Merge branch 'main' into dependabot/pip/requirements/CI/numpy-1.22.4

popsim-consortium · Jun 1, 2022 · a0f40e0 · a0f40e0
2 parents 5d20e03 + f76b1c7
commit a0f40e0
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diff --git a/docs/_ext/speciescatalog.py b/docs/_ext/speciescatalog.py
@@ -428,6 +428,7 @@ def model_image(self, species, model):
         os.makedirs(f"parameter_images/{species.id}/", exist_ok=True)
         img_name = f"parameter_images/{species.id}/{mid}.png"
         plt.savefig(img_name, dpi=150)
+        plt.close()
         section = nodes.image(uri=img_name)
         return section
 

diff --git a/docs/catalog.rst b/docs/catalog.rst
@@ -46,8 +46,16 @@ Then, if you feel ready, make an issue on our
 
 .. speciescatalog:: AnoCar
 
+.. speciescatalog:: AnoGam
+
+.. speciescatalog:: ApiMel
+
 .. speciescatalog:: AraTha
 
+.. speciescatalog:: BosTau
+
+.. speciescatalog:: CaeEle
+
 .. speciescatalog:: CanFam
 
 .. speciescatalog:: ChlRei
@@ -66,6 +74,8 @@ Then, if you feel ready, make an issue on our
 
 .. speciescatalog:: HomSap
 
+.. speciescatalog:: PapAnu
+
 .. speciescatalog:: PonAbe
 
 .. speciescatalog:: StrAga

diff --git a/docs/development.rst b/docs/development.rst
@@ -1108,6 +1108,13 @@ to him until directed).
          --retainIntermediates
 
 
+.. note::
+
+    The ``GeneticMap`` named ``"SalomeAveraged_TAIR10"`` for ``"AraTha"``
+    was generated by aligning the TAIR7 and TAIR10 with ``"minimap2"``,
+    and lifting the recombination rates on TAIR7 to TAIR10 with
+    ``"paftools.js liftover"``.
+
 
 .. _sec_development_dfe_model:
 

diff --git a/docs/parameter_tables/AnoGam/GabonAg1000G_1A17.csv b/docs/parameter_tables/AnoGam/GabonAg1000G_1A17.csv
@@ -0,0 +1,4 @@
+Population size,"4,069,863","Modern population size"
+Population size,"205,766","Mean coalescence time / 4"
+"Generation time (yrs.)",1/11,"Generation time"
+"Mutation rate (subst/gen)",3.5e-9,"Mutation rate"