Pioneer tutorial updates (empirical impedance model and nonlinear spr…

…ing) (#362)

* Update CONTRIBUTING.md to indicate PRs should be to the new `dev` branch

* Update RELEASING.md to reflect new workflow with the `dev` branch

* Set Default uniform_shift to False (#313)

* Make uniform shift default false and fix test_core

* Allow for non-uniform shift for impedance

* update docstrings (#326)

* damping naming and consistently change radiation damping (#328)

* run CI + codeQL on dev PRs/pushses

* Fix test failures (#330)

* fix tests

* fix pioneer

* actually test power solution for irregular wave (#327)

* Update test_integration with new scaling (#333)

* Phase Realizations Demo and Docs (#315)

* Pioneer tutorial realizations demo

Add frequency array and realization study to beginning of pioneer tutorial

* Update pioneer

* Clean pioneer and update docs

* remove print

* Units

* Update pioneer plots

* Waves before frequencies

* Explain less frequencies

* Minor updates

* Update pioneer

* Merge branch 'dev' of https://github.com/sandialabs/WecOptTool into phases_demo

* issue 321 fd_to_td() bug (#329)

* bug bix : DC and Nyquist frequency should not be devided by two before ifft


* Changed td_to_fd to scale single sided frequency components rather than TD signal

* minor bug fix from issue332 #332

* nodf -> ndof (#334)

* add DOI for Daniel's paper (#336)

* Tutorial cleanup (#339)

* run CI on PRs against dev branch

* revamped tutorial 1, including fix for #293

* more tutorial cleanup and editorial changes

* more cleanup and incorporated changes in #315

* fixed tutorial 2 colormaps

* finishing touches

* reverted a few accidental changes

* fixes as per Jeff's review comments

---------

Co-authored-by: Ryan Coe <rcoe@sandia.gov>

* Utils dev - replaces old utilities PR (#343)

* run CI on PRs against dev branch

* coppied fundamental utility files

* import utilities module

* added utilities funtions to tut1

* added bem plot from utils

* added bem plot from utils

* updated sankey plot

* updated check_radiation_damping

* cleared outputs

* corrected bug

* changed Zi to hydro_impedance to be consistent with our variables name python convention

* PR review edits

* add grid to plots

* removed draft functions in utilities.py

* typo

* Fixed one more typo I found while reviewing Daniel's changes

---------

Co-authored-by: Ryan Coe <rcoe@sandia.gov>
Co-authored-by: Michael Devin <michaelcdevin@outlook.com>

* Post process docstrings; use loops for multiple realizations (#337)

* post_processing docstrings

- examples
- parameters (order)

* handle multiple phase realizations internally

* Update wecopttool/core.py

* making outputs lists

* Update implementation to function with tutorial 1 for now

* Update tutorials

* Update LUPA

* Make sure same WEC is passed in

* Add test_utilities

Revert "Add test_utilities"

This reverts commit 27399f0.

* Update utilities module

* Update utilities

* Update test_utilities

* Update tutorial 1 utilities call

---------

Co-authored-by: Carlos A. Michelén Ströfer <cmichel@sandia.gov>
Co-authored-by: Carlos A. Michelén Ströfer <c.michelen.strofer@gmail.com>
Co-authored-by: jtgrasb <jtgrasb@sandia.gov>
Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>

* v3.0.0

* Lower tolerance for new test to fix CI failing occasionally

* hyperlinks no longer have formatting, plus other small adjustments (#348)

* Merge to dev, not main (#349)

* Dev version of documentation site (#347)

* added initial file changes based on sphinx_multiversion docs and WEC-Sim implementation

* removed sphinx-multiversion since it is no longer supported and made manual multiversion

* now uses absolute paths, commented out linkcheck for debugging

* fixed docstring errors in utilities module

* updating files again that somehow got reverted

* fixing path in conf.py

* don't run tutorials (will revert later)

* handle file moves correctly, fixed if statement to make other versions appear

* fixed two bugs in versions template

* reverted temp changes, changes latest to main

* switched latest to main

* main branch now in root directory of pages

* fixed URLs with change from last commit

* make other branches visible before building

* switched main branch tag for more testing

* fixed typo

* switched dev branch to an existing branch

* renamed main to latest, changed version.html file name to avoid confusion

* added prints about moving files so Sphinx output isn't misleading

* fixed typo with quotations

* changed versions.html name back because that broke things I guess

* modified contributing documentation to reflect changes

* add logic to remove duplicate 'latest' branch

* Fixed pathing when already on latest

* remove typo

* Troubleshooting complete, switching back to correct branches for deployment

* Removed extra word in docstring

* removed redundant function

* fixed pathing so returns to same file (and fixes tutorial/API docs)

* changed latest branch for demonstration

* switched back latest branch for deployment

* updated with new Capytaine docs URL

* Add warnings when adding inertia and hydrostatic stiffness automatically (#346)

* Add data and update tutorial 4

* CI workflow cleanup (#352)

* removed conda environment from workflows since newer capytaine/wavespectra work with Windows

* fixed unnecessary capitalization

* still create CI conda environment to fix Mac environment failures

* added conda env fully back in, push workflow deploys docs, split PR workflow

* conda environment activates again

* mambaforge instead of miniforge

* manual cache reset

* reset to older version of setup-miniconda to troubleshoot

* Specify NumPy version <2.0 since it breaks autograd

* v3.0.1 (#360)

* Revert "v3.0.1 (#360)" (#361)

This reverts commit f79ff8b.

* Update pyproject.toml

* Update pioneer tutorial with nl spring and empirical model

* Clear outputs

* Consolidate empirical data and fix small issues

* Remove consolidation file

---------

Co-authored-by: Carlos A. Michelén Ströfer <cmichel@sandia.gov>
Co-authored-by: Ryan Coe <rcoe@sandia.gov>
Co-authored-by: Daniel Gaebele <86246113+dtgaebe@users.noreply.github.com>
Co-authored-by: Michael Devin <michaelcdevin@outlook.com>
Co-authored-by: Carlos A. Michelén Ströfer <c.michelen.strofer@gmail.com>
Co-authored-by: mcdevin <mcdevin@sandia.gov>