.wdrt_dt, self.wdrt_period, method=methods | ||
| # ) | ||
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| # close = [] | ||
| # for method in methods: | ||
| # close.append( | ||
| # np.allclose( | ||
| # np_copulas[f"{method}_x1"], | ||
| # self.wdrt_copulas[f"{method}_x1"], | ||
| # atol=0.13, | ||
| # ) | ||
| # ) | ||
| # close.append( | ||
| # np.allclose( | ||
| # np_copulas[f"{method}_x2"], | ||
| # self.wdrt_copulas[f"{method}_x2"], | ||
| # atol=0.13, | ||
| # ) | ||
| # ) | ||
| # self.assertTrue(all(close)) | ||
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| # def test_kde_copulas(self): | ||
| # kde_copula = wave.contours.environmental_contours( | ||
| # self.wdrt_Hm0, | ||
| # self.wdrt_Te, | ||
| # self.wdrt_dt, | ||
| # self.wdrt_period, | ||
| # method=["bivariate_KDE"], | ||
| # bandwidth=[0.23, 0.23], | ||
| # ) | ||
| # log_kde_copula = wave.contours.environmental_contours( | ||
| # self.wdrt_Hm0, | ||
| # self.wdrt_Te, | ||
| # self.wdrt_dt, | ||
| # self.wdrt_period, | ||
| # method=["bivariate_KDE_log"], | ||
| # bandwidth=[0.02, 0.11], | ||
| # ) | ||
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| # close = [ | ||
| # np.allclose( | ||
| # kde_copula["bivariate_KDE_x1"], self.wdrt_copulas["bivariate_KDE_x1"] | ||
| # ), | ||
| # np.allclose( | ||
| # kde_copula["bivariate_KDE_x2"], self.wdrt_copulas["bivariate_KDE_x2"] | ||
| # ), | ||
| # np.allclose( | ||
| # log_kde_copula["bivariate_KDE_log_x1"], | ||
| # self.wdrt_copulas["bivariate_KDE_log_x1"], | ||
| # ), | ||
| # np.allclose( | ||
| # log_kde_copula["bivariate_KDE_log_x2"], | ||
| # self.wdrt_copulas["bivariate_KDE_log_x2"], | ||
| # ), | ||
| # ] | ||
| # self.assertTrue(all(close)) | ||
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should these tests still be commented? Let's remove or add back in
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Good Catch. These should be added back. They are a significant source of time during testing.
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Noting here some non-black related changes, @ssolson add anything else I've missed that you did. We've largely discussed all of these and they aren't issues, but noting for future reference:
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Thank you for documenting all these. |
Adam as I mentioned in the meeting I uninstalled the pre-commit as I found it slow. I just reinstalled it and I did not get any conflicts. |
That sounds good, thanks for checking. I just wanted to make sure that it could work, even if its slow since we call it out as an option in the readme. |
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Once the commented tests are back in this should be good to go! Thanks @ssolson |
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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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This PR adds starts to address formatting issues in MHKiT by adding black:
This PR adds black because it will automatically format our files allowing our users to focus on coding and letting black fix the formatting issues automatically.
To adhere to black formatting developers can install and run black from the terminal manually, they can install black as an extension in their IDE such as VS code, or they can enable enable the pre-commit hook.
What this PR changes:
black .formatting on the repo