apply codestyle changes

Author: zStupan

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+ci:
+  autofix_prs: true
+  autoupdate_schedule: monthly
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: check-ast
+      - id: check-docstring-first
+
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.10.1
+    hooks:
+      - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.3
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]

CODE_OF_CONDUCT.md

@@ -119,11 +119,11 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
 [https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
 
-Community Impact Guidelines were inspired by 
+Community Impact Guidelines were inspired by
 [Mozilla's code of conduct enforcement ladder][Mozilla CoC].
 
 For answers to common questions about this code of conduct, see the FAQ at
-[https://www.contributor-covenant.org/faq][FAQ]. Translations are available 
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
 at [https://www.contributor-covenant.org/translations][translations].
 
 [homepage]: https://www.contributor-covenant.org

docs/_static/output_sample.csv

@@ -8,4 +8,4 @@ antecedent,consequent,fitness,support,confidence,lift,coverage,rhs_support,convi
 "[Rings([1, 29]), Shucked weight([0.001, 1.488])]","[Viscera weight([0.0005, 0.76])]",1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.3333333333333333,0.9997605937275557,0.5,0.0,-1.0
 "[Shucked weight([0.001, 1.488]), Rings([1, 29])]","[Whole weight([0.002, 2.8255]), Viscera weight([0.0005, 0.76])]",1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.4444444444444444,0.9997605937275557,0.6826061944859854,0.0,-1.0
 "[Rings([1, 29]), Whole weight([0.002, 2.8255])]","[Viscera weight([0.0005, 0.76])]",1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.3333333333333333,0.9997605937275557,0.5,0.0,-1.0
-"[Shucked weight([0.001, 1.488])]","[Height([0.0, 1.13]), Viscera weight([0.0005, 0.76])]",1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.3333333333333333,0.9997605937275557,0.7924812503605781,0.0,-1.0
+"[Shucked weight([0.001, 1.488])]","[Height([0.0, 1.13]), Viscera weight([0.0005, 0.76])]",1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.3333333333333333,0.9997605937275557,0.7924812503605781,0.0,-1.0

docs/api/text.rst

@@ -3,4 +3,4 @@ Text
 
 .. automodule:: niaarm.text
     :members:
-    :show-inheritance:
+    :show-inheritance:

docs/api/visualize.rst

@@ -3,4 +3,4 @@ Visualize
 
 .. automodule:: niaarm.visualize
     :members:
-    :show-inheritance:
+    :show-inheritance:

docs/cli.rst

@@ -110,4 +110,3 @@ E.g. (for the above run):
     Average length of antecedent: 1.97723292469352
     Average length of consequent: 1.5604203152364273
     Run Time: 6.4538s
-

docs/conf.py

@@ -12,55 +12,61 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath("../"))
 
 # -- Project information -----------------------------------------------------
 
-project = 'NiaARM'
-copyright = '2022-2023, Žiga Stupan, Iztok Fister Jr.'
-author = 'Žiga Stupan, Iztok Fister Jr.'
+project = "NiaARM"
+copyright = "2022-2023, Žiga Stupan, Iztok Fister Jr."
+author = "Žiga Stupan, Iztok Fister Jr."
 
 # The full version, including alpha/beta/rc tags
-release = '0.3.3'
+release = "0.3.3"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx_rtd_theme', 'sphinxcontrib.bibtex', 'sphinx.ext.napoleon']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx_rtd_theme",
+    "sphinxcontrib.bibtex",
+    "sphinx.ext.napoleon",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Bibtex
-bibtex_bibfiles = ['refs.bib']
+bibtex_bibfiles = ["refs.bib"]
 
 # Bibliography style
-bibtex_default_style = 'unsrt'
+bibtex_default_style = "unsrt"
 
 # Add logo for project
-html_logo = '_static/logo.png'
+html_logo = "_static/logo.png"
 html_theme_options = {
-    'logo_only': True,
-    'display_version': False,
+    "logo_only": True,
+    "display_version": False,
 }

docs/documentation.rst

@@ -8,4 +8,4 @@ To locally generate and preview documentation run the following commands in the
     poetry install --extras docs
     poetry run sphinx-build ./docs ./docs/_build
 
-If the build of the documentation is successful, you can preview the documentation in the docs/_build folder by clicking the ``index.html`` file.
+If the build of the documentation is successful, you can preview the documentation in the docs/_build folder by clicking the ``index.html`` file.

docs/installation.rst

@@ -16,6 +16,12 @@ run the following command from the root of the cloned project:
 
     $ poetry install
 
+To also install the documentation dependencies run:
+
+.. code:: sh
+
+    $ poetry install --with docs
+
 All of the project's dependencies should be installed and the project
 ready for further development. **Note that Poetry creates a separate
 virtual environment for your project.**
@@ -26,11 +32,13 @@ Dependencies
 +----------------+--------------+------------+
 | Package        | Version      | Platform   |
 +================+==============+============+
-| niapy          | ^2.0.1       | All        |
+| niapy          | ^2.0.5       | All        |
 +----------------+--------------+------------+
-| pandas         | ^1.3.5       | All        |
+| pandas         | ^2.1.1       | All        |
 +----------------+--------------+------------+
-| numpy          | ^1.21.5      | All        |
+| numpy          | ^1.26.1      | All        |
++----------------+--------------+------------+
+| nltk           | ^3.8.1       | All        |
 +----------------+--------------+------------+
 
 Development Dependencies
@@ -39,18 +47,50 @@ Development Dependencies
 +--------------------+-----------+------------+
 | Package            | Version   | Platform   |
 +====================+===========+============+
-| Pytest             | ^7.0.1    | Any        |
+| pre-commit         | ^3.5.0    | Any        |
++--------------------+-----------+------------+
+
+Test Dependencies
+~~~~~~~~~~~~~~~~~
+
++--------------------+-----------+------------+
+| Package            | Version   | Platform   |
++====================+===========+============+
+| pytest             | ^7.4.2    | Any        |
++--------------------+-----------+------------+
+| pytest-cov         | ^7.4.2    | Any        |
++--------------------+-----------+------------+
+| pytest-randomly    | ^7.4.2    | Any        |
 +--------------------+-----------+------------+
 
-Extras
-~~~~~~
+Documentation dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 +------------------------------+--------------+------------+
 | Package                      | Version      | Platform   |
 +==============================+==============+============+
-| Sphinx                       | ^4.4.0       | Any        |
+| sphinx                       | ^7.2.6       | Any        |
 +------------------------------+--------------+------------+
 | sphinx-rtd-theme             | ^1.0.0       | Any        |
 +------------------------------+--------------+------------+
 | sphinxcontrib-bibtex         | ^2.4.1       | Any        |
 +------------------------------+--------------+------------+
+
+
+Pre-commit hooks
+~~~~~~~~~~~~~~~~
+
+We use pre-commit hooks for formatting and linting. You can install the pre-commit hooks with:
+
+.. code:: sh
+
+    $ pre-commit install
+
+
+Once the pre-commit hooks are installed and configured, they will automatically run before each git commit. If any hook fails, the commit will be aborted, and you'll need to address the issues raised by the hooks.
+
+To manually run the pre-commit hooks on all files, use the following command:
+
+.. code:: sh
+
+    $ pre-commit run --all-files

examples/basic_run.py

@@ -4,7 +4,7 @@
 from niapy.task import Task, OptimizationType
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # load and preprocess the dataset from csv
     data = Dataset("datasets/Abalone.csv")
 
@@ -13,14 +13,24 @@
     # features represent the list of features, while transactions depicts the list of transactions
     # the following 4 elements represent weights (support, confidence, coverage, shrinkage)
     # A weight of 0.0 means that criteria are omitted and are, therefore, excluded from the fitness function
-    problem = NiaARM(data.dimension, data.features, data.transactions, metrics=('support', 'confidence'), logging=True)
+    problem = NiaARM(
+        data.dimension,
+        data.features,
+        data.transactions,
+        metrics=("support", "confidence"),
+        logging=True,
+    )
 
     # build niapy task
-    task = Task(problem=problem, max_iters=30, optimization_type=OptimizationType.MAXIMIZATION)
+    task = Task(
+        problem=problem, max_iters=30, optimization_type=OptimizationType.MAXIMIZATION
+    )
 
     # use Differential Evolution (DE) algorithm from the NiaPy library
     # see full list of available algorithms: https://github.com/NiaOrg/NiaPy/blob/master/Algorithms.md
-    algo = DifferentialEvolution(population_size=50, differential_weight=0.5, crossover_probability=0.9)
+    algo = DifferentialEvolution(
+        population_size=50, differential_weight=0.5, crossover_probability=0.9
+    )
 
     # run algorithm
     best = algo.run(task=task)
@@ -29,4 +39,4 @@
     problem.rules.sort()
 
     # export all rules to csv
-    problem.rules.to_csv('output.csv')
+    problem.rules.to_csv("output.csv")