Merge branch 'main' of https://github.com/Kuanhao-Chao/splam into main

README.md

@@ -4,7 +4,7 @@
 </p>
 
 
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) ![version](https://img.shields.io/badge/version-v.1.0.1-blue) [![GitHub Downloads](https://img.shields.io/github/downloads/Kuanhao-Chao/splam/total.svg?style=social&logo=github&label=Download)](https://github.com/Kuanhao-Chao/splam/releases) ![os](https://img.shields.io/badge/platform-macOS_/Linux-green.svg) [![](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Kuanhao-Chao/splam/blob/main/notebook/splam_example.ipynb)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) ![version](https://img.shields.io/badge/version-v.1.0.2-blue) [![GitHub Downloads](https://img.shields.io/github/downloads/Kuanhao-Chao/splam/total.svg?style=social&logo=github&label=Download)](https://github.com/Kuanhao-Chao/splam/releases) ![os](https://img.shields.io/badge/platform-macOS_/Linux-green.svg) [![](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Kuanhao-Chao/splam/blob/main/notebook/splam_example.ipynb)
 
 <!-- <a href="https://colab.research.google.com/github/Kuanhao-Chao/splam/blob/main/notebook/splam_example.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a> -->
 
@@ -48,21 +48,29 @@ There are two main use case scenarios:
 
 ## <a name="documentation"></a>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading">#</a>
 📒 The full user manual is available **[here](http://ccb.jhu.edu/splam/)**
+
+
+
+
+
 <section id="table-of-contents" class="">
 <h3>Table of contents<a class="headerlink" href="#table-of-contents" title="Permalink to this heading">#</a></h3>
+
+
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html">Installation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#system-requirements">System requirements</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#install-through-pip">Install through pip</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#install-from-source">Install from source</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#install-through-conda">Install through conda</a></li>
-<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#check-splam-installation">Verify installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#check-splam-installation">Check Splam installation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/installation.html#now-you-are-ready-to-go">Now, you are ready to go !</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/quickstart.html">Quick Start Guide</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/quickstart.html#super-quick-start-3-lines-of-code">Super-Quick Start (3 lines)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/quickstart.html#super-quick-start-3-lines-of-code">Super-Quick Start (3 lines of code)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/quickstart.html#try-splam-on-google-colab">Try Splam on Google Colab</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/alignment_evaluation.html">Alignment file evaluation &amp; cleanup (<code class="code docutils literal notranslate"><span class="pre">BAM</span></code>)</a><ul>
@@ -85,18 +93,19 @@ There are two main use case scenarios:
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/annotation_evaluation.html#what-s-next">What's next?</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/generalization.html">Splam generalizes on non-human species</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/generalization.html#example-running-splam-on-house-mouse-mus-musculus">Example: Running Splam on house mouse (<em>Mus musculus</em>)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/generalization.html#explanation-splam-s-performance-on-non-human-species">Explanation: Splam's performance on non-human species</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/behind_scenes.html">Behind the scenes</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/behind_scenes.html#data-curation">Data curation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/behind_scenes.html#model-architecture">Model architecture</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/behind_scenes.html#splam-training-testing">Splam training &amp; testing</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/behind_scenes.html#reference">Reference</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/generalization.html">Splam generalizes on non-human species</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/generalization.html#test">Test</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/how_to_page.html">Q &amp; A</a></li>
+<li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/how_to_page.html">Q &amp; A ...</a></li>
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/function_manual.html">User Manual</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/function_manual.html#splam">splam</a></li>
 <li class="toctree-l2"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/function_manual.html#splam-extract">splam extract</a></li>
@@ -108,7 +117,6 @@ There are two main use case scenarios:
 <li class="toctree-l1"><a class="reference internal" href="http://ccb.jhu.edu/splam/content/contact.html">Contact</a></li>
 </ul>
 </div>
-</section>
 
 <br>
 

docs/source/index.rst

@@ -51,8 +51,8 @@ Splam's tutorial
 .. image:: https://img.shields.io/badge/License-MIT-yellow.svg
     :target: https://img.shields.io/badge/License-MIT-yellow.svg
 
-.. image:: https://img.shields.io/badge/version-v.1.0.1-blue
-    :target: https://img.shields.io/badge/version-v.1.0.1-blue
+.. image:: https://img.shields.io/badge/version-v.1.0.2-blue
+    :target: https://img.shields.io/badge/version-v.1.0.2-blue
 
 .. image:: https://img.shields.io/github/downloads/Kuanhao-Chao/splam/total.svg?style=social&logo=github&label=Download
     :target: https://img.shields.io/github/downloads/Kuanhao-Chao/splam/total.svg?style=social&logo=github&label=Download

src/setup.py

@@ -7,7 +7,7 @@
 from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
-VERSION = "1.0.1"
+VERSION = "1.0.2"
 
 # Convert distutils Windows platform specifiers to CMake -A arguments
 PLAT_TO_CMAKE = {

src/splam/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.2'

src/splam/header.py

@@ -8,4 +8,4 @@
 __license__ = "MIT"
 __maintainer__ = "developer"
 __status__ = "Kuan-Hao Chao"
-__version__ = "1.0.1"
+__version__ = "1.0.2"