Add code diff chain visualization

.gitignore

@@ -177,6 +177,7 @@ BBOB*.zip
 /run/
 /setup/
 .vscode/
+.python-version
 _site/
 
 # Apple File System

data.csv

@@ -0,0 +1,101 @@
+,id,fitness,name,description,configspace,generation,feedback,error,parent_ids,operator,metadata,task_prompt,method_name,problem_name,seed,_id,cummax_fitness,eval
+0,18084962-51ed-4376-8b09-caa9e3c69568,5.955078389147237,AutoCorrCandidate,"Generates a nearly-optimal non-negative function by leveraging a piecewise-constant structure with optimized heights over a central region, tapering to zero at the edges to reduce autocorrelation.",,0,"C1 ratio = 5.95508, best known = 1.5053",,[],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,0,5.955078389147237,1
+1,43b5aacb-4de5-45a9-b846-f2331c03b92f,2.108060230292329,AutoCorrCandidate,"Refines the piecewise-constant function by optimizing the heights of the central, tapering, and edge regions to minimize autocorrelation.",,1,"C1 ratio = 2.10806, best known = 1.5053",,['18084962-51ed-4376-8b09-caa9e3c69568'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,1,5.955078389147237,2
+2,f053dcc7-b434-43ac-a0d0-0167c7569ed2,2.244990298343852,AutoCorrCandidate,"Optimizes a piecewise-constant function with central flat, tapered, and constant-height edge regions, incorporating a dynamically adjusted sigmoid taper and refined parameter bounds to further minimize autocorrelation.",,2,"C1 ratio = 2.24499, best known = 1.5053",,['43b5aacb-4de5-45a9-b846-f2331c03b92f'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,2,5.955078389147237,3
+3,dc80fb23-aa09-4b26-9a7a-1c0f535b08a9,2.14625421730855,AutoCorrCandidate,"Optimizes a piecewise-constant function with a central flat region, cosine tapers, and optimized edge values using a more robust optimizer and a refined parameterization, adding a small constant offset to avoid zero values, and using a larger number of iterations.",,3,"C1 ratio = 2.14625, best known = 1.5053",,['43b5aacb-4de5-45a9-b846-f2331c03b92f'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,3,5.955078389147237,4
+4,7e44f5a8-b458-4b51-9e44-87cbd6e3307f,0.0,AutoCorrCandidate,Optimizes a piecewise-constant function with an added Gaussian component and refined tapering to minimize autocorrelation.,,4,calc-error Integral ∫f must be > 0 for C1,calc-failed,['43b5aacb-4de5-45a9-b846-f2331c03b92f'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,4,5.955078389147237,5
+5,d236ef84-7086-4204-882b-7151cddc3692,2.072361474351445,AutoCorrCandidate,"Optimizes a piecewise-quadratic function with a central flat region, tapering quadratic sections, and constant edges to minimize autocorrelation.",,5,"C1 ratio = 2.07236, best known = 1.5053",,['43b5aacb-4de5-45a9-b846-f2331c03b92f'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,5,5.955078389147237,6
+6,617268ca-e233-47c4-9a64-e6889dc5560b,2.000000000000122,AutoCorrCandidate,"Optimizes a piecewise-cubic function with smooth transitions between regions by directly controlling the function values at key points, aiming for a flatter autocorrelation peak.",,6,"C1 ratio = 2, best known = 1.5053",,['d236ef84-7086-4204-882b-7151cddc3692'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,6,5.955078389147237,7
+7,01594200-c881-458f-b751-38ebd030cf6c,10.0,AutoCorrCandidate,"Optimizes a raised cosine function with adjustable parameters for a flatter autocorrelation peak, simplifying the parameter space for faster convergence.",,7,"C1 ratio = 10, best known = 1.5053",,['617268ca-e233-47c4-9a64-e6889dc5560b'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,7,10.0,8
+8,06529ca8-7515-41b3-bfca-120341bfc009,2.000000000000957,AutoCorrCandidate,Optimize a piecewise-quadratic function with a central flat region and parabolic tapers to minimize autocorrelation peak relative to integrated function square.,,8,"C1 ratio = 2, best known = 1.5053",,['617268ca-e233-47c4-9a64-e6889dc5560b'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,8,10.0,9
+9,f2400a0c-cca8-4bb5-9498-b669eb35e167,0.0,AutoCorrCandidate,Optimizes a piecewise-linear function with a central flat region and linearly decaying edges to minimize the autocorrelation peak relative to the integral squared.,,9,"exec-error could not broadcast input array from shape (240,) into shape (120,)",exec-failed,['617268ca-e233-47c4-9a64-e6889dc5560b'],,{},"
+
+Write a python class with function `__call__`, that returns a list of floats f of length N.
+- Where N is number of bins over [-1/4, 1/4] with discretization of dx = 0.5 / N.
+- Auto-convolution of `g = dx * conv(f, f, mode=""full"")`, where g lies in range [-1/2, 1/2].
+- Optimise for objective of minimize  max_t (f*f)(t) / (∫ f)^2, where all entries in the list f must be greater than or equal to 0 and do not normalise the f, scaling does not change the score.
+- Symmetry or piecewise-constant structure is allowed if helpful.
+- Set N = 600 as default.
+
+",LLaMEA,auto_corr_ineq_1,0,9,10.0,10

iohblade/plots.py

@@ -4,12 +4,11 @@
 import os
 from collections import Counter
 
-import plotly.graph_objects as go
-
 import jsonlines
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import plotly.graph_objects as go
 import seaborn as sns
 from scipy.stats import ttest_ind
 from sklearn.decomposition import PCA
@@ -680,6 +679,140 @@ def plotly_code_evolution(
     return fig
 
 
+def code_diff_chain(
+    run_data: pd.DataFrame, solution_id: str
+) -> list[dict[str, pd.Series | str]]:
+    """Return diffs along the lineage of ``solution_id``.
+
+    The function follows the first parent of each solution until the root is
+    reached. For every parent-child pair a unified diff of their code is
+    produced.
+
+    Args:
+        run_data: DataFrame containing at least ``id``, ``parent_ids`` and
+            ``code`` columns. ``name``, ``generation`` and ``fitness`` are
+            optional but will be preserved if present.
+        solution_id: Identifier of the final solution.
+
+    Returns:
+        A list of dictionaries ordered from the first ancestor to
+        ``solution_id``. Each dictionary has ``parent`` and ``child`` keys with
+        the respective rows and a ``diff`` key containing a unified diff string.
+    """
+
+    data = run_data.copy()
+    data["parent_ids"] = data["parent_ids"].apply(
+        lambda x: ast.literal_eval(x) if isinstance(x, str) else x
+    )
+    data = data.set_index("id", drop=False)
+    if solution_id not in data.index:
+        raise ValueError(f"Unknown solution_id: {solution_id}")
+
+    chain: list[dict[str, pd.Series | str]] = []
+    current = solution_id
+
+    while True:
+        row = data.loc[current]
+        parents = row["parent_ids"]
+        if not parents:
+            break
+        parent_id = parents[0]
+        parent_row = data.loc[parent_id]
+        parent_code = parent_row["code"]
+        current_code = row["code"]
+        parent_lines = parent_code.splitlines()
+        current_lines = current_code.splitlines()
+        diff_lines = difflib.unified_diff(
+            parent_lines,
+            current_lines,
+            fromfile=str(parent_id),
+            tofile=str(current),
+            lineterm="",
+            n=max(len(parent_lines), len(current_lines)),
+        )
+        chain.append(
+            {"parent": parent_row, "child": row, "diff": "\n".join(diff_lines)}
+        )
+        current = parent_id
+
+    chain.reverse()
+    return chain
+
+
+def get_code_lineage(run_data: pd.DataFrame, solution_id: str) -> list[pd.Series]:
+    """Return lineage of an individual with id ``solution_id``, across generation.
+
+    The function follows the first parent of each solution until the root is
+    reached. Generating a chin from first generation to the last generation.
+    Args:
+        run_data: DataFrame containing at least ``id``, ``parent_ids`` and
+            ``code`` columns. ``name``, ``generation`` and ``fitness`` are
+            optional but will be preserved if present.
+        solution_id: Identifier of the final solution.
+
+    Returns:
+        A list of pd.Series `rows` that present individual lineage in ascending order, oldest -> newest.
+    """
+    data = run_data.copy()
+    data["parent_ids"] = data["parent_ids"].apply(
+        lambda x: ast.literal_eval(x) if isinstance(x, str) else x
+    )
+    data = data.set_index("id", drop=False)
+    if solution_id not in data.index:
+        raise ValueError(f"Unknown solution_id: {solution_id}")
+
+    lineage: list[pd.Series] = []
+    id = solution_id
+    while id:
+        try:
+            parent = data.loc[data["id"] == id].iloc[0]
+        except:
+            parent = None
+        if parent is not None:
+            lineage.append(parent)
+        pid = parent["parent_ids"]
+        if pid:
+            id = pid[0]
+        else:
+            id = None
+    return lineage[::-1]
+
+
+def print_code_diff_chain(run_data: pd.DataFrame, solution_id: str) -> None:
+    """Print the code diff chain for ``solution_id``."""
+
+    chain = code_diff_chain(run_data, solution_id)
+    if not chain:
+        return
+    root = chain[0]["parent"]
+    print(
+        "Initial {p} (gen {pg}, fit {pf})".format(
+            p=root.get("name", root["id"]),
+            pg=root.get("generation", "?"),
+            pf=root.get("fitness", "?"),
+        )
+    )
+    print(root["code"])
+    print()
+    for step, entry in enumerate(chain, start=1):
+        parent = entry["parent"]
+        child = entry["child"]
+        diff = entry["diff"]
+        print(
+            "Step {step}: {p} (gen {pg}, fit {pf}) -> {c} (gen {cg}, fit {cf})".format(
+                step=step,
+                p=parent.get("name", parent["id"]),
+                pg=parent.get("generation", "?"),
+                pf=parent.get("fitness", "?"),
+                c=child.get("name", child["id"]),
+                cg=child.get("generation", "?"),
+                cf=child.get("fitness", "?"),
+            )
+        )
+        print(diff)
+        print()
+
+
 def plot_boxplot_fitness(
     logger: ExperimentLogger, y_label="Fitness", x_label="Method", problems=None
 ):