Merge pull request #27 from Serapieum-of-alex/more-distributions

More distributions

Author: MAfarrag

.pre-commit-config.yaml

@@ -43,12 +43,12 @@ repos:
 #    hooks:
 #      - id: isort
 #        name: "[py   - format] isort"
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.4
-    hooks:
-      - id: docformatter
-        name: "[py   - format] docformatter"
-        args: [ -i, --wrap-summaries, "0" ]
+#  - repo: https://github.com/PyCQA/docformatter
+#    rev: v1.4
+#    hooks:
+#      - id: docformatter
+#        name: "[py   - format] docformatter"
+#        args: [ -i, --wrap-summaries, "0" ]
 
   - repo: https://github.com/PyCQA/pydocstyle
     rev: 6.1.1
@@ -57,12 +57,12 @@ repos:
         name: "[py   - check] pydocstyle"
         files: ^Hapi/
 
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
     hooks:
       - id: flake8
         name: "[py   - check] flake8"
-        language_version: python3.9
+#        language_version: python3.9
         exclude: ^(examples/|tests/)
 
   #- repo: https://github.com/psf/black
@@ -74,7 +74,7 @@ repos:
     hooks:
       - id: black
         name: "[py   - format] black"
-        language_version: python3.9
+#        language_version: python3.9
   - repo: https://github.com/lovesegfault/beautysh
     rev: v6.2.1
     hooks:
@@ -108,7 +108,7 @@ repos:
     hooks:
       - id: pytest-check
         name: pytest-check
-        entry: pytest -vvv --cov=Hapi
+        entry: pytest -vvv --cov=statista
         language: system
         pass_filenames: false
         always_run: true

HISTORY.rst

@@ -24,3 +24,13 @@ History
 
 * add eva (Extreme value analysis) module
 * fix bug in obtaining distribution parameters using optimization method
+
+
+0.3.0 (2023-02-19)
+------------------
+
+* add documentations for both GEV and gumbel distributions.
+* add lmoment parameter estimation method for all distributions.
+* add exponential and normal distributions
+* modify the pdf, cdf, and probability plot plots
+* create separate plot and confidence_interval modules.

README.md

@@ -26,15 +26,19 @@ statista
 
 Main Features
 -------------
-  - Statistical Distributions (GEV/GUMBL)
-  - Parameter estimation Lmoments/ML/MOM
+  - Statistical Distributions
+    - GEV
+    - GUMBL
+    - Normal
+    - Exponential
+  - Parameter estimation methods
+    - Lmoments
+    - ML
+    - MOM
   - One-at-time (O-A-T) Sensitivity analysis.
   - Sobol visualization
-  - Statistical Metrics
-
-Future work
--------------
-  - More distributions
+  - Statistical descriptors
+  - Extreme value analysis
 
 
 Installing statista
@@ -61,7 +65,7 @@ pip install git+https://github.com/MAfarrag/statista
 ## pip
 to install the last release you can easly use pip
 ```
-pip install statista==0.2.0
+pip install statista==0.3.0
 ```
 
 Quick start

docs/conf.py

@@ -8,18 +8,18 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
+
 import os
 import sys
 
 # import sphinx_rtd_theme
 
 # General information about the project.
-project = "pyramids"
+project = "statista"
 author = "Mostafa Farrag"
 
 # copyright = u"2013-2019, "
 
-
 html_theme = "sphinxdoc"
 # html_theme = "agogo"
 html_theme_path = ["."]
@@ -28,7 +28,7 @@
 # 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.insert(0, os.path.abspath("../pyramids"))
+sys.path.insert(0, os.path.abspath("../statista"))
 sys.path.insert(0, os.path.abspath(".."))
 sys.path.insert(0, os.path.abspath("../examples"))
 
@@ -37,7 +37,7 @@
 # os.path.abspath to make it absolute, like shown here.
 sys.path.append(os.path.abspath("sphinxext"))
 
-# import pyramids
+# import statista
 
 
 # -- General configuration -----------------------------------------------------
@@ -48,13 +48,19 @@
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
-    "matplotlib.sphinxext.plot_directive",
-    "sphinx.ext.todo",
-    "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
-    "sphinx.ext.graphviz",
-    "sphinx.ext.doctest",
-    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.imgmath",
+    "easydev.copybutton",
+    # "matplotlib.sphinxext.plot_directive",
+    # "sphinx.ext.todo",
+    # "sphinx.ext.mathjax",
+    # "sphinx.ext.graphviz",
+    # "sphinx.ext.doctest",
+    # "sphinx.ext.autosectionlabel",
+    "numpydoc",
+    "nbsphinx",
 ]
 
 autosectionlabel_prefix_document = True
@@ -117,7 +123,9 @@
 
 # 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"
+html_theme = "pydata_sphinx_theme"
+
 
 # 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
@@ -137,7 +145,7 @@
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 """
-html_logo = "images/pyramids.png"
+html_logo = "images/statista.png"
 """
 # 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
@@ -164,7 +172,13 @@
 # html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-# html_sidebars = {}
+html_sidebars = {
+    "**": [
+        "globaltoc.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -197,16 +211,20 @@
 html_file_suffix = ".html"
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "pyramidsdoc"
+htmlhelp_basename = "statistadoc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
-
-
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ("index", "pyramids.tex", "pyramids Documentation", "Mostafa Farrag", "report")
+    (
+        "index",
+        "statista.tex",
+        "statista Documentation",
+        "Mostafa Farrag",
+        "report",
+    )
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -234,7 +252,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "pyramids", "pyramids Documentation", [author], 1)]
+man_pages = [("index", "statista", "statista Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -248,10 +266,9 @@
 texinfo_documents = [
     (
         "index",
-        "pyramids",
-        "pyramids Documentation",
+        "statista",
+        "statista Documentation",
         "Mostafa Farrag",
-        "pyramids",
         "One line description of project.",
         "Miscellaneous",
     )
@@ -277,5 +294,5 @@
     #    "netCDF4_utils",
     #    "netcdftime",
     #    "pyproj",
-    #    "pyramids.version",
+    #    "statista.version",
 ]

docs/distributions.rst

@@ -0,0 +1,56 @@
+#############
+Distributions
+#############
+
+********************************************
+Generalized extreme value distribution (GEV)
+********************************************
+
+- The generalised extreme value (or generalized extreme value) distribution characterises the behaviour of ‘block
+    maxima’
+
+probability density function (pdf)
+==================================
+
+.. math::
+     f(x) = \frac{1}{\sigma}\ast{Q(x)}^{\xi+1}\ast e^{-Q(x)}
+
+
+.. math::
+     Q(x) =
+        \begin{cases}
+        {(1+\xi(\frac{x-\mu}{\delta}))}^\frac{-1}{\xi}  & \quad \text{if } \xi \text{ \neq 0}\\
+        e^{-(\frac{x-\mu}{\delta})}                     & \quad \text{if } \xi \text{ = 0}
+        \end{cases}
+
+- where
+    - :math: `\sigma` is the scale parameter
+    - :math: `\mu` is the location parameter
+    - :math: `\delta` is the scale parameter
+
+
+Cumulative distribution function (cdf)
+======================================
+
+.. math::
+    F(x)=e^{-Q(x)}
+
+*******************
+Gumbel Distribution
+*******************
+
+- The Gumbel distribution is a special case of the `Generalized extreme value distribution (GEV)`_ when the shape
+    parameter :math: `\sigma` equals zero.
+
+probability density function (pdf)
+==================================
+
+.. math::
+     f(x) = \frac{1}{\sigma} \ast { {e}^{-(\frac{x-\mu}{\delta}) - {e}^{- (\frac{x-\mu}{\delta})} }}
+
+
+Cumulative distribution function (cdf)
+======================================
+
+.. math::
+    F(x) = {e}^{- {e}^{- (\frac{x-\mu}{\delta})} }

docs/environment.yml

@@ -1,10 +1,13 @@
 channels:
   - conda-forge
 dependencies:
-  - python >=3.9.0
-  - pip >=21.3.1
-  - matplotlib >=3.4.2,<3.6.0
-#  - pandas >=1.3.2,<1.4.3
-#  - pip:
-#      - geoplot >=0.5.1
-#      - loguru >=0.5.3
+  - python >=3.9,<3.11
+  - pip >=22.3.1
+  - pandas
+  - numpy==1.20.*
+  - numpydoc==1.1.0
+  - typing-extensions==3.10.*
+  - pip:
+    - pydata-sphinx-theme
+    - nbsphinx
+    - easydev

docs/images/sensitivityAnalysis1.png

@@ -6,22 +6,22 @@ Current release info
   :target: https://pypi.org/project/statista/0.1.2/
 
 
-.. image:: https://img.shields.io/conda/v/conda-forge/hapi?label=conda-forge
+.. image:: https://img.shields.io/conda/v/conda-forge/statista?label=conda-forge
   :target: https://pypi.org/project/statista/0.1.2/
 
 
 .. image:: https://img.shields.io/pypi/pyversions/statista
   :target: https://pypi.org/project/statista/0.1.2/
 
 
-.. image:: https://img.shields.io/github/forks/mafarrag/hapi?style=social   :alt: GitHub forks
+.. image:: https://img.shields.io/github/forks/mafarrag/statista?style=social   :alt: GitHub forks
 
 
-.. image:: https://anaconda.org/conda-forge/hapi/badges/downloads.svg
-  :target: https://anaconda.org/conda-forge/hapi
+.. image:: https://anaconda.org/conda-forge/statista/badges/downloads.svg
+  :target: https://anaconda.org/conda-forge/statista
 
 
-.. image:: https://img.shields.io/conda/vn/conda-forge/hapi   :alt: Conda (channel only)
+.. image:: https://img.shields.io/conda/vn/conda-forge/statista   :alt: Conda (channel only)
   :target: https://pypi.org/project/statista/0.1.2/
 
 
@@ -37,8 +37,8 @@ Current release info
   :alt: PyPI
 
 
-.. image:: https://anaconda.org/conda-forge/hapi/badges/platforms.svg
-  :target: https://anaconda.org/conda-forge/hapi
+.. image:: https://anaconda.org/conda-forge/statista/badges/platforms.svg
+  :target: https://anaconda.org/conda-forge/statista
 
 
 .. image:: https://static.pepy.tech/personalized-badge/statista?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads
@@ -81,6 +81,6 @@ Main Features
    :hidden:
    :maxdepth: 1
 
-   Installation <00Installation.rst>
-   Tutorial <03tutorial.rst>
-   GIS <05GIS.rst>
+   Installation <installation.rst>
+   Distributions <distributions.rst>
+   Sensitivity analysis <sensitivity_analysis.rst>