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DOC: updated release notes

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Frederic Fortier
2018-02-08 01:17:12 -05:00
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@@ -107,77 +95,204 @@
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<h1>Install<a class="headerlink" href="#install" title="Permalink to this headline"></a></h1>
@@ -243,23 +358,23 @@ to a folder you can remember. Make sure that the file gets saved with the
saved the above <code class="docutils literal"><span class="pre">python2.7-environment.yml</span></code> file.</p>
</li>
<li><p class="first">Install using this file. This step can take about 5-10 minutes to install.</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>conda env create -f python2.7-environment.yml
<div class="highlight-bash"><div class="highlight"><pre>conda env create -f python2.7-environment.yml
</pre></div>
</div>
</li>
<li><p class="first">Activate the environment (which you need to do every time you start a new
session to run Catalyst):</p>
<p><strong>Linux or MacOS:</strong></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">source</span> activate catalyst
<div class="highlight-bash"><div class="highlight"><pre><span class="nb">source </span>activate catalyst
</pre></div>
</div>
<p><strong>Windows:</strong></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>activate catalyst
<div class="highlight-bash"><div class="highlight"><pre>activate catalyst
</pre></div>
</div>
</li>
<li><p class="first">Verify that Catalyst is install correctly:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>catalyst --version
<div class="highlight-bash"><div class="highlight"><pre>catalyst --version
</pre></div>
</div>
<p>which should display the current version.</p>
@@ -275,32 +390,32 @@ with the following steps:</p>
<li><p class="first">If the above installation failed, and you have a partially set up catalyst
environment, remove it first. If you are starting from scratch, proceed to
step #2:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>conda env remove --name catalyst
<div class="highlight-bash"><div class="highlight"><pre>conda env remove --name catalyst
</pre></div>
</div>
</li>
<li><p class="first">Create the environment:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>conda create --name catalyst <span class="nv">python</span><span class="o">=</span><span class="m">2</span>.7 scipy zlib
<div class="highlight-bash"><div class="highlight"><pre>conda create --name catalyst <span class="nv">python</span><span class="o">=</span>2.7 scipy zlib
</pre></div>
</div>
</li>
<li><p class="first">Activate the environment:</p>
<p><strong>Linux or MacOS:</strong></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">source</span> activate catalyst
<div class="highlight-bash"><div class="highlight"><pre><span class="nb">source </span>activate catalyst
</pre></div>
</div>
<p><strong>Windows:</strong></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>activate catalyst
<div class="highlight-bash"><div class="highlight"><pre>activate catalyst
</pre></div>
</div>
</li>
<li><p class="first">Install the Catalyst inside the environment:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>pip install enigma-catalyst matplotlib
<div class="highlight-bash"><div class="highlight"><pre>pip install enigma-catalyst matplotlib
</pre></div>
</div>
</li>
<li><p class="first">Verify that Catalyst is installed correctly:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>catalyst --version
<div class="highlight-bash"><div class="highlight"><pre>catalyst --version
</pre></div>
</div>
<p>which should display the current version.</p>
@@ -330,14 +445,14 @@ distribution, refer to the <a class="reference internal" href="#conda"><span>Ins
that you install in a <a class="reference external" href="https://virtualenv.readthedocs.org/en/latest">virtualenv</a>. The <a class="reference external" href="http://docs.python-guide.org/en/latest/">Hitchhiker&#8217;s Guide to
Python</a> provides an <a class="reference external" href="http://docs.python-guide.org/en/latest/dev/virtualenvs/">excellent tutorial on virtualenv</a>. Here&#8217;s a
summarized version:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install virtualenv
$ virtualenv catalyst-venv
$ <span class="nb">source</span> ./catalyst-venv/bin/activate
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install virtualenv
<span class="nv">$ </span>virtualenv catalyst-venv
<span class="nv">$ </span><span class="nb">source</span> ./catalyst-venv/bin/activate
</pre></div>
</div>
<p>Once you&#8217;ve installed the necessary additional dependencies for your system
(<a class="reference internal" href="#linux"><span>GNU/Linux Requirements</span></a>, <a class="reference internal" href="#macos"><span>MacOS Requirements</span></a> or <a class="reference internal" href="#windows"><span>Windows Requirements</span></a>) <strong>and have activated your virtualenv</strong>, you should be able to simply run</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install enigma-catalyst matplotlib
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install enigma-catalyst matplotlib
</pre></div>
</div>
<p>Note that in the command above we install two different packages. The second
@@ -352,11 +467,11 @@ recommend you install it, as well.</p>
<dd>Package enigma-catalyst cannot be found</dd>
<dt><strong>Solution</strong>:</dt>
<dd><p class="first">Make sure you have the most up-to-date version of pip installed, by running:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install --upgrade pip
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install --upgrade pip
</pre></div>
</div>
<p>On Windows, the recommended command is:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ python -m pip install --upgrade pip
<div class="last highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>python -m pip install --upgrade pip
</pre></div>
</div>
</dd>
@@ -366,10 +481,10 @@ recommend you install it, as well.</p>
<dt><strong>Issue</strong>:</dt>
<dd><p class="first">Package enigma-catalyst cannot still be found, even after upgrading pip
(see above), with an error similar to:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>Downloading/unpacking enigma-catalyst
<div class="last highlight-bash"><div class="highlight"><pre>Downloading/unpacking enigma-catalyst
Could not find a version that satisfies the requirement enigma-catalyst
<span class="o">(</span>from versions: <span class="m">0</span>.1.dev9, <span class="m">0</span>.2.dev2, <span class="m">0</span>.1.dev4, <span class="m">0</span>.1.dev5, <span class="m">0</span>.1.dev3,
<span class="m">0</span>.2.dev1, <span class="m">0</span>.1.dev8, <span class="m">0</span>.1.dev6<span class="o">)</span>
<span class="o">(</span>from versions: 0.1.dev9, 0.2.dev2, 0.1.dev4, 0.1.dev5, 0.1.dev3,
0.2.dev1, 0.1.dev8, 0.1.dev6<span class="o">)</span>
Cleaning up...
No distributions matching the version <span class="k">for</span> enigma-catalyst
</pre></div>
@@ -381,7 +496,7 @@ to only find stable versions by default. Since Catalyst is in alpha
version, pip cannot find a matching version that satisfies the installation
requirements. The solution is to include the <cite>&#8211;pre</cite> flag to include
pre-release and development versions:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ pip install --pre enigma-catalyst
<div class="last highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install --pre enigma-catalyst
</pre></div>
</div>
</dd>
@@ -392,7 +507,7 @@ pre-release and development versions:</p>
<dd>Package enigma-catalyst fails to install because of outdated setuptools</dd>
<dt><strong>Solution</strong>:</dt>
<dd><p class="first">Upgrade to the most up-to-date setuptools package by running:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ pip install --upgrade pip setuptools
<div class="last highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install --upgrade pip setuptools
</pre></div>
</div>
</dd>
@@ -405,7 +520,7 @@ pre-release and development versions:</p>
<dd><p class="first">Download <a class="reference external" href="https://github.com/enigmampc/catalyst/blob/master/etc/requirements.txt">requirements.txt</a>
(click on the <em>Raw</em> button and Right click -&gt; Save As...) and use it to
install all the required dependencies by running:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ pip install -r requirements.txt
<div class="last highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install -r requirements.txt
</pre></div>
</div>
</dd>
@@ -420,7 +535,7 @@ install all the required dependencies by running:</p>
for the proper build and installation of package dependencies. The solution
is to install python-dev, which is independent of the virtual environment.
In Ubuntu, you would need to run:</p>
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ sudo apt-get install python-dev
<div class="last highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo apt-get install python-dev
</pre></div>
</div>
</dd>
@@ -431,21 +546,21 @@ In Ubuntu, you would need to run:</p>
<span id="pipenv"></span><h2>Installing with <code class="docutils literal"><span class="pre">pipenv</span></code><a class="headerlink" href="#installing-with-pipenv" title="Permalink to this headline"></a></h2>
<p>Installing Catalyst via <code class="docutils literal"><span class="pre">pipenv</span></code> is perhaps easier that installing it via
<code class="docutils literal"><span class="pre">pip</span></code> itself but you need to install <code class="docutils literal"><span class="pre">pipenv</span></code> first via <code class="docutils literal"><span class="pre">pip</span></code>.</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install pipenv
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install pipenv
</pre></div>
</div>
<p>Once <code class="docutils literal"><span class="pre">pipenv</span></code> is installed you can proceed by creating a project folder and
installing Catalyst on that project automagically as follows:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ mkdir project
$ <span class="nb">cd</span> project
$ pipenv --two
$ pipenv install enigma-catalyst matplotlib
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>mkdir project
<span class="nv">$ </span><span class="nb">cd </span>project
<span class="nv">$ </span>pipenv --two
<span class="nv">$ </span>pipenv install enigma-catalyst matplotlib
</pre></div>
</div>
<p>Until now the workflow compared to <code class="docutils literal"><span class="pre">pip</span></code> is almost identical, the difference
is that you don&#8217;t need to load manually any virtualenv however you need to use
the <cite>pipenv run</cite> prefix to run the <cite>catalyst</cite> command as follows:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pipenv run catalyst --version
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pipenv run catalyst --version
</pre></div>
</div>
<p>If you want to know more about <code class="docutils literal"><span class="pre">pipenv</span></code> go to the <a class="reference external" href="https://github.com/pypa/pipenv">pipenv github repo</a></p>
@@ -454,29 +569,29 @@ the <cite>pipenv run</cite> prefix to run the <cite>catalyst</cite> command as f
<span id="linux"></span><h2>GNU/Linux Requirements<a class="headerlink" href="#gnu-linux-requirements" title="Permalink to this headline"></a></h2>
<p>On <a class="reference external" href="https://www.debian.org/misc/children-distros">Debian-derived</a> Linux distributions, you can acquire all the necessary
binary dependencies from <code class="docutils literal"><span class="pre">apt</span></code> by running:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo apt-get install libatlas-base-dev python-dev gfortran pkg-config libfreetype6-dev
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo apt-get install libatlas-base-dev python-dev gfortran pkg-config libfreetype6-dev
</pre></div>
</div>
<p>On recent <a class="reference external" href="https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives">RHEL-derived</a> derived Linux distributions (e.g. Fedora), the
following should be sufficient to acquire the necessary additional
dependencies:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo dnf install atlas-devel gcc-c++ gcc-gfortran libgfortran python-devel redhat-rep-config
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo dnf install atlas-devel gcc-c++ gcc-gfortran libgfortran python-devel redhat-rep-config
</pre></div>
</div>
<p>On <a class="reference external" href="https://www.archlinux.org/">Arch Linux</a>, you can acquire the additional dependencies via <code class="docutils literal"><span class="pre">pacman</span></code>:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pacman -S lapack gcc gcc-fortran pkg-config
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pacman -S lapack gcc gcc-fortran pkg-config
</pre></div>
</div>
<div class="section" id="amazon-linux-ami-notes">
<h3>Amazon Linux AMI Notes<a class="headerlink" href="#amazon-linux-ami-notes" title="Permalink to this headline"></a></h3>
<p>The packages <code class="docutils literal"><span class="pre">pip</span></code> and <code class="docutils literal"><span class="pre">setuptools</span></code> that come shipped by default are very
outdated. Thus, you first need to run:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install --upgrade pip setuptools
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install --upgrade pip setuptools
</pre></div>
</div>
<p>The default installation is also missing the C and C++ compilers, which you
install by:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo yum install gcc gcc-c++
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo yum install gcc gcc-c++
</pre></div>
</div>
<p>Then you should follow the regular installation instructions outlined at the
@@ -493,14 +608,14 @@ to <a class="reference external" href="http://docs.python-guide.org/en/latest/">
which explains how to install Python with the <a class="reference external" href="http://brew.sh">Homebrew</a> manager.</p>
<p>Assuming you&#8217;ve installed Python with Homebrew, you&#8217;ll also likely need the
following brew packages:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ brew install freetype pkg-config gcc openssl
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>brew install freetype pkg-config gcc openssl
</pre></div>
</div>
<div class="section" id="macos-virtualenv-conda-matplotlib">
<h3>MacOS + virtualenv/conda + matplotlib<a class="headerlink" href="#macos-virtualenv-conda-matplotlib" title="Permalink to this headline"></a></h3>
<p>The first time that you try to run an algorithm that loads the <code class="docutils literal"><span class="pre">matplotlib</span></code>
library, you may get the following error:</p>
<div class="highlight-text"><div class="highlight"><pre><span></span>RuntimeError: Python is not installed as a framework. The Mac OS X backend
<div class="highlight-text"><div class="highlight"><pre>RuntimeError: Python is not installed as a framework. The Mac OS X backend
will not be able to function correctly if Python is not installed as a
framework. See the Python documentation for more information on installing
Python as a framework on Mac OS X. Please either reinstall Python as a
@@ -512,7 +627,7 @@ information.
</div>
<p>This is a <code class="docutils literal"><span class="pre">matplotlib</span></code>-specific error, that will go away once you run the
following command:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">echo</span> <span class="s2">&quot;backend: TkAgg&quot;</span> &gt; ~/.matplotlib/matplotlibrc
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span><span class="nb">echo</span> <span class="s2">&quot;backend: TkAgg&quot;</span> &gt; ~/.matplotlib/matplotlibrc
</pre></div>
</div>
<p>in order to override the default <code class="docutils literal"><span class="pre">MacOS</span></code> backend for your system, which
@@ -582,12 +697,12 @@ update Catalyst frequently. Once installed, Catalyst can easily be updated as a
<code class="docutils literal"><span class="pre">pip</span></code> package regardless of the environemnt used for installation. Make sure
you activate your environment first as you did in your first install, and then
execute:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip uninstall enigma-catalyst
$ pip install enigma-catalyst
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip uninstall enigma-catalyst
<span class="nv">$ </span>pip install enigma-catalyst
</pre></div>
</div>
<p>Alternatively, you could update Catalyst issuing the following command:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ pip install -U enigma-catalyst
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>pip install -U enigma-catalyst
</pre></div>
</div>
<p>but this command will also upgrade all the Catalyst dependencies to the latest
@@ -617,19 +732,15 @@ and you get a hint on how to solve it.</li>
</div>
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@@ -639,10 +750,9 @@ and you get a hint on how to solve it.</li>
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@@ -663,8 +773,7 @@ and you get a hint on how to solve it.</li>
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