Packaging and numpy>=2

.gitignore

@@ -21,4 +21,15 @@ ECT_*
 *.PNG
 _build/
 dist/
-wakis.egg-info/
+wakis.egg-info/
+.venv
+.coverage
+coverage.xml
+*.pyc
+*.pyo
+*.pyd
+*.so
+.Python
+*.ipynb_checkpoints
+htmlcov/
+uv.lock

MANIFEST.in

@@ -4,7 +4,4 @@ include pyproject.toml
 include *.md
 
 # Include the license file
-include LICENSE.txt
-
-# Include requirements
-include requirements.txt
+include LICENSE

Makefile

@@ -0,0 +1,52 @@
+# wakis Makefile
+
+
+# Colors for output
+RED := \033[0;31m
+GREEN := \033[0;32m
+YELLOW := \033[1;33m
+NC := \033[0m # No Color
+
+.PHONY: help install install-gpu clean docs
+
+# Based on https://gist.github.com/prwhite/8168133?permalink_comment_id=4718682#gistcomment-4718682
+
+## (Default) Print listing of key targets with their descriptions
+help:
+	@printf "\n\033[1;33mwakis Makefile\033[0m\n"
+	@printf "\n\033[1;34mUsage:\033[0m \033[1;33mmake <target>\033[0m\n\n"
+	@awk '\
+		/^## / { \
+			desc = substr($$0, 4); \
+			getline nextline; \
+			if (match(nextline, /^([a-zA-Z0-9._-]+):/)) { \
+				target = substr(nextline, RSTART, RLENGTH-1); \
+				printf "  \033[34m%-20s\033[0m %s\n", target, desc; \
+			} \
+		} \
+	' $(MAKEFILE_LIST)
+
+## Install Python dependencies
+install:
+	@echo -e "Installing Python dependencies..."
+	@pip install -e  .[full]
+
+## Install Python dependencies
+install-gpu:
+	@echo -e "Installing Python dependencies with GPU support..."
+	@pip install -e  .[full-gpu]
+
+## Remove temporary and generated files
+clean:
+	@echo -e "Cleaning up directory..."
+	@rm -rf __pycache__ .ruff_cache .pytest_cache *.egg-info .html *.html coverage.xml .coverage .mypy_cache results
+	@ cd docs && make -s clean
+
+
+## Run Python tests
+test:
+	pytest -s
+
+## Build documentation
+docs:
+	cd docs && make html

README.md

@@ -98,8 +98,7 @@ Create a dedicated **conda environment** and install dependencies:
 cd wakis/
 conda create --name wakis-env python=3.11
 conda activate wakis-env
-pip install -r requirements.txt
-pip install -e .  # install wakis in editable mode
+pip install -e .[notebook, tests, docs]  # install wakis in editable mode
 pip install neffint iddefix bihc  # Optional tools
 ```
 🛠️ **Want to contribute?**  To merge your changes into `main`, create a **Pull Request (PR)** following our [PR template](https://github.com/ImpedanCEI/wakis/blob/main/.github/pull_request_template.md).

docs/conf.py

@@ -10,87 +10,90 @@
 # 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.
 #
-import sys, os
-sys.path.insert(0, os.path.abspath('../../wakis/'))
-#sys.path.insert(0, os.path.abspath("../wakis"))
+import sys
+import os
+
+sys.path.insert(0, os.path.abspath("../../wakis/"))
+# sys.path.insert(0, os.path.abspath("../wakis"))
 sys.path.insert(0, os.path.abspath("../"))
-sys.path.append(os.path.abspath('..'))
+sys.path.append(os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
 
-project = 'wakis'
-copyright = '2024, CERN, BE-ABP-CEI'
-author = 'Elena de la Fuente, Lorenzo Giacomel, Giovanni Iadarola, Carlo Zannini'
+project = "wakis"
+copyright = "2024, CERN, BE-ABP-CEI"
+author = "Elena de la Fuente, Lorenzo Giacomel, Giovanni Iadarola, Carlo Zannini"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0'
+release = "1.0"
 
 # -- 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.ext.autosummary',
-              'sphinx.ext.doctest',
-              'sphinx.ext.extlinks',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.mathjax', #for eqs
-              'sphinx.ext.napoleon', 
-              'sphinx.ext.todo',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.githubpages',
-              'sphinx_copybutton',
-              #'sphinxemoji',
-              'myst_parser', #for markdown
-              'sphinx_design',
-              'sphinx_last_updated_by_git', 
-] 
-
-autodoc_preserve_defaults = True #preserves default args as in source code
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",  # for eqs
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx_copybutton",
+    #'sphinxemoji',
+    "myst_parser",  # for markdown
+    "sphinx_design",
+    "sphinx_last_updated_by_git",
+]
+
+autodoc_preserve_defaults = True  # preserves default args as in source code
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-myst_enable_extensions = ["dollarmath","html_admonition", "colon_fence"]
-#myst_enable_extensions = ["deflist", "dollarmath"]
+templates_path = ["_templates"]
+myst_enable_extensions = ["dollarmath", "html_admonition", "colon_fence"]
+# myst_enable_extensions = ["deflist", "dollarmath"]
 
 # The suffix of source filenames.
 
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.md': 'markdown',
+    ".rst": "restructuredtext",
+    ".md": "markdown",
 }
 
 # 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"]
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-#project = u'wakis'
-#copyright = u'2024, CERN, BE-ABP-CEI'
+# project = u'wakis'
+# copyright = u'2024, CERN, BE-ABP-CEI'
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- 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_static_path = ['img']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["img"]
 html_logo = "img/wakis-logo-pinkwhite.png"
 html_theme_options = {
-    'logo_only': True,
-    'home_page_in_toc': True,
-    'display_version': False,
-    'collapse_navigation': False,
-    'navigation_depth': 1,
+    "logo_only": True,
+    "home_page_in_toc": True,
+    "display_version": False,
+    "collapse_navigation": False,
+    "navigation_depth": 1,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -99,75 +102,73 @@
 # html_static_path = ['_static']
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'ReadtheDocsTemplatedoc'
+htmlhelp_basename = "ReadtheDocsTemplatedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
-'''
+"""
 latex_documents = [
   ('index', 'ReadtheDocsTemplate.tex', u'Read the Docs Template Documentation',
    u'Read the Docs', 'manual'),
 ]
-'''
+"""
 # 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
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
-'''
+"""
 texinfo_documents = [
   ('index', 'ReadtheDocsTemplate', u'Read the Docs Template Documentation',
    u'Read the Docs', 'ReadtheDocsTemplate', 'One line description of project.',
    'Miscellaneous'),
 ]
-'''
+"""
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
 
 
-# -- Extension configuration -------------------------------------------------
+# -- Extension configuration -------------------------------------------------