Merge pull request #1034 from aabiddanda/main

Generated catalog figures for each published demographic model

docs/_ext/speciescatalog.py

@@ -15,6 +15,7 @@
 from sphinx.util import logging
 
 import stdpopsim
+import os
 
 logger = logging.getLogger(__name__)
 
@@ -401,6 +402,30 @@ def model_section(self, species, model):
         section += self.model_parameter_table(species, model)
         return [target, section]
 
+    def model_image(self, species, model):
+        import demesdraw
+        import matplotlib.pyplot as plt
+
+        mid = self.get_demographic_model_id(species, model)
+        _, ax = plt.subplots(1, 1, figsize=(4, 4), tight_layout=True)
+        # Conversion into demes object for easier plotting
+        graph = model.model.to_demes()
+        demesdraw.tubes(graph, ax=ax, log_time=True)
+        ax.set_title(f"{model.id}", fontsize=10)
+        ax.set_xticklabels(
+            [p.name for p in model.populations],
+            rotation=45,
+            ha="right",
+            rotation_mode="anchor",
+            fontsize=10,
+        )
+        ax.set_ylabel("Time (generations)", fontsize=10)
+        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)
+        section = nodes.image(uri=img_name)
+        return section
+
     def run(self):
         species = stdpopsim.get_species(self.arguments[0])
         sid = f"sec_catalog_{species.id}"
@@ -427,6 +452,7 @@ def run(self):
         models_section += self.models_table(species)
         for i, model in enumerate(species.demographic_models):
             models_section += self.model_section(species, model)
+            models_section += self.model_image(species, model)
             if i < len(species.demographic_models) - 1:
                 models_section += nodes.transition()
         section += models_section

docs/development.rst

@@ -407,7 +407,7 @@ message:
     hint: 'git pull ...') before pushing again.
     hint: See the 'Note about fast-forwards' in 'git push --help' for details.
 
-**DO NOT LISTEN TO GIT IN THIS CASE!** Git is giving you is **terrible advice**
+**DO NOT LISTEN TO GIT IN THIS CASE!** Git is giving you **terrible advice**
 which will mess up your branch. What we need to do is replace the state of
 the branch ``topic_branch_name`` on your fork on GitHub (the ``upstream`` remote)
 with the state of your local branch, ``topic_branch_name``. We do this

environment.yml

@@ -16,6 +16,7 @@ dependencies:
         - msprime
         - scikit-allel
         - matplotlib
+        - demesdraw
         - slim
         # load the stdpopsim Github repository as a library using pip
         - pip:

requirements/CI/requirements.txt

@@ -20,3 +20,5 @@ numpy==1.21.2
 scikit-allel==1.3.5
 zarr==2.10.0
 biopython==1.79
+demes==0.1.2
+demesdraw==0.1.4

requirements/development.txt

@@ -24,3 +24,5 @@ numpy
 scikit-allel
 zarr>=2.4
 biopython
+demes==0.1.2
+demesdraw==0.1.4

stdpopsim/catalog/HomSap/demographic_models.py

@@ -13,7 +13,7 @@
 
 # population definitions that are reused.
 _yri_population = stdpopsim.Population(
-    id="YRI", description="1000 Genomes YRI (Yorubans)"
+    id="YRI", description="1000 Genomes YRI (Yoruba)"
 )
 _ceu_population = stdpopsim.Population(
     id="CEU",