sync dev with main

[andybeet]

PRs into dev contained all info we needed. They have already been reviewed. If you've got this far we're in good shape!

List PRs

List the PRs that made it into dev that are waiting to be pulled into main:

• PR Contaminant uptake #78 which fixes [Bug Report]: Contaminant uptake and transfer not happening correctly #76

Types of changes

What types of changes does code introduce? Put an x in the boxes that apply.
This will inform the new release number.

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation Update (if none of the other choices apply)

Reviewer instructions

The underlying PRs should already have been reviewed.

If this is a New Feature, Breaking change, or a bug fix, the Atlantis Manual will need to be updated to reflect these changes.
Now would be a good time to create an issue in the Atlantis Manual repo and begin documenting your changes.

• I've created an issue
• This is NA

[hmorzaria]

@eafulton This commit includes a bug fix for your review to the contaminant code. In the Puget Sound Model and NoBA there were issues with some invertebrate and macroalgae groups not taking up contaminants. First, we thought it was just a problem with parametrization because the Salish Sea model didn't have that problem. After trying different parameter combinations, we realized the model differences were an issue of how the models were set up to favor uptake (PAHs) vs transfer (mostly PCBs and Mercury). We then identified several issues, including feeding vs. when prey had contaminants, the timing of contaminants being taken up and written into the array, and dead organisms' contaminants not being transferred to carrion.
I ran the code fixes with the Puget Sound model, and now all groups have contaminants. Raisha checked the code fix and ran it with her model, and it works fine

[hmorzaria]

@eafulton ready for your review, see comment above. Talked to @cecilieha yesterday, and she has tested the bug fix in NoBA and it solved all her issues. Her invert groups now uptake contaminants.