Maternal transfer

[hmorzaria]

Your commits explain the who, what, where and when of these changes. Your code shows the how. You do not need to reiterate this. This PR should complete the big picture by telling the why.

Justification

Updated CHANGELOG to match recent merge in dev

If it fixes a bug or resolves a feature request, be sure to link to the issue below.

Types of changes

What types of changes does your code introduce? Put an x in the boxes that apply

• Other change (if none of the other choices apply)
  Documentation

Further comments

• This is NA

Reviewer instructions:

Assign at least 2 reviewers:

• one of which should be a maintainer,
• the others should be familiar with the subject changes. Please add these under the assignees field

Please detail the process reviewers will need to follow to properly test these changes. It is especially helpful to identify the exact code needed to conduct a local build/review/test and to specify any aspects of the testing that may not be obvious.

[Copilot]

Pull request overview

This PR updates example and core ecology/contaminants code around “maternal transfer”/migration handling, and refreshes repository documentation/log artifacts to reflect recent development work.

Changes:

• Adjusts migration/movement logic and initialization in atmovement.c, including handling for returning migrants and stock selection.
• Adds defensive/diagnostic changes in contaminant settler handling and allocation initialization (atContaminants.c, atForcedMovement.c).
• Updates examples/docs: makes the ReactiveAtlantis R example use project-relative paths, updates CHANGELOG.md, and removes valgrind log artifacts.

Reviewed changes

Copilot reviewed 5 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
example/VMPA_setas_biol_fishing_Trunk.prm	Minor formatting/line alignment tweak in the example parameter file.
example/valgrind14.log	Removes committed valgrind output (log artifact).
example/valgrind12.log	Removes committed valgrind output (log artifact).
example/valgrind11.log	Removes committed valgrind output (log artifact).
example/ReactiveAtlantisToolExample.R	Switches to here::here() paths for a more portable R example.
CHANGELOG.md	Adds commit-level changelog entries describing recent fixes/changes.
atlantis/atecology/atmovement.c	Initializes variables and adjusts migration-return/recruit handling.
atlantis/atecology/atForcedMovement.c	Changes allocation from malloc to calloc for force-move entries.
atlantis/atecology/atContaminants.c	Adds additional cohort/flag handling and bounds checks in settler contaminant logic.

Suppressed comments (2)

example/ReactiveAtlantisToolExample.R:41

• outputFolder_original is referenced here, but that directory doesn’t exist in the repository (the included baseline is outputFolderPristine). This makes the example fail unless the reviewer guesses the intended path.

prm.file    <-  here::here("example","VMPA_setas_biol_fishing_Trunk.prm")
diet.file   <- here::here("example","outputFolder_original","outputSETASDietCheck.txt")
food.web(diet.file, grp.csv)

CHANGELOG.md:35

• Typo: “bing used” should be “being used”.

- if (stock_id < 0) {stock_id = 0;} so stock id would be defined before bing used as it was causing a memory loss

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[andybeet]

@hmorzaria. Not sure i understand what this is.
It is also a PR into main not dev
Also it looks like your other reviewer, (copilot) has multiple suggestions for your review.

[hmorzaria]

@andybeet I corrected the pull request so it is going to DEV. This pull request was supposed to be only for the CHANGELOG; the other changes are in #70, which Beth already reviewed and merged into DEV. I was expecting Copilot to only look at the CHANGELOG, but it looked at all the changes in the branch within #70. I accepted Copilot suggestions that fixed redundancies, except one that I think changes the code from what Beth had already reviewed.

[andybeet]

Still not following. If Beth already approved a PR which adds this content in atContaminants.c (and the other R file in this PR), why is this PR removing it? Won't dev end up NOT having this code in it? Don't we want it? I would think this PR should just be a changelog.md change.

[hmorzaria]

Closed to make a documentation only pull request