Use ruff for formatting and linting (#7)

* Remove catchall except

* Fix ruff checks

* Remove wildcard imports

* Ruff format

* Check format with ruff

* Add ruff badge

* pytest

* pytest

Author: relf

.github/workflows/linting.yml

@@ -23,8 +23,7 @@ jobs:
         pip install -r requirements.txt
         pip install -e .
 
-    - name: Check format with black
+    - name: Check format with ruff
       run: |
-        black --version
-        black --diff pyDOE3
-        black --check pyDOE3
+        ruff --version
+        ruff check

.github/workflows/tests.yml

@@ -32,5 +32,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest --doctest-modules
+        pytest --doctest-modules pyDOE3
+        pytest tests
+
 

README.md

@@ -4,6 +4,7 @@ pyDOE3: An experimental design package for python
 [![Tests](https://github.com/relf/pyDOE3/actions/workflows/tests.yml/badge.svg)](https://github.com/relf/pyDOE3/actions/workflows/tests.yml)
 [![Documentation](https://readthedocs.org/projects/pydoe3/badge/?version=latest)](https://pydoe3.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/709347557.svg)](https://zenodo.org/doi/10.5281/zenodo.10958492)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 `pyDOE3` is a fork of the [`pyDOE2`](https://github.com/clicumu/pyDOE2) package
 that is designed to help the scientist, engineer, statistician, etc., to
@@ -61,7 +62,7 @@ individuals for use with Scilab:
 
 `pyDOE` was converted to Python by the following individual:
 
-- Copyright (c) 2014, Abraham D. Lee & timsimst
+- Copyright (c) 2014, Abraham D. Lee
 
 The following individuals forked and worked on `pyDOE2`:
 

doc/conf.py

@@ -13,16 +13,17 @@
 
 from datetime import date
 
-import sys, os
+import sys
+import os
 
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath(".."))
 
 import pyDOE3
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.append(os.path.abspath('.'))
+# sys.path.append(os.path.abspath('.'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -31,152 +32,152 @@
 extensions = []
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8'
+# source_encoding = 'utf-8'
 
 # The master toctree document.
-master_doc = 'index_TOC'
+master_doc = "index_TOC"
 
 # General information about the project.
-project = u'pyDOE3'
-if date.today().year!=2013:
-    copyright = u'2013–%d, Abraham Lee' % date.today().year
+project = "pyDOE3"
+if date.today().year != 2013:
+    copyright = "2013–%d, Abraham Lee" % date.today().year
 else:
-    copyright = u'2013, Abraham Lee'
+    copyright = "2013, Abraham Lee"
 
 # 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 = '1'
+version = "1"
 # The full version, including alpha/beta/rc tags.
 release = pyDOE3.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 # List of directories, relative to source directory, that shouldn't be searched
 # for source files.
-exclude_trees = ['_build']
+exclude_trees = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'sphinxdoc'
+html_theme = "sphinxdoc"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 # html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'favicon.ico'
+html_favicon = "favicon.ico"
 
 # 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"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_use_modindex = True
+# html_use_modindex = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pyDOEPythonPackagedoc'
+htmlhelp_basename = "pyDOEPythonPackagedoc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
@@ -187,17 +188,17 @@
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True

pyDOE3/__init__.py

@@ -17,16 +17,38 @@
 The following individuals forked pyDOE and works on `pyDOE2`:
 
 - Copyright (C) 2018 - Rickard Sjoegren and Daniel Svensson
-
 """
 
-from ._version import __version__
-
-from pyDOE3.doe_box_behnken import *
-from pyDOE3.doe_composite import *
-from pyDOE3.doe_factorial import *
-from pyDOE3.doe_lhs import *
-from pyDOE3.doe_fold import *
-from pyDOE3.doe_plackett_burman import *
-from pyDOE3.var_regression_matrix import *
+from pyDOE3.doe_box_behnken import bbdesign
+from pyDOE3.doe_composite import ccdesign
+from pyDOE3.doe_factorial import (
+    fullfact,
+    ff2n,
+    fracfact,
+    fracfact_by_res,
+    fracfact_opt,
+    fracfact_aliasing,
+    alias_vector_indices,
+)
+from pyDOE3.doe_lhs import lhs
+from pyDOE3.doe_fold import fold
+from pyDOE3.doe_plackett_burman import pbdesign
+from pyDOE3.var_regression_matrix import var_regression_matrix
 from pyDOE3.doe_gsd import gsd
+
+__all__ = [
+    "bbdesign",
+    "ccdesign",
+    "fullfact",
+    "ff2n",
+    "fracfact",
+    "fracfact_by_res",
+    "fracfact_opt",
+    "fracfact_aliasing",
+    "alias_vector_indices",
+    "lhs",
+    "fold",
+    "pbdesign",
+    "var_regression_matrix",
+    "gsd",
+]

pyDOE3/build_regression_matrix.py

@@ -6,10 +6,10 @@
     Copyright (C) 2010 - 2011 - INRIA - Michael Baudin
     Copyright (C) 2009 - Yann Collette
     Copyright (C) 2009 - CEA - Jean-Marc Martinez
-    
+
     website: forge.scilab.org/index.php/p/scidoe/sourcetree/master/macros
 
-Much thanks goes to these individuals. It has been converted to Python by 
+Much thanks goes to these individuals. It has been converted to Python by
 Abraham Lee.
 """
 

pyDOE3/doe_box_behnken.py

@@ -6,10 +6,10 @@
     Copyright (C) 2010 - 2011 - INRIA - Michael Baudin
     Copyright (C) 2009 - Yann Collette
     Copyright (C) 2009 - CEA - Jean-Marc Martinez
-    
+
     website: forge.scilab.org/index.php/p/scidoe/sourcetree/master/macros
 
-Much thanks goes to these individuals. It has been converted to Python by 
+Much thanks goes to these individuals. It has been converted to Python by
 Abraham Lee.
 """
 
@@ -77,12 +77,12 @@ def bbdesign(n, center=None):
     for i in range(n - 1):
         for j in range(i + 1, n):
             Index = Index + 1
-            H[
-                max([0, (Index - 1) * H_fact.shape[0]]) : Index * H_fact.shape[0], i
-            ] = H_fact[:, 0]
-            H[
-                max([0, (Index - 1) * H_fact.shape[0]]) : Index * H_fact.shape[0], j
-            ] = H_fact[:, 1]
+            H[max([0, (Index - 1) * H_fact.shape[0]]) : Index * H_fact.shape[0], i] = (
+                H_fact[:, 0]
+            )
+            H[max([0, (Index - 1) * H_fact.shape[0]]) : Index * H_fact.shape[0], j] = (
+                H_fact[:, 1]
+            )
 
     if center is None:
         if n <= 16: