From 9c28823f1065374a0bec22819d1f7a5fbf8c25f7 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Thu, 16 Oct 2025 09:58:19 +0100
Subject: [PATCH 1/5] Added support for Python 3.13 and included tox

---
 .github/CONTRIBUTING.md         | 47 ---------------------------
 .github/workflows/ci-tests.yaml |  2 +-
 .readthedocs.yaml               |  2 +-
 CONTRIBUTING.md                 | 57 +++++++++++++++++++++++++++++++++
 README.md                       | 34 +++++---------------
 causal_testing/__main__.py      |  5 ++-
 causal_testing/main.py          |  3 ++
 docs/source/requirements.txt    |  6 +++-
 pyproject.toml                  | 37 ++++++++++++++++++---
 9 files changed, 111 insertions(+), 82 deletions(-)
 delete mode 100644 .github/CONTRIBUTING.md
 create mode 100644 CONTRIBUTING.md

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
deleted file mode 100644
index 24e368fc..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,47 +0,0 @@
-# Contributing to Causal Testing Framework
-
-### Questions
-Ask any questions about the Causal Testing Framework or surrounding concepts on the
-[discussions board](https://github.com/CITCOM-project/CausalTestingFramework/discussions). Before opening a new
-discussion, please see whether a relevant one already exists - someone may have answered your question already.
-
-### Reporting Bugs and Making Suggestions
-Upon identifying any bugs or features that could be improved, please open an 
-[issue](https://github.com/CITCOM-project/CausalTestingFramework/issues) and label with bug or suggestion. Every issue
-should clearly explain the bug or feature to be improved and, where necessary, instructions to replicate.
-
-### Making a Pull Request
-In order to directly contribute to the Causal Testing Framework, the following steps must be taken:
-1. Create a new [branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository).
-   - This branch should have a name that describes the feature which is changed or added.
-   - Work directly onto this branch, making sure that you follow our style guidelines outlined below.
-2. Open a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) 
-   from your branch to the main branch.
-   - Explain the changes made or feature added.
-   - [Request a review](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/requesting-a-pull-request-review).
-   - The pull request will have to pass our [continuous integration (CI) checks](#continuous-integration-ci) and receive an 
-     approving review, which will be determined by our [review guidelines]().
-     
-### Continuous Integration (CI)
-Upon pushing or pulling, the following GitHub actions will be triggered:
-    - Build: install Python dependencies
-    - Linting: check style guidelines have been met.
-    - Testing: run unit and regression tests.
-
-### Coding Style
-In the Causal Testing Framework, we aim to provide highly reusable and easily maintainable packages. To this end,
-we ask contributors to stick to the following guidelines:
-1. Make small and frequent changes rather than verbose and infrequent changes.
-2. Favour readable and informative variable, method, and class names over concise names.
-3. Use logging instead of print.
-4. For every method and class, include detailed docstrings following the 
-   [reStructuredText/Sphinx](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html) guidelines.
-5. Add credit and license information where existing code has been used (in the method or class docstring).
-6. If a method implements a specific algorithm/technique from a paper, add a citation to the docstring.
-7. Use [variable](https://www.python.org/dev/peps/pep-0008/#variable-annotations) and [function](https://www.python.org/dev/peps/pep-0008/#function-annotations)
-   annotations.
-8. All methods should be thoroughly tested with PyTest (see [Testing]() below).
-9. Optionally run `autopep8 causal_testing` to prevent linter errors.
-10. Optionally run `isort causal_testing` to ensure imports are done in the right order (this will also help prevent linter errors).
-11. Format code using `black causal_testing`.
-12. Linting code using `pylint causal_testing` is advised.
diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml
index dc1403c1..31bd8503 100644
--- a/.github/workflows/ci-tests.yaml
+++ b/.github/workflows/ci-tests.yaml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 2f7254ef..53cec224 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.13"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 00000000..9862f4fc
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,57 @@
+# How to Contribute
+
+### Questions
+Please ask any questions about the Causal Testing Framework or surrounding concepts on the
+[discussions board](https://github.com/CITCOM-project/CausalTestingFramework/discussions). Before opening a new
+discussion, please see whether a relevant one already exists - someone may have answered your question already.
+
+### Reporting Bugs and Making Suggestions
+Upon identifying any bugs or features that could be improved, please open an 
+[issue](https://github.com/CITCOM-project/CausalTestingFramework/issues) and label with bug or feature suggestion. Every issue
+should clearly explain the bug or feature to be improved and, where necessary, instructions to replicate. We also
+provide templates for each scenario when creating an issue.
+
+### Contributing to the Codebase
+To contribute to our work, please ensure the following:
+
+1. [Fork the repository](https://help.github.com/articles/fork-a-repo/) into your own GitHub account, and [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) it to your local machine.
+2. [Create a new branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository) in your forked repository. Give this branch an appropriate name, and create commits that describe the changes.
+3. [Push your changes](https://docs.github.com/en/get-started/using-git/pushing-commits-to-a-remote-repository) to your new branch in your remote fork, compare with `CausalTestingFramework/main`, and ensure any conflicts are resolved.
+4. Create a draft [pull request](https://docs.github.com/en/get-started/quickstart/hello-world#opening-a-pull-request) from your branch, and ensure you have [linked](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/autolinked-references-and-urls) it to any relevant issues in your description.
+     
+### Continuous Integration (CI) and Code Quality
+Our CI/CD tests include:
+    - Build: Install the necessary Python and runtime dependencies.
+    - Linting: [pylint](https://pypi.org/project/pylint/) is employed for our code linter and analyser.
+    - Testing: We use the [unittest]() module to develop our tests and the [pytest](https://pytest.org/en/latest/) framework as our test discovery.
+    - Formatting: We use [black](https://pypi.org/project/black/) for our code formatting.
+
+To find the other (optional) developer dependencies, please check `pyproject.toml`.
+
+### Coding Style
+In the Causal Testing Framework, we aim to provide highly reusable and easily maintainable packages. To this end,
+we ask contributors to stick to the following guidelines:
+1. Make small and frequent changes rather than verbose and infrequent changes.
+2. Favour readable and informative variable, method, and class names over concise names.
+3. Use logging instead of print.
+4. For every method and class, include detailed docstrings following the 
+   [reStructuredText/Sphinx](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html) guidelines.
+5. Add credit and license information where existing code has been used (in the method or class docstring).
+6. If a method implements a specific algorithm/technique from a paper, add a citation to the docstring.
+7. Use [variable](https://www.python.org/dev/peps/pep-0008/#variable-annotations) and [function](https://www.python.org/dev/peps/pep-0008/#function-annotations)
+   annotations.
+8. All methods should be thoroughly tested with PyTest (see [Testing]() below).
+9. Optionally run `autopep8 causal_testing` to prevent linter errors.
+10. Optionally run `isort causal_testing` to ensure imports are done in the right order (this will also help prevent linter errors).
+11. Format code using `black causal_testing`.
+12. Linting code using `pylint causal_testing` is advised.
+
+### Compatibility Testing Across Python Versions with tox
+
+For compatibility testing Python versions, we use [tox](https://pypi.org/project/tox/) to automate 
+testing across all supported Python versions (3.10, 3.11, 3.12, and 3.13):
+
+- **Install tox**: `pip install tox`.
+- **Test all versions**: `tox` (runs tests on all Python versions + linting in the root folder).
+- **Test specific version**: `tox -e py313` (or py310, py311, py312).
+- **Quick iteration**: Use `pytest` directly for fast testing during development.
\ No newline at end of file
diff --git a/README.md b/README.md
index 5d31817c..80639e67 100644
--- a/README.md
+++ b/README.md
@@ -12,13 +12,12 @@
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.07739/status.svg)](https://doi.org/10.21105/joss.07739)
 [![DOI](https://img.shields.io/badge/doi-10.26180/5c6e1160b8d8a-blue.svg?style=flat&labelColor=whitesmoke&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAB8AAAAfCAYAAAAfrhY5AAAJsklEQVR42qWXd1DTaRrHf%2BiB2Hdt5zhrAUKz4IKEYu9IGiGFFJJQ0gkJCAKiWFDWBRdFhCQUF3UVdeVcRQEBxUI3yY9iEnQHb3bdW1fPubnyz%2F11M7lvEHfOQee2ZOYzPyDv%2B3yf9%2Fk95YX4fx%2BltfUt08GcFEuPR4U9hDDZ%2FVngIlhb%2FSiI6InkTgLzgDcgfvtnovhH4BzoVlrbwr55QnhCtBW4QHXnFrZbPBaQoBh4%2FSYH2EnpBEtqcDMVzB93wA%2F8AFwa23XFGcc8CkT3mxz%2BfXWtq9T9IQlLIXYEuHojudb%2BCM7Hgdq8ydi%2FAHiBXyY%2BLjwFlAEnS6Jnar%2FvnQVhvdzasad0eKvWZKe8hvDB2ofLZ%2FZEcWsh%2BhyIuyO5Bxs2iZIE4nRv7NWAb0EO8AC%2FWPxjYAWuOEX2MSXZVgPxzmRL3xKz3ScGpx6p6QnOx4mDIFqO0w6Q4fEhO5IzwxlSwyD2FYHzwAW%2BAZ4fEsf74gCumykwNHskLM7taQxLYjjIyy8MUtraGhTWdkfhkFJqtvuVl%2F9l2ZquDfEyrH8B0W06nnpH3JtIyRGpH1iJ6SfxDIHjRXHJmdQjLpfHeN54gnfFx4W9QRnovx%2FN20aXZeTD2J84hn3%2BqoF2Tqr14VqTPUCIcP%2B5%2Fly4qC%2BUL3sYxSvNj1NwsVYPsWdMUfomsdkYm3Tj0nbV0N1wRKwFe1MgKACDIBdMAhPE%2FwicwNWxll8Ag40w%2BFfhibJkGHmutjYeQ8gVlaN%2BjO51nDysa9TwNUFMqaGbKdRJZFfOJSp6mkRKsv0rRIpEVWjAvyFkxNOEpwvcAVPfEe%2Bl8ojeNTx3nXLBcWRrYGxSRjDEk0VlpxYrbe1ZmaQ5xuT0u3r%2B2qe5j0J5uytiZPGsRL2Jm32AldpxPUNJ3jmmsN4x62z1cXrbedXBQf2yvIFCeZrtyicZZG2U2nrrBJzYorI2EXLrvTfCSB43s41PKEvbZDEfQby6L4JTj%2FfIwam%2B4%2BwucBu%2BDgNK05Nle1rSt9HvR%2FKPC4U6LTfvUIaip1mjIa8fPzykii23h2eanT57zQ7fsyYH5QjywwlooAUcAdOh5QumgTHx6aAO7%2FL52eaQNEShrxfhL6albEDmfhGflrsT4tps8gTHNOJbeDeBlt0WJWDHSgxs6cW6lQqyg1FpD5ZVDfhn1HYFF1y4Eiaqa18pQf3zzYMBhcanlBjYfgWNayAf%2FASOgklu8bmgD7hADrk4cRlOL7NSOewEcbqSmaivT33QuFdHXj5sdvjlN5yMDrAECmdgDWG2L8P%2BAKLs9ZLZ7dJda%2BB4Xl84t7QvnKfvpXJv9obz2KgK8dXyqISyV0sXGZ0U47hOA%2FAiigbEMECJxC9aoKp86re5O5prxOlHkcksutSQJzxZRlPZmrOKhsQBF5zEZKybUC0vVjG8PqOnhOq46qyDTDnj5gZBriWCk4DvXrudQnXQmnXblebhAC2cCB6zIbM4PYgGl0elPSgIf3iFEA21aLdHYLHUQuVkpgi02SxFdrG862Y8ymYGMvXDzUmiX8DS5vKZyZlGmsSgQqfLub5RyLNS4zfDiZc9Edzh%2FtCE%2BX8j9k%2FqWB071rcZyMImne1SLkL4GRw4UPHMV3jjwEYpPG5uW5fAEot0aTSJnsGAwHJi2nvF1Y5OIqWziVCQd5NT7t6Q8guOSpgS%2Fa1dSRn8JGGaCD3BPXDyQRG4Bqhu8XrgAp0yy8DMSvvyVXDgJcJTcr1wQ2BvFKf65jqhvmxXUuDpGBlRvV36XvGjQzLi8KAKT2lYOnmxQPGorURSV0NhyTIuIyqOmKTMhQ%2BieEsgOgpc4KBbfDM4B3SIgFljvfHF6cef7qpyLBXAiQcXvg5l3Iunp%2FWv4dH6qFziO%2BL9PbrimQ9RY6MQphEfGUpOmma7KkGzuS8sPUFnCtIYcKCaI9EXo4HlQLgGrBjbiK5EqMj2AKWt9QWcIFMtnVvQVDQV9lXJJqdPVtUQpbh6gCI2Ov1nvZts7yYdsnvRgxiWFOtNJcOMVLn1vgptVi6qrNiFOfEjHCDB3J%2BHDLqUB77YgQGwX%2Fb1eYna3hGKdlqJKIyiE4nSbV8VFgxmxR4b5mVkkeUhMgs5YTi4ja2XZ009xJRHdkfwMi%2BfocaancuO7h%2FMlcLOa0V%2FSw6Dq47CumRQAKhgbOP8t%2BMTjuxjJGhXCY6XpmDDFqWlVYbQ1aDJ5Cptdw4oLbf3Ck%2BdWkVP0LpH7s9XLPXI%2FQX8ws%2Bj2In63IcRvOOo%2BTTjiN%2BlssfRsanW%2B3REVKoavBOAPTXABW4AL7e4NygHdpAKBscmlDh9Jysp4wxbnUNna3L3xBvyE1jyrGIkUHaqQMuxhHElV6oj1picvgL1QEuS5PyZTEaivqh5vUCKJqOuIgPFGESns8kyFk7%2FDxyima3cYxi%2FYOQCj%2F%2B9Ms2Ll%2Bhn4FmKnl7JkGXQGDKDAz9rUGL1TIlBpuJr9Be2JjK6qPzyDg495UxXYF7JY1qKimw9jWjF0iV6DRIqE%2B%2FeWG0J2ofmZTk0mLYVd4GLiFCOoKR0Cg727tWq981InYynvCuKW43aXgEjofVbxIqrm0VL76zlH3gQzWP3R3Bv9oXxclrlO7VVtgBRpSP4hMFWJ8BrUSBCJXC07l40X4jWuvtc42ofNCxtlX2JH6bdeojXgTh5TxOBKEyY5wvBE%2BACh8BtOPNPkApjoxi5h%2B%2FFMQQNpWvZaMH7MKFu5Ax8HoCQdmGkJrtnOiLHwD3uS5y8%2F2xTSDrE%2F4PT1yqtt6vGe8ldMBVMEPd6KwqiYECHDlfbvzphcWP%2BJiZuL5swoWQYlS%2Br7Yu5mNUiGD2retxBi9fl6RDGn4Ti9B1oyYy%2BMP5G87D%2FCpRlvdnuy0PY6RC8BzTA40NXqckQ9TaOUDywkYsudxJzPgyDoAWn%2BB6nEFbaVxxC6UXjJiuDkW9TWq7uRBOJocky9iMfUhGpv%2FdQuVVIuGjYqACbXf8aa%2BPeYNIHZsM7l4s5gAQuUAzRUoT51hnH3EWofXf2vkD5HJJ33vwE%2FaEWp36GHr6GpMaH4AAPuqM5eabH%2FhfG9zcCz4nN6cPinuAw6IHwtvyB%2FdO1toZciBaPh25U0ducR2PI3Zl7mokyLWKkSnEDOg1x5fCsJE9EKhH7HwFNhWMGMS7%2BqxyYsbHHRUDUH4I%2FAheQY7wujJNnFUH4KdCju83riuQeHU9WEqNzjsJFuF%2FdTDAZ%2FK7%2F1WaAU%2BAWymT59pVMT4g2AxcwNa0XEBDdBDpAPvgDIH73R25teeuAF5ime2Ul0OUIiG4GpSAEJeYW9wDTf43wfwHgHLKJoPznkwAAAABJRU5ErkJggg%3D%3D)](http://doi.org/10.15131/shef.data.24427516.v2)
 
-Causal testing is a causal inference-driven framework for functional black-box testing. This framework utilises
-graphical causal inference (CI) techniques for the specification and functional testing of software from a black-box
-perspective. In this framework, we use causal directed acyclic graphs (DAGs) to express the anticipated cause-effect
-relationships amongst the inputs and outputs of the system-under-test and the supporting mathematical framework to
-design statistical procedures capable of making causal inferences. Each causal test case focuses on the causal effect of
-an intervention made to the system-under test. That is, a prescribed change to the input configuration of the
-system-under-test that is expected to cause a change to some output(s).
+The Causal Testing Framework is comprised of a :term:`causal inference`-driven architecture designed for functional black-box testing.
+It leverages graphical causal inference (CI) techniques to specify and evaluate software behaviour from a black-box perspective.
+Within this framework, causal directed acyclic graphs (DAGs) are used to represent the expected cause–effect relationships between
+the inputs and outputs of the system under test, supported by mathematical foundations for designing statistical procedures that
+enable causal inference. Each causal test case targets the causal effect of a specific intervention on the system under test--that is,
+a deliberate modification to the input configuration expected to produce a corresponding change in one or more outputs.
 
 ![Causal Testing Workflow](images/schematic-dark.png#gh-dark-mode-only)
 ![Causal Testing Workflow](images/schematic.png#gh-light-mode-only)
@@ -26,9 +25,7 @@ system-under-test that is expected to cause a change to some output(s).
 ## Installation
 
 ### Requirements
-- Python 3.10, 3.11 and 3.12
-
-- Microsoft Visual C++ 14.0+ (Windows only).
+- Python 3.10, 3.11, 3.12 and 3.13
 
 To install the latest stable release of the Causal Testing Framework:
 
@@ -55,7 +52,7 @@ pip install -e . # For editable install, useful for development work
 For more information on how to use the Causal Testing Framework, please refer to our [documentation](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest).  
 
 >[!NOTE]
->We recommend you use a 64 bit OS (standard in most modern machines) as we have had reports of the installation crashing on some 32 bit Debian installations.
+>We recommend you use a 64-bit OS (standard in most modern machines) as we have had reports of the installation crashing on legacy 32-bit Debian systems.
 
 ## Usage
 >[!NOTE]
@@ -86,7 +83,6 @@ The paper citation should be the Causal Testing Framework [paper](https://dl.acm
 and the software citation should contain the specific Figshare [DOI](https://orda.shef.ac.uk/articles/software/CITCOM_Software_Release/24427516) of the version used in your work.
 
 
-
 <details>
   <summary><b>BibTeX Citations</b></summary>
 
@@ -127,20 +123,6 @@ and the software citation should contain the specific Figshare [DOI](https://ord
 
 </details>
 
-## How to Contribute
-
-To contribute to our work, please ensure the following:
-
-1. [Fork the repository](https://help.github.com/articles/fork-a-repo/) into your own GitHub account, and [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) it to your local machine.
-2. [Create a new branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository) in your forked repository. Give this branch an appropriate name, and create commits that describe the changes.
-3. [Push your changes](https://docs.github.com/en/get-started/using-git/pushing-commits-to-a-remote-repository) to your new branch in your remote fork, compare with `CausalTestingFramework/main`, and ensure any conflicts are resolved.
-4. Create a draft [pull request](https://docs.github.com/en/get-started/quickstart/hello-world#opening-a-pull-request) from your branch, and ensure you have [linked](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/autolinked-references-and-urls) it to any relevant issues in your description.
-
-We use the [unittest]() module to develop our tests and the [pytest](https://pytest.org/en/latest/) framework as our test discovery, [pylint](https://pypi.org/project/pylint/) for our code analyser, and [black](https://pypi.org/project/black/) for our code formatting.
-To find the other (optional) developer dependencies, please check `pyproject.toml`.
-
-
-
 ## Acknowledgements
 
 The Causal Testing Framework is supported by the UK's Engineering and Physical Sciences Research Council (EPSRC),
diff --git a/causal_testing/__main__.py b/causal_testing/__main__.py
index bfe3fd1f..4e8bee0f 100644
--- a/causal_testing/__main__.py
+++ b/causal_testing/__main__.py
@@ -4,6 +4,7 @@
 import tempfile
 import json
 import os
+from pathlib import Path
 
 from causal_testing.testing.metamorphic_relation import generate_causal_tests
 from .main import setup_logging, parse_args, CausalTestingPaths, CausalTestingFramework, Command
@@ -68,7 +69,9 @@ def main() -> None:
                 with open(file_path, "r", encoding="utf-8") as f:
                     all_results.extend(json.load(f))
 
-            # Save the final stitched results to your desired location
+            output_path = Path(args.output)
+            output_path.parent.mkdir(parents=True, exist_ok=True)
+
             with open(args.output, "w", encoding="utf-8") as f:
                 json.dump(all_results, f, indent=4)
     else:
diff --git a/causal_testing/main.py b/causal_testing/main.py
index 3cbbf493..1d3f3ccf 100644
--- a/causal_testing/main.py
+++ b/causal_testing/main.py
@@ -418,6 +418,9 @@ def save_results(self, results: List[CausalTestResult], output_path: str = None)
             output_path = self.paths.output_path
         logger.info(f"Saving results to {output_path}")
 
+        # Create parent directory if it doesn't exist
+        Path(output_path).parent.mkdir(parents=True, exist_ok=True)
+
         # Load original test configs to preserve test metadata
         with open(self.paths.test_config_path, "r", encoding="utf-8") as f:
             test_configs = json.load(f)
diff --git a/docs/source/requirements.txt b/docs/source/requirements.txt
index 3f2d7e9a..25212ac5 100644
--- a/docs/source/requirements.txt
+++ b/docs/source/requirements.txt
@@ -1,4 +1,8 @@
 Sphinx==7.2.6
 myst-parser==2.0.0
 sphinx-autoapi==3.0.0
-sphinx-rtd-theme==2.0.0
\ No newline at end of file
+sphinx-rtd-theme==2.0.0
+nbsphinx==0.9.7
+ipykernel==6.30.1
+pandoc==2.4
+sphinxcontrib-mermaid==1.0.0
diff --git a/pyproject.toml b/pyproject.toml
index 9a845844..60359d61 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,16 +11,16 @@ name = "causal_testing_framework"
 authors = [{ name = "The CITCOM team" }]
 description = "A framework for causal testing using causal directed acyclic graphs."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 license = { text = "MIT" }
 keywords = ["causal inference", "verification"]
 dependencies = [
-    "lifelines~=0.29.0",
+    "lifelines~=0.30.0",
     "networkx>=3.4,<3.5",
-    "numpy~=1.26",
+    "numpy>=1.2.6, <=2.2.0",
     "pandas>=2.1",
     "scikit_learn~=1.4",
-    "scipy>=1.12.0,<1.14.0",
+    "scipy>=1.12.0,<=1.16.2",
     "statsmodels~=0.14",
     "tabulate~=0.9",
     "pydot~=2.0",
@@ -29,6 +29,7 @@ dependencies = [
     "sympy~=1.13.1",
     "pyarrow~=19.0.1",
     "fastparquet~=2024.11.0",
+    "tqdm~=4.67.1"
 ]
 dynamic = ["version"]
 
@@ -41,10 +42,14 @@ dev = [
     "black",
     "autoapi",
     "myst-parser",
+    "sphinx",
     "sphinx-autoapi",
     "sphinx_rtd_theme",
-    "tqdm",
+    "nbsphinx",
+    "ipykernel",
+    "pandoc",
 ]
+
 test = [
   "covasim~=3.0.7",
 ]
@@ -75,3 +80,25 @@ minversion = "6.0"
 python_files=[
     "test_*.py",
     "example_*.py"]
+
+[tool.tox]
+requires = ["tox>=4.19"]
+env_list = ["3.10", "3.11", "3.12", "3.13"]
+skip_missing_interpreters = false  # fail if devs don’t have all required Python versions
+
+# Base configuration for all test environments
+[tool.tox.env_run_base]
+description = "Run pytest under {base_python}"
+extras = ["dev", "test"]
+deps = ["pytest"]
+commands = [["pytest"]]
+
+# Automatically test for type-checking (TODO: enable type checking in env_list in the future)
+[tool.tox.env.type]
+description = "Run type checks with mypy on the codebase"
+deps = [
+    "mypy==1.18.2",
+    "types-cachetools>=5.5.0.20240820",
+    "types-chardet>=5.0.4.6"
+]
+commands = [["mypy", "causal_testing"], ["mypy", "tests"]]
\ No newline at end of file

From f68d27b02211c82b1972076b1071ca7a9eb27767 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 17 Oct 2025 10:22:14 +0100
Subject: [PATCH 2/5] Included pre-commit workflow

---
 .pre-commit-config.yaml                       | 39 ++++++++++++
 .pylintrc                                     | 42 +++++++++----
 CONTRIBUTING.md                               | 59 +++++++++++++++----
 README.md                                     |  2 +-
 causal_testing/__main__.py                    |  7 ++-
 .../abstract_regression_estimator.py          |  6 +-
 .../estimation/cubic_spline_estimator.py      |  4 +-
 causal_testing/estimation/effect_estimate.py  |  1 +
 .../estimation/experimental_estimator.py      |  3 +-
 .../genetic_programming_regression_fitter.py  | 12 ++--
 .../instrumental_variable_estimator.py        |  1 +
 causal_testing/estimation/ipcw_estimator.py   |  3 +-
 .../estimation/linear_regression_estimator.py |  6 +-
 .../logistic_regression_estimator.py          |  2 +-
 causal_testing/main.py                        | 18 +++---
 causal_testing/specification/causal_dag.py    |  3 +-
 causal_testing/specification/variable.py      |  1 +
 .../surrogate/causal_surrogate_assisted.py    |  4 +-
 .../surrogate/surrogate_search_algorithms.py  |  3 +-
 causal_testing/testing/base_test_case.py      |  1 +
 causal_testing/testing/causal_effect.py       |  1 +
 .../testing/causal_test_adequacy.py           |  7 ++-
 causal_testing/testing/causal_test_case.py    |  5 +-
 .../testing/metamorphic_relation.py           |  6 +-
 causal_testing/utils/validation.py            |  1 +
 pyproject.toml                                | 10 +---
 26 files changed, 170 insertions(+), 77 deletions(-)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..26c772d4
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,39 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  # Black
+  - repo: https://github.com/psf/black
+    rev: 25.9.0
+    hooks:
+      - id: black
+        args: ['--line-length=120', '--target-version=py310']
+        files: ^causal_testing/
+
+  # isort
+  - repo: https://github.com/pycqa/isort
+    rev: 7.0.0
+    hooks:
+      - id: isort
+        args: ['--profile', 'black', '--line-length', '120']
+        files: ^causal_testing/
+
+  # Pylint
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args: ['--max-line-length=120', '--max-positional-arguments=12']
+        files: ^causal_testing/
diff --git a/.pylintrc b/.pylintrc
index 4ab81c8c..ddb6341a 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -82,14 +82,15 @@ persistent=yes
 
 # Minimum Python version to use for version dependent checks. Will default to
 # the version used to run pylint.
-py-version=3.9
+py-version=3.10
 
 # Discover python modules and packages in the file system subtree.
 recursive=no
 
 # When enabled, pylint would attempt to guess common misconfiguration and emit
 # user-friendly hints instead of false-positive error messages.
-suggestion-mode=yes
+# REMOVED: suggestion-mode is deprecated and not recognized in newer versions
+# suggestion-mode=yes
 
 # Allow loading of arbitrary C extensions. Extensions are imported into the
 # active Python interpreter and may run arbitrary code.
@@ -154,6 +155,9 @@ disable=raw-checker-failed,
         use-symbolic-message-instead,
         logging-fstring-interpolation,
         import-error,
+        too-many-positional-arguments,
+        unbalanced-tuple-unpacking,
+        possibly-used-before-assignment,
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
@@ -244,7 +248,14 @@ good-names=i,
            df,
            Run,
            z3,
-           _
+           _,
+           x,
+           y,
+           z,
+           e,
+           ax,
+           fig,
+           id
 
 # Good variable names regexes, separated by a comma. If names match any regex,
 # they will always be accepted
@@ -338,10 +349,10 @@ exclude-too-few-public-methods=
 ignored-parents=
 
 # Maximum number of arguments for function / method.
-max-args=5
+max-args=12
 
 # Maximum number of attributes for a class (see R0902).
-max-attributes=7
+max-attributes=10
 
 # Maximum number of boolean expressions in an if statement (see R0916).
 max-bool-expr=5
@@ -350,22 +361,22 @@ max-bool-expr=5
 max-branches=12
 
 # Maximum number of locals for function / method body.
-max-locals=15
+max-locals=20
 
 # Maximum number of parents for a class (see R0901).
 max-parents=7
 
 # Maximum number of public methods for a class (see R0904).
-max-public-methods=20
+max-public-methods=25
 
 # Maximum number of return / yield for function / method body.
 max-returns=6
 
 # Maximum number of statements in function / method body.
-max-statements=50
+max-statements=60
 
 # Minimum number of public methods for a class (see R0903).
-min-public-methods=2
+min-public-methods=1
 
 
 [EXCEPTIONS]
@@ -394,7 +405,7 @@ indent-string='    '
 max-line-length=120
 
 # Maximum number of lines in a module.
-max-module-lines=1000
+max-module-lines=1500
 
 # Allow the body of a class to be on the same line as the declaration if body
 # contains single statement.
@@ -538,7 +549,11 @@ contextmanager-decorators=contextlib.contextmanager
 # List of members which are set dynamically and missed by pylint inference
 # system, and so shouldn't trigger E1101 when accessed. Python regular
 # expressions are accepted.
-generated-members=
+generated-members=deap.creator.*,
+                  deap.tools.*,
+                  networkx.graphml,
+                  networkx.*,
+                  deap.base.Toolbox.*,
 
 # Tells whether to warn about missing members when the owner of the attribute
 # is inferred to be None.
@@ -561,7 +576,7 @@ ignored-checks-for-mixins=no-member,
 # List of class names for which member attributes should not be checked (useful
 # for classes with dynamically set attributes). This supports the use of
 # qualified names.
-ignored-classes=optparse.Values,thread._local,_thread._local,argparse.Namespace
+ignored-classes=optparse.Values,thread._local,_thread._local,argparse.Namespace,deap.creator,deap.base.Toolbox
 
 # Show a hint with possible names when a member name was not found. The aspect
 # of finding the hint is based on edit distance.
@@ -613,3 +628,6 @@ init-import=no
 # List of qualified module names which can have objects that can redefine
 # builtins.
 redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io
+
+[causal_testing.specification.causal_dag]
+disable=no-member
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 9862f4fc..60315106 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -6,7 +6,7 @@ Please ask any questions about the Causal Testing Framework or surrounding conce
 discussion, please see whether a relevant one already exists - someone may have answered your question already.
 
 ### Reporting Bugs and Making Suggestions
-Upon identifying any bugs or features that could be improved, please open an 
+Upon identifying any bugs or features that could be improved, please open an
 [issue](https://github.com/CITCOM-project/CausalTestingFramework/issues) and label with bug or feature suggestion. Every issue
 should clearly explain the bug or feature to be improved and, where necessary, instructions to replicate. We also
 provide templates for each scenario when creating an issue.
@@ -18,7 +18,7 @@ To contribute to our work, please ensure the following:
 2. [Create a new branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository) in your forked repository. Give this branch an appropriate name, and create commits that describe the changes.
 3. [Push your changes](https://docs.github.com/en/get-started/using-git/pushing-commits-to-a-remote-repository) to your new branch in your remote fork, compare with `CausalTestingFramework/main`, and ensure any conflicts are resolved.
 4. Create a draft [pull request](https://docs.github.com/en/get-started/quickstart/hello-world#opening-a-pull-request) from your branch, and ensure you have [linked](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/autolinked-references-and-urls) it to any relevant issues in your description.
-     
+
 ### Continuous Integration (CI) and Code Quality
 Our CI/CD tests include:
     - Build: Install the necessary Python and runtime dependencies.
@@ -28,30 +28,65 @@ Our CI/CD tests include:
 
 To find the other (optional) developer dependencies, please check `pyproject.toml`.
 
+### Pre-commit Hooks
+We use [pre-commit](https://pre-commit.com/) to automatically run code quality checks before each commit. This ensures consistent code style and catches issues early.
+
+Automated checks include:
+
+- Trailing whitespace removal.
+- End-of-file fixing.
+- YAML and TOML validation.
+- Black formatting.
+- isort import sorting.
+- Pylint code analysis.
+
+To use pre-commit:
+```bash
+# Install pre-commit hooks (one-time setup of .pre-commit-config.yaml)
+pre-commit install
+
+# Manually run hooks on all files (optional)
+pre-commit run --all-files
+```
+
 ### Coding Style
 In the Causal Testing Framework, we aim to provide highly reusable and easily maintainable packages. To this end,
 we ask contributors to stick to the following guidelines:
 1. Make small and frequent changes rather than verbose and infrequent changes.
 2. Favour readable and informative variable, method, and class names over concise names.
 3. Use logging instead of print.
-4. For every method and class, include detailed docstrings following the 
+4. For every method and class, include detailed docstrings following the
    [reStructuredText/Sphinx](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html) guidelines.
 5. Add credit and license information where existing code has been used (in the method or class docstring).
 6. If a method implements a specific algorithm/technique from a paper, add a citation to the docstring.
 7. Use [variable](https://www.python.org/dev/peps/pep-0008/#variable-annotations) and [function](https://www.python.org/dev/peps/pep-0008/#function-annotations)
    annotations.
 8. All methods should be thoroughly tested with PyTest (see [Testing]() below).
-9. Optionally run `autopep8 causal_testing` to prevent linter errors.
-10. Optionally run `isort causal_testing` to ensure imports are done in the right order (this will also help prevent linter errors).
-11. Format code using `black causal_testing`.
-12. Linting code using `pylint causal_testing` is advised.
+9. Code formatting and linting is handled automatically by pre-commit hooks (see above).
+
+### Manual Code Quality Checks (Optional)
+While pre-commit handles most formatting automatically, you can run these commands manually if needed:
+
+```bash
+# Format code
+black causal_testing
+
+# Sort imports
+isort causal_testing
+
+# Run linter
+pylint causal_testing
+
+# Run tests
+pytest
+```
 
 ### Compatibility Testing Across Python Versions with tox
 
-For compatibility testing Python versions, we use [tox](https://pypi.org/project/tox/) to automate 
+For compatibility testing Python versions, we use [tox](https://pypi.org/project/tox/) to automate
 testing across all supported Python versions (3.10, 3.11, 3.12, and 3.13):
 
-- **Install tox**: `pip install tox`.
-- **Test all versions**: `tox` (runs tests on all Python versions + linting in the root folder).
-- **Test specific version**: `tox -e py313` (or py310, py311, py312).
-- **Quick iteration**: Use `pytest` directly for fast testing during development.
\ No newline at end of file
+- Install tox: `pip install tox`.
+- Test all versions: `tox` (runs tests on all Python versions + linting in the root folder).
+- Test specific version: `tox -e py313` (or py310, py311, py312).
+- Quick iteration: Use `pytest` directly for fast testing during development.
diff --git a/README.md b/README.md
index 80639e67..545dfb8f 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,7 @@ git checkout tags/<tag> -b <branch>
 pip install . # For core API only
 pip install -e . # For editable install, useful for development work
 ```
-For more information on how to use the Causal Testing Framework, please refer to our [documentation](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest).  
+For more information on how to use the Causal Testing Framework, please refer to our [documentation](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest).
 
 >[!NOTE]
 >We recommend you use a 64-bit OS (standard in most modern machines) as we have had reports of the installation crashing on legacy 32-bit Debian systems.
diff --git a/causal_testing/__main__.py b/causal_testing/__main__.py
index 4e8bee0f..77bb11a2 100644
--- a/causal_testing/__main__.py
+++ b/causal_testing/__main__.py
@@ -1,13 +1,14 @@
 """This module contains the main entrypoint functionality to the Causal Testing Framework."""
 
-import logging
-import tempfile
 import json
+import logging
 import os
+import tempfile
 from pathlib import Path
 
 from causal_testing.testing.metamorphic_relation import generate_causal_tests
-from .main import setup_logging, parse_args, CausalTestingPaths, CausalTestingFramework, Command
+
+from .main import CausalTestingFramework, CausalTestingPaths, Command, parse_args, setup_logging
 
 
 def main() -> None:
diff --git a/causal_testing/estimation/abstract_regression_estimator.py b/causal_testing/estimation/abstract_regression_estimator.py
index 53597a0f..e0bdb8b9 100644
--- a/causal_testing/estimation/abstract_regression_estimator.py
+++ b/causal_testing/estimation/abstract_regression_estimator.py
@@ -1,15 +1,15 @@
 """This module contains the RegressionEstimator, which is an abstract class for concrete regression estimators."""
 
 import logging
-from typing import Any
 from abc import abstractmethod
+from typing import Any
 
 import pandas as pd
-from statsmodels.regression.linear_model import RegressionResultsWrapper
 from patsy import dmatrix  # pylint: disable = no-name-in-module
+from statsmodels.regression.linear_model import RegressionResultsWrapper
 
-from causal_testing.specification.variable import Variable
 from causal_testing.estimation.abstract_estimator import Estimator
+from causal_testing.specification.variable import Variable
 from causal_testing.testing.base_test_case import BaseTestCase
 
 logger = logging.getLogger(__name__)
diff --git a/causal_testing/estimation/cubic_spline_estimator.py b/causal_testing/estimation/cubic_spline_estimator.py
index 2fec6496..1b7d8607 100644
--- a/causal_testing/estimation/cubic_spline_estimator.py
+++ b/causal_testing/estimation/cubic_spline_estimator.py
@@ -6,9 +6,9 @@
 
 import pandas as pd
 
-from causal_testing.specification.variable import Variable
-from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
 from causal_testing.estimation.effect_estimate import EffectEstimate
+from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
+from causal_testing.specification.variable import Variable
 from causal_testing.testing.base_test_case import BaseTestCase
 
 logger = logging.getLogger(__name__)
diff --git a/causal_testing/estimation/effect_estimate.py b/causal_testing/estimation/effect_estimate.py
index ad89abd3..865ecd61 100644
--- a/causal_testing/estimation/effect_estimate.py
+++ b/causal_testing/estimation/effect_estimate.py
@@ -3,6 +3,7 @@
 """
 
 from dataclasses import dataclass
+
 import pandas as pd
 
 
diff --git a/causal_testing/estimation/experimental_estimator.py b/causal_testing/estimation/experimental_estimator.py
index e94959d0..f8ed77a8 100644
--- a/causal_testing/estimation/experimental_estimator.py
+++ b/causal_testing/estimation/experimental_estimator.py
@@ -1,7 +1,8 @@
 """This module contains the ExperimentalEstimator class for directly interacting with the system under test."""
 
-from typing import Any
 from abc import abstractmethod
+from typing import Any
+
 import pandas as pd
 
 from causal_testing.estimation.abstract_estimator import Estimator
diff --git a/causal_testing/estimation/genetic_programming_regression_fitter.py b/causal_testing/estimation/genetic_programming_regression_fitter.py
index b8a52e8d..782dbc68 100644
--- a/causal_testing/estimation/genetic_programming_regression_fitter.py
+++ b/causal_testing/estimation/genetic_programming_regression_fitter.py
@@ -4,20 +4,18 @@
 """
 
 import copy
+import random
 from inspect import isclass
 from operator import add, mul
-import random
 
-import patsy
 import numpy as np
 import pandas as pd
-import statsmodels.formula.api as smf
+import patsy
 import statsmodels
+import statsmodels.formula.api as smf
 import sympy
-
-from deap import base, creator, tools, gp
-
-from numpy import power, log
+from deap import base, creator, gp, tools
+from numpy import log, power
 
 
 def reciprocal(x: float) -> float:
diff --git a/causal_testing/estimation/instrumental_variable_estimator.py b/causal_testing/estimation/instrumental_variable_estimator.py
index 2b5eaf2d..c7775363 100644
--- a/causal_testing/estimation/instrumental_variable_estimator.py
+++ b/causal_testing/estimation/instrumental_variable_estimator.py
@@ -3,6 +3,7 @@
 
 import logging
 from math import ceil
+
 import pandas as pd
 import statsmodels.api as sm
 
diff --git a/causal_testing/estimation/ipcw_estimator.py b/causal_testing/estimation/ipcw_estimator.py
index ab038df1..1e4040a0 100644
--- a/causal_testing/estimation/ipcw_estimator.py
+++ b/causal_testing/estimation/ipcw_estimator.py
@@ -4,7 +4,6 @@
 from typing import Any
 from uuid import uuid4
 
-
 import numpy as np
 import pandas as pd
 import statsmodels.formula.api as smf
@@ -12,8 +11,8 @@
 
 from causal_testing.estimation.abstract_estimator import Estimator
 from causal_testing.estimation.effect_estimate import EffectEstimate
-from causal_testing.testing.base_test_case import BaseTestCase
 from causal_testing.specification.variable import Variable
+from causal_testing.testing.base_test_case import BaseTestCase
 
 logger = logging.getLogger(__name__)
 
diff --git a/causal_testing/estimation/linear_regression_estimator.py b/causal_testing/estimation/linear_regression_estimator.py
index fcc1d8ae..7869c4de 100644
--- a/causal_testing/estimation/linear_regression_estimator.py
+++ b/causal_testing/estimation/linear_regression_estimator.py
@@ -5,12 +5,12 @@
 
 import pandas as pd
 import statsmodels.formula.api as smf
-from patsy import dmatrix, ModelDesc  # pylint: disable = no-name-in-module
+from patsy import ModelDesc, dmatrix  # pylint: disable = no-name-in-module
 
-from causal_testing.specification.variable import Variable
-from causal_testing.estimation.genetic_programming_regression_fitter import GP
 from causal_testing.estimation.abstract_regression_estimator import RegressionEstimator
 from causal_testing.estimation.effect_estimate import EffectEstimate
+from causal_testing.estimation.genetic_programming_regression_fitter import GP
+from causal_testing.specification.variable import Variable
 from causal_testing.testing.base_test_case import BaseTestCase
 
 logger = logging.getLogger(__name__)
diff --git a/causal_testing/estimation/logistic_regression_estimator.py b/causal_testing/estimation/logistic_regression_estimator.py
index f4f14725..bd95b35f 100644
--- a/causal_testing/estimation/logistic_regression_estimator.py
+++ b/causal_testing/estimation/logistic_regression_estimator.py
@@ -6,8 +6,8 @@
 import pandas as pd
 import statsmodels.formula.api as smf
 
-from causal_testing.estimation.effect_estimate import EffectEstimate
 from causal_testing.estimation.abstract_regression_estimator import RegressionEstimator
+from causal_testing.estimation.effect_estimate import EffectEstimate
 
 logger = logging.getLogger(__name__)
 
diff --git a/causal_testing/main.py b/causal_testing/main.py
index 1d3f3ccf..be2b0dc6 100644
--- a/causal_testing/main.py
+++ b/causal_testing/main.py
@@ -3,25 +3,25 @@
 import argparse
 import json
 import logging
-from enum import Enum
 from dataclasses import dataclass
+from enum import Enum
 from pathlib import Path
-from typing import Dict, Any, Optional, List, Union, Sequence
+from typing import Any, Dict, List, Optional, Sequence, Union
 
-from tqdm import tqdm
-import pandas as pd
 import numpy as np
+import pandas as pd
+from tqdm import tqdm
 
+from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
+from causal_testing.estimation.logistic_regression_estimator import LogisticRegressionEstimator
 from causal_testing.specification.causal_dag import CausalDAG
+from causal_testing.specification.causal_specification import CausalSpecification
 from causal_testing.specification.scenario import Scenario
 from causal_testing.specification.variable import Input, Output
-from causal_testing.specification.causal_specification import CausalSpecification
-from causal_testing.testing.causal_test_case import CausalTestCase
 from causal_testing.testing.base_test_case import BaseTestCase
-from causal_testing.testing.causal_effect import NoEffect, SomeEffect, Positive, Negative
+from causal_testing.testing.causal_effect import Negative, NoEffect, Positive, SomeEffect
+from causal_testing.testing.causal_test_case import CausalTestCase
 from causal_testing.testing.causal_test_result import CausalTestResult
-from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
-from causal_testing.estimation.logistic_regression_estimator import LogisticRegressionEstimator
 
 logger = logging.getLogger(__name__)
 
diff --git a/causal_testing/specification/causal_dag.py b/causal_testing/specification/causal_dag.py
index 42327051..e2692f9b 100644
--- a/causal_testing/specification/causal_dag.py
+++ b/causal_testing/specification/causal_dag.py
@@ -4,7 +4,7 @@
 
 import logging
 from itertools import combinations
-from typing import Union, Set, Generator
+from typing import Generator, Set, Union
 
 import networkx as nx
 
@@ -13,7 +13,6 @@
 from .scenario import Scenario
 from .variable import Output
 
-
 Node = Union[str, int]  # Node type hint: A node is a string or an int
 
 logger = logging.getLogger(__name__)
diff --git a/causal_testing/specification/variable.py b/causal_testing/specification/variable.py
index 3642ea83..4fb27b13 100644
--- a/causal_testing/specification/variable.py
+++ b/causal_testing/specification/variable.py
@@ -1,6 +1,7 @@
 """This module contains the Variable abstract class, as well as its concrete extensions: Input, Output and Meta."""
 
 from __future__ import annotations
+
 from abc import ABC
 from collections.abc import Callable
 from typing import TypeVar
diff --git a/causal_testing/surrogate/causal_surrogate_assisted.py b/causal_testing/surrogate/causal_surrogate_assisted.py
index 8a97d2cf..1a3911dc 100644
--- a/causal_testing/surrogate/causal_surrogate_assisted.py
+++ b/causal_testing/surrogate/causal_surrogate_assisted.py
@@ -3,10 +3,12 @@
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from typing import Callable
+
 import pandas as pd
+
+from causal_testing.estimation.cubic_spline_estimator import CubicSplineRegressionEstimator
 from causal_testing.specification.causal_specification import CausalSpecification
 from causal_testing.testing.base_test_case import BaseTestCase
-from causal_testing.estimation.cubic_spline_estimator import CubicSplineRegressionEstimator
 
 
 @dataclass
diff --git a/causal_testing/surrogate/surrogate_search_algorithms.py b/causal_testing/surrogate/surrogate_search_algorithms.py
index 19e2e8f0..3b2c14ba 100644
--- a/causal_testing/surrogate/surrogate_search_algorithms.py
+++ b/causal_testing/surrogate/surrogate_search_algorithms.py
@@ -3,10 +3,11 @@
 # Fitness functions are required to be iteratively defined, including all variables within.
 
 from operator import itemgetter
+
 from pygad import GA
 
-from causal_testing.specification.causal_specification import CausalSpecification
 from causal_testing.estimation.cubic_spline_estimator import CubicSplineRegressionEstimator
+from causal_testing.specification.causal_specification import CausalSpecification
 from causal_testing.surrogate.causal_surrogate_assisted import SearchAlgorithm
 
 
diff --git a/causal_testing/testing/base_test_case.py b/causal_testing/testing/base_test_case.py
index 8838b932..aca1b376 100644
--- a/causal_testing/testing/base_test_case.py
+++ b/causal_testing/testing/base_test_case.py
@@ -1,6 +1,7 @@
 """This module contains the BaseTestCase dataclass, which stores the information required for identification"""
 
 from dataclasses import dataclass
+
 from causal_testing.specification.variable import Variable
 from causal_testing.testing.effect import Effect
 
diff --git a/causal_testing/testing/causal_effect.py b/causal_testing/testing/causal_effect.py
index 9d6a4c09..8ca60154 100644
--- a/causal_testing/testing/causal_effect.py
+++ b/causal_testing/testing/causal_effect.py
@@ -4,6 +4,7 @@
 
 from abc import ABC, abstractmethod
 from collections.abc import Iterable
+
 import numpy as np
 
 from causal_testing.testing.causal_test_result import CausalTestResult
diff --git a/causal_testing/testing/causal_test_adequacy.py b/causal_testing/testing/causal_test_adequacy.py
index fcbc8f00..f64d1dea 100644
--- a/causal_testing/testing/causal_test_adequacy.py
+++ b/causal_testing/testing/causal_test_adequacy.py
@@ -3,14 +3,15 @@
 """
 
 import logging
-from itertools import combinations
 from copy import deepcopy
+from itertools import combinations
+
 import pandas as pd
-from numpy.linalg import LinAlgError
 from lifelines.exceptions import ConvergenceError
+from numpy.linalg import LinAlgError
 
-from causal_testing.specification.causal_dag import CausalDAG
 from causal_testing.estimation.abstract_estimator import Estimator
+from causal_testing.specification.causal_dag import CausalDAG
 from causal_testing.testing.causal_test_case import CausalTestCase
 
 logger = logging.getLogger(__name__)
diff --git a/causal_testing/testing/causal_test_case.py b/causal_testing/testing/causal_test_case.py
index 08895b76..0b75ea12 100644
--- a/causal_testing/testing/causal_test_case.py
+++ b/causal_testing/testing/causal_test_case.py
@@ -2,12 +2,11 @@
 
 import logging
 
-from causal_testing.testing.causal_effect import CausalEffect
-from causal_testing.testing.base_test_case import BaseTestCase
 from causal_testing.estimation.abstract_estimator import Estimator
+from causal_testing.testing.base_test_case import BaseTestCase
+from causal_testing.testing.causal_effect import CausalEffect
 from causal_testing.testing.causal_test_result import CausalTestResult
 
-
 logger = logging.getLogger(__name__)
 
 
diff --git a/causal_testing/testing/metamorphic_relation.py b/causal_testing/testing/metamorphic_relation.py
index 5d20e3e2..09eaac86 100644
--- a/causal_testing/testing/metamorphic_relation.py
+++ b/causal_testing/testing/metamorphic_relation.py
@@ -3,12 +3,12 @@
 defined in our ICST paper [https://eprints.whiterose.ac.uk/195317/].
 """
 
+import json
+import logging
 from dataclasses import dataclass
-from typing import Iterable
 from itertools import combinations
-import logging
-import json
 from multiprocessing import Pool
+from typing import Iterable
 
 import networkx as nx
 
diff --git a/causal_testing/utils/validation.py b/causal_testing/utils/validation.py
index 63df5dc3..2fd0bb66 100644
--- a/causal_testing/utils/validation.py
+++ b/causal_testing/utils/validation.py
@@ -1,6 +1,7 @@
 """This module contains the CausalValidator class for performing Quantitive Bias Analysis techniques"""
 
 import math
+
 import numpy as np
 from scipy.stats import t
 from statsmodels.regression.linear_model import RegressionResultsWrapper
diff --git a/pyproject.toml b/pyproject.toml
index 60359d61..42ae59c3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,7 +35,6 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "autopep8",
     "isort",
     "pytest",
     "pylint",
@@ -48,6 +47,7 @@ dev = [
     "nbsphinx",
     "ipykernel",
     "pandoc",
+    "pre-commit"
 ]
 
 test = [
@@ -69,12 +69,6 @@ find = {}
 line-length = 120
 target-version = ["py310"]
 
-[tool.autopep8]
-max_line_length = 120
-in-place = true
-recursive = true
-aggressive = 3
-
 [tool.pytest.ini_options]
 minversion = "6.0"
 python_files=[
@@ -101,4 +95,4 @@ deps = [
     "types-cachetools>=5.5.0.20240820",
     "types-chardet>=5.0.4.6"
 ]
-commands = [["mypy", "causal_testing"], ["mypy", "tests"]]
\ No newline at end of file
+commands = [["mypy", "causal_testing"], ["mypy", "tests"]]

From b466100a6e018cb2b8ee9467f07aea8e34aee587 Mon Sep 17 00:00:00 2001
From: Farhad Allian <39086289+f-allian@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:19:23 +0100
Subject: [PATCH 3/5] Update README.md

Co-authored-by: Michael Foster <13611658+jmafoster1@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 545dfb8f..8c4c0634 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.07739/status.svg)](https://doi.org/10.21105/joss.07739)
 [![DOI](https://img.shields.io/badge/doi-10.26180/5c6e1160b8d8a-blue.svg?style=flat&labelColor=whitesmoke&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAB8AAAAfCAYAAAAfrhY5AAAJsklEQVR42qWXd1DTaRrHf%2BiB2Hdt5zhrAUKz4IKEYu9IGiGFFJJQ0gkJCAKiWFDWBRdFhCQUF3UVdeVcRQEBxUI3yY9iEnQHb3bdW1fPubnyz%2F11M7lvEHfOQee2ZOYzPyDv%2B3yf9%2Fk95YX4fx%2BltfUt08GcFEuPR4U9hDDZ%2FVngIlhb%2FSiI6InkTgLzgDcgfvtnovhH4BzoVlrbwr55QnhCtBW4QHXnFrZbPBaQoBh4%2FSYH2EnpBEtqcDMVzB93wA%2F8AFwa23XFGcc8CkT3mxz%2BfXWtq9T9IQlLIXYEuHojudb%2BCM7Hgdq8ydi%2FAHiBXyY%2BLjwFlAEnS6Jnar%2FvnQVhvdzasad0eKvWZKe8hvDB2ofLZ%2FZEcWsh%2BhyIuyO5Bxs2iZIE4nRv7NWAb0EO8AC%2FWPxjYAWuOEX2MSXZVgPxzmRL3xKz3ScGpx6p6QnOx4mDIFqO0w6Q4fEhO5IzwxlSwyD2FYHzwAW%2BAZ4fEsf74gCumykwNHskLM7taQxLYjjIyy8MUtraGhTWdkfhkFJqtvuVl%2F9l2ZquDfEyrH8B0W06nnpH3JtIyRGpH1iJ6SfxDIHjRXHJmdQjLpfHeN54gnfFx4W9QRnovx%2FN20aXZeTD2J84hn3%2BqoF2Tqr14VqTPUCIcP%2B5%2Fly4qC%2BUL3sYxSvNj1NwsVYPsWdMUfomsdkYm3Tj0nbV0N1wRKwFe1MgKACDIBdMAhPE%2FwicwNWxll8Ag40w%2BFfhibJkGHmutjYeQ8gVlaN%2BjO51nDysa9TwNUFMqaGbKdRJZFfOJSp6mkRKsv0rRIpEVWjAvyFkxNOEpwvcAVPfEe%2Bl8ojeNTx3nXLBcWRrYGxSRjDEk0VlpxYrbe1ZmaQ5xuT0u3r%2B2qe5j0J5uytiZPGsRL2Jm32AldpxPUNJ3jmmsN4x62z1cXrbedXBQf2yvIFCeZrtyicZZG2U2nrrBJzYorI2EXLrvTfCSB43s41PKEvbZDEfQby6L4JTj%2FfIwam%2B4%2BwucBu%2BDgNK05Nle1rSt9HvR%2FKPC4U6LTfvUIaip1mjIa8fPzykii23h2eanT57zQ7fsyYH5QjywwlooAUcAdOh5QumgTHx6aAO7%2FL52eaQNEShrxfhL6albEDmfhGflrsT4tps8gTHNOJbeDeBlt0WJWDHSgxs6cW6lQqyg1FpD5ZVDfhn1HYFF1y4Eiaqa18pQf3zzYMBhcanlBjYfgWNayAf%2FASOgklu8bmgD7hADrk4cRlOL7NSOewEcbqSmaivT33QuFdHXj5sdvjlN5yMDrAECmdgDWG2L8P%2BAKLs9ZLZ7dJda%2BB4Xl84t7QvnKfvpXJv9obz2KgK8dXyqISyV0sXGZ0U47hOA%2FAiigbEMECJxC9aoKp86re5O5prxOlHkcksutSQJzxZRlPZmrOKhsQBF5zEZKybUC0vVjG8PqOnhOq46qyDTDnj5gZBriWCk4DvXrudQnXQmnXblebhAC2cCB6zIbM4PYgGl0elPSgIf3iFEA21aLdHYLHUQuVkpgi02SxFdrG862Y8ymYGMvXDzUmiX8DS5vKZyZlGmsSgQqfLub5RyLNS4zfDiZc9Edzh%2FtCE%2BX8j9k%2FqWB071rcZyMImne1SLkL4GRw4UPHMV3jjwEYpPG5uW5fAEot0aTSJnsGAwHJi2nvF1Y5OIqWziVCQd5NT7t6Q8guOSpgS%2Fa1dSRn8JGGaCD3BPXDyQRG4Bqhu8XrgAp0yy8DMSvvyVXDgJcJTcr1wQ2BvFKf65jqhvmxXUuDpGBlRvV36XvGjQzLi8KAKT2lYOnmxQPGorURSV0NhyTIuIyqOmKTMhQ%2BieEsgOgpc4KBbfDM4B3SIgFljvfHF6cef7qpyLBXAiQcXvg5l3Iunp%2FWv4dH6qFziO%2BL9PbrimQ9RY6MQphEfGUpOmma7KkGzuS8sPUFnCtIYcKCaI9EXo4HlQLgGrBjbiK5EqMj2AKWt9QWcIFMtnVvQVDQV9lXJJqdPVtUQpbh6gCI2Ov1nvZts7yYdsnvRgxiWFOtNJcOMVLn1vgptVi6qrNiFOfEjHCDB3J%2BHDLqUB77YgQGwX%2Fb1eYna3hGKdlqJKIyiE4nSbV8VFgxmxR4b5mVkkeUhMgs5YTi4ja2XZ009xJRHdkfwMi%2BfocaancuO7h%2FMlcLOa0V%2FSw6Dq47CumRQAKhgbOP8t%2BMTjuxjJGhXCY6XpmDDFqWlVYbQ1aDJ5Cptdw4oLbf3Ck%2BdWkVP0LpH7s9XLPXI%2FQX8ws%2Bj2In63IcRvOOo%2BTTjiN%2BlssfRsanW%2B3REVKoavBOAPTXABW4AL7e4NygHdpAKBscmlDh9Jysp4wxbnUNna3L3xBvyE1jyrGIkUHaqQMuxhHElV6oj1picvgL1QEuS5PyZTEaivqh5vUCKJqOuIgPFGESns8kyFk7%2FDxyima3cYxi%2FYOQCj%2F%2B9Ms2Ll%2Bhn4FmKnl7JkGXQGDKDAz9rUGL1TIlBpuJr9Be2JjK6qPzyDg495UxXYF7JY1qKimw9jWjF0iV6DRIqE%2B%2FeWG0J2ofmZTk0mLYVd4GLiFCOoKR0Cg727tWq981InYynvCuKW43aXgEjofVbxIqrm0VL76zlH3gQzWP3R3Bv9oXxclrlO7VVtgBRpSP4hMFWJ8BrUSBCJXC07l40X4jWuvtc42ofNCxtlX2JH6bdeojXgTh5TxOBKEyY5wvBE%2BACh8BtOPNPkApjoxi5h%2B%2FFMQQNpWvZaMH7MKFu5Ax8HoCQdmGkJrtnOiLHwD3uS5y8%2F2xTSDrE%2F4PT1yqtt6vGe8ldMBVMEPd6KwqiYECHDlfbvzphcWP%2BJiZuL5swoWQYlS%2Br7Yu5mNUiGD2retxBi9fl6RDGn4Ti9B1oyYy%2BMP5G87D%2FCpRlvdnuy0PY6RC8BzTA40NXqckQ9TaOUDywkYsudxJzPgyDoAWn%2BB6nEFbaVxxC6UXjJiuDkW9TWq7uRBOJocky9iMfUhGpv%2FdQuVVIuGjYqACbXf8aa%2BPeYNIHZsM7l4s5gAQuUAzRUoT51hnH3EWofXf2vkD5HJJ33vwE%2FaEWp36GHr6GpMaH4AAPuqM5eabH%2FhfG9zcCz4nN6cPinuAw6IHwtvyB%2FdO1toZciBaPh25U0ducR2PI3Zl7mokyLWKkSnEDOg1x5fCsJE9EKhH7HwFNhWMGMS7%2BqxyYsbHHRUDUH4I%2FAheQY7wujJNnFUH4KdCju83riuQeHU9WEqNzjsJFuF%2FdTDAZ%2FK7%2F1WaAU%2BAWymT59pVMT4g2AxcwNa0XEBDdBDpAPvgDIH73R25teeuAF5ime2Ul0OUIiG4GpSAEJeYW9wDTf43wfwHgHLKJoPznkwAAAABJRU5ErkJggg%3D%3D)](http://doi.org/10.15131/shef.data.24427516.v2)
 
-The Causal Testing Framework is comprised of a :term:`causal inference`-driven architecture designed for functional black-box testing.
+The Causal Testing Framework is composed of a :term:`causal inference`-driven architecture designed for functional black-box testing.
 It leverages graphical causal inference (CI) techniques to specify and evaluate software behaviour from a black-box perspective.
 Within this framework, causal directed acyclic graphs (DAGs) are used to represent the expected cause–effect relationships between
 the inputs and outputs of the system under test, supported by mathematical foundations for designing statistical procedures that

From 268f35f10e8448433b522eb17fafbcb31fa27af1 Mon Sep 17 00:00:00 2001
From: Farhad Allian <39086289+f-allian@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:19:35 +0100
Subject: [PATCH 4/5] Update CONTRIBUTING.md

Co-authored-by: Michael Foster <13611658+jmafoster1@users.noreply.github.com>
---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 60315106..ceaf96a0 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ discussion, please see whether a relevant one already exists - someone may have
 Upon identifying any bugs or features that could be improved, please open an
 [issue](https://github.com/CITCOM-project/CausalTestingFramework/issues) and label with bug or feature suggestion. Every issue
 should clearly explain the bug or feature to be improved and, where necessary, instructions to replicate. We also
-provide templates for each scenario when creating an issue.
+provide templates for common scenarios when creating an issue.
 
 ### Contributing to the Codebase
 To contribute to our work, please ensure the following:

From 638c92c6ef003f4d42d92141a51958d1f5bb8470 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 17 Oct 2025 11:30:50 +0100
Subject: [PATCH 5/5] Fixes to PR suggestions

---
 .pre-commit-config.yaml | 1 +
 pyproject.toml          | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 26c772d4..c048887f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,6 +10,7 @@ repos:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
+        files: \.py$
 
   # Black
   - repo: https://github.com/psf/black
diff --git a/pyproject.toml b/pyproject.toml
index 42ae59c3..63b1f8bb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,6 +69,10 @@ find = {}
 line-length = 120
 target-version = ["py310"]
 
+[tool.isort]
+profile = "black"
+line_length = 120
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 python_files=[