Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
mhasoba committed Oct 24, 2024
1 parent d785456 commit f6a6c9c
Show file tree
Hide file tree
Showing 47 changed files with 674 additions and 660 deletions.
2 changes: 1 addition & 1 deletion .buildinfo
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# 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: 99ae3a8de8eb267aa492261c626d4ad9
config: 40be6e96d990e312dca40f6c890edbc8
tags: 645f666f9bcd5a90fca523b33c5a78b7
7 changes: 2 additions & 5 deletions Stats-Intro.html
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@

<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=a3416100" />
<link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=3943d584" />
<link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
Expand All @@ -45,13 +45,10 @@
<script src="_static/documentation_options.js?v=9eb32ce0"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/togglebutton.js?v=3e7854f7"></script>
<script src="_static/clipboard.min.js?v=a7894cd8"></script>
<script src="_static/copybutton.js?v=f281be69"></script>
<script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
<script src="_static/togglebutton.js?v=4a39c7ea"></script>
<script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
<script src="_static/design-tabs.js?v=f930bc37"></script>
<script>const THEBE_JS_URL = "https://unpkg.com/[email protected]/lib/index.js"; const thebe_selector = ".thebe,.cell"; const thebe_selector_input = "pre"; const thebe_selector_output = ".output, .cell_output"</script>
Expand Down
215 changes: 165 additions & 50 deletions _sources/notebooks/Appendix-Assessment.md

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions _sources/notebooks/Appendix-MiniProj.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
"source": [
"## Introduction \n",
"\n",
"The computing Miniproject gives you an opportunity to try the \"whole nine yards\" of *asking and answering* a scientific question in biology (potentially involving multiple sub-questions/hypotheses) in a **fully reproducible way**. It will in essence give you an opportunity to perform a useful \"dry run\" of executing your actual Dissertation project. *It is an opportunity to do apply the computational methods you have been learning to a biological problem.*\n",
"The computing Miniproject gives you an opportunity to try the \"whole nine yards\" of *asking and answering* a scientific question in biology (potentially involving multiple sub-questions/hypotheses) in a **fully reproducible way**. It will in essence give you an opportunity to perform a useful \"dry run\" of executing your actual Dissertation project. *It is an opportunity to apply the computational methods you have been learning to a biological problem.*\n",
"\n",
"\n",
"## Objectives\n",
Expand Down Expand Up @@ -2861,7 +2861,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"version": "3.12.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
Expand Down
138 changes: 69 additions & 69 deletions _static/pygments.css
Original file line number Diff line number Diff line change
Expand Up @@ -3,77 +3,77 @@ html[data-theme="light"] .highlight td.linenos .normal { color: inherit; backgro
html[data-theme="light"] .highlight span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
html[data-theme="light"] .highlight td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
html[data-theme="light"] .highlight span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
html[data-theme="light"] .highlight .hll { background-color: #fae4c2 }
html[data-theme="light"] .highlight { background: #fefefe; color: #080808 }
html[data-theme="light"] .highlight .c { color: #515151 } /* Comment */
html[data-theme="light"] .highlight .err { color: #a12236 } /* Error */
html[data-theme="light"] .highlight .k { color: #6730c5 } /* Keyword */
html[data-theme="light"] .highlight .l { color: #7f4707 } /* Literal */
html[data-theme="light"] .highlight .n { color: #080808 } /* Name */
html[data-theme="light"] .highlight .o { color: #00622f } /* Operator */
html[data-theme="light"] .highlight .p { color: #080808 } /* Punctuation */
html[data-theme="light"] .highlight .ch { color: #515151 } /* Comment.Hashbang */
html[data-theme="light"] .highlight .cm { color: #515151 } /* Comment.Multiline */
html[data-theme="light"] .highlight .cp { color: #515151 } /* Comment.Preproc */
html[data-theme="light"] .highlight .cpf { color: #515151 } /* Comment.PreprocFile */
html[data-theme="light"] .highlight .c1 { color: #515151 } /* Comment.Single */
html[data-theme="light"] .highlight .cs { color: #515151 } /* Comment.Special */
html[data-theme="light"] .highlight .gd { color: #005b82 } /* Generic.Deleted */
html[data-theme="light"] .highlight .hll { background-color: #7971292e }
html[data-theme="light"] .highlight { background: #fefefe; color: #545454 }
html[data-theme="light"] .highlight .c { color: #797129 } /* Comment */
html[data-theme="light"] .highlight .err { color: #d91e18 } /* Error */
html[data-theme="light"] .highlight .k { color: #7928a1 } /* Keyword */
html[data-theme="light"] .highlight .l { color: #797129 } /* Literal */
html[data-theme="light"] .highlight .n { color: #545454 } /* Name */
html[data-theme="light"] .highlight .o { color: #008000 } /* Operator */
html[data-theme="light"] .highlight .p { color: #545454 } /* Punctuation */
html[data-theme="light"] .highlight .ch { color: #797129 } /* Comment.Hashbang */
html[data-theme="light"] .highlight .cm { color: #797129 } /* Comment.Multiline */
html[data-theme="light"] .highlight .cp { color: #797129 } /* Comment.Preproc */
html[data-theme="light"] .highlight .cpf { color: #797129 } /* Comment.PreprocFile */
html[data-theme="light"] .highlight .c1 { color: #797129 } /* Comment.Single */
html[data-theme="light"] .highlight .cs { color: #797129 } /* Comment.Special */
html[data-theme="light"] .highlight .gd { color: #007faa } /* Generic.Deleted */
html[data-theme="light"] .highlight .ge { font-style: italic } /* Generic.Emph */
html[data-theme="light"] .highlight .gh { color: #005b82 } /* Generic.Heading */
html[data-theme="light"] .highlight .gh { color: #007faa } /* Generic.Heading */
html[data-theme="light"] .highlight .gs { font-weight: bold } /* Generic.Strong */
html[data-theme="light"] .highlight .gu { color: #005b82 } /* Generic.Subheading */
html[data-theme="light"] .highlight .kc { color: #6730c5 } /* Keyword.Constant */
html[data-theme="light"] .highlight .kd { color: #6730c5 } /* Keyword.Declaration */
html[data-theme="light"] .highlight .kn { color: #6730c5 } /* Keyword.Namespace */
html[data-theme="light"] .highlight .kp { color: #6730c5 } /* Keyword.Pseudo */
html[data-theme="light"] .highlight .kr { color: #6730c5 } /* Keyword.Reserved */
html[data-theme="light"] .highlight .kt { color: #7f4707 } /* Keyword.Type */
html[data-theme="light"] .highlight .ld { color: #7f4707 } /* Literal.Date */
html[data-theme="light"] .highlight .m { color: #7f4707 } /* Literal.Number */
html[data-theme="light"] .highlight .s { color: #00622f } /* Literal.String */
html[data-theme="light"] .highlight .na { color: #912583 } /* Name.Attribute */
html[data-theme="light"] .highlight .nb { color: #7f4707 } /* Name.Builtin */
html[data-theme="light"] .highlight .nc { color: #005b82 } /* Name.Class */
html[data-theme="light"] .highlight .no { color: #005b82 } /* Name.Constant */
html[data-theme="light"] .highlight .nd { color: #7f4707 } /* Name.Decorator */
html[data-theme="light"] .highlight .ni { color: #00622f } /* Name.Entity */
html[data-theme="light"] .highlight .ne { color: #6730c5 } /* Name.Exception */
html[data-theme="light"] .highlight .nf { color: #005b82 } /* Name.Function */
html[data-theme="light"] .highlight .nl { color: #7f4707 } /* Name.Label */
html[data-theme="light"] .highlight .nn { color: #080808 } /* Name.Namespace */
html[data-theme="light"] .highlight .nx { color: #080808 } /* Name.Other */
html[data-theme="light"] .highlight .py { color: #005b82 } /* Name.Property */
html[data-theme="light"] .highlight .nt { color: #005b82 } /* Name.Tag */
html[data-theme="light"] .highlight .nv { color: #a12236 } /* Name.Variable */
html[data-theme="light"] .highlight .ow { color: #6730c5 } /* Operator.Word */
html[data-theme="light"] .highlight .pm { color: #080808 } /* Punctuation.Marker */
html[data-theme="light"] .highlight .w { color: #080808 } /* Text.Whitespace */
html[data-theme="light"] .highlight .mb { color: #7f4707 } /* Literal.Number.Bin */
html[data-theme="light"] .highlight .mf { color: #7f4707 } /* Literal.Number.Float */
html[data-theme="light"] .highlight .mh { color: #7f4707 } /* Literal.Number.Hex */
html[data-theme="light"] .highlight .mi { color: #7f4707 } /* Literal.Number.Integer */
html[data-theme="light"] .highlight .mo { color: #7f4707 } /* Literal.Number.Oct */
html[data-theme="light"] .highlight .sa { color: #00622f } /* Literal.String.Affix */
html[data-theme="light"] .highlight .sb { color: #00622f } /* Literal.String.Backtick */
html[data-theme="light"] .highlight .sc { color: #00622f } /* Literal.String.Char */
html[data-theme="light"] .highlight .dl { color: #00622f } /* Literal.String.Delimiter */
html[data-theme="light"] .highlight .sd { color: #00622f } /* Literal.String.Doc */
html[data-theme="light"] .highlight .s2 { color: #00622f } /* Literal.String.Double */
html[data-theme="light"] .highlight .se { color: #00622f } /* Literal.String.Escape */
html[data-theme="light"] .highlight .sh { color: #00622f } /* Literal.String.Heredoc */
html[data-theme="light"] .highlight .si { color: #00622f } /* Literal.String.Interpol */
html[data-theme="light"] .highlight .sx { color: #00622f } /* Literal.String.Other */
html[data-theme="light"] .highlight .sr { color: #a12236 } /* Literal.String.Regex */
html[data-theme="light"] .highlight .s1 { color: #00622f } /* Literal.String.Single */
html[data-theme="light"] .highlight .ss { color: #005b82 } /* Literal.String.Symbol */
html[data-theme="light"] .highlight .bp { color: #7f4707 } /* Name.Builtin.Pseudo */
html[data-theme="light"] .highlight .fm { color: #005b82 } /* Name.Function.Magic */
html[data-theme="light"] .highlight .vc { color: #a12236 } /* Name.Variable.Class */
html[data-theme="light"] .highlight .vg { color: #a12236 } /* Name.Variable.Global */
html[data-theme="light"] .highlight .vi { color: #a12236 } /* Name.Variable.Instance */
html[data-theme="light"] .highlight .vm { color: #7f4707 } /* Name.Variable.Magic */
html[data-theme="light"] .highlight .il { color: #7f4707 } /* Literal.Number.Integer.Long */
html[data-theme="light"] .highlight .gu { color: #007faa } /* Generic.Subheading */
html[data-theme="light"] .highlight .kc { color: #7928a1 } /* Keyword.Constant */
html[data-theme="light"] .highlight .kd { color: #7928a1 } /* Keyword.Declaration */
html[data-theme="light"] .highlight .kn { color: #7928a1 } /* Keyword.Namespace */
html[data-theme="light"] .highlight .kp { color: #7928a1 } /* Keyword.Pseudo */
html[data-theme="light"] .highlight .kr { color: #7928a1 } /* Keyword.Reserved */
html[data-theme="light"] .highlight .kt { color: #797129 } /* Keyword.Type */
html[data-theme="light"] .highlight .ld { color: #797129 } /* Literal.Date */
html[data-theme="light"] .highlight .m { color: #797129 } /* Literal.Number */
html[data-theme="light"] .highlight .s { color: #008000 } /* Literal.String */
html[data-theme="light"] .highlight .na { color: #797129 } /* Name.Attribute */
html[data-theme="light"] .highlight .nb { color: #797129 } /* Name.Builtin */
html[data-theme="light"] .highlight .nc { color: #007faa } /* Name.Class */
html[data-theme="light"] .highlight .no { color: #007faa } /* Name.Constant */
html[data-theme="light"] .highlight .nd { color: #797129 } /* Name.Decorator */
html[data-theme="light"] .highlight .ni { color: #008000 } /* Name.Entity */
html[data-theme="light"] .highlight .ne { color: #7928a1 } /* Name.Exception */
html[data-theme="light"] .highlight .nf { color: #007faa } /* Name.Function */
html[data-theme="light"] .highlight .nl { color: #797129 } /* Name.Label */
html[data-theme="light"] .highlight .nn { color: #545454 } /* Name.Namespace */
html[data-theme="light"] .highlight .nx { color: #545454 } /* Name.Other */
html[data-theme="light"] .highlight .py { color: #007faa } /* Name.Property */
html[data-theme="light"] .highlight .nt { color: #007faa } /* Name.Tag */
html[data-theme="light"] .highlight .nv { color: #d91e18 } /* Name.Variable */
html[data-theme="light"] .highlight .ow { color: #7928a1 } /* Operator.Word */
html[data-theme="light"] .highlight .pm { color: #545454 } /* Punctuation.Marker */
html[data-theme="light"] .highlight .w { color: #545454 } /* Text.Whitespace */
html[data-theme="light"] .highlight .mb { color: #797129 } /* Literal.Number.Bin */
html[data-theme="light"] .highlight .mf { color: #797129 } /* Literal.Number.Float */
html[data-theme="light"] .highlight .mh { color: #797129 } /* Literal.Number.Hex */
html[data-theme="light"] .highlight .mi { color: #797129 } /* Literal.Number.Integer */
html[data-theme="light"] .highlight .mo { color: #797129 } /* Literal.Number.Oct */
html[data-theme="light"] .highlight .sa { color: #008000 } /* Literal.String.Affix */
html[data-theme="light"] .highlight .sb { color: #008000 } /* Literal.String.Backtick */
html[data-theme="light"] .highlight .sc { color: #008000 } /* Literal.String.Char */
html[data-theme="light"] .highlight .dl { color: #008000 } /* Literal.String.Delimiter */
html[data-theme="light"] .highlight .sd { color: #008000 } /* Literal.String.Doc */
html[data-theme="light"] .highlight .s2 { color: #008000 } /* Literal.String.Double */
html[data-theme="light"] .highlight .se { color: #008000 } /* Literal.String.Escape */
html[data-theme="light"] .highlight .sh { color: #008000 } /* Literal.String.Heredoc */
html[data-theme="light"] .highlight .si { color: #008000 } /* Literal.String.Interpol */
html[data-theme="light"] .highlight .sx { color: #008000 } /* Literal.String.Other */
html[data-theme="light"] .highlight .sr { color: #d91e18 } /* Literal.String.Regex */
html[data-theme="light"] .highlight .s1 { color: #008000 } /* Literal.String.Single */
html[data-theme="light"] .highlight .ss { color: #007faa } /* Literal.String.Symbol */
html[data-theme="light"] .highlight .bp { color: #797129 } /* Name.Builtin.Pseudo */
html[data-theme="light"] .highlight .fm { color: #007faa } /* Name.Function.Magic */
html[data-theme="light"] .highlight .vc { color: #d91e18 } /* Name.Variable.Class */
html[data-theme="light"] .highlight .vg { color: #d91e18 } /* Name.Variable.Global */
html[data-theme="light"] .highlight .vi { color: #d91e18 } /* Name.Variable.Instance */
html[data-theme="light"] .highlight .vm { color: #797129 } /* Name.Variable.Magic */
html[data-theme="light"] .highlight .il { color: #797129 } /* Literal.Number.Integer.Long */
html[data-theme="dark"] .highlight pre { line-height: 125%; }
html[data-theme="dark"] .highlight td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
html[data-theme="dark"] .highlight span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
Expand Down
Loading

0 comments on commit f6a6c9c

Please sign in to comment.