2239 lines
61 KiB
HTML
2239 lines
61 KiB
HTML
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<title>ob-julia: high quality julia org-mode support</title>
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<meta name="author" content="Nicolò Balzarotti" />
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#org-div-home-and-up
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<style>pre.src-julia:before { content: 'julia'; }</style>
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<script type="text/javascript">
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/*
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@licstart The following is the entire license notice for the
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JavaScript code in this tag.
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any later version. The code is distributed WITHOUT ANY WARRANTY;
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without even the implied warranty of MERCHANTABILITY or FITNESS
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FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
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As additional permission under GNU GPL version 3 section 7, you
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may distribute non-source (e.g., minimized or compacted) forms of
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through which recipients can access the Corresponding Source.
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@licend The above is the entire license notice
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*/
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</head>
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<body>
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<div id="content">
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<h1 class="title">ob-julia: high quality julia org-mode support</h1>
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<div id="table-of-contents">
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org36bfcd8">1. ob-julia</a></li>
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<li><a href="#orgabd302e">2. How it works</a></li>
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<li><a href="#org2d55a4b">3. Implemented features</a>
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<ul>
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<li><a href="#org08ced76">3.1. Session (<code>:session none</code>, <code>:session</code>, <code>:session session-name</code>)</a></li>
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<li><a href="#org6b34a8f">3.2. Async (<code>:async</code> <code>:async yes</code>, <code>:async t</code>)</a></li>
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<li><a href="#org1cc6d26">3.3. Variables input (<code>:var</code>), Standard output</a>
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<ul>
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<li><a href="#org3dc535d">3.3.1. Inputs</a></li>
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</ul>
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</li>
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<li><a href="#orgcc48829">3.4. Directory (<code>:dir</code>)</a></li>
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<li><a href="#org45b73dd">3.5. Error management</a></li>
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<li><a href="#org6e84a66">3.6. Using (<code>:using</code>) and Import (<code>:import</code>)</a></li>
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<li><a href="#org1053058">3.7. Results (<code>:results output</code>, <code>:results file</code>, )</a></li>
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<li><a href="#orgce3b792">3.8. Supported Types</a></li>
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<li><a href="#org4346a6b">3.9. File output & Inlining</a>
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<ul>
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<li><a href="#org58644e0">3.9.1. Inlining (<code>:inline no</code>, <code>:inline</code>, <code>:inline format</code>)</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li><a href="#orgde8118c">4. Issues and Missing features</a></li>
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<li><a href="#orgcbcfb68">5. Credits</a></li>
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</ul>
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</div>
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</div>
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<div id="outline-container-org36bfcd8" class="outline-2">
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<h2 id="org36bfcd8"><span class="section-number-2">1</span> ob-julia</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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See <a href="#org2d55a4b">3</a> for more details.
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</p>
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</div>
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</div>
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<div id="outline-container-orgabd302e" class="outline-2">
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<h2 id="orgabd302e"><span class="section-number-2">2</span> How it works</h2>
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<div class="outline-text-2" id="text-2">
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<ol class="org-ol">
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<li>Code block is saved to a temporary file (under /tmp)</li>
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<li>Decide whether we need to start a new julia process or not
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<ol class="org-ol">
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<li>If session is "none", don't use a session (code under /tmp will
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be passed to <code>julia -L initfile src-block.jl</code>). This does not
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require ess. The command is customized by
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<code>org-babel-julia-command</code>)</li>
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<li>If session is nil, use default session name
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(customized by <code>org-babel-julia-default-session</code>)</li>
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<li>If session has a values, use it's name</li>
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</ol></li>
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<li>Check if we want to use a session or not. Check if the session
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exists. Start the session accordingly.</li>
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<li>Is the evaluation async?
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<ol class="org-ol">
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<li>YES:
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<ol class="org-ol">
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<li>Register a filter function</li>
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<li>Return immediately, printing a ref to the evaluation.
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The ref is in the form: <code>julia-async:$uuid:$tmpfile</code>
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<ul class="org-ul">
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<li>uuid: identifier of this evaluation, used to find out where to
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insert again results</li>
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<li>tmpfile: the path where the output will be saved. This is
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useful both for debugging purposes and so that we do not need
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to store an object that maps computations to files. The
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process-filter look for the uuid, and then inserts <code>$tmpfile</code>.</li>
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</ul></li>
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</ol></li>
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<li>NO: Run the code, wait for the results. Insert the results.</li>
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</ol></li>
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</ol>
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</div>
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</div>
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|
<div id="outline-container-org2d55a4b" class="outline-2">
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<h2 id="org2d55a4b"><span class="section-number-2">3</span> Implemented features</h2>
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<div class="outline-text-2" id="text-3">
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</div>
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<div id="outline-container-org08ced76" class="outline-3">
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<h3 id="org08ced76"><span class="section-number-3">3.1</span> Session (<code>:session none</code>, <code>:session</code>, <code>:session session-name</code>)</h3>
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<div class="outline-text-3" id="text-3-1">
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<p>
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|
By default code is executed without a session. The advantage is that
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you do not requires <code>emacs-ess</code> to run julia code with ob-julia. But
|
|
sessions (especially for julia, where speed comes from compiled code)
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|
are available. The same behaviour is obtained by setting the <code>:session</code>
|
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header to <code>none</code>.
|
|
</p>
|
|
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|
<p>
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|
You can enable sessions with the <code>:session</code> argument. Without
|
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parameters, the session used is named after
|
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<code>org-babel-julia-default-session</code> (<code>*julia*</code> by default). With a
|
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parameter, the name is earmuffed (a star is prepended and appended).
|
|
</p>
|
|
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<p>
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|
The REPL is kept sane. There's no cluttering (you don't see all the
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code executed that is required by ob-julia to have results), history
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|
is preserved (you can <code>C-S-up</code> to see the list of org-src block
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|
evaluated), and results are shown (this can be customized by
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|
<code>org-babel-julia-silent-repl</code>).
|
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</p>
|
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</div>
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</div>
|
|
|
|
<div id="outline-container-org6b34a8f" class="outline-3">
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<h3 id="org6b34a8f"><span class="section-number-3">3.2</span> Async (<code>:async</code> <code>:async yes</code>, <code>:async t</code>)</h3>
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<div class="outline-text-3" id="text-3-2">
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|
<p>
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|
Async works both with and without <code>:session</code>.
|
|
</p>
|
|
|
|
<p>
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|
The best combination of features is combining session with
|
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<code>:async</code>. Async allows code evaluation in background (you can continue
|
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using emacs while julia compute results).
|
|
</p>
|
|
|
|
<p>
|
|
You can change buffer or even narrow it while the evaluation
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|
completes: the result is added automatically as soon as julia
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finishes. Multiple evaluation are queued automatically (thanks to
|
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ess). Cache is supported (evaluating the same code-block twice does
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not re-trigger evaluation, even if the code is still running).
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</p>
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|
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|
<p>
|
|
It's not possible to have async blocks with <code>:results silent</code>. I'm
|
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currently using this to distinguish between active src block and
|
|
variable resolution (when a <code>:var</code> refer to an async block, the block
|
|
cannot be executed asynchonously. So we need to distinguish between
|
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the two. This is the only way I was able to find, if you know better
|
|
please tell me).
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</p>
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|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">sleep(1)
|
|
<span style="color: #8b2252;">"It works!"</span>
|
|
</pre>
|
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</div>
|
|
|
|
<pre class="example">
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|
It works!
|
|
</pre>
|
|
|
|
|
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<div class="org-src-container">
|
|
<pre class="src src-julia">sleep(1)
|
|
<span style="color: #8b2252;">"It works!"</span>
|
|
</pre>
|
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</div>
|
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|
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<pre class="example">
|
|
It works!
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
Here the same, without the session
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">sleep(1)
|
|
<span style="color: #8b2252;">"It works!"</span>
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
It works!
|
|
</pre>
|
|
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">sleep(1)
|
|
<span style="color: #8b2252;">"It works!"</span>
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
It works!
|
|
</pre>
|
|
|
|
|
|
|
|
<p>
|
|
Asynchronous evaluation is automatically disabled on export, or when a
|
|
code block depends on one (<code>:var</code>)
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org1cc6d26" class="outline-3">
|
|
<h3 id="org1cc6d26"><span class="section-number-3">3.3</span> Variables input (<code>:var</code>), Standard output</h3>
|
|
<div class="outline-text-3" id="text-3-3">
|
|
</div>
|
|
<div id="outline-container-org3dc535d" class="outline-4">
|
|
<h4 id="org3dc535d"><span class="section-number-4">3.3.1</span> Inputs</h4>
|
|
<div class="outline-text-4" id="text-3-3-1">
|
|
<p>
|
|
Those are example inputs that will be used later, to check whether
|
|
import+export pipeline works as expected.
|
|
</p>
|
|
|
|
<p>
|
|
A table
|
|
</p>
|
|
|
|
<table id="org35deea2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">a</th>
|
|
<th scope="col" class="org-right">b</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right"> </td>
|
|
<td class="org-right"> </td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
A matrix (no hline)
|
|
</p>
|
|
|
|
<table id="org145e0c5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
A column
|
|
</p>
|
|
|
|
<table id="orge510b86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
A row
|
|
</p>
|
|
|
|
<table id="org9a52593" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
A list
|
|
</p>
|
|
|
|
<ul class="org-ul">
|
|
<li>1</li>
|
|
<li>2</li>
|
|
<li>3</li>
|
|
<li>4</li>
|
|
</ul>
|
|
</div>
|
|
|
|
<ol class="org-ol">
|
|
<li><a id="orgcadfe14"></a>Table<br />
|
|
<div class="outline-text-5" id="text-3-3-1-1">
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">table
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">a</th>
|
|
<th scope="col" class="org-right">b</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right"> </td>
|
|
<td class="org-right"> </td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
As you can see, the table automatically adds the hline after the
|
|
header. This is a heuristic that might fail (might be triggered for
|
|
matrix, might not trigger on tables), so you can manually
|
|
force/disable it with the <code>:results table</code> or <code>:results matrix</code> param.
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">table
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">a</td>
|
|
<td class="org-right">b</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right"> </td>
|
|
<td class="org-right"> </td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</li>
|
|
|
|
<li><a id="orgd402086"></a>Row<br />
|
|
<div class="outline-text-5" id="text-3-3-1-2">
|
|
<p>
|
|
Column, Rows, and Matrix export works just fine (tests in session sync, session async
|
|
and without session).
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org5f960b7">row
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="orgb68478b">row
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org7733fbb">row
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</li>
|
|
|
|
<li><a id="org3180867"></a>Column<br />
|
|
<div class="outline-text-5" id="text-3-3-1-3">
|
|
<p>
|
|
Works both with synchronous evaluation
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org3c1fdbd">column
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
asynchronous evaluation
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org04805eb">column
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
and without a session
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org5628a9d">column
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</li>
|
|
|
|
<li><a id="org14530c2"></a>Matrix<br />
|
|
<div class="outline-text-5" id="text-3-3-1-4">
|
|
<p>
|
|
Sync
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="orgf312a0d">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
Just like for tables, you can control header hline line with the
|
|
results param.
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">1</th>
|
|
<th scope="col" class="org-right">2</th>
|
|
<th scope="col" class="org-right">3</th>
|
|
<th scope="col" class="org-right">4</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
Async
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="orga168090">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
No session
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org40d06a2">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">1</th>
|
|
<th scope="col" class="org-right">2</th>
|
|
<th scope="col" class="org-right">3</th>
|
|
<th scope="col" class="org-right">4</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">3</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</li>
|
|
|
|
<li><a id="orgfe7813a"></a>List<br />
|
|
<div class="outline-text-5" id="text-3-3-1-5">
|
|
<p>
|
|
List are parsed as columns
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-emacs-lisp">list
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<code>:results list</code> return the list (just like R). It's not perfect with
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">list
|
|
</pre>
|
|
</div>
|
|
|
|
<ul class="org-ul">
|
|
<li>(1)</li>
|
|
<li>(2)</li>
|
|
<li>(3)</li>
|
|
<li>(4)</li>
|
|
</ul>
|
|
</div>
|
|
</li>
|
|
|
|
<li><a id="orgb2b4371"></a>Table<br />
|
|
<div class="outline-text-5" id="text-3-3-1-6">
|
|
<p>
|
|
There are two ways in which tables can be passed to Julia:
|
|
</p>
|
|
<ul class="org-ul">
|
|
<li>Array{NamedTuple}</li>
|
|
<li>Dictionary</li>
|
|
</ul>
|
|
|
|
<p>
|
|
I like the NamedTuple approach, but if you don't like it you can
|
|
customize the variable <code>org-babel-julia-table-as-dict</code>. In both cases,
|
|
if you <a href="#org6e84a66">:import</a> DataFrames, you can construct a DataFrame from both.
|
|
</p>
|
|
|
|
<p>
|
|
TOOD: I miss the julia code for printing Array{NamedTuple}.
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">table
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">a</th>
|
|
<th scope="col" class="org-right">b</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-right">1</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right"> </td>
|
|
<td class="org-right"> </td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-right">4</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
Also, it's nice that a single NamedTuple can represent a table:
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">table[2]
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">a</th>
|
|
<th scope="col" class="org-right">b</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-right">2</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgcc48829" class="outline-3">
|
|
<h3 id="orgcc48829"><span class="section-number-3">3.4</span> Directory (<code>:dir</code>)</h3>
|
|
<div class="outline-text-3" id="text-3-4">
|
|
<p>
|
|
Each source block is evaluated in it's :dir param
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">pwd()
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
/tmp
|
|
</pre>
|
|
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">pwd()
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
/
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
If unspecified, the directory is session's one
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">pwd()
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
/home/nixo/dotfiles/emacs/.emacs.d/extra/ob-julia
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
Changing dir from julia code still works
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">cd(<span style="color: #8b2252;">"/"</span>)
|
|
realpath(<span style="color: #8b2252;">"."</span>)
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
/
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
but is ephemeral (like fort the <code>:dir</code> param)
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">realpath(<span style="color: #8b2252;">"."</span>)
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
/home/nixo/dotfiles/emacs/.emacs.d/extra/ob-julia
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
This is obtained by wrapping the src block in a <code>cd()</code> call:
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">cd(folder) <span style="color: #a020f0;">do</span>
|
|
block
|
|
<span style="color: #a020f0;">end</span>
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org45b73dd" class="outline-3">
|
|
<h3 id="org45b73dd"><span class="section-number-3">3.5</span> Error management</h3>
|
|
<div class="outline-text-3" id="text-3-5">
|
|
<p>
|
|
If the block errors out,
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org35390b6">x
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">UndefVarError(:x)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org9e87d69">1 + <span style="color: #8b2252;">"ciao"</span>
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">MethodError(+</td>
|
|
<td class="org-left">(1</td>
|
|
<td class="org-left">ciao)</td>
|
|
<td class="org-right">0x0000000000006426)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
|
|
<col class="org-right" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">MethodError(+</td>
|
|
<td class="org-left">(1</td>
|
|
<td class="org-left">ciao)</td>
|
|
<td class="org-right">0x0000000000006420)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
It works in async
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">x
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">UndefVarError(:x)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
On external process (sync)
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">x
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">UndefVarError(:x)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
and on external process (async)
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">x
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-left" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-left">ERROR</td>
|
|
<td class="org-left">UndefVarError(:x)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
Error management can still be improved for helping with debug (see
|
|
scimax).
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org6e84a66" class="outline-3">
|
|
<h3 id="org6e84a66"><span class="section-number-3">3.6</span> Using (<code>:using</code>) and Import (<code>:import</code>)</h3>
|
|
<div class="outline-text-3" id="text-3-6">
|
|
<p>
|
|
To include dependencies, you can use <code>:using</code> and <code>:import</code>.
|
|
</p>
|
|
|
|
<p>
|
|
Because of how the julia code is actually implemented, in order to use
|
|
specialized exports (e.g., DataFrames, see ) you need the
|
|
modules to be available <span class="underline">before</span> the block gets evaluated. The problem
|
|
can be solved in 2 (or 3 ways):
|
|
</p>
|
|
<ul class="org-ul">
|
|
<li>Evaluating a block with using/import, then the other block</li>
|
|
<li>Using the header arguments</li>
|
|
<li>Fixing the Julia code :D</li>
|
|
</ul>
|
|
|
|
<p>
|
|
to use <code>:import</code>, you need to pass arguments quoted:
|
|
</p>
|
|
<pre class="example">
|
|
:using DataFrames Query :import "FileIO: load" "Plots: plot"
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org1053058" class="outline-3">
|
|
<h3 id="org1053058"><span class="section-number-3">3.7</span> Results (<code>:results output</code>, <code>:results file</code>, )</h3>
|
|
<div class="outline-text-3" id="text-3-7">
|
|
<p>
|
|
The default is to return the value:
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">10
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
10
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
If results is output, it's included the stdout (what's printed in the
|
|
terminal). (This part still needs some work to be useful.)
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">10
|
|
</pre>
|
|
</div>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">println(10)
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
10
|
|
</pre>
|
|
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">println(<span style="color: #8b2252;">"a"</span>)
|
|
|
|
<span style="color: #8b2252;">"10"</span>
|
|
|
|
println(<span style="color: #8b2252;">"b"</span>)
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
a
|
|
b
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
Error (results output)
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">This will throw an error
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
Base.Meta.ParseError("extra token \"will\" after end of expression")
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
Another error (result ouptut)
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">print(one(3,3))
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
MethodError(one, (3, 3), 0x0000000000006426)
|
|
</pre>
|
|
|
|
|
|
<p>
|
|
A matrix
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">print(ones(3,3))
|
|
</pre>
|
|
</div>
|
|
|
|
<pre class="example">
|
|
[1.0 1.0 1.0; 1.0 1.0 1.0; 1.0 1.0 1.0]
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgce3b792" class="outline-3">
|
|
<h3 id="orgce3b792"><span class="section-number-3">3.8</span> Supported Types</h3>
|
|
<div class="outline-text-3" id="text-3-8">
|
|
<p>
|
|
Adding new types is easy (you need to define an <code>orgshow()</code> function for
|
|
your type. See <a href="init.jl#MissingReference">init.jl</a>). There's a simple mechanism that allows to
|
|
define method on non-yet-existing types <a href="init.jl#MissingReference">example</a>.
|
|
</p>
|
|
|
|
<p>
|
|
The current version supports a couple of useful type: DataFrames and
|
|
Plots. ob-julia needs community support to add more types: please help!
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-org4346a6b" class="outline-3">
|
|
<h3 id="org4346a6b"><span class="section-number-3">3.9</span> File output & Inlining</h3>
|
|
<div class="outline-text-3" id="text-3-9">
|
|
<p>
|
|
There's native support for writing output to file. For unkown file
|
|
types, instead of inserting the output in the buffer it's written to the file.
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">zeros(3,3)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<a href="readme/output.html">readme/output.html</a>
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">zeros(3,3)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<a href="readme/output.csv">readme/output.csv</a>
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia"><span style="color: #228b22;">Dict</span>(10 => 10)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<a href="readme/output.csv">readme/output.csv</a>
|
|
</p>
|
|
|
|
<p>
|
|
Saving plots requires the Plots library. You can require it with the
|
|
<code>:using</code> <a href="#org6e84a66">header</a>. There's the custom <code>:size "tuple"</code> header argument for
|
|
specifying the output size. It <span class="underline">must</span> be placed inside parentheses, and
|
|
it's evaluated as julia object (that means it can contains variables
|
|
and expressions).
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">plot(matrix)
|
|
</pre>
|
|
</div>
|
|
|
|
|
|
<div class="figure">
|
|
<p><img src="readme/output-plot.png" alt="output-plot.png" />
|
|
</p>
|
|
</div>
|
|
|
|
<p>
|
|
Matrix also has an automatic conversion (when Plots is loaded), so you
|
|
don't even need to pass it to the <code>plot()</code> function (there's a generic
|
|
fallback that tries to plot anything saved to png or svg).
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
|
|
<div class="figure">
|
|
<p><object type="image/svg+xml" data="readme/output-matrix.svg" class="org-svg">
|
|
Sorry, your browser does not support SVG.</object>
|
|
</p>
|
|
</div>
|
|
|
|
<p>
|
|
Plots can also manage errors (in a visually-disturbing way).
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">this_is_undefined
|
|
</pre>
|
|
</div>
|
|
|
|
|
|
<div class="figure">
|
|
<p><object type="image/svg+xml" data="readme/output-undef.svg" class="org-svg">
|
|
Sorry, your browser does not support SVG.</object>
|
|
</p>
|
|
</div>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">another_undefined_but_async
|
|
</pre>
|
|
</div>
|
|
|
|
|
|
<div class="figure">
|
|
<p><img src="readme/output-undef.png" alt="output-undef.png" />
|
|
</p>
|
|
</div>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia" id="org998d143">DataFrame(x = 1:10, y = (0:9) .+ <span style="color: #8b2252;">'a'</span>)
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">x</th>
|
|
<th scope="col" class="org-left">y</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-left">a</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-left">b</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
<td class="org-left">c</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-left">d</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">5</td>
|
|
<td class="org-left">e</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">6</td>
|
|
<td class="org-left">f</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">7</td>
|
|
<td class="org-left">g</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">8</td>
|
|
<td class="org-left">h</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">9</td>
|
|
<td class="org-left">i</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">10</td>
|
|
<td class="org-left">j</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">DataFrame(table)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<a href="readme/output-table.csv">readme/output-table.csv</a>
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">data
|
|
</pre>
|
|
</div>
|
|
|
|
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
|
|
|
|
|
<colgroup>
|
|
<col class="org-right" />
|
|
|
|
<col class="org-left" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th scope="col" class="org-right">x</th>
|
|
<th scope="col" class="org-left">y</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td class="org-right">1</td>
|
|
<td class="org-left">a</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">2</td>
|
|
<td class="org-left">b</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">3</td>
|
|
<td class="org-left">c</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">4</td>
|
|
<td class="org-left">d</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">5</td>
|
|
<td class="org-left">e</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">6</td>
|
|
<td class="org-left">f</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">7</td>
|
|
<td class="org-left">g</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">8</td>
|
|
<td class="org-left">h</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">9</td>
|
|
<td class="org-left">i</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td class="org-right">10</td>
|
|
<td class="org-left">j</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
|
|
<div id="outline-container-org58644e0" class="outline-4">
|
|
<h4 id="org58644e0"><span class="section-number-4">3.9.1</span> Inlining (<code>:inline no</code>, <code>:inline</code>, <code>:inline format</code>)</h4>
|
|
<div class="outline-text-4" id="text-3-9-1">
|
|
<p>
|
|
Output to file and Inlining are different things but nicely fit
|
|
together to solve the same problem: inserting images or other objects
|
|
inside the buffer.
|
|
</p>
|
|
|
|
<p>
|
|
If your type can be represented inside the exported format (like
|
|
images as svg/base-64 encoded pngs inside <code>.html</code>, tex plots in a <code>.tex</code>
|
|
file), the <code>:inline</code> header is what you need. The behaviour changes
|
|
based depending on your interactive use and on the desired output
|
|
format.
|
|
</p>
|
|
|
|
<p>
|
|
TODO: right now :results raw is required on export. How do we fix it?
|
|
</p>
|
|
|
|
<p>
|
|
Examples: :inline keyword alone, in interactive evaluation, the output
|
|
inserted in the buffer is the usual.
|
|
</p>
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<table style="width:100%"><tr><th>1</th><th>2</th><th>3</th><th>4</tr><tr><th>1</th><th>2</th><th>3</th><th>4</table>
|
|
</p>
|
|
|
|
<p>
|
|
But when you export the output to html, the output will be processed
|
|
<span class="underline">by julia</span>, and inserted in the buffer (or a different representation
|
|
for different export formats). This is not of much use with tables
|
|
(even if you can customize the export, e.g. by passing the :width
|
|
keyword), but is wonderful for pictures. If a result can be inserted
|
|
in multiple ways (picture in html can be both inline png or svg), you
|
|
can specify the desired format by passing the argument to the :inline
|
|
keyword (like <code>:inline svg</code>). In this case, the processed output is
|
|
inserted also in interactive sessions.
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">matrix
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<table style="width:10%"><tr><th>1</th><th>2</th><th>3</th><th>4</tr><tr><th>1</th><th>2</th><th>3</th><th>4</table>
|
|
</p>
|
|
|
|
<p>
|
|
Plots default to inline png
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">plot(matrix)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<?xml version="1.0" encoding="utf-8"?>
|
|
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="600" height="400" viewBox="0 0 2400 1600">
|
|
<defs>
|
|
<clipPath id="clip0700">
|
|
<rect x="0" y="0" width="2400" height="1600"/>
|
|
</clipPath>
|
|
</defs>
|
|
<path clip-path="url(#clip0700)" d="
|
|
M0 1600 L2400 1600 L2400 0 L0 0 Z
|
|
" fill="#ffffff" fill-rule="evenodd" fill-opacity="1"/>
|
|
<defs>
|
|
<clipPath id="clip0701">
|
|
<rect x="480" y="0" width="1681" height="1600"/>
|
|
</clipPath>
|
|
</defs>
|
|
<path clip-path="url(#clip0700)" d="
|
|
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" fill="#ffffff" fill-rule="evenodd" fill-opacity="1"/>
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<defs>
|
|
<clipPath id="clip0702">
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|
<rect x="113" y="47" width="2240" height="1441"/>
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</clipPath>
|
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</defs>
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<polyline clip-path="url(#clip0702)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
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<g clip-path="url(#clip0700)">
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</g>
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<g clip-path="url(#clip0700)">
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<g clip-path="url(#clip0700)">
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</g>
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<g clip-path="url(#clip0700)">
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<path clip-path="url(#clip0700)" d="
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|
|
"/>
|
|
<polyline clip-path="url(#clip0700)" style="stroke:#009af9; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,191.244 2157.93,191.244
|
|
"/>
|
|
<g clip-path="url(#clip0700)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 208.744)" x="2181.93" y="208.744">y1</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip0700)" style="stroke:#e26f46; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,251.724 2157.93,251.724
|
|
"/>
|
|
<g clip-path="url(#clip0700)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 269.224)" x="2181.93" y="269.224">y2</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip0700)" style="stroke:#3da44d; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,312.204 2157.93,312.204
|
|
"/>
|
|
<g clip-path="url(#clip0700)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 329.704)" x="2181.93" y="329.704">y3</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip0700)" style="stroke:#c271d2; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,372.684 2157.93,372.684
|
|
"/>
|
|
<g clip-path="url(#clip0700)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 390.184)" x="2181.93" y="390.184">y4</text>
|
|
</g>
|
|
</svg>
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
But you can also force svg (Since it's multiline, :wrap it with <code>:wrap html</code>)
|
|
</p>
|
|
|
|
<div class="org-src-container">
|
|
<pre class="src src-julia">plot(matrix)
|
|
</pre>
|
|
</div>
|
|
|
|
<p>
|
|
<?xml version="1.0" encoding="utf-8"?>
|
|
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="600" height="400" viewBox="0 0 2400 1600">
|
|
<defs>
|
|
<clipPath id="clip1000">
|
|
<rect x="0" y="0" width="2400" height="1600"/>
|
|
</clipPath>
|
|
</defs>
|
|
<path clip-path="url(#clip1000)" d="
|
|
M0 1600 L2400 1600 L2400 0 L0 0 Z
|
|
" fill="#ffffff" fill-rule="evenodd" fill-opacity="1"/>
|
|
<defs>
|
|
<clipPath id="clip1001">
|
|
<rect x="480" y="0" width="1681" height="1600"/>
|
|
</clipPath>
|
|
</defs>
|
|
<path clip-path="url(#clip1000)" d="
|
|
M113.754 1487.47 L2352.76 1487.47 L2352.76 47.2441 L113.754 47.2441 Z
|
|
" fill="#ffffff" fill-rule="evenodd" fill-opacity="1"/>
|
|
<defs>
|
|
<clipPath id="clip1002">
|
|
<rect x="113" y="47" width="2240" height="1441"/>
|
|
</clipPath>
|
|
</defs>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
177.122,1487.47 177.122,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
705.189,1487.47 705.189,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
1233.26,1487.47 1233.26,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
1761.32,1487.47 1761.32,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
2289.39,1487.47 2289.39,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
113.754,1446.71 2352.76,1446.71
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
113.754,993.811 2352.76,993.811
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|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
113.754,540.908 2352.76,540.908
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#000000; stroke-width:2; stroke-opacity:0.1; fill:none" points="
|
|
113.754,88.0053 2352.76,88.0053
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,1487.47 2352.76,1487.47
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,1487.47 113.754,47.2441
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
177.122,1487.47 177.122,1465.87
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
705.189,1487.47 705.189,1465.87
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|
"/>
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|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
1233.26,1487.47 1233.26,1465.87
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
1761.32,1487.47 1761.32,1465.87
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2289.39,1487.47 2289.39,1465.87
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,1446.71 147.339,1446.71
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,993.811 147.339,993.811
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,540.908 147.339,540.908
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
113.754,88.0053 147.339,88.0053
|
|
"/>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:middle;" transform="rotate(0, 177.122, 1541.47)" x="177.122" y="1541.47">1.00</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:middle;" transform="rotate(0, 705.189, 1541.47)" x="705.189" y="1541.47">1.25</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:middle;" transform="rotate(0, 1233.26, 1541.47)" x="1233.26" y="1541.47">1.50</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:middle;" transform="rotate(0, 1761.32, 1541.47)" x="1761.32" y="1541.47">1.75</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:middle;" transform="rotate(0, 2289.39, 1541.47)" x="2289.39" y="1541.47">2.00</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:end;" transform="rotate(0, 89.7545, 1464.21)" x="89.7545" y="1464.21">1</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:end;" transform="rotate(0, 89.7545, 1011.31)" x="89.7545" y="1011.31">2</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:end;" transform="rotate(0, 89.7545, 558.408)" x="89.7545" y="558.408">3</text>
|
|
</g>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:end;" transform="rotate(0, 89.7545, 105.505)" x="89.7545" y="105.505">4</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#009af9; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
177.122,1446.71 2289.39,1446.71
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#e26f46; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
177.122,993.811 2289.39,993.811
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#3da44d; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
177.122,540.908 2289.39,540.908
|
|
"/>
|
|
<polyline clip-path="url(#clip1002)" style="stroke:#c271d2; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
177.122,88.0053 2289.39,88.0053
|
|
"/>
|
|
<path clip-path="url(#clip1000)" d="
|
|
M1989.93 433.164 L2280.76 433.164 L2280.76 130.764 L1989.93 130.764 Z
|
|
" fill="#ffffff" fill-rule="evenodd" fill-opacity="1"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#000000; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
1989.93,433.164 2280.76,433.164 2280.76,130.764 1989.93,130.764 1989.93,433.164
|
|
"/>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#009af9; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,191.244 2157.93,191.244
|
|
"/>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 208.744)" x="2181.93" y="208.744">y1</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#e26f46; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,251.724 2157.93,251.724
|
|
"/>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 269.224)" x="2181.93" y="269.224">y2</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#3da44d; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,312.204 2157.93,312.204
|
|
"/>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 329.704)" x="2181.93" y="329.704">y3</text>
|
|
</g>
|
|
<polyline clip-path="url(#clip1000)" style="stroke:#c271d2; stroke-width:4; stroke-opacity:1; fill:none" points="
|
|
2013.93,372.684 2157.93,372.684
|
|
"/>
|
|
<g clip-path="url(#clip1000)">
|
|
<text style="fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;" transform="rotate(0, 2181.93, 390.184)" x="2181.93" y="390.184">y4</text>
|
|
</g>
|
|
</svg>
|
|
|
|
</p>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<div id="outline-container-orgde8118c" class="outline-2">
|
|
<h2 id="orgde8118c"><span class="section-number-2">4</span> Issues and Missing features</h2>
|
|
<div class="outline-text-2" id="text-4">
|
|
<ul class="org-ul">
|
|
<li>No automated tests yet</li>
|
|
<li>Not tested with remote host</li>
|
|
<li>Variable resolution of src-block is synchronous. If your :async src
|
|
block depends on another :async src block, the latter is evaluated
|
|
synchronously, then former asynchonously. This could be implemented
|
|
by using a simple queue, where next item is started in the
|
|
process-filter and where variables starting with julia-async: are
|
|
replaced. Right now I don't feel the need (if results are cached,
|
|
things already feels good).</li>
|
|
<li>For async evaluation to work the session must be started from
|
|
ob-julia (or you must register the filter function manually,
|
|
undocumented).</li>
|
|
<li><code>:results output</code> is implemented but untested. I rarely find it
|
|
useful.</li>
|
|
<li>import/using errors are not reported</li>
|
|
</ul>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgcbcfb68" class="outline-2">
|
|
<h2 id="orgcbcfb68"><span class="section-number-2">5</span> Credits</h2>
|
|
<div class="outline-text-2" id="text-5">
|
|
<p>
|
|
This project originally started as a fork of
|
|
<a href="https://github.com/astahlman/ob-async/">astahlman/ob-async</a>. However, because of changes in new version of Org
|
|
Mode, julia 1.0 release and unsupported features, I decided to start
|
|
over.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
<div id="postamble" class="status">
|
|
<p class="author">Author: Nicolò Balzarotti</p>
|
|
<p class="date">Created: 2019-10-29 Tue 11:56</p>
|
|
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
|
</div>
|
|
</body>
|
|
</html>
|