Refactor + tests (#6)

- Minor codebase clean-up
- Slight reorganisation of examples + tests so that we don't break stuff by accident
- CI tests

examples/bdd/generators/old_syntax/gen_abstract.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+"""
+Generator for the Abstract Pipeline benchmark.
+
+Produces a reaction system modelling a pipeline of N modules,
+each cycling through entities a -> y,b -> c -> d before passing
+activation to the next module. The final reaction requires all
+modules to have completed (all y_i present).
+
+NOTE: generates old-syntax input (context-entities, initial-contexts,
+rsctl-property) which is not compatible with the current parser.
+"""
+
+import argparse
+
+
+def generate(n, variant):
+    out = "reactions {\n"
+    out += "\t{ {x},{s} -> {a1} };\n"
+
+    for i in range(1, n + 1):
+        out += "\t{{ {{a{i}}},{{s}} -> {{y{i}}} }};\n".format(i=i)
+        out += "\t{{ {{a{i}}},{{s}} -> {{b{i}}} }};\n".format(i=i)
+        out += "\t{{ {{b{i}}},{{s}} -> {{c{i}}} }};\n".format(i=i)
+        out += "\t{{ {{c{i}}},{{s}} -> {{d{i}}} }};\n".format(i=i)
+        out += "\t{{ {{d{i},y{i}}},{{s}} -> {{a{j}}} }};\n".format(i=i, j=i + 1)
+        out += "\t{{ {{y{i}}},{{s}} -> {{y{i}}} }};\n".format(i=i)
+
+    final_reactants = "a" + str(n + 1)
+    for i in range(1, n + 1):
+        final_reactants += ",y" + str(i)
+    out += "\t{{ {{{r}}},{{s}} -> {{r}} }};\n".format(r=final_reactants)
+    out += "}\n"
+
+    if variant == 1:
+        out += "context-entities { s }\n"
+    elif variant == 2:
+        ctx = "s"
+        for i in range(1, n + 1):
+            if i % 2 == 0:
+                ctx += ",a" + str(i)
+        out += "context-entities {{ {} }}\n".format(ctx)
+
+    out += "initial-contexts { {x} }\n"
+    out += "rsctl-property { E[{}]F(r) }\n"
+
+    return out
+
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument("n", type=int, help="number of pipeline modules")
+    parser.add_argument("variant", type=int, choices=[1, 2],
+        help="context variant (1: minimal, 2: extended)")
+    args = parser.parse_args()
+
+    print(generate(args.n, args.variant))
+
+
+if __name__ == "__main__":
+    main()