working on julia export

Author: matthiaskoenig

src/sbmlutils/converters/odefac.py

@@ -467,6 +467,24 @@ def to_R(self, r_file: Optional[Path] = None) -> str:
 
         return content
 
+    def to_julia(self, jl_file: Optional[Path] = None) -> str:
+        """Write ODEs to julia.
+
+        Generated files can be used as an input for DifferentialEquations.jl
+        https://docs.sciml.ai/DiffEqDocs/stable/
+
+        """
+        content = self._render_template(
+            template_file="odefac_template.jl",
+            index_offset=1,
+            replace_symbols=True,
+        )
+        if jl_file:
+            with open(jl_file, "w") as f:
+                f.write(content)
+
+        return content
+
     def to_markdown(self, md_file: Optional[Path] = None) -> str:
         """Write ODEs to markdown."""
         content = self._render_template(

src/sbmlutils/resources/converters/odefac_template.jl

@@ -0,0 +1,41 @@
+# -------------------------------------------------------------------------------------
+# Autogenerated ODE definition from SBML file with sbmlutils
+# (https://github.com/matthiaskoenig/sbmlutils).
+#
+#    model: {{ model.getId() }}
+# -------------------------------------------------------------------------------------
+
+module {{ model.getId() }}
+    export p, x0, f_dxdt, xids, pids, yids
+
+    # ids
+    xids = [{% for id in xids %}"{{ id }}"{% if not loop.last %}, {% endif %}{% endfor %}]
+    pids = [{% for id in pids %}"{{ id }}"{% if not loop.last %}, {% endif %}{% endfor %}]
+
+    # initial conditions
+    x0 = [
+    {% for id in xids %}
+      {{ x0[id] }}{% if not loop.last %},{% endif %}      # x0[{{ loop.index }}] {{ id }}
+    {% endfor %}
+    ]
+
+    # parameters
+    p = [
+    {% for id in pids %}
+      {{ p[id] }}{% if not loop.last %},{% endif %}      # p[{{ loop.index }}] {{ id }}
+    {% endfor %}
+    ]
+
+    # odes
+    function f_dxdt(dx, x, p, t)
+        {% for id in yids %}
+        {{ id }} = {{ y[id] }}      # y[{{ loop.index }}] {{ id }}
+        {% endfor %}
+
+        {% for id in xids %}
+        dx[{{loop.index}}] = {{ dx[id] }}     # dx[{{ loop.index }}] {{ id }}
+        {% endfor %}
+
+    end
+
+end