feat(API): updated documentation, overhauled API

BREAKING CHANGE: Total API overhaul for final (at this time) release

.github/workflows/update_wiki.yml

@@ -3,11 +3,8 @@ name: Deploy Wiki
 on:
   workflow_dispatch:
   push:
-    # Trigger only when wiki directory changes
     paths:
-      - 'wiki/pages/**'
-
-    # Trigger only on main
+      - 'wiki/**'
     branches: [ main ]
 
 jobs:
@@ -16,35 +13,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install tools to build whl package
-      run: |
-        pip install sdist
-
-    - name: Build whl package
-      run: |
-        python setup.py sdist bdist_wheel
-      env:
-        SEMANTIC_VERSION: 1.0.0   # not actually 1.0.0, but has no impact on wiki-building
-
-    - name: Install do-calculus package
-      run: |
-        pip install -e .
-      env:
-        SEMANTIC_VERSION: 1.0.0   # not actually 1.0.0, but has no impact on wiki-building
-
-    - name: Build Pages (replace stubs)
-      run: |
-        python ./wiki/build_wiki.py
-
     - name: Push Wiki Changes
-      uses: Andrew-Chen-Wang/github-wiki-action@v2
+      uses: Andrew-Chen-Wang/github-wiki-action@v3
       env:
-        WIKI_DIR: wiki/pages/
+        WIKI_DIR: wiki/
         GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         GH_MAIL: ${{ secrets.EMAIL }}
         GH_NAME: ${{ github.repository_owner }}

README.md

@@ -28,3 +28,12 @@
 * **Contact**: [braden.dubois@usask.ca](mailto:braden.dubois@usask.ca)
 
 See the [wiki](https://github.com/bradendubois/do-calculus/wiki) to get started.
+
+
+## Development Status
+
+A full overhaul has been completed, and marks important milestones in my life and (consequently) this project's. Development on this project is halted until further notice, barring further changes to my own life, or necessary bug fixes and/or security fixes.
+
+## Acknowledgements
+
+This project represents approximately two years of part- and full-time work as part of an indescribably fulfilling undergraduate research project. This project was done under the supervision of Dr. Eric Neufeld from approximately Spring 2020 - Winter 2022. Without Dr. Neufeld's support, guidance, patience, expertise (and of course, funding), this project would never have been started, let alone completed. I cannot overstate my appreciation - you've changed my academic and professional path, and provided me with so many wonderful experiences and memories that I will never forget. Thanks, Eric.

archive/README.md

@@ -0,0 +1,5 @@
+# Archive
+
+Contained here is some old code that built a (now-outdated) wiki that I don't have the heart to delete.
+
+Don't rely on it expecting accurate information.

do/identification/API.py

@@ -5,7 +5,7 @@
 from ..core.Variables import Intervention, Outcome
 
 from .LatentGraph import latent_transform
-from .Identification import Identification
+from .Identification import Identification, simplify_expression
 from .PExpression import PExpression, TemplateExpression
 
 
@@ -62,7 +62,6 @@ def _process(current: Union[PExpression, TemplateExpression], known: Mapping[str
                 return t
 
         result = _process(expression, {v.name: v.outcome for v in y} | {v.name: v.outcome for v in x})
-
         return (result, expression.proof()) if include_proof else result
 
     def proof(self, y: Set[Outcome], x: Set[Intervention], model: Model) -> str:

do/identification/LatentGraph.py

@@ -179,29 +179,29 @@ def latent_transform(g: Graph, u: Set[str]):
         reduction = False
 
         remove = set()
-        for u in Un:
+        for un in Un:
 
-            parents = [edge[0] for edge in E if edge[1] == u]       # Edges : parent -> u
-            children = [edge[1] for edge in E if edge[0] == u]      # Edges : u -> child
+            parents = [edge[0] for edge in E if edge[1] == un]       # Edges : parent -> u
+            children = [edge[1] for edge in E if edge[0] == un]      # Edges : u -> child
 
             # All parents are unobservable, all children are observable, at least one parent
             if all(x in u for x in parents) and len(parents) > 0 and all(x not in u for x in children):
                 reduction = True
 
                 # Remove edges from parents to u
                 for parent in parents:
-                    E.remove((parent, u))
+                    E.remove((parent, un))
 
                 # Remove edges from u to children
                 for child in children:
-                    E.remove((u, child))
+                    E.remove((un, child))
 
                 # Replace with edge from edge parent to each child
                 for cr in product(parents, children):
                     E.add((cr[0], cr[1]))
 
                 # U can be removed entirely from graph
-                remove.add(u)
+                remove.add(un)
 
         V -= remove
         Un -= remove
@@ -229,4 +229,5 @@ def latent_transform(g: Graph, u: Set[str]):
             a, b = child_edges[i], child_edges[(i + 1) % len(child_edges)]
             E_Bidirected.add((a[1], b[1]))
 
+    print(V, u)
     return LatentGraph(V, E, E_Bidirected, [x for x in g.topology_sort() if x in V - u])

examples/2-backdoor-paths/deconfound.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+
+from do import API
+
+api = API()
+
+file = Path("pearl-3.4.yml")
+model = api.instantiate_model(file)
+
+backdoors = api.backdoors({"Xi"}, {"Xj"}, model.graph())
+assert len(backdoors) > 0, "No backdoor paths detected!"
+assert not api.blocks({"Xi"}, {"Xj"}, model.graph(), set()), "This should not block all paths!" 
+
+for path in backdoors:
+    print("Path:", path)
+
+backdoors = api.backdoors({"Xi"}, {"Xj"}, model.graph(), {"X1", "X4"})
+assert len(backdoors) == 0, "Expected this to block!"
+assert api.blocks({"Xi"}, {"Xj"}, model.graph(), {"X1", "X4"}), "This should block!"

examples/2-backdoor-paths/pearl-3.4.yml

@@ -0,0 +1,116 @@
+name: 'Pearl: Figure 3.4'
+endogenous:
+  X1:
+    outcomes:
+    - x1
+    - ~x1
+    parents: []
+    table: [
+      [x1, 0.4],
+      [~x1, 0.6]
+    ]
+  X2:
+    outcomes:
+    - x2
+    - ~x2
+    parents: []
+    table: [
+      [x2, 0.15],
+      [~x2, 0.85]
+    ]
+  X3:
+    outcomes:
+    - x3
+    - ~x3
+    parents:
+    - X1
+    table: [
+      [x3, x1, 0.1],
+      [x3, ~x1, 0.3],
+      [~x3, x1, 0.9],
+      [~x3, ~x1, 0.7]
+    ]
+  X4:
+    outcomes:
+    - x4
+    - ~x4
+    parents:
+    - X1
+    - X2
+    table: [
+      [x4, x1, x2, 0.7],
+      [x4, x1, ~x2, 0.9],
+      [x4, ~x1, x2, 0.55],
+      [x4, ~x1, ~x2, 0.15],
+      [~x4, x1, x2, 0.3],
+      [~x4, x1, ~x2, 0.1],
+      [~x4, ~x1, x2, 0.45],
+      [~x4, ~x1, ~x2, 0.85]
+   ]
+  X5:
+    outcomes:
+    - x5
+    - ~x5
+    parents:
+    - X2
+    table: [
+      [x5, x2, 0.8],
+      [x5, ~x2, 0.25],
+      [~x5, x2, 0.2],
+      [~x5, ~x2, 0.75]
+    ]
+  X6:
+    outcomes:
+    - x6
+    - ~x6
+    parents:
+    - Xi
+    table: [
+      [x6, xi, 0.9],
+      [x6, ~xi, 0.25],
+      [~x6, xi, 0.1],
+      [~x6, ~xi, 0.75]
+   ]
+  Xi:
+    outcomes:
+    - xi
+    - ~xi
+    parents:
+    - X3
+    - X4
+    table: [
+      [xi, x3, x4, 0.5],
+      [xi, x3, ~x4, 0.65],
+      [xi, ~x3, x4, 0.1],
+      [xi, ~x3, ~x4, 0.25],
+      [~xi, x3, x4, 0.5],
+      [~xi, x3, ~x4, 0.35],
+      [~xi, ~x3, x4, 0.9],
+      [~xi, ~x3, ~x4, 0.75]
+    ]
+  Xj:
+    outcomes:
+    - xj
+    - ~xj
+    parents:
+    - X6
+    - X4
+    - X5
+    table: [
+      [xj, x6, x4, x5, 0.0],
+      [xj, x6, x4, ~x5, 0.25],
+      [xj, x6, ~x4, x5, 0.7],
+      [xj, x6, ~x4, ~x5, 0.45],
+      [xj, ~x6, x4, x5, 0.15],
+      [xj, ~x6, x4, ~x5, 0.8],
+      [xj, ~x6, ~x4, x5, 0.95],
+      [xj, ~x6, ~x4, ~x5, 0.05],
+      [~xj, x6, x4, x5, 1.0],
+      [~xj, x6, x4, ~x5, 0.75],
+      [~xj, x6, ~x4, x5, 0.3],
+      [~xj, x6, ~x4, ~x5, 0.55],
+      [~xj, ~x6, x4, x5, 0.85],
+      [~xj, ~x6, x4, ~x5, 0.2],
+      [~xj, ~x6, ~x4, x5, 0.05],
+      [~xj, ~x6, ~x4, ~x5, 0.95]
+    ]

examples/3-latent/3.4-latent.yml

@@ -0,0 +1,90 @@
+name: 'Pearl: Figure 3.4'
+endogenous:
+  X1:
+    outcomes:
+    - x1
+    - ~x1
+    parents: []
+    table: [
+      [x1, 0.4],
+      [~x1, 0.6]
+    ]
+  X2:
+    outcomes:
+    - x2
+    - ~x2
+    parents: []
+    table: [
+      [x2, 0.15],
+      [~x2, 0.85]
+    ]
+  X3:
+    outcomes:
+    - x3
+    - ~x3
+    table: [
+      [x3, 0.1],
+      [~x3, 0.9],
+    ]
+  X4:
+    outcomes:
+    - x4
+    - ~x4
+    parents:
+    - Xi
+    table: [
+      [x4, xi, 0.9],
+      [x4, ~xi, 0.25],
+      [~x4, xi, 0.1],
+      [~x4, ~xi, 0.75]
+   ]
+  Xi:
+    outcomes:
+    - xi
+    - ~xi
+    parents:
+    - X1
+    - X2
+    table: [
+      [xi, x1, x2, 0.5],
+      [xi, x1, ~x2, 0.65],
+      [xi, ~x1, x2, 0.1],
+      [xi, ~x1, ~x2, 0.25],
+      [~xi, x1, x2, 0.5],
+      [~xi, x1, ~x2, 0.35],
+      [~xi, ~x1, x2, 0.9],
+      [~xi, ~x1, ~x2, 0.75]
+    ]
+  Xj:
+    outcomes:
+    - xj
+    - ~xj
+    parents:
+    - X2
+    - X3
+    - X4
+    table: [
+      [xj, x2, x3, x4, 0.0],
+      [xj, x2, x3, ~x4, 0.25],
+      [xj, x2, ~x3, x4, 0.7],
+      [xj, x2, ~x3, ~x4, 0.45],
+      [xj, ~x2, x3, x4, 0.15],
+      [xj, ~x2, x3, ~x4, 0.8],
+      [xj, ~x2, ~x3, x4, 0.95],
+      [xj, ~x2, ~x3, ~x4, 0.05],
+      [~xj, x2, x3, x4, 1.0],
+      [~xj, x2, x3, ~x4, 0.75],
+      [~xj, x2, ~x3, x4, 0.3],
+      [~xj, x2, ~x3, ~x4, 0.55],
+      [~xj, ~x2, x3, x4, 0.85],
+      [~xj, ~x2, x3, ~x4, 0.2],
+      [~xj, ~x2, ~x3, x4, 0.05],
+      [~xj, ~x2, ~x3, ~x4, 0.95]
+    ]
+exogenous:
+  U1:
+  - X1
+  - X2
+  U2:
+  - X2
+  - X3

examples/3-latent/deconfound.py

@@ -0,0 +1,16 @@
+from pathlib import Path
+
+from do import API, Expression, Intervention, Outcome
+
+api = API()
+
+file = Path("3.4-latent.yml")
+model = api.instantiate_model(file)
+
+xj = Outcome("Xj", "xj")
+xi = Intervention("Xi", "xi")
+e = Expression(xj, [xi])
+
+result, proof = api.identification([xj], [xi], model)
+print(result)
+print(proof)