Merge pull request #5 from INGEOTEC/develop

Missing imports

.readthedocs.yaml

@@ -0,0 +1,9 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "miniconda3-4.7"
+
+conda:
+  environment: environment.yml

CompStats/__init__.py

@@ -13,5 +13,5 @@
 # limitations under the License.
 __version__ = '0.0.4'
 from CompStats.bootstrap import StatisticSamples
-from CompStats.measurements import CI
-from CompStats.performance import performance, difference, plot_performance, plot_difference
+from CompStats.measurements import CI, difference_p_value
+from CompStats.performance import performance, difference, all_differences, plot_performance, plot_difference

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = CompStats
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

@@ -0,0 +1,178 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+import CompStats
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'CompStats'
+copyright = '2024, Sergio Nava, Mario Graff, Hugo Jair Escalante'
+author = 'Sergio Nava-Muñoz, Mario Graff, Hugo Jair Escalante'
+
+# The short X.Y version
+version = CompStats.__version__
+# The full version, including alpha/beta/rc tags
+release = version
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.doctest',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.intersphinx'    
+]
+
+intersphinx_mapping = {}
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+highlight_language = 'python'
+# autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_class_signature = 'separated'
+add_function_parentheses = False
+add_module_names = False
+
+# -- 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 = 'classic'
+
+# 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 = {
+    "rightsidebar": "false",
+    "relbarbgcolor": "black",
+    "sidebarbgcolor": "white",
+    "sidebartextcolor": "black"
+}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'CompStatsdoc'
+html_logo = 'ingeotec.png'
+
+
+# -- 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': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (master_doc, 'CompStats.tex', 'CompStats Documentation',
+     'Sergio Nava-Muñoz, Mario Graff, Hugo Jair Escalante', '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, 'CompStats', 'CompStats Documentation',
+     [author], 1)
+]
+
+
+# -- 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 = [
+    (master_doc, 'CompStats', 'CompStats Documentation',
+     author, 'CompStats', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

docs/source/index.rst

@@ -0,0 +1,112 @@
+.. _CompStats:
+
+====================================
+CompStats
+====================================
+.. image:: https://github.com/INGEOTEC/CompStats/actions/workflows/test.yaml/badge.svg
+		:target: https://github.com/INGEOTEC/CompStats/actions/workflows/test.yaml
+
+.. image:: https://coveralls.io/repos/github/INGEOTEC/CompStats/badge.svg?branch=develop
+		:target: https://coveralls.io/github/INGEOTEC/CompStats?branch=develop
+
+.. image:: https://badge.fury.io/py/CompStats.svg
+		:target: https://badge.fury.io/py/CompStats
+
+.. image:: https://readthedocs.org/projects/compstats/badge/?version=latest
+		:target: https://compstats.readthedocs.io/en/latest/?badge=latest
+
+
+CompStats
+
+Quickstart Guide
+====================================
+
+The first step is to install CompStats, which is described below.
+
+Installing CompStats
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The first step is to install the library, which can be done using the `conda package manager <https://conda-forge.org/>`_ with the following instruction. 
+
+.. code:: bash
+
+	  conda install -c conda-forge CompStats
+
+A more general approach to installing CompStats is through the use of the command pip, as illustrated in the following instruction. 
+
+.. code:: bash
+
+	  pip install CompStats
+
+
+Performance
+^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: python
+
+    >>> from CompStats import performance, plot_performance
+    >>> from CompStats.tests.test_performance import DATA
+    >>> from sklearn.metrics import f1_score
+    >>> import pandas as pd
+    >>> df = pd.read_csv(DATA)
+    >>> score = lambda y, hy: f1_score(y, hy, average='weighted')
+    >>> perf = performance(df, score=score)
+    >>> ins = plot_performance(perf)
+
+
+.. image:: performance.png
+
+
+Performance Comparison
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: python
+
+    >>> from CompStats import performance, difference, plot_difference
+    >>> from CompStats.tests.test_performance import DATA
+    >>> from sklearn.metrics import f1_score
+    >>> import pandas as pd
+    >>> df = pd.read_csv(DATA)
+    >>> score = lambda y, hy: f1_score(y, hy, average='weighted')
+    >>> perf = performance(df, score=score)
+    >>> diff = difference(perf)
+    >>> ins = plot_difference(diff)
+
+.. image:: difference.png
+
+
+The difference p-value can be estimated with the following instruction.
+
+
+.. code-block:: python
+
+    >>> from CompStats.measurements import difference_p_value
+    >>> p_values = difference_p_value(diff)
+    >>> p_values['BoW']
+    0.22
+    >>> p_values['StackBoW']
+    0.104
+
+
+Citing
+==========
+
+If you find CompStats useful for any academic/scientific purpose, we would appreciate citations to the following reference:
+
+.. code:: bibtex
+
+    @article{Nava:2023,
+    title = {{Comparison of Classifiers in Challenge Scheme}},
+    year = {2023},
+    journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
+    author = {Nava-Mu{\~{n}}oz, Sergio and Graff Guerrero, Mario and Escalante, Hugo Jair},
+    pages = {89--98},
+    volume = {13902 LNCS},
+    publisher = {Springer Science and Business Media Deutschland GmbH},
+    url = {https://link.springer.com/chapter/10.1007/978-3-031-33783-3_9},
+    isbn = {9783031337826},
+    doi = {10.1007/978-3-031-33783-3{\_}9/COVER},
+    issn = {16113349},
+    keywords = {Bootstrap, Challenges, Performance}
+    }
+