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/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..c048887f
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,40 @@
+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
+        files: \.py$
+
+  # 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/.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..ceaf96a0
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,92 @@
+# 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 common scenarios 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`.
+
+### 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
+   [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. 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
+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.
diff --git a/README.md b/README.md
index 5d31817c..8c4c0634 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 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
+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:
 
@@ -52,10 +49,10 @@ 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 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..77bb11a2 100644
--- a/causal_testing/__main__.py
+++ b/causal_testing/__main__.py
@@ -1,12 +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:
@@ -68,7 +70,9 @@ 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/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 3cbbf493..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__)
 
@@ -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/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/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..63b1f8bb 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",
@@ -29,22 +29,27 @@ dependencies = [
     "sympy~=1.13.1",
     "pyarrow~=19.0.1",
     "fastparquet~=2024.11.0",
+    "tqdm~=4.67.1"
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "autopep8",
     "isort",
     "pytest",
     "pylint",
     "black",
     "autoapi",
     "myst-parser",
+    "sphinx",
     "sphinx-autoapi",
     "sphinx_rtd_theme",
-    "tqdm",
+    "nbsphinx",
+    "ipykernel",
+    "pandoc",
+    "pre-commit"
 ]
+
 test = [
   "covasim~=3.0.7",
 ]
@@ -64,14 +69,34 @@ find = {}
 line-length = 120
 target-version = ["py310"]
 
-[tool.autopep8]
-max_line_length = 120
-in-place = true
-recursive = true
-aggressive = 3
+[tool.isort]
+profile = "black"
+line_length = 120
 
 [tool.pytest.ini_options]
 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"]]