Merge pull request #445 from jamesmartini/develop

support custom variables in user_function

src/cogent3/app/composable.py

@@ -678,10 +678,14 @@ def __init__(self, func, input_types, output_types, data_types=None):
         )
         self.func = func
 
+    def func(self, *args, **kwargs):
+        self._func(self, *args, **kwargs)
+
     def __str__(self):
         name = self.func.__name__
         module = self.func.__module__
         return f"user_function(name='{name}', module='{module}')"
 
     def __repr__(self):
         return str(self)
+

tests/test_app/test_composable.py

@@ -300,6 +300,19 @@ def foo(self, val, *args, **kwargs):
     def bar(self, val, *args, **kwargs):
         return val.distance_matrix(calc="hamming", show_progress=False)
 
+    def _demo(self, ctx, expect):
+        self.assertEqual(ctx.frame_start, expect)
+        return expect
+
+    def test_user_function_custom_variables(self):
+        demo = user_function(
+            self._demo, ("aligned", "serialisable"), ("aligned", "serialisable")
+        )
+        foo = demo
+        frame_start = 2
+        foo.frame_start = frame_start
+        foo(frame_start)
+
     def test_user_function(self):
         """composable functions should be user definable"""
         from cogent3 import make_aligned_seqs