378 bug nan in reportsso for sexratio in hermaphroditism model with second growth morph

[Rick-Methot-NOAA]

Concisely (20 words or less) describe the issue

reporting of sex ratio in report.sso could produce nan because it was only using area 1 numbers

Please Link issue(s)

#378
resolves #[add issue number number], resolves #[optional second issue number if more than 1 issue addressed.]
#378

What tests have been done? Upload any model input files created for testing in a zip file, if possible.

visual examination of biology in endyr report table

What tests/review still need to be done? Who can do it, and by when is it needed (ideally)?

none

Has any new code been documented?

yes
If not, please add documentation before submitting the Pull Request.

• I have documented any new code added (or no new code was added)

is there an input change for users to Stock Synthesis?

no

• Yes, there was an input change

If so, please provide an example of the new inputs needed.

[New example stock synthesis input goes here]

Check which is true. This PR requires:

• no further changes to r4ss
• no further changes to the manual
• no further changes to SSI (the SS3 GUI)
• no further changes to the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI that are needed (if not checked):

Inform users that output is now area_specific. Column header format is now: sex_ratio_area:X

If changes are needed in the change log, please fill in the table here:

Action	Topics	Type
[fix, new, or revise]	[e.g., biology. Use issue label options.]	[input, output, and/or calc, or ALL]

Additional information (optional):

[Rick-Methot-NOAA]

@iantaylor-NOAA @e-gugliotti-NOAA
Looks like r4ss will need a tweak to accommodate the changed number of columns for a >1 area model and/or for the change in column name from "sex_ratio" to "sex_ratio_area:X"

[e-perl-NOAA]

@Rick-Methot-NOAA @iantaylor-NOAA Kathryn and I are working on this. It looks like its might be more of an issue with github actions.

[nschindler-noaa]

This looks okay to me - no change to SSI.

[e-perl-NOAA]

@Rick-Methot-NOAA Kathryn and I have worked on this today and the problem is solved (adding - name: install libcurl
run: sudo apt-get install -y libcurl4-openssl-dev to test-r4ss-with-ss3 as well as updating the env with the env from the ghactions for r workflow) though it's not showing up here. The action that failed needed to be run manually to get it to work once it was updated. The successful run can be found here.

[Rick-Methot-NOAA]

good work. Nothing like jumping into a problem on your first SS3 PR to get you introduced to the system.

[e-perl-NOAA]

Approved now that the gh actions have successfully passed.

[Rick-Methot-NOAA]

@e-gugliotti-NOAA Can you check to see if the manual shows that sex_ratio is now reported by area in the biology output table of report.sso?

[e-perl-NOAA]

@Rick-Methot-NOAA It currently does not. Would this need to go in the general biology section of the report portion of the manual or the biology at age section like mentioned in Ian's bug?

[Rick-Methot-NOAA]

It is report:47 for biology at age.

Also check to see if r4ss will read the multiple columns.