Merge branch 'temporal-shenanigans' of github.com:CITCOM-project/CausalTestingFramework into temporal-shenanigans

Author: jmafoster1

.github/workflows/ci-tests-drafts.yaml

@@ -15,25 +15,22 @@ jobs:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python using Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Install package and dependencies
-        run: |
-          python --version
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+       python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+          python -m pip install --upgrade pip
           pip install -e .
           pip install -e .[test]
           pip install pytest pytest-cov
-        shell: bash -l {0}
-      - name: Test with pytest
-        run: |
-          pytest --cov=causal_testing --cov-report=xml
-        shell: bash -l {0}
-      - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v2
-        with:
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+    - name: Test with pytest
+      run: |
+        pytest --cov=causal_testing --cov-report=xml
+    - name: "Upload coverage to Codecov"
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci-tests.yaml

@@ -20,25 +20,23 @@ jobs:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python using Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Install package and dependencies
-        run: |
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
           python --version
+          python -m pip install --upgrade pip
           pip install -e .
           pip install -e .[test]
           pip install pytest pytest-cov
-        shell: bash -l {0}
-      - name: Test with pytest
-        run: |
-          pytest --cov=causal_testing --cov-report=xml
-        shell: bash -l {0}
-      - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v2
-        with:
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+    - name: Test with pytest
+      run: |
+        pytest --cov=causal_testing --cov-report=xml
+    - name: "Upload coverage to Codecov"
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -25,7 +25,7 @@ system-under-test that is expected to cause a change to some output(s).
 ## Installation
 
 ### Requirements
-- Python 3.9 and 3.10 only.
+- Python 3.9, 3.10, 3.11 and 3.12
 
 - Microsoft Visual C++ 14.0+ (Windows only).
 

causal_testing/surrogate/causal_surrogate_assisted.py

@@ -3,13 +3,12 @@
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from typing import Callable
-
+import pandas as pd
 from causal_testing.data_collection.data_collector import ObservationalDataCollector
 from causal_testing.specification.causal_specification import CausalSpecification
 from causal_testing.testing.base_test_case import BaseTestCase
 from causal_testing.testing.estimators import CubicSplineRegressionEstimator
 
-
 @dataclass
 class SimulationResult:
     """Data class holding the data and result metadata of a simulation"""
@@ -18,6 +17,11 @@ class SimulationResult:
     fault: bool
     relationship: str
 
+    def to_dataframe(self) -> pd.DataFrame:
+        """Convert the simulation result data to a pandas DataFrame"""
+        data_as_lists = {k: v if isinstance(v, list) else [v] for k,v in self.data.items()}
+        return pd.DataFrame(data_as_lists)
+
 
 class SearchAlgorithm(ABC):  # pylint: disable=too-few-public-methods
     """Class to be inherited with the search algorithm consisting of a search function and the fitness function of the
@@ -87,14 +91,14 @@ def execute(
 
             self.simulator.startup()
             test_result = self.simulator.run_with_config(candidate_test_case)
+            test_result_df = test_result.to_dataframe()
             self.simulator.shutdown()
 
             if custom_data_aggregator is not None:
                 if data_collector.data is not None:
                     data_collector.data = custom_data_aggregator(data_collector.data, test_result.data)
             else:
-                data_collector.data = data_collector.data.append(test_result.data, ignore_index=True)
-
+                data_collector.data = pd.concat([data_collector.data, test_result_df], ignore_index=True)
             if test_result.fault:
                 print(
                     f"Fault found between {surrogate.treatment} causing {surrogate.outcome}. Contradiction with "

docs/source/installation.rst

@@ -3,7 +3,7 @@ Getting started
 
 Requirements
 ---------------
-* Python 3.9 and 3.10 only.
+* Python 3.9, 3.10, 3.11 and 3.12
 * `Microsoft Visual C++ <https://docs.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist>`_ 14.0+ (Windows only).
 
 

tests/surrogate_tests/test_causal_surrogate_assisted.py

@@ -231,4 +231,7 @@ def shutdown(self):
         pass
 
 def data_double_aggregator(data, new_data):
-    return data.append(new_data, ignore_index=True).append(new_data, ignore_index=True)
+    """Previously used data.append(new_data), however, pandas version >2 requires pd.concat() since append is now a private method. 
+       Converting new_data to a pd.DataFrame is required to use pd.concat(). """
+    new_data = pd.DataFrame([new_data])
+    return pd.concat([data, new_data, new_data], ignore_index=True)