misc: Add and run pre-commit

Author: daavoo

.github/workflows/tests.yaml

@@ -32,11 +32,11 @@ jobs:
       run: |
         pip install pytest
         pip install pytest-cov
-  
-        pytest --cov=pyntcloud --cov-report=xml --cov-append tests/unit 
-        pytest --cov=pyntcloud --cov-report=xml --cov-append tests/integration 
 
-    - name: Upload coverage to Codecov  
+        pytest --cov=pyntcloud --cov-report=xml --cov-append tests/unit
+        pytest --cov=pyntcloud --cov-report=xml --cov-append tests/integration
+
+    - name: Upload coverage to Codecov
       if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.11'
       run: bash <(curl -s https://codecov.io/bash) -t $TOKEN -B $REF
       env:

.gitignore

@@ -61,4 +61,4 @@ docs/_build
 \.idea/
 
 \.pytest_cache/
-pythonenv*
+pythonenv*

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+        args: ['--assume-in-merge']
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+      - id: sort-simple-yaml
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.9.10'
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        exclude: CODE_OF_CONDUCT.md

docs/conf.py

@@ -22,7 +22,7 @@
 
 import sphinx_bootstrap_theme
 
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- General configuration ------------------------------------------------
@@ -36,40 +36,40 @@
 # ones.
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
 ]
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'pyntcloud'
-copyright = 'HAKUNA MATATA'
-author = 'David de la Iglesia Castro'
+project = "pyntcloud"
+copyright = "HAKUNA MATATA"
+author = "David de la Iglesia Castro"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.3'
+version = "0.1.3"
 # The full version, including alpha/beta/rc tags.
-release = '0.1.3'
+release = "0.1.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -81,10 +81,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -95,7 +95,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'bootstrap'
+html_theme = "bootstrap"
 html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 html_logo = "images/pyntcloud_logo_small.png"
 
@@ -112,7 +112,7 @@
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pyntclouddoc'
+htmlhelp_basename = "pyntclouddoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -121,15 +121,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -139,19 +136,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pyntcloud.tex', 'pyntcloud Documentation',
-     'David de la Iglesia Castro', 'manual'),
+    (
+        master_doc,
+        "pyntcloud.tex",
+        "pyntcloud Documentation",
+        "David de la Iglesia Castro",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pyntcloud', 'pyntcloud Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pyntcloud", "pyntcloud Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -160,7 +159,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pyntcloud', 'pyntcloud Documentation',
-     author, 'pyntcloud', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pyntcloud",
+        "pyntcloud Documentation",
+        author,
+        "pyntcloud",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]

docs/filters_dev.rst

@@ -25,7 +25,7 @@ Filters are used by the method:
 Take a look at the source code in order to get a general overview of how filters are being used. All filters are classes and all have the same
 methods.
 
-The sections below will guide you trough the filters module explaining how you can create your own filters or where you need
+The sections below will guide you through the filters module explaining how you can create your own filters or where you need
 to look in order to modify existing ones.
 
 Base Class
@@ -37,7 +37,7 @@ All filters must inherit from the base class `Filter` and implement its abstract
 
 The base class is located at pyntcloud/filters/base.py
 
-.. autoclass:: Filter     
+.. autoclass:: Filter
 
 At the very least, all filters receive a PyntCloud when they are instantiated.
 
@@ -64,14 +64,14 @@ methods of the Filter base class.
 
 For example, in the f_kdtree submodule there is a Filter_KDTree class from which all the filters that require a KDTree inherit.
 
-.. autoclass:: Filter_KDTree     
+.. autoclass:: Filter_KDTree
 
 If you don't find a submodule that extracts the information that your new filter needs, create a new one using as guideline one of the existing ones.
 
 Specific Filter Class
 =====================
 
-Once you have a submodule base class that extracts the right information, you have to actually create the specific class 
+Once you have a submodule base class that extracts the right information, you have to actually create the specific class
 for your filter, inheriting from the submodule base class and overriding the `Filter.compute` method.
 
 If the computation of your filter requires some parameters from the user, you should override the `__init__` method in order to accept those

docs/introduction.rst

@@ -49,7 +49,7 @@ common point cloud processing operations:
 
 -   sampling
 
--   :ref:`scalar_fields` / :ref:`scalar_fields_dev` 
+-   :ref:`scalar_fields` / :ref:`scalar_fields_dev`
 
 -   :ref:`structures` / :ref:`structures_dev`
 

docs/io_dev.rst

@@ -2,4 +2,4 @@
 
 =========
 I/O - Dev
-=========
+=========

docs/structures_dev.rst

@@ -2,4 +2,4 @@
 
 ================
 Structures - Dev
-================
+================

examples/[scalar_fields] eigenvalues.ipynb

@@ -167,7 +167,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "anky_cloud = anky.get_sample(\"mesh_random\", n=100000, rgb=True, normals=True, as_PyntCloud=True)"
+    "anky_cloud = anky.get_sample(\n",
+    "    \"mesh_random\", n=100000, rgb=True, normals=True, as_PyntCloud=True\n",
+    ")"
    ]
   },
   {
@@ -319,9 +321,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "eigenvalues = anky_cloud.add_scalar_field(\n",
-    "    \"eigen_values\", \n",
-    "    k_neighbors=k_neighbors)"
+    "eigenvalues = anky_cloud.add_scalar_field(\"eigen_values\", k_neighbors=k_neighbors)"
    ]
   },
   {

examples/[scalar_fields] normals.ipynb

@@ -167,7 +167,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "anky_cloud = anky.get_sample(\"mesh_random\", n=100000, rgb=True, normals=True, as_PyntCloud=True)"
+    "anky_cloud = anky.get_sample(\n",
+    "    \"mesh_random\", n=100000, rgb=True, normals=True, as_PyntCloud=True\n",
+    ")"
    ]
   },
   {