Adk pass

[andrewkern]

Opening this as a draft PR because I'd like to get some feedback on my reorganization of the paper up to the "Updates to stdpopsim" section.

In reading through where the paper was at, I was unhappy with how we were trying to straddle this being about stdpopsim vs a general guide to simulation. I've tried to be a bit bolder in this intro reorganization to move the paper more towards being about stdpopsim.

@gphocs-dev @lauterbur @dschride @petrelharp @jeromekelleher, others-- what do you think of what I've done so far here to the tone? i'm going to keep going but could use some feedback I think

[gregorgorjanc]

@andrewkern @gphocs-dev I have checked out this PR and revised the Bos Taurus section. How do I push my changes?

ggorjanc@S37-81T5G3QP adding-species-manuscript-mine % gh pr checkout 49
? Which should be the base repository (used for e.g. querying issues) for this directory? popsim-consortium/adding-species-manuscript
remote: Enumerating objects: 30, done.
remote: Counting objects: 100% (30/30), done.
remote: Compressing objects: 100% (18/18), done.
remote: Total 30 (delta 17), reused 25 (delta 12), pack-reused 0
Unpacking objects: 100% (30/30), 57.78 KiB | 71.00 KiB/s, done.
From https://github.com/popsim-consortium/adding-species-manuscript
 * [new ref]         refs/pull/49/head -> adk_pass
Switched to branch 'adk_pass'
ggorjanc@S37-81T5G3QP adding-species-manuscript-mine % git add adding-species-manuscript.Rproj 
ggorjanc@S37-81T5G3QP adding-species-manuscript-mine % git add references.bib 
ggorjanc@S37-81T5G3QP adding-species-manuscript-mine % git commit -m "Reviewing Bos Taurus changes"                     
[adk_pass 4d7ad7d] Reviewing Bos Taurus changes
 2 files changed, 877 insertions(+), 850 deletions(-)
 create mode 100644 adding-species-manuscript.Rproj
ggorjanc@S37-81T5G3QP adding-species-manuscript-mine % git push
remote: Permission to andrewkern/adding-species-manuscript.git denied to gregorgorjanc.
fatal: unable to access 'https://github.com/andrewkern/adding-species-manuscript.git/': The requested URL returned error: 403

[andrewkern]

@gregorgorjanc -- you could open a PR with your changes against the main branch of the popsim-consortium repo-- i haven't yet edited the Bos section

[andrewkern]

alternatively you could open a PR against my branch and I could incorporate there, but I think it's cleaner for you to open your PR against main

[gregorgorjanc]

@andrewkern you made some changes hence I pulled your PR, but I am not clear how a make a PR against your PR?

[andrewkern]

submit a PR against this branch: https://github.com/andrewkern/adding-species-manuscript/tree/adk_pass

[igronau]

I'm going to spend much of the next few days in transition, but I'll try to take some time to review when I get a chance

[andrewkern]

Okay and meanwhile I will keep going through the doc on my editing pass.

[lauterbur]

I will take a look this evening or (more likely) tomorrow. We have had a lot of back and forth about which side of the general guidelines/stdpopsim specific line this belongs on, hence the current straddling. I think it would be a good idea to make a final decision on that before doing too much more restructuring, because we have already gone from one side to the other and back again.

[andrewkern]

okay so at this point I've gone once through the doc and taken care of most (all?) of @gphocs-dev's queries.

@dschride sent me some comments via email that i will incorporate next to this PR but they are mostly small. Once those are in I will squash.

[andrewkern]

Okay this is ready for review / merge / etc

[andrewkern]

Okay thanks @igronau. I will merge this PR.

@dschride I believe the ball is now yours.