Merge pull request #1059 from izabelcavassim/doc_dfe

added DFE description to the catalog docs

docs/_ext/speciescatalog.py

@@ -36,6 +36,9 @@ def get_genetic_map_id(self, species, genetic_map):
     def get_annotation_id(self, species, annotation):
         return f"sec_catalog_{species.id}_annotations_{annotation.id}".lower()
 
+    def get_dfe_id(self, species, dfe):
+        return f"sec_catalog_{species.id}_dfes_{dfe.id}".lower()
+
     def get_target(self, tid):
         """
         Returns a target node for the specified ID.
@@ -493,27 +496,94 @@ def annotation_table(self, species):
 
         return table
 
+    def dfe_section(self, species, dfe):
+        dfe_id = self.get_dfe_id(species, dfe)
+        target = self.get_target(dfe_id)
+        section = nodes.section(ids=[dfe_id])
+        section += nodes.title(text=dfe.id)
+        section += nodes.paragraph(text=dfe.description)
+        section += nodes.rubric(text="Citations")
+        section += self.citation_list(dfe)
+        return [target, section]
+
+    def dfes_table(self, species):
+        table = nodes.table()
+        tgroup = nodes.tgroup(cols=3)
+        colspec = nodes.colspec(colwidth=1)
+        tgroup.append(colspec)
+        colspec = nodes.colspec(colwidth=1)
+        tgroup.append(colspec)
+        colspec = nodes.colspec(colwidth=1)
+        tgroup.append(colspec)
+
+        table += tgroup
+
+        thead = nodes.thead()
+        tgroup += thead
+        row = nodes.row()
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="ID")
+        row += entry
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Year")
+        row += entry
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Description")
+        row += entry
+
+        thead.append(row)
+
+        rows = []
+
+        for dfe in species.dfes:
+            row = nodes.row()
+            rows.append(row)
+
+            dfe_id = self.get_dfe_id(species, dfe)
+            entry = nodes.entry()
+            para = nodes.paragraph()
+            entry += para
+            para += nodes.reference(internal=True, refid=dfe_id, text=dfe.id)
+            row += entry
+
+            entry = nodes.entry()
+            entry += nodes.paragraph(text=dfe.citations[0].year)
+            row += entry
+
+            entry = nodes.entry()
+            para = nodes.paragraph()
+            entry += nodes.paragraph(text=dfe.description)
+            row += entry
+
+        tbody = nodes.tbody()
+        tbody.extend(rows)
+        tgroup += tbody
+
+        return table
+
     def run(self):
+        # species:
         species = stdpopsim.get_species(self.arguments[0])
         sid = f"sec_catalog_{species.id}"
         species_target = self.get_target(sid)
         section = nodes.section(ids=[sid], names=[sid])
         section += nodes.title(text=species.name)
         section += self.species_summary(species)
-
+        # genomes:
         genome_section = nodes.section(ids=[f"sec_catalog_{species.id}_genome"])
         genome_section += nodes.title(text="Genome")
         genome_section += self.chromosomes_table(species)
         section += genome_section
         section += nodes.transition()
-
+        # genetic maps:
         maps_section = nodes.section(ids=[f"sec_catalog_{species.id}_genetic_maps"])
         maps_section += nodes.title(text="Genetic Maps")
         maps_section += self.genetic_maps_table(species)
         for gmap in species.genetic_maps:
             maps_section += self.genetic_map_section(species, gmap)
         section += maps_section
         section += nodes.transition()
+        # demographic models:
         models_section = nodes.section(ids=[f"sec_catalog_{species.id}_models"])
         models_section += nodes.title(text="Demographic Models")
         models_section += self.models_table(species)
@@ -523,13 +593,22 @@ def run(self):
             if i < len(species.demographic_models) - 1:
                 models_section += nodes.transition()
         section += models_section
+        # annotation:
         annot_section = nodes.section(ids=[f"sec_catalog_{species.id}_annotations"])
         annot_section += nodes.title(text="Annotations")
         annot_section += self.annotation_table(species)
         for an in species.annotations:
             annot_section += self.annotation_section(species, an)
         section += annot_section
         section += nodes.transition()
+        # DFE:
+        dfes_section = nodes.section(ids=[f"sec_catalog_{species.id}_dfe"])
+        dfes_section += nodes.title(text="Distribution of Fitness Effects (DFEs)")
+        dfes_section += self.dfes_table(species)
+        for i, dfe in enumerate(species.dfes):
+            dfes_section += self.dfe_section(species, dfe)
+        section += dfes_section
+        section += nodes.transition()
         return [species_target, section]