Add almond species and demographic model

[jorgemasgomez]

No description provided.

[gregorgorjanc]

Issue for this PR is at #1730

[codecov]

Codecov Report

❌ Patch coverage is 56.66667% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 99.55%. Comparing base (9534946) to head (679f43a).

Files with missing lines	Patch %	Lines
stdpopsim/catalog/PruDul/demographic_models.py	0.00%	13 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1729      +/-   ##
==========================================
- Coverage   99.81%   99.55%   -0.27%     
==========================================
  Files         142      146       +4     
  Lines        4873     4903      +30     
  Branches      472      473       +1     
==========================================
+ Hits         4864     4881      +17     
- Misses          6       19      +13     
  Partials        3        3              

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[gregorgorjanc]

@jorgemasgomez good job on squashing the above points. Let me know when you are done with all the points and then we will QC this via the test file.

[jorgemasgomez]

In relation to the genome information, the v3 assembly of the ‘Texas’ cultivar is the most recent one. It is a phased genome assembly, therefore the reported genome length corresponds to the average length of both haplotypes.

[jorgemasgomez]

Regarding the demographic model, data points for population size over time were obtained by digitizing the line plot shown in Figure S8a.

[gregorgorjanc]

@jorgemasgomez these changes look all very good and correct (I have cross-checked everything on my end). I left few minor editing nitpicks for you to accept;)

@petrelharp how should we handle this PR - it has:

• species addition from @jorgemasgomez
• species QC from me, but @jorgemasgomez also included the test file based on my review here (I have cross-checked everything and left page or URL crumbs so it's easy to follow)
• demographic model addition from @jorgemasgomez

I have not yet QCed the demographic model. I propose I QC this part as well and we merge in this PR as all 4 things in on (species addition & QC and demographic model & QC). Or should we split this out into separate PRs?

[jorgemasgomez]

@gregorgorjanc I have accepted and addressed the nitpicks! :)