Added Support for Python 3.13

.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

.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/

.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

.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:

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.