deploy: 1b59f12

_sources/contributing.md

@@ -0,0 +1,26 @@
+# Contributing
+
+This is a laboratory website maintained by the SIMEXP team. Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. You can contribute in the ways listed below.
+
+## Improve the content
+
+Fixing typos or suggestion changes to the text is very much appreciated. The layout can always be improved too! Whether you directly implement the changes or just make a general suggestion, do not hesitate to raise an issue.
+
+## Add content
+
+The SIMEXP website can always use more documentation on the laboratory operations. Any other idea is also welcome.
+
+## Get Started
+
+Ready to contribute? Here's how to set up `SIMEXP website` for local development.
+
+1. Fork the repo on GitHub.
+2. Clone your fork locally.
+3. Install your local copy into a virtualenv, e.g., using `virtualenvwrapper` or `conda`.
+4. Create a branch for local development and make changes locally.
+5. Commit your changes and push your branch to GitHub.
+6. Submit a pull request through the GitHub website.
+
+## Code of Conduct
+
+Please note that the SIMEXP website project is released with a [Code of Conduct](coc.md). By contributing to this project you agree to abide by its terms.

_sources/manifesto.md

@@ -2,6 +2,7 @@
 
 Academia means different things to different people. The laboratory for brain simulation and exploration (SIMEXP) is founded on a fairly opinionated, and possibly unusual view of what academia is. This document tries to make the SIMEXP academic values explicit. It does not mean that everybody at SIMEXP shares all of these values, or operates under a particular value at all times. These values are rather guiding principles for many key aspects of the operations of the lab, and form a baseline for expectations.
 
+![Hacking](images/hacking.png)
 ## The hacker way
 Sharing is a key aspect of all academic communities, but how that sharing works varies widely. Lots of academic collaborations are transactional in nature, with people exchanging one contribution for another. Original founders of free software and the hacker movement operate under very different, simple rules. If you want to learn about something, just ask and you can expect an answer. The day somebody wants to learn something from you, you are expected to help that person. Don’t try to balance out what you get and give to a particular person. By helping others, you’re just building up karma, doing good to your community and the world. A corollary of that collaborative ethos is to strive to openly share as much research material as possible, data, code and ideas. The sharing process is greatly facilitated by adopting tools designed for sharing in your daily research activities (“open by design”).
 
@@ -11,6 +12,7 @@ Some laboratories operate under pretty strict labor division, with technical ass
 ## Automate all the things
 Neural data science requires us to iterate analyses a lot, to explore new ideas, replicate analyses on new datasets, and test the impact of various hyper-parameters. This means that data analysis operations should be automated to the greatest extent possible.  
 
+![Brain art](images/brain_art.jpg)
 ## The academic game is not the endgame
 Academia is a highly competitive environment. Some individuals end up focussing their work based on the metrics used to assess them, out of fear of not surviving the game, or simply thinking that it is what the academic community expects them to do. This means that many labs expend considerable energy towards publishing in high impact-factor journals, apply to awards, attend as many conferences as possible, get invited presentations, and sit on many committees, amongst others. The SIMEXP lab does of course support the careers of lab members, whether academic or not, and makes strategic investment of resources towards these metrics. But it is critical to not lose sight that pretty much none of us went into academia to work towards these metrics. The endgame of SIMEXP is to solve problems, namely prognosis of Alzheimer’s disease, and building human-like artificial neural networks. The academic game is a means to these ends. Nothing more. We aim to keep our collective and individual academic boats afloat with bare minimum required efforts, and are committed to not let the academic game ruin the fun and joy we have doing research. We rightfully trust that doing elite research, prioritizing quality over quantity, is all it really takes to strive inside and outside of academia anyway.
 

coc.html

@@ -173,8 +173,8 @@
 <li class="toctree-l1"><a class="reference internal" href="manifesto.html">Manifesto</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Code of conduct</a></li>
 <li class="toctree-l1"><a class="reference internal" href="members.html">Members</a></li>
-<li class="toctree-l1"><a class="reference internal" href="CONTRIBUTING.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="publications.html">Publications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
 </ul>
 
     </div>

CONTRIBUTING.html → contributing.html

@@ -62,12 +62,11 @@
 const thebe_selector_output = ".output, .cell_output"
 </script>
     <script async="async" src="_static/sphinx-thebe.js"></script>
-    <script>DOCUMENTATION_OPTIONS.pagename = 'CONTRIBUTING';</script>
+    <script>DOCUMENTATION_OPTIONS.pagename = 'contributing';</script>
     <link rel="shortcut icon" href="_static/favicon.png"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Publications" href="publications.html" />
-    <link rel="prev" title="Members" href="members.html" />
+    <link rel="prev" title="Publications" href="publications.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -173,8 +172,8 @@
 <li class="toctree-l1"><a class="reference internal" href="manifesto.html">Manifesto</a></li>
 <li class="toctree-l1"><a class="reference internal" href="coc.html">Code of conduct</a></li>
 <li class="toctree-l1"><a class="reference internal" href="members.html">Members</a></li>
-<li class="toctree-l1 current active"><a class="current reference internal" href="#">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="publications.html">Publications</a></li>
+<li class="toctree-l1 current active"><a class="current reference internal" href="#">Contributing</a></li>
 </ul>
 
     </div>
@@ -246,7 +245,7 @@
 
 
 
-      <li><a href="https://github.com/simexp/simexp.github.io/issues/new?title=Issue%20on%20page%20%2FCONTRIBUTING.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/simexp/simexp.github.io/issues/new?title=Issue%20on%20page%20%2Fcontributing.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -276,7 +275,7 @@
 
 
 
-      <li><a href="_sources/CONTRIBUTING.md" target="_blank"
+      <li><a href="_sources/contributing.md" target="_blank"
    class="btn btn-sm btn-download-source-button dropdown-item"
    title="Download source file"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -370,11 +369,8 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#report-bugs">Report Bugs</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#fix-bugs">Fix Bugs</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#implement-features">Implement Features</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#write-documentation">Write Documentation</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submit-feedback">Submit Feedback</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#improve-the-content">Improve the content</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#add-content">Add content</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#get-started">Get Started</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#code-of-conduct">Code of Conduct</a></li>
 </ul>
@@ -390,60 +386,30 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="contributing">
 <h1>Contributing<a class="headerlink" href="#contributing" title="Permalink to this heading">#</a></h1>
-<p>Contributions are welcome, and they are greatly appreciated! Every little bit
-helps, and credit will always be given. You can contribute in the ways listed below.</p>
-<section id="report-bugs">
-<h2>Report Bugs<a class="headerlink" href="#report-bugs" title="Permalink to this heading">#</a></h2>
-<p>Report bugs using GitHub issues.</p>
-<p>If you are reporting a bug, please include:</p>
-<ul class="simple">
-<li><p>Your operating system name and version.</p></li>
-<li><p>Any details about your local setup that might be helpful in troubleshooting.</p></li>
-<li><p>Detailed steps to reproduce the bug.</p></li>
-</ul>
-</section>
-<section id="fix-bugs">
-<h2>Fix Bugs<a class="headerlink" href="#fix-bugs" title="Permalink to this heading">#</a></h2>
-<p>Look through the GitHub issues for bugs. Anything tagged with “bug” and “help
-wanted” is open to whoever wants to implement it.</p>
-</section>
-<section id="implement-features">
-<h2>Implement Features<a class="headerlink" href="#implement-features" title="Permalink to this heading">#</a></h2>
-<p>Look through the GitHub issues for features. Anything tagged with “enhancement”
-and “help wanted” is open to whoever wants to implement it.</p>
-</section>
-<section id="write-documentation">
-<h2>Write Documentation<a class="headerlink" href="#write-documentation" title="Permalink to this heading">#</a></h2>
-<p>SIMEXP website could always use more documentation, whether as part of the
-official SIMEXP website docs, in docstrings, or even on the web in blog posts,
-articles, and such.</p>
+<p>This is a laboratory website maintained by the SIMEXP team. Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. You can contribute in the ways listed below.</p>
+<section id="improve-the-content">
+<h2>Improve the content<a class="headerlink" href="#improve-the-content" title="Permalink to this heading">#</a></h2>
+<p>Fixing typos or suggestion changes to the text is very much appreciated. The layout can always be improved too! Whether you directly implement the changes or just make a general suggestion, do not hesitate to raise an issue.</p>
 </section>
-<section id="submit-feedback">
-<h2>Submit Feedback<a class="headerlink" href="#submit-feedback" title="Permalink to this heading">#</a></h2>
-<p>The best way to send feedback is to file an issue on GitHub.</p>
-<p>If you are proposing a feature:</p>
-<ul class="simple">
-<li><p>Explain in detail how it would work.</p></li>
-<li><p>Keep the scope as narrow as possible, to make it easier to implement.</p></li>
-<li><p>Remember that this is a volunteer-driven project, and that contributions
-are welcome :)</p></li>
-</ul>
+<section id="add-content">
+<h2>Add content<a class="headerlink" href="#add-content" title="Permalink to this heading">#</a></h2>
+<p>The SIMEXP website can always use more documentation on the laboratory operations. Any other idea is also welcome.</p>
 </section>
 <section id="get-started">
 <h2>Get Started<a class="headerlink" href="#get-started" title="Permalink to this heading">#</a></h2>
 <p>Ready to contribute? Here’s how to set up <code class="docutils literal notranslate"><span class="pre">SIMEXP</span> <span class="pre">website</span></code> for local development.</p>
 <ol class="arabic simple">
 <li><p>Fork the repo on GitHub.</p></li>
 <li><p>Clone your fork locally.</p></li>
-<li><p>Install your local copy into a virtualenv, e.g., using <code class="docutils literal notranslate"><span class="pre">conda</span></code>.</p></li>
+<li><p>Install your local copy into a virtualenv, e.g., using <code class="docutils literal notranslate"><span class="pre">virtualenvwrapper</span></code> or <code class="docutils literal notranslate"><span class="pre">conda</span></code>.</p></li>
 <li><p>Create a branch for local development and make changes locally.</p></li>
 <li><p>Commit your changes and push your branch to GitHub.</p></li>
 <li><p>Submit a pull request through the GitHub website.</p></li>
 </ol>
 </section>
 <section id="code-of-conduct">
 <h2>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Permalink to this heading">#</a></h2>
-<p>Please note that the SIMEXP website project is released with a <span class="xref myst">Contributor Code of Conduct</span>. By contributing to this project you agree to abide by its terms.</p>
+<p>Please note that the SIMEXP website project is released with a <a class="reference internal" href="coc.html"><span class="doc std std-doc">Code of Conduct</span></a>. By contributing to this project you agree to abide by its terms.</p>
 </section>
 </section>
 
@@ -478,22 +444,13 @@ <h2>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Permalin
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="members.html"
+       href="publications.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Members</p>
-      </div>
-    </a>
-    <a class="right-next"
-       href="publications.html"
-       title="next page">
-      <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
         <p class="prev-next-title">Publications</p>
       </div>
-      <i class="fa-solid fa-angle-right"></i>
     </a>
 </div>
                 </footer>
@@ -510,11 +467,8 @@ <h2>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Permalin
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#report-bugs">Report Bugs</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#fix-bugs">Fix Bugs</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#implement-features">Implement Features</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#write-documentation">Write Documentation</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#submit-feedback">Submit Feedback</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#improve-the-content">Improve the content</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#add-content">Add content</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#get-started">Get Started</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#code-of-conduct">Code of Conduct</a></li>
 </ul>

genindex.html

@@ -170,8 +170,8 @@
 <li class="toctree-l1"><a class="reference internal" href="manifesto.html">Manifesto</a></li>
 <li class="toctree-l1"><a class="reference internal" href="coc.html">Code of conduct</a></li>
 <li class="toctree-l1"><a class="reference internal" href="members.html">Members</a></li>
-<li class="toctree-l1"><a class="reference internal" href="CONTRIBUTING.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="publications.html">Publications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
 </ul>
 
     </div>

intro.html

@@ -172,8 +172,8 @@
 <li class="toctree-l1"><a class="reference internal" href="manifesto.html">Manifesto</a></li>
 <li class="toctree-l1"><a class="reference internal" href="coc.html">Code of conduct</a></li>
 <li class="toctree-l1"><a class="reference internal" href="members.html">Members</a></li>
-<li class="toctree-l1"><a class="reference internal" href="CONTRIBUTING.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="publications.html">Publications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
 </ul>
 
     </div>