diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
new file mode 100644
index 0000000..50d26fc
--- /dev/null
+++ b/.github/workflows/pypi-publish.yml
@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+ release:
+ types: [published]
+
+permissions:
+ contents: read
+
+jobs:
+ deploy:
+
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python
+ uses: actions/setup-python@v3
+ with:
+ python-version: '3.x'
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install build
+ - name: Build package
+ run: python -m build --sdist --wheel --outdir dist/
+ - name: Publish package
+ uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+ with:
+ user: __token__
+ password: ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
new file mode 100644
index 0000000..e6cd345
--- /dev/null
+++ b/.github/workflows/unit_test.yml
@@ -0,0 +1,33 @@
+on:
+ pull_request:
+ types: [opened, reopened, synchronize, edited]
+ workflow_dispatch:
+
+jobs:
+ build:
+ name: unit_test
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ['3.8','3.9','3.10']
+ steps:
+ - name: Install Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: "3.x"
+ - name: Checkout repo
+ uses: actions/checkout@v3
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ - name: Install dependencies
+ shell: bash
+ run: |
+ python3 -m pip install --upgrade pip
+ python3 -m pip install Bottleneck
+ python3 -m pip install --upgrade setuptools
+ cd $GITHUB_WORKSPACE
+ pip install .
+ - name: Run unit tests
+ shell: bash
+ run: |
+ python3 -m unittest discover griml
diff --git a/.gitignore b/.gitignore
index 8e68576..c8aebfa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,24 +1,9 @@
-
*.tif
other/out/*
other/datasets/*
other/old/*
-src/examples/getHagenBrae.py
-src/examples/analyse.py
-src/examples/getHagenBrae_dask.py
-src/examples/getMargin.py
-src/examples/getMarginGIMP.py
-src/examples/getTimeSeries.py
-src/examples/margin.py
-src/examples/process_old.py
-src/examples/sar_water.py
-*.docx
-src/griml/examples/analyse.py
-src/griml/examples/getHagenBrae.py
-src/griml/examples/getHagenBrae_dask.py
-src/griml/examples/getMargin.py
-src/griml/examples/getMarginGIMP.py
-src/griml/examples/getTimeSeries.py
-src/griml/examples/margin.py
-src/griml/examples/process_old.py
-src/griml/examples/sar_water.py
+other/iml_2017/*
+other/hagen_brae/*
+other/lake_temperature/*
+other/south_greenland/*
+src/griml/examples/*
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..9f55fec
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+ os: ubuntu-22.04
+ tools:
+ python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+ configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+ install:
+ - requirements: docs/requirements.txt
+
+formats:
+ - pdf
+ - epub
diff --git a/dist/griml-0.0.1-py3-none-any.whl b/dist/griml-0.0.1-py3-none-any.whl
deleted file mode 100644
index b01b9ba..0000000
Binary files a/dist/griml-0.0.1-py3-none-any.whl and /dev/null differ
diff --git a/dist/griml-0.0.1.tar.gz b/dist/griml-0.0.1.tar.gz
deleted file mode 100644
index 31bbdf9..0000000
Binary files a/dist/griml-0.0.1.tar.gz and /dev/null differ
diff --git a/docs/Makefile b/docs/Makefile
index d0c3cbf..d4bb2cb 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -5,8 +5,8 @@
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
-SOURCEDIR = source
-BUILDDIR = build
+SOURCEDIR = .
+BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
diff --git a/docs/build/.buildinfo b/docs/build/.buildinfo
deleted file mode 100644
index 3f31abd..0000000
--- a/docs/build/.buildinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: a1f544b9a74526735edfbe417308855a
-tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
deleted file mode 100644
index 0cca8af..0000000
Binary files a/docs/build/.doctrees/environment.pickle and /dev/null differ
diff --git a/docs/build/.doctrees/index.doctree b/docs/build/.doctrees/index.doctree
deleted file mode 100644
index beafd5d..0000000
Binary files a/docs/build/.doctrees/index.doctree and /dev/null differ
diff --git a/docs/build/.doctrees/modules.doctree b/docs/build/.doctrees/modules.doctree
deleted file mode 100644
index 5ca7050..0000000
Binary files a/docs/build/.doctrees/modules.doctree and /dev/null differ
diff --git a/docs/build/_sources/index.rst.txt b/docs/build/_sources/index.rst.txt
deleted file mode 100644
index f52e0b1..0000000
--- a/docs/build/_sources/index.rst.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-.. GrIML documentation master file, created by
- sphinx-quickstart on Tue Apr 26 16:51:31 2022.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-GrIML
-=====
-
-A Python package for classifying lakes and compiling lake inventories, under the GrIML project (Investigating Greenland's ice marginal lakes under a changing climate).
-
-.. toctree::
- :maxdepth: 2
- :caption: Contents:
-
- modules
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/build/_sources/modules.rst.txt b/docs/build/_sources/modules.rst.txt
deleted file mode 100644
index aafa617..0000000
--- a/docs/build/_sources/modules.rst.txt
+++ /dev/null
@@ -1,56 +0,0 @@
-Modules
-=======
-
-dem module
-----------
-
-.. automodule:: dem
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-lake module
------------
-
-.. automodule:: lake
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-process module
---------------
-
-.. automodule:: process
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-retrieve module
----------------
-
-.. automodule:: retrieve
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-sar module
-----------
-
-.. automodule:: sar
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-vis module
-----------
-
-.. automodule:: vis
- :members:
- :undoc-members:
- :show-inheritance:
-
diff --git a/docs/build/_static/basic.css b/docs/build/_static/basic.css
deleted file mode 100644
index bf18350..0000000
--- a/docs/build/_static/basic.css
+++ /dev/null
@@ -1,906 +0,0 @@
-/*
- * basic.css
- * ~~~~~~~~~
- *
- * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
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diff --git a/docs/build/_static/dialog-note.png b/docs/build/_static/dialog-note.png
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index 5a6336d..0000000
Binary files a/docs/build/_static/dialog-note.png and /dev/null differ
diff --git a/docs/build/_static/dialog-seealso.png b/docs/build/_static/dialog-seealso.png
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index 97553a8..0000000
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index cfbc280..0000000
Binary files a/docs/build/_static/dialog-todo.png and /dev/null differ
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deleted file mode 100644
index a75afea..0000000
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diff --git a/docs/build/_static/dialog-warning.png b/docs/build/_static/dialog-warning.png
deleted file mode 100644
index 8bb7d8d..0000000
Binary files a/docs/build/_static/dialog-warning.png and /dev/null differ
diff --git a/docs/build/_static/doctools.js b/docs/build/_static/doctools.js
deleted file mode 100644
index e509e48..0000000
--- a/docs/build/_static/doctools.js
+++ /dev/null
@@ -1,326 +0,0 @@
-/*
- * doctools.js
- * ~~~~~~~~~~~
- *
- * Sphinx JavaScript utilities for all documentation.
- *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
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-/**
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- */
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-
-/**
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- * an installed firebug like debugger
-if (!window.console || !console.firebug) {
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- window.console = {};
- for (var i = 0; i < names.length; ++i)
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-}
- */
-
-/**
- * small helper function to urldecode strings
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- */
-jQuery.urldecode = function(x) {
- if (!x) {
- return x
- }
- return decodeURIComponent(x.replace(/\+/g, ' '));
-};
-
-/**
- * small helper function to urlencode strings
- */
-jQuery.urlencode = encodeURIComponent;
-
-/**
- * This function returns the parsed url parameters of the
- * current request. Multiple values per key are supported,
- * it will always return arrays of strings for the value parts.
- */
-jQuery.getQueryParameters = function(s) {
- if (typeof s === 'undefined')
- s = document.location.search;
- var parts = s.substr(s.indexOf('?') + 1).split('&');
- var result = {};
- for (var i = 0; i < parts.length; i++) {
- var tmp = parts[i].split('=', 2);
- var key = jQuery.urldecode(tmp[0]);
- var value = jQuery.urldecode(tmp[1]);
- if (key in result)
- result[key].push(value);
- else
- result[key] = [value];
- }
- return result;
-};
-
-/**
- * highlight a given string on a jquery object by wrapping it in
- * span elements with the given class name.
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-jQuery.fn.highlightText = function(text, className) {
- function highlight(node, addItems) {
- if (node.nodeType === 3) {
- var val = node.nodeValue;
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- !jQuery(node.parentNode).hasClass(className) &&
- !jQuery(node.parentNode).hasClass("nohighlight")) {
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- var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
- if (isInSVG) {
- span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
- } else {
- span = document.createElement("span");
- span.className = className;
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- node.parentNode.insertBefore(span, node.parentNode.insertBefore(
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- "target": rect});
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- }
- }
- else if (!jQuery(node).is("button, select, textarea")) {
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- highlight(this, addItems);
- });
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- }
- var addItems = [];
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- highlight(this, addItems);
- });
- for (var i = 0; i < addItems.length; ++i) {
- jQuery(addItems[i].parent).before(addItems[i].target);
- }
- return result;
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-
-/*
- * backward compatibility for jQuery.browser
- * This will be supported until firefox bug is fixed.
- */
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-
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- /(webkit)[ \/]([\w.]+)/.exec(ua) ||
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- /(msie) ([\w.]+)/.exec(ua) ||
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- [];
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- this.highlightSearchWords();
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- if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
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- },
-
- /**
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- },
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- /**
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- $('div[id] > :header:first').each(function() {
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- /**
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- else
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- }).css('display', '');
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- togglers.click();
- }
- },
-
- /**
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- */
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- url.searchParams.delete('highlight');
- window.history.replaceState({}, '', url);
- },
-
- /**
- * make the url absolute
- */
- makeURL : function(relativeURL) {
- return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
- },
-
- /**
- * get the current relative url
- */
- getCurrentURL : function() {
- var path = document.location.pathname;
- var parts = path.split(/\//);
- $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this === '..')
- parts.pop();
- });
- var url = parts.join('/');
- return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
- },
-
- initOnKeyListeners: function() {
- $(document).keydown(function(event) {
- var activeElementType = document.activeElement.tagName;
- // don't navigate when in search box, textarea, dropdown or button
- if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
- && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
- && !event.shiftKey) {
- switch (event.keyCode) {
- case 37: // left
- var prevHref = $('link[rel="prev"]').prop('href');
- if (prevHref) {
- window.location.href = prevHref;
- return false;
- }
- break;
- case 39: // right
- var nextHref = $('link[rel="next"]').prop('href');
- if (nextHref) {
- window.location.href = nextHref;
- return false;
- }
- break;
- }
- }
- });
- }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
- Documentation.init();
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diff --git a/docs/build/_static/documentation_options.js b/docs/build/_static/documentation_options.js
deleted file mode 100644
index 23fc755..0000000
--- a/docs/build/_static/documentation_options.js
+++ /dev/null
@@ -1,12 +0,0 @@
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- VERSION: '0.0.1',
- LANGUAGE: 'None',
- COLLAPSE_INDEX: false,
- BUILDER: 'html',
- FILE_SUFFIX: '.html',
- LINK_SUFFIX: '.html',
- HAS_SOURCE: true,
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- NAVIGATION_WITH_KEYS: false
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\ No newline at end of file
diff --git a/docs/build/_static/epub.css b/docs/build/_static/epub.css
deleted file mode 100644
index 165f41d..0000000
--- a/docs/build/_static/epub.css
+++ /dev/null
@@ -1,310 +0,0 @@
-/*
- * default.css_t
- * ~~~~~~~~~~~~~
- *
- * Sphinx stylesheet -- default theme.
- *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
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-/* -- page layout ----------------------------------------------------------- */
-
-body {
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-
-div.body {
- background-color: {{ theme_bgcolor }};
- color: {{ theme_textcolor }};
- padding: 0 20px 30px 20px;
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-
-{%- if theme_rightsidebar|tobool %}
-div.bodywrapper {
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-}
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-
-div.footer {
- color: {{ theme_footertextcolor }};
- width: 100%;
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- font-size: 75%;
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- color: {{ theme_footertextcolor }};
- text-decoration: underline;
-}
-
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- background-color: {{ theme_relbarbgcolor }};
- line-height: 30px;
- color: {{ theme_relbartextcolor }};
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-
-div.related a {
- color: {{ theme_relbarlinkcolor }};
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-
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- {%- endif %}
- {%- if theme_rightsidebar|tobool %}
- float: right;
- {%- if theme_stickysidebar|tobool %}
- right: 0;
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- {%- endif %}
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-
-{%- if theme_stickysidebar|tobool %}
-/* this is nice, but it it leads to hidden headings when jumping
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- color: {{ theme_sidebartextcolor }};
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- font-size: 1em;
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-
-{% if theme_collapsiblesidebar|tobool %}
-/* for collapsible sidebar */
-div#sidebarbutton {
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-{% endif %}
-
-/* -- hyperlink styles ------------------------------------------------------ */
-
-a {
- color: {{ theme_linkcolor }};
- text-decoration: none;
-}
-
-a:visited {
- color: {{ theme_visitedlinkcolor }};
- text-decoration: none;
-}
-
-a:hover {
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-
-{% if theme_externalrefs|tobool %}
-a.external {
- text-decoration: none;
- border-bottom: 1px dashed {{ theme_linkcolor }};
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-
-a.external:hover {
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- border-bottom: none;
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- border-bottom: 1px dashed {{ theme_visitedlinkcolor }};
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-{% endif %}
-
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-div.body h5,
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- color: {{ theme_headtextcolor }};
- border-bottom: 1px solid #ccc;
- margin: 20px -20px 10px -20px;
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- border: 1px solid #ac9;
- border-left: none;
- border-right: none;
-}
-
-code {
- background-color: #ecf0f3;
- padding: 0 1px 0 1px;
- font-size: 0.95em;
-}
-
-th {
- background-color: #ede;
-}
-
-.warning code {
- background: #efc2c2;
-}
-
-.note code {
- background: #d6d6d6;
-}
-
-.viewcode-back {
- font-family: {{ theme_bodyfont }};
-}
-
-div.viewcode-block:target {
- background-color: #f4debf;
- border-top: 1px solid #ac9;
- border-bottom: 1px solid #ac9;
-}
diff --git a/docs/build/_static/file.png b/docs/build/_static/file.png
deleted file mode 100644
index a858a41..0000000
Binary files a/docs/build/_static/file.png and /dev/null differ
diff --git a/docs/build/_static/footerbg.png b/docs/build/_static/footerbg.png
deleted file mode 100644
index 1fbc873..0000000
Binary files a/docs/build/_static/footerbg.png and /dev/null differ
diff --git a/docs/build/_static/headerbg.png b/docs/build/_static/headerbg.png
deleted file mode 100644
index e1051af..0000000
Binary files a/docs/build/_static/headerbg.png and /dev/null differ
diff --git a/docs/build/_static/ie6.css b/docs/build/_static/ie6.css
deleted file mode 100644
index 74baa5d..0000000
--- a/docs/build/_static/ie6.css
+++ /dev/null
@@ -1,7 +0,0 @@
-* html img,
-* html .png{position:relative;behavior:expression((this.runtimeStyle.behavior="none")&&(this.pngSet?this.pngSet=true:(this.nodeName == "IMG" && this.src.toLowerCase().indexOf('.png')>-1?(this.runtimeStyle.backgroundImage = "none",
-this.runtimeStyle.filter = "progid:DXImageTransform.Microsoft.AlphaImageLoader(src='" + this.src + "',sizingMethod='image')",
-this.src = "_static/transparent.gif"):(this.origBg = this.origBg? this.origBg :this.currentStyle.backgroundImage.toString().replace('url("','').replace('")',''),
-this.runtimeStyle.filter = "progid:DXImageTransform.Microsoft.AlphaImageLoader(src='" + this.origBg + "',sizingMethod='crop')",
-this.runtimeStyle.backgroundImage = "none")),this.pngSet=true)
-);}
diff --git a/docs/build/_static/jquery-3.5.1.js b/docs/build/_static/jquery-3.5.1.js
deleted file mode 100644
index 5093733..0000000
--- a/docs/build/_static/jquery-3.5.1.js
+++ /dev/null
@@ -1,10872 +0,0 @@
-/*!
- * jQuery JavaScript Library v3.5.1
- * https://jquery.com/
- *
- * Includes Sizzle.js
- * https://sizzlejs.com/
- *
- * Copyright JS Foundation and other contributors
- * Released under the MIT license
- * https://jquery.org/license
- *
- * Date: 2020-05-04T22:49Z
- */
-( function( global, factory ) {
-
- "use strict";
-
- if ( typeof module === "object" && typeof module.exports === "object" ) {
-
- // For CommonJS and CommonJS-like environments where a proper `window`
- // is present, execute the factory and get jQuery.
- // For environments that do not have a `window` with a `document`
- // (such as Node.js), expose a factory as module.exports.
- // This accentuates the need for the creation of a real `window`.
- // e.g. var jQuery = require("jquery")(window);
- // See ticket #14549 for more info.
- module.exports = global.document ?
- factory( global, true ) :
- function( w ) {
- if ( !w.document ) {
- throw new Error( "jQuery requires a window with a document" );
- }
- return factory( w );
- };
- } else {
- factory( global );
- }
-
-// Pass this if window is not defined yet
-} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
-// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
-// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
-// enough that all such attempts are guarded in a try block.
-"use strict";
-
-var arr = [];
-
-var getProto = Object.getPrototypeOf;
-
-var slice = arr.slice;
-
-var flat = arr.flat ? function( array ) {
- return arr.flat.call( array );
-} : function( array ) {
- return arr.concat.apply( [], array );
-};
-
-
-var push = arr.push;
-
-var indexOf = arr.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var fnToString = hasOwn.toString;
-
-var ObjectFunctionString = fnToString.call( Object );
-
-var support = {};
-
-var isFunction = function isFunction( obj ) {
-
- // Support: Chrome <=57, Firefox <=52
- // In some browsers, typeof returns "function" for HTML