updating insall docs and requirements

README.rst

@@ -13,7 +13,7 @@ CRNT4SBML
         :target: https://crnt4sbml.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
-CRNT4SBML is an easily installable Python based package available on Mac and Windows. CRNT4SBML is concentrated on
+CRNT4SBML is an easily installable Python based package available on MacOS and Windows. CRNT4SBML is concentrated on
 providing a simple workflow for the testing of core CRNT methods directed at detecting bistability in cell signaling
 pathways endowed with mass action kinetics.
 

docs/_build/html/_sources/installation.rst.txt

@@ -56,27 +56,36 @@ One can now see a directory called "crnt4sbml\_env" is created in the directory
 
 We can now activate this environment as follows:
 
-On Mac:
+On MacOS:
 
-.. code-block:: console
+    .. code-block:: console
 
-    $ source /path/to/python_environments/crnt4sbml_env/bin/activate
+        $ source /path/to/python_environments/crnt4sbml_env/bin/activate
 
 On Windows:
 
-.. code-block:: console
+    .. code-block:: console
 
-    $ path\to\crnt4sbml_env\Scripts\activate
+        $ path\to\crnt4sbml_env\Scripts\activate
 
 Note, in case you are using PowerShell, make sure its policy is updated by executing command as administrator
 ``Set-ExecutionPolicy RemoteSigned``. On the command line one should now see "(crnt4sbml_env)" on the left side of the
 command line, which indicates that one is now working in the virtual environment.
 
+Stable Release
+---------------
+
 Once the environment is activated, one can now install CRNT4SBML as follows:
 
-.. code-block:: console
+On MacOS:
+    .. code-block:: console
+
+        $ pip install crnt4sbml[MacOS]
 
-    $ pip install crnt4sbml
+On Windows:
+    .. code-block:: console
+
+        $ pip install crnt4sbml[Windows]
 
 note that this will install crnt4sbml in the virtual environment crnt4sbml_env. One can only use crnt4sbml within this
 environment. If one wants to stop using the virtual environment, the following command can be used:
@@ -88,36 +97,37 @@ environment. If one wants to stop using the virtual environment, the following c
 "(base)" should show up on the left of the command line. One can then use the environment by using the "source" command
 above.
 
-Stable release
---------------
-
-crnt4sbml can be obtained through a standard `pip`_ install as follows:
-
-.. code-block:: console
+Working Version
+----------------
 
-    $ pip install crnt4sbml
+The current working version of crnt4sbml can be downloaded from the `Github repo`_.
 
-This will always install the most recent stable release. Note that crnt4sbml has only been tested with Python version
-3.7.
+Once the environment is activated, one can now install CRNT4SBML as follows:
 
-.. _pip: https://pip.pypa.io
+On MacOS:
+    .. code-block:: console
 
-From sources
-------------
+        $ pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg=crnt4sbml[MacOS]
 
-The sources for crnt4sbml can be downloaded from the `Github repo`_.
+On Windows:
+    .. code-block:: console
 
-You can also clone the public repository:
+        $ pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg=crnt4sbml[Windows]
 
-.. code-block:: console
+On Linux:
+    .. code-block:: console
 
-    $ git clone https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git
+        $ pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg=crnt4sbml[Linux]
 
-Once you have a copy of the source, you can install it with:
+note that this will install crnt4sbml in the virtual environment crnt4sbml_env. One can only use crnt4sbml within this
+environment. If one wants to stop using the virtual environment, the following command can be used:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ deactivate
 
+"(base)" should show up on the left of the command line. One can then use the environment by using the "source" command
+above.
 
 .. _Github repo: https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML
+.. _pip: https://pip.pypa.io

docs/_build/html/index.html

@@ -187,8 +187,8 @@ <h1>Welcome to CRNT4SBML’s documentation!<a class="headerlink" href="#welcome-
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#requirements">Requirements</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#creating-a-virtual-environment">Creating a Virtual Environment</a></li>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#stable-release">Stable release</a></li>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#from-sources">From sources</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#stable-release">Stable Release</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#working-version">Working Version</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="detect_bistability.html">Steps for Detecting Bistability</a></li>

docs/_build/html/installation.html

@@ -90,8 +90,8 @@
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#creating-a-virtual-environment">Creating a Virtual Environment</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#stable-release">Stable release</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#from-sources">From sources</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#stable-release">Stable Release</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#working-version">Working Version</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="detect_bistability.html">Steps for Detecting Bistability</a></li>
@@ -224,21 +224,37 @@ <h2>Creating a Virtual Environment<a class="headerlink" href="#creating-a-virtua
 on Mac and “C:\Users\your_user_name\AppData\Local \Programs\Python\Python37\python.exe” on Windows.
 One can now see a directory called “crnt4sbml_env” is created in the directory python_environments.</p>
 <p>We can now activate this environment as follows:</p>
-<p>On Mac:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">source</span> /path/to/python_environments/crnt4sbml_env/bin/activate
+<p>On MacOS:</p>
+<blockquote>
+<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">source</span> /path/to/python_environments/crnt4sbml_env/bin/activate
 </pre></div>
 </div>
+</div></blockquote>
 <p>On Windows:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> path<span class="se">\t</span>o<span class="se">\c</span>rnt4sbml_env<span class="se">\S</span>cripts<span class="se">\a</span>ctivate
+<blockquote>
+<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> path<span class="se">\t</span>o<span class="se">\c</span>rnt4sbml_env<span class="se">\S</span>cripts<span class="se">\a</span>ctivate
 </pre></div>
 </div>
+</div></blockquote>
 <p>Note, in case you are using PowerShell, make sure its policy is updated by executing command as administrator
 <code class="docutils literal notranslate"><span class="pre">Set-ExecutionPolicy</span> <span class="pre">RemoteSigned</span></code>. On the command line one should now see “(crnt4sbml_env)” on the left side of the
 command line, which indicates that one is now working in the virtual environment.</p>
+</div>
+<div class="section" id="stable-release">
+<h2>Stable Release<a class="headerlink" href="#stable-release" title="Permalink to this headline">¶</a></h2>
 <p>Once the environment is activated, one can now install CRNT4SBML as follows:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install crnt4sbml
+<dl class="docutils">
+<dt>On MacOS:</dt>
+<dd><div class="first last highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install crnt4sbml<span class="o">[</span>MacOS<span class="o">]</span>
+</pre></div>
+</div>
+</dd>
+<dt>On Windows:</dt>
+<dd><div class="first last highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install crnt4sbml<span class="o">[</span>Windows<span class="o">]</span>
 </pre></div>
 </div>
+</dd>
+</dl>
 <p>note that this will install crnt4sbml in the virtual environment crnt4sbml_env. One can only use crnt4sbml within this
 environment. If one wants to stop using the virtual environment, the following command can be used:</p>
 <div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> deactivate
@@ -247,26 +263,34 @@ <h2>Creating a Virtual Environment<a class="headerlink" href="#creating-a-virtua
 <p>“(base)” should show up on the left of the command line. One can then use the environment by using the “source” command
 above.</p>
 </div>
-<div class="section" id="stable-release">
-<h2>Stable release<a class="headerlink" href="#stable-release" title="Permalink to this headline">¶</a></h2>
-<p>crnt4sbml can be obtained through a standard <a class="reference external" href="https://pip.pypa.io">pip</a> install as follows:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install crnt4sbml
+<div class="section" id="working-version">
+<h2>Working Version<a class="headerlink" href="#working-version" title="Permalink to this headline">¶</a></h2>
+<p>The current working version of crnt4sbml can be downloaded from the <a class="reference external" href="https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML">Github repo</a>.</p>
+<p>Once the environment is activated, one can now install CRNT4SBML as follows:</p>
+<dl class="docutils">
+<dt>On MacOS:</dt>
+<dd><div class="first last highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg<span class="o">=</span>crnt4sbml<span class="o">[</span>MacOS<span class="o">]</span>
 </pre></div>
 </div>
-<p>This will always install the most recent stable release. Note that crnt4sbml has only been tested with Python version
-3.7.</p>
+</dd>
+<dt>On Windows:</dt>
+<dd><div class="first last highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg<span class="o">=</span>crnt4sbml<span class="o">[</span>Windows<span class="o">]</span>
+</pre></div>
 </div>
-<div class="section" id="from-sources">
-<h2>From sources<a class="headerlink" href="#from-sources" title="Permalink to this headline">¶</a></h2>
-<p>The sources for crnt4sbml can be downloaded from the <a class="reference external" href="https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML">Github repo</a>.</p>
-<p>You can also clone the public repository:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git clone https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git
+</dd>
+<dt>On Linux:</dt>
+<dd><div class="first last highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pip install git+https://github.com/PNNL-Comp-Mass-Spec/CRNT4SBML.git#egg<span class="o">=</span>crnt4sbml<span class="o">[</span>Linux<span class="o">]</span>
 </pre></div>
 </div>
-<p>Once you have a copy of the source, you can install it with:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> python setup.py install
+</dd>
+</dl>
+<p>note that this will install crnt4sbml in the virtual environment crnt4sbml_env. One can only use crnt4sbml within this
+environment. If one wants to stop using the virtual environment, the following command can be used:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> deactivate
 </pre></div>
 </div>
+<p>“(base)” should show up on the left of the command line. One can then use the environment by using the “source” command
+above.</p>
 </div>
 </div>
 

docs/_build/html/readme.html

@@ -184,7 +184,7 @@ <h1>CRNT4SBML<a class="headerlink" href="#crnt4sbml" title="Permalink to this he
 <a class="reference external image-reference" href="https://pypi.python.org/pypi/crnt4sbml"><img alt="https://img.shields.io/pypi/v/crnt4sbml.svg" src="https://img.shields.io/pypi/v/crnt4sbml.svg" /></a>
 <a class="reference external image-reference" href="https://travis-ci.org/PNNL-Comp-Mass-Spec/CRNT4SBML"><img alt="https://img.shields.io/travis/PNNL-Comp-Mass-Spec/CRNT4SBML.svg" src="https://img.shields.io/travis/PNNL-Comp-Mass-Spec/CRNT4SBML.svg" /></a>
 <a class="reference external image-reference" href="https://crnt4sbml.readthedocs.io/en/latest/?badge=latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/crnt4sbml/badge/?version=latest" /></a>
-<p>CRNT4SBML is an easily installable Python based package available on Mac and Windows. CRNT4SBML is concentrated on
+<p>CRNT4SBML is an easily installable Python based package available on MacOS and Windows. CRNT4SBML is concentrated on
 providing a simple workflow for the testing of core CRNT methods directed at detecting bistability in cell signaling
 pathways endowed with mass action kinetics.</p>
 <ul class="simple">