Convert examples to new syntax

examples/example-5-11

+# Example 5.11 in journal paper
+{square,circle,triangle} x PX
+
+s1: (square, {})
+t1: (triangle, {c1, c2, c3})
+t2: (triangle, {c1, c3})
+c1: (circle, {s1})
+c2: (circle, {c3})
+c3: (circle, {})

examples/example.yaml

-functor: "{box,circle,triangle} x PX"
-
-morphisms:
-- - box            # 0: s1
-  - triangle       # 1: t1
-  - triangle       # 2: t2
-  - circle         # 3: c1
-  - circle         # 4: c2
-  - circle         # 5: c3
-- - []
-  - [3, 4, 5]
-  - [3, 4]
-  - [0]
-  - [5]
-  - []

examples/pp-non-zippable

+# Example 5.10 in journal paper
+{circled, normal} x P(PX)
+
+a1: (normal, {{a2, a3}, {a4, a5}})
+a2: (circled, {})
+a3: (normal, {{a6}})
+a4: (normal, {})
+a5: (normal, {{a7}})
+a6: (normal, {})
+a7: (circled, {})
+
+b1: (normal, {{b2, b3}, {b4, b5}})
+b2: (circled, {})
+b3: (normal, {{b6}})
+b4: (normal, {})
+b5: (normal, {{b7}})
+b6: (circled, {})
+b7: (normal, {})

examples/pp-non-zippable.yaml

-# Example 4.6
-functor: "{a,b} x P(PX)"
-
-morphisms:
-- - a                           # 0: a1
-  - b                           # 1: a2
-  - a                           # 2: a3
-  - a                           # 3: a4
-  - a                           # 4: a5
-  - a                           # 5: a6
-  - b                           # 6: a7
-  - a                           # 7: b1
-  - b                           # 8: b2
-  - a                           # 9: b3
-  - a                           # 10: b4
-  - a                           # 11: b5
-  - b                           # 12: b6
-  - a                           # 13: b7
-- - [0,1]                       # 0: a1
-  - []                          # 1: a2
-  - [2]                         # 2: a3
-  - []                          # 3: a4
-  - [3]                         # 4: a5
-  - []                          # 5: a6
-  - []                          # 6: a7
-  - [4,5]                       # 7: b1
-  - []                          # 8: b2
-  - [6]                         # 9: b3
-  - []                          # 10: b4
-  - [7]                         # 11: b5
-  - []                          # 12: b6
-  - []                          # 13: b7
-- - [1,2]                       # 0 -> [a2,a3]
-  - [3,4]                       # 1 -> [a4,a5]
-  - [5]                         # 2 -> [a6]
-  - [6]                         # 3 -> [a7]
-  - [8,9]                       # 4 -> [b2,b3]
-  - [10,11]                     # 5 -> [b4,b5]
-  - [12]                        # 6 -> [b6]
-  - [13]                        # 7 -> [b7]

examples/valmari-fig3

+# This is Figure 3 from "Simple O(m log n) Time Markov Chain Lumping"
+# by Valmari and Franceschinis.
+{B1, B2, B345, B6}x(ℝ^X)
+
+# elements of the same block are numbered from top to bottom
+b6_1: (B6  , { b3_2: 1.0 })
+b6_2: (B6  , { b4: 1.0 })
+b3_1: (B345, { b1: 1.0 })
+b3_2: (B345, { b1: 1.0 })
+b4:   (B345, { b2: 0.5, b5: 0.5 })
+b5:   (B345, { b5: 1.0 })
+b1:   (B1  , { b1: 1.0 })
+b2:   (B2  , { b2: 1.0 })

examples/valmari-fig3.yaml

-# This is Figure 3 from "Simple O(m log n) Time Markov Chain Lumping"
-# by Valmari and Franceschinis.
-functor: "{a,b,c,d}x(ℝ^X)"
-
-morphisms:
-- - d
-  - d
-  - c
-  - c
-  - c
-  - c
-  - a
-  - b
-- - {3: 1}
-  - {4: 1}
-  - {6: 1}
-  - {6: 1}
-  - {7: 0.5, 5: 0.5}
-  - {5: 1}
-  - {6: 1}
-  - {7: 1}