* Update calls to grid formatting

* run on develop

In an oversight in merging #193 the docstring was updated for the
type of return_year in return_year_value but the corresponding
assertion was not.

Tests for the types of the two input parameters have been added to
try to avoid a simular situation occuring the future.

* Require previous version of NetCDF4.

* Merge Master into Develop (#179)

* Include last day of year (#160)

Include the last day of the year when using years parameter. Fixes #154.

* Timezone Bug fix: remove `.replace()` for `.astimezone()` (#161)

* Bug fix: remove timezone replace for astimezone

* add pytz to required packages

* Fix: Pandas latest (#159)

* Plot each col in DataFrame individually

* Remove numpy and pandas version requirements

* WDRT (#141)

* Working version of Gaussian Copula

* Create dedicated function for iso probs and quantiles

* Contour plots worsk for single and multiple contours

* Gumbel Copula.

* Clayton Copula

* Rosenblatt Copula

* Guass and gumbel general copula

* Add support for nonparametric gaussian, clayton, and gumbel copulas

* Require statsmodel for nonparametric KDE copulas

* Small changes

* Fix bug in KDE log transformation

* Adding docstrings

* All doc strings updated

* Add markers option to contours plotting

* Add Copula tests comparing to WDRTresults

* Fix x1, x2 pts bug in KDE contour, clean up

* Example showing the calculation of all copla methods and comparing to WDRT results

* Simplifications and lanuguage cleanup

* Add statsmodel

* Add testing data files

* In plot envrionmental contors convert x1,x2 to values if a Series is passed

* Docstring typo corrections

* Corrected notebook description typos.

* module and example for short-term extreme distributions

* docstrings for short-term extreme functions

* fixes #140 Speedup surface elevation calculation.

* correction to surface_elevation

* elevation

* minor fixes based on review comments

* add environmental_contours to init

* Remove WDRT functionality

* All WDRT contour functionality can be called from one function

* Rework tests for new contour functions setup and location

* Move all contour example into this file

* Update to work with new structure.

* Remove all commented out wdrt functions from resource

* No changes made. Reverting back.

* Have PCA method use general fit. Adds PCAmethod to fit method but can also accept the PCA dictionary. General Docstring Cleanup

* Update discussion around the use of the copula method.

* Remove copula stand alone notebook

* minor formmating changes

* Remove test bugs created from merge with origin

* Import env contours into resource module and adjust test, examples, ect to function with tthe new structure

* Uncommented tests

* Remove reference to import the env contours module

* fixing minor typo

* Move env contours to _file and adjust package to handle new structure

* Minor formatting cleanup

* Cleanup unsed packages and variables

* intial mler upload

* formalize functions

* add tests and example

* sampling rate to averaging period

* rename MLER example

* working

* merging

* WDRT functions and examples finalized. Missing tests.

* integrate mler into extreme

* fixes tests?

* fix tests

* fix tests

* fix full sea state example?

* test contour samples

* test sample full seastate

* random seed

* test long term extreme

* expand MLER functionality

* test short-term extremes

* fix mler tests

* MLER test error

* mler fix 2

* update formats and asserts

* further cleanup of countours.py for consistency, typos, and pep8

* run tests?

* fix test?

* change lists to np.array so they pass the assert statements

* clean extreme.py for consistency, pep8

* points_per_interval should be int

* typing in examples

* full sea state example: make it easier to follow, add more explanation, and use consistent naming

* contour example: make it easier to follow, add more explanation, and use consistent naming

* Alias ste function and minor formatting.

* naming convention

* rename example

* ste example

* allow weights to be np.array

* allow weights to be np.ndarray

Co-authored-by: ssolson <[email protected]>
Co-authored-by: ssolson <[email protected]>
Co-authored-by: rpauly18 <[email protected]>
Co-authored-by: hivanov-nrel <[email protected]>

* DOLfYN IO (#126)

* input output files
+ testing

* Code update

* Test reformatting

* Testing paths

* dependency switch from h5netcdf to netcdf4

* Code cleanup

* Test import fix

* Minor docstring edits

* Add dolfyn test data

* Test fixes for mhkit

* Removing uneeded test files, improving consistency

* Not sure why these files didn't upload

* Organizational changes and clarifications. Request for additional clarification

* Dolfyn codebase updates

* Dolfyn example notebooks update

* Testing updates

* Update example datafile

* Latest dolfyn v0.13.0 updates

* Name change

* input output files
+ testing

* Code update

* Organizational changes and clarifications. Request for additional clarification

* Dolfyn codebase updates

* fix bug and make faster. Un-hard-code default seed/phase.

* fix tests

* delete commented out tests

* retrigger checks

* Checkpoint push

* New dolfyn data files

* Reorganize dolfyn testing

* pytest install for warnings tests

* Final update for IO

* Remove future updates

* Ensure file compression runs

* Update numpy dependency

* trying numpy v1.22

* changing numpy requirements

* Remake unittest test cases

* Save format options

* Add dolfyn view to notebooks

* Decode remaining binary ad2cp variables

* DOLfYN 1.0.0 dependency

Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: ssolson <[email protected]>
Co-authored-by: Michelen <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: rpauly18 <[email protected]>

* regenerate WDRT examples (#163)

* updating version number in package

* fixing dolfyn imports from pip

* updating version number for bug fix

* NDBC Metocean data (#152)

* catch extra header in ndbc data

* NDBC cwind example

* update unit catch in request_data

* update gust plot to show more data

* add tests to read cwind with and without units

* move graphics import to ndbc module and fix capitalization

* use resample, add gridlines, rename variables, replace NDBC nans up front

* rename wind_example to metocean_example

* adding "Develop" branch to PR

Co-authored-by: Carlos A. Michelén Ströfer <[email protected]>
Co-authored-by: rpauly18 <[email protected]>
Co-authored-by: hivanov-nrel <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: rpauly18 <[email protected]>
Co-authored-by: Adam Keester <[email protected]>

* Test Suite Restructure (#174)

* test_wave file to folder with individual feature files

* Move io tests into io folder

* Send plots to a plots folder

* Move resource characterizations plot tests into resource metrics file

* move load tests to folder

* move power tests to folder

* move river tests to folder

* move tidal tests to folder

* move utils tests to folder

* add inits so that tests pick up the tests in subfolders

* Require previous netCDF4 release.

* FIx data directory path

* Fix data directory path

* Fix load data directory path

* Remove relpath call to see if it fixes Windows test suite issues

* Remove relpath from the rest of io tests in wave

* DOLfYN source code (#169)

* Initial push

* Latest bugfixes

* Remove phase-in text

* Update docstrings

* Readability, imports

* Make functions public

* Docstring updates

* Fix test oversight

* Fix docstring

* Missing timestamp fix for classic Nortek

* Docstring updates

* Renaming functions per mhkit standards

* Single array vs binned array functions

* Reorganizing analysis code

* Update invalid orientation matrix warning

* Add config details to dataset attributes

* dolfyn bugfixes

Co-authored-by: jmcvey3 <[email protected]>

* Delft 3D Timestep to Seconds Function (#168)

* fixing file history

* fixing file history

* fixing file history

* made revisions from ssolson review

* changed time_stamp to timestamp

* updated varible names

* updated variable names

* fixed syntax line 63

* umdated variable name

* fixed typos in doc strings

* ssolson review 5-26-2022

* deleted excessive code in get_all_data

* chaged TI to a % from a fraction

* adjusted TI test to be a %

* fixed doc string for TI function

* Docstring adjustments

* updated doc strings

* Make convert_time a hidden func, make 2 functions to access it

* Minor changes to get_lay_data docstring and formatting

* small changes

* remove print from create_points

* example notebook clean up

* fixed merge confilics

* updated after merge

* final developmet barnach merge updates

* deleated space

* Delete test_river.py

* added coverage to test

* updated min and max plot labels

Co-authored-by: Browning <[email protected]>
Co-authored-by: ssolson <[email protected]>

* NetCDF4 (#181)

* Use conda TEST env on Py 3.7, 3.8, 3.9

* Use pip install with Py 3.8 and 3.9.

* Updates for WEC-Sim v5.0 (#185)

* update read_wecsim for WEC-Sim v5.0

* add cable class

* update notebook with results

* add try-except for Morrison (v4.1) vs Morison (v4.2+)

* add cable check and dataset to wave tests

* update cable dataset

* updated variable names

* updated variable names

* updated variable names

* fixed a few docstring typos

* updated s1 to water level

* updated s1 to waterlevel

* updated s1 to waterlevel

* updated s1 to water level

* updated s1 to waterlever

* fixed typo depth to waterdepth

* D3d Tanana Transect Example

* Fix pip install tests (#194)

* Require previous version of NetCDF4.

* Use original pre install for environemnt in pip tests

* Only test pip

* No loading shell PATH

* Do not upgrade h5py

* Set NETCDF to 1.5.8

* pytest and coverage

* yaml syntax fix

* Change need to pip-build

* Control coverage and test via rc files

* Move configuration file to workflows directory

* Move configuration file to workflows directory

* Specify the location of configuration files in coverage/pytest call

* run conda & pip, pass both to coveralls

* conda bash -l {0}

* Add hindcast build which runs serial

* configuration files for hindcast run

* Specify hindcast configuration for hindcast build

* Remove version specification from hindcast calls

* Specify configuration files to include/omit hindcast accordingly

* Change job name

* Fix configuration to hindcast file not test

* Use all OS and py versions in tests

* pandas <=1.5.0

* xarray <=2022.9.0

* Only hindcast

* Clean up package install

* Fixing hypy and h5pyd to previous versions

* Run limited other tests

* No hindcast tests

* remove hindcast comments and coveralls call

* remove py3.8 from pip build

* requirements.txt netCDF <= 1.5.8

* Add function to compute value at a given return period (#193)

* Run CI on push to Develop (#200)

* added optional edge interpolation with nearest

* updated z to water depth

* Dolfyn general updates (#186)

* Initial push

* Latest bugfixes

* Remove phase-in text

* Update docstrings

* Readability, imports

* Make functions public

* Docstring updates

* Fix test oversight

* Fix docstring

* Missing timestamp fix for classic Nortek

* Docstring updates

* Renaming functions per mhkit standards

* Single array vs binned array functions

* Reorganizing analysis code

* Update invalid orientation matrix warning

* Add config details to dataset attributes

* dolfyn bugfixes

* ADV updates
:

* Update compression option for netcdf4

* Remove compression options

* Fix clean function

* Set functions as private

* Move stress functions to ADV dir

* Add bottleneck to reqs

* Minor changes

* Remove old functions

* Code simplification

* Update examples

* Make functions public

* Add bottleneck to dependencies

* Fix notebook

* Bugfix for beam vars

Co-authored-by: jmcvey3 <[email protected]>

* RDI reader, logging, duty cycle motion correction

* Delft3D z calculation (#190)

* updated variable names

* updated variable names

* updated variable names

* fixed a few docstring typos

* updated s1 to water level

* updated s1 to waterlevel

* updated s1 to waterlevel

* updated s1 to water level

* updated s1 to waterlever

* fixed typo depth to waterdepth

* added edges = nearest example

* added edges = nearest option in variable interpolate

* updated z to waterdepth

* added edges= nearest example

Co-authored-by: Browning <[email protected]>

* Directional NDBC  (#197)

* working on directional NDBC

* clean up functions. Write docstrings. Write assert statements. Write tests. Create Tutorial.

* docstring and asserts for plotting function

* add dolfyn, currenly will not run on the branch need jmcvey3 trdi_5beam

* found river bottom and removed data below

* Bug Fix: Averaging histogram bin and wave energy (#205)

* Fix averaging bug
* Add outline to bin counts text for better contrast
* Update plotting function and plot in example notebook

* Fix: update variable name to remove reference before assignment error (#208)

* update wave.contours.samples_contour to not get variable referenced before assignment error

Co-authored-by: Graham Penrose <[email protected]>

* HSDS (#211)

Adds hindcast tests back into the test suite. The NREL HSDS API issues were resolved by creating multiple calls to the API for direction wave spectrum requests. Additionally, an exponential back-off time was implemented to retry calls with an increased wait time between calls.

Co-authored-by: Adam Keester <[email protected]>

* Provide function to convert from Te to Tp using ITTC approximation (#210)

* Provide function to convert from Te to Tp using ITTC approximation

* Apply suggestions from code review

Co-authored-by: Adam Keester <[email protected]>

* Updates

* Force float32 datatype

* added downsampelind comparison and tried contourf

* D3D tanana data

* tanana transect 2

* tanana transect 3

* Docstring formatting

* Metocean module - WIND Toolkit (#187)

* initial script

* update wind_toolkit with 4 regions and 1-hr or 5-min data

* update parameters of wind_toolkit functions

* compare NDBC and WIND metocean data

* fix typo in wpto hindcast example

* finish metocean example and add results

* add wind_toolkit to wave/io/__init__.py

* update WIND Toolkit parameter list

* initial test structure for WIND toolkit

* finish metocean example

* add function to plot each region

* wind toolkit tests and test data

* add tests for misc wind_toolkit MHKiT functions and cases

* fix wind toolkit tests

* add elevation_to_string utility function

* misc cleanup

* clarify available parameters

* add users lat_lon to plot_region visualization

* update example with new functions

* add numpy dependency back in

* Ingnore the new hindcast folder

* Include only the new hindcast folder

* Move hindcast tests to hindcast folder

* Specify exclusion of hindcast from standard coverage

* update hindcast coverage

* remove unnecessary header

* move hindcast and wind_toolkit to wave/io/hindcast

* update .coveragerc files

* update paths for new wave.io.hindcast directory

Co-authored-by: ssolson <[email protected]>

* Change 'default' docstring default

* Remove old comments

* updated code to match Energies paper

* Review

* Boat transect image

* updated variable names

* Dolfyn updates (#212)

* RDI reader, logging, duty cycle motion correction

* Updates

* Force float32 datatype

* Docstring formatting

* Change 'default' docstring default

* Remove old comments

* updated variable names

* updated variable names added to discriptions

* Clean up and suggestions

* added to the examples

* TRTS study edits

* code and discription updates

* Edits and TODOs

* moved files, updated discriptions

* readding Delft3D_example notebook

* added USGS discharge

* updated doc strings

* example updates and move data files

* updated doc strings and Error equations

* updated doc strings

* pulled down development branch

* updated figure visibility

* updated figure at L2 equation

* restor old version

* updated L2 eqation and intro fig

* updated L2 eqation and intro fig

* updated L2 equation

* pulled in Develope branch

* updated figure formate

---------

Co-authored-by: ssolson <[email protected]>
Co-authored-by: ssolson <[email protected]>
Co-authored-by: Carlos A. Michelén Ströfer <[email protected]>
Co-authored-by: rpauly18 <[email protected]>
Co-authored-by: hivanov-nrel <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: jmcvey3 <[email protected]>
Co-authored-by: rpauly18 <[email protected]>
Co-authored-by: Adam Keester <[email protected]>
Co-authored-by: Browning <[email protected]>
Co-authored-by: Mark Bruggemann <[email protected]>
Co-authored-by: Graham Penrose <[email protected]>

* Fix skipping data bug

* check if data is none

* date parsing with datetime.strptime

* date list using a list comprehension

* more efficient DataFrame concatenation

* module docstring

* add tests and lint

Supersedes #166 by @ryancoe to incorporate his suggested changes:

Update the wave.io.hindcast.request_wpto_directional_spectrum function to:

added gid to the metadata and added a description of gid to the docstring
General linting

Addresses #76 by adding a function get_buoy_metadata to the ndbc submodule.

This PR adds needed tests and updates the PACWAVE example to show how to call the metadata.

Co-authored-by: ssolson <[email protected]>

Approve this README as discussed at NREL meeting

Create functions for a mooring module:

 read MoorDyn OUT file
 read MoorDyn input file
 calculate lay length
 create 3d animation
 create 2d animation
---------

Co-authored-by: ssolson <[email protected]>

* Prevent nan values for zero-frequency component in spectrum

Previously providing a zero frequency when creating a spectrum (JONSWAP or Pierson Moskowitz) produced a NaN value. This is due the f^-5 and f^-4 terms in the calculation.

The zero frequency is a valid input and is important when calculating the surface elevation from the spectrum. We know, however, that the zero frequency should __always__ have zero amplitude as the surface elevation has a mean of zero.

This change ensures that if a zero frequency is provided, the amplitude is set to zero.

* Compute surface elevation using IFFT

Previously the surface elevation was only computed using the 'sum of sines' method. This has been found to be prohibitively slow when computing long duration surface elevation traces.

This commit introduces the capability to compute the surface elevation using the more computationally efficient IFFT. The IFFT routine is used by default if no frequency bins are provided and the input frequency vector is equally spaced.

For example a 1hr sea state realisation at 20Hz took 11s to compute using the 'sum of sines' and 0.007s using the IFFT.

Fixes #229

* add docstrings to surface_elevation

* update surface_elevation calls in examples

---------

Co-authored-by: akeeste <[email protected]>

A slew of bugfixes and inconsistency cleanup, as well as including ADCP turbulence functionality for #227

Changelog:

Bugfixes

Added check to ensure n_bin is shorter than the total data length when calling dolfyn.TimeBinner.reshape
Added checks to ensure n_fft and n_fft_coh can't be greater than n_bin
Fixed bug where dolfyn.adp.nan_beyond_surface overtrimmed TRDI instrument data
Fixed bug where dolfyn.ADVBinner.cross_spectral_density would fail if n_fft != n_fft_coh
Improved robustness of Nortek Signature reader for deployments not measuring water velocity
log file extension changed from ".log" to ".dolfyn.log"
API/Useability

Calculation of depth from pressure sensor updated to use linear approximation of the equation of state, rather than EOS-80
Added warnings for ADV motion and turbulence functions
Updated dataset.velds.U_dir shortcut to automatically convert "degrees CCW from X/East/streamwise" to "degrees CW from X/North/streamwise"
dolfyn.ADVBinner.cross_spectral_density now returns frequency coordinate coh_freq instead of freq
Added ADCP turbulence functions
Added function to calculate Doppler noise to ADV turbulence functions
Added "beam_angle" attribute to Nortek Signature datasets
Saved full Nortek Signature "config" dictionary as json string in attributes
Added warning if "rotate_vars" attribute not found
Standardized variable metadata based on CF conventions

Tidal power performance capabilities specified in IEC/TS 6200-200.

Also includes bugfixes, docstring clarifications, and useability edits for the Tidal module in general that I came across from a users standpoint. Changelog as follows:

Bugfixes:
- Standardized function inputs to accept both numpy.ndarrays and pandas.Series (some functions already have this implemented).
- Fixed assertions so that if a numpy array is supplied, the following assertions that rely on pandas don't fail (some functions already have this implemented).
- Added a (temporary) fix so that assertions can handle nans
- Fixed river.performance capture area calculation the multiplies by instead of dividing by 4.
- Fixed a misnamed variable in tidal.performance.principal_flow_directions.
- Corrected the "Returns" statement in the tidal.performance.principal_flow_directions docstring and added a "Notes" section.

API/useability
- Added 'ax' argument passthrough to tidal.graphics.plot_rose and tidal.graphics.plot_joint_prob_distribution to enable more complex matplotlib capabilities outside of the function.
- Added check and updated docstring in tidal.performance.principal_flow_directions to make sure directions are between 0 and 360 degrees, which the function requires.

* Added release to pypi github actions workflow

* Fix badges on pypi

* Fix README broken link