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Replaces anaconda python installation with miniforge
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Adds a basic python environment
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@dpshelio
dpshelio committed Sep 6, 2024
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84 changes: 63 additions & 21 deletions _includes/install_instructions/python.html
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Expand Up @@ -13,7 +13,7 @@ <h3>Python</h3>
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
<a href="https://www.anaconda.com/download/success">Anaconda</a>,
<a href="https://conda-forge.org/download/">Conda-forge</a>,
an all-in-one installer.
</p>

Expand All @@ -30,7 +30,7 @@ <h3>Python</h3>
{% endcomment %}
<p>
We will teach Python using the <a href="https://jupyter.org/">Jupyter Notebook</a>,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Miniforge). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
<a href="https://jupyter-notebook.readthedocs.io/en/stable/notebook.html#browser-compatibility">supported</a>
Expand All @@ -48,33 +48,73 @@ <h3>Python</h3>
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="python-windows">
<ol>
<li>Open <a href="https://www.anaconda.com/download/success">https://www.anaconda.com/download/success</a> with your web browser.</li>
<li>Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer <em>Anaconda3-...-Windows-x86_64.exe</em>)</li>
<li>Install Python 3 by running the Anaconda Installer, using all of the defaults for installation <em>except</em> make sure to check <strong>Add Anaconda to my PATH environment variable</strong>.</li>
<li>Open <a href="https://conda-forge.org/download/">https://conda-forge.org/download/</a> with your web browser.</li>
<li>Download the Miniforge for Windows installer</li>
<li>Double click on the downloaded file (Something like, <code>Minforge3-Windows-x86_64.exe</code>)</li>
<li>If you get a "Windows protected your PC" pop-up from Microsoft Defender SmartScreen, click on "More info" and select "Run anyway"</li>
<li>Follow through the installer using all of the defaults for installation <em>except</em> make sure to check <strong>Add Miniforge3 to my PATH environment variable</strong>.</li>
{% comment %}
<li>Search for the application "Miniforge Prompt", open it and run: <code>conda install jupyter</code> and click <kbd>Enter</kbd> when asked for confirmation.</li>
if we want to add an icon, it can be done with:
https://medium.com/@kostal91/create-a-desktop-shortcut-for-jupyterlab-on-windows-9fcabcfa0d3f - easier and more convenient using %userprofile% variable rather than users\%username%
and need to update miniconda for miniforge
Also, the https://pypi.org/project/start-jupyter-cm/ could be helpful.
{% endcomment %}
<li>Download the <a href="./data/swc_environment.yml" download>environment file</a>.<br>
(The following steps requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
</li>
<li>Search for the application "Miniforge Prompt", open it and run: <code>conda env create -f .\Downloads\swc_environment.yml</code></li>
<li>Close the terminal window.</li>
</ol>
<h4>Video Tutorial</h4>
<div class="yt-wrapper2">
<div class="yt-wrapper">
<iframe type="text/html" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" src="https://www.youtube-nocookie.com/embed/xxQ0mzZ8UvA?modestbranding=1&playsinline=1&iv_load_policy=3&rel=0" class="yt-frame" allowfullscreen></iframe>
</div>
</div>
</article>
<article role="tabpanel" class="tab-pane" id="python-macos">
<ol>
<li>Open <a href="https://www.anaconda.com/download/success">https://www.anaconda.com/download/success</a> with your web browser.</li>
<li>Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).</li>
<li>Install Python 3 by running the Anaconda Installer using all of the defaults for installation.</li>
<li>Open <a href="https://conda-forge.org/download/">https://conda-forge.org/download/</a> with your web browser.</li>
<li>Download the appropriate Miniforge installer for macOS<br>
(The following steps requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
</li>
<li>
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., <code>cd ~/Downloads</code>).
</li>
<li>
Type <pre>bash Miniforge3-</pre> and then press
<kbd>Tab</kbd> to autocomplete the full file name. The name of
file you just downloaded should appear.
</li>
<li>
Press <kbd>Enter</kbd>
(or <kbd>Return</kbd> depending on your keyboard).
You will follow the text-only prompts.
To move through the text, press <kbd>Spacebar</kbd>.
Type <code>yes</code> and press enter to approve the license.
Press <kbd>Enter</kbd> (or <kbd>Return</kbd>)
to approve the default location
for the files.
Type <code>yes</code> and press
<kbd>Enter</kbd> (or <kbd>Return</kbd>)
to prepend Anaconda to your <code>PATH</code>
(this makes the Anaconda distribution the default Python).
</li>
<li>Download the <a href="./data/swc_environment.yml" download>environment file</a>.</li>
<li>On the terminal run: <code>conda env create -f ~/Downloads/swc_environment.yml</code></li>
<li>
Close the terminal window.
</li>
</ol>
<h4>Video Tutorial</h4>
<div class="yt-wrapper2">
<div class="yt-wrapper">
<iframe type="text/html" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" src="https://www.youtube-nocookie.com/embed/TcSAln46u9U?modestbranding=1&playsinline=1&iv_load_policy=3&rel=0" class="yt-frame" allowfullscreen></iframe>
</div>
</div>
</article>
<article role="tabpanel" class="tab-pane" id="python-linux">
<ol>
<li>Open <a href="https://www.anaconda.com/download/success">https://www.anaconda.com/download/success</a> with your web browser.</li>
<li>Open <a href="https://conda-forge.org/download/">https://conda-forge.org/download/</a> with your web browser.</li>
<li>Download the appropriate Miniforge installer for Linux<br>
(The following steps requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
</li>
<li>Download the Anaconda Installer with Python 3 for Linux.<br>
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
Expand Down Expand Up @@ -103,6 +143,8 @@ <h4>Video Tutorial</h4>
to prepend Anaconda to your <code>PATH</code>
(this makes the Anaconda distribution the default Python).
</li>
<li>Download the <a href="./data/swc_environment.yml" download>environment file</a>.</li>
<li>Search for the application "Miniforge Prompt", open it and run: <code>conda env create -f ~/Downloads/swc_environment.yml</code></li>
<li>
Close the terminal window.
</li>
Expand Down
9 changes: 9 additions & 0 deletions data/swc_environment.yml
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@@ -0,0 +1,9 @@
name: swc
channels:
- conda-forge
dependencies:
- ipykernel
- jupyer
- matplotlib
- numpy
- pandas

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