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Merge pull request #92 from scicloj/notespace-cleanup
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Notespace cleanup
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@genmeblog
genmeblog committed Apr 24, 2024
2 parents 3c520bb + b8f64f6 commit 44154e8
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12 changes: 3 additions & 9 deletions README.md
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Expand Up @@ -118,13 +118,7 @@ Note however that:

## Tutorials

* [Intro](https://scicloj.github.io/clojisr/doc/clojisr/v1/tutorial-test/)

* [A tutorial about generating R code from Clojure](https://scicloj.github.io/clojisr/doc/clojisr/v1/codegen-test/)

* [Titanic tutorial #0](https://scicloj.github.io/clojisr/doc/clojisr/v1/titanic0-test/)

* [Dataset transfer](https://scicloj.github.io/clojisr/doc/clojisr/v1/dataset-test/)
* The tutorials are now organized in [a book](https://scicloj.github.io/clojisr).

* More examples -- see the [clojisr-examples repo](https://github.com/scicloj/clojisr-examples#list-of-examples)

Expand Down Expand Up @@ -158,7 +152,7 @@ Also we run [a stream](https://clojurians.zulipchat.com/#narrow/stream/224816-cl

## Testing

The code tests are embedded in the [tutorials](#tutorials) and are run when they are rendered (using [notespace](https://github.com/scicloj/notespace)). This way we make sure that tests and documentation are in sync.
The tests are regular clojure.test tests, but are auto-genedated from the tutorials.

## Tools used

Expand All @@ -168,7 +162,7 @@ Working on this project, we enjoyed the following tools (partial list):

* [clj-kondo](https://github.com/borkdude/clj-kondo) for code quality control

* [notespace](https://github.com/scicloj/notespace) for documentation and tests
* [Clay](https://scicloj.github.io/clay/) for documentation and test generation

## License

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3 changes: 1 addition & 2 deletions deps.edn
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Expand Up @@ -9,8 +9,7 @@
:paths ["src"]
:aliases {:dev {:extra-paths ["resources" "notebooks"]
:jvm-opts ["-Dclojure.tools.logging.factory=clojure.tools.logging.impl/jul-factory"]
:extra-deps {scicloj/notespace {:mvn/version "2.0.0-alpha5"}
org.scicloj/clay {:mvn/version "2-beta8"}
:extra-deps {org.scicloj/clay {:mvn/version "2-beta8"}
io.github.nextjournal/clerk {:mvn/version "0.7.418"}}}
:test {:extra-paths ["test"]
:extra-deps {io.github.cognitect-labs/test-runner
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22 changes: 11 additions & 11 deletions docs/clojisr.v1.tutorials.codegen.html
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Expand Up @@ -271,7 +271,7 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="r-code-as-a-string"><span
<div class="sourceCode" id="cb6"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>(r <span class="st">"mean(rnorm(100000,mean=1.0,sd=3.0))"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb7"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] <span class="fl">1.006405</span></span>
<div class="sourceCode" id="cb7"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] <span class="fl">0.993209</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="sourceClojure">
Expand All @@ -280,7 +280,7 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="r-code-as-a-string"><span
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="st"> f(abc)"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb9"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] -<span class="fl">0.9791201</span></span>
<div class="sourceCode" id="cb9"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] -<span class="fl">0.9940711</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>As mentioned above, every <code>r</code> call creates RObject and R variable which keeps result of the execution.</p>
Expand All @@ -297,15 +297,15 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="r-code-as-a-string"><span
<div class="sourceCode" id="cb13"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>(<span class="at">:object-name</span> result)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb14"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$xc3ede4017d834b02"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb14"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x71e90738f6d4485e"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Let’s use the var name string to see what it represents.</p>
<div class="sourceClojure">
<div class="sourceCode" id="cb15"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>(r (<span class="at">:object-name</span> result))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb16"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a> [<span class="dv">1</span>] -<span class="fl">1.0509587</span> -<span class="fl">0.7279353</span> <span class="fl">0.1352645</span> -<span class="fl">2.1315183</span> -<span class="fl">1.1095648</span> -<span class="fl">1.2226944</span></span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a> [<span class="dv">7</span>] <span class="fl">1.6877214</span> <span class="fl">0.1063141</span> -<span class="fl">0.4282806</span> <span class="fl">1.3858847</span></span>
<div class="sourceCode" id="cb16"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a> [<span class="dv">1</span>] <span class="fl">0.07702078</span> -<span class="fl">0.15438780</span> -<span class="fl">1.09161854</span> <span class="fl">1.72482688</span> -<span class="fl">0.04943640</span> <span class="fl">1.35407181</span></span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a> [<span class="dv">7</span>] <span class="fl">1.26637556</span> -<span class="fl">0.91809940</span> -<span class="fl">2.06403479</span> -<span class="fl">0.75490144</span></span>
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Now let us move to discussing the ROBject data type.</p>
Expand Down Expand Up @@ -515,7 +515,7 @@ <h3 data-number="3.3.1" class="anchored" data-anchor-id="primitive-data-types"><
<div class="sourceCode" id="cb67"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb67-1"><a href="#cb67-1" aria-hidden="true" tabindex="-1"></a>(-&gt;code (r <span class="st">"1+2"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb68"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb68-1"><a href="#cb68-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x91a7d6e9e33640f0"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb68"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb68-1"><a href="#cb68-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x0a63e42c8b1445bb"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Date/time is converted to a string.</p>
<div class="sourceClojure">
Expand Down Expand Up @@ -668,21 +668,21 @@ <h4 data-number="3.3.2.1" class="anchored" data-anchor-id="tagged-vectors"><span
<span id="cb95-2"><a href="#cb95-2" aria-hidden="true" tabindex="-1"></a> r r-&gt;clj)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb96"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb96-1"><a href="#cb96-1" aria-hidden="true" tabindex="-1"></a>[#object[java.<span class="kw">time</span>.LocalDateTime <span class="bn">0x3d564d48</span> <span class="st">"2011-11-02T00:33:11"</span>]]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb96"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb96-1"><a href="#cb96-1" aria-hidden="true" tabindex="-1"></a>[#object[java.<span class="kw">time</span>.LocalDateTime <span class="bn">0x4e4d5c6e</span> <span class="st">"2011-11-02T00:33:11"</span>]]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="sourceClojure">
<div class="sourceCode" id="cb97"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb97-1"><a href="#cb97-1" aria-hidden="true" tabindex="-1"></a>(<span class="kw">-&gt;</span> [:!lt #inst <span class="st">"2011-11-01T22:33:11"</span>]</span>
<span id="cb97-2"><a href="#cb97-2" aria-hidden="true" tabindex="-1"></a> r r-&gt;clj)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb98"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb98-1"><a href="#cb98-1" aria-hidden="true" tabindex="-1"></a>[#object[java.<span class="kw">time</span>.LocalDateTime <span class="bn">0x5e2a4d04</span> <span class="st">"2011-11-02T00:33:11"</span>]]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb98"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb98-1"><a href="#cb98-1" aria-hidden="true" tabindex="-1"></a>[#object[java.<span class="kw">time</span>.LocalDateTime <span class="bn">0x244a668</span> <span class="st">"2011-11-02T00:33:11"</span>]]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>When a vector is big enough, it is transfered not directly as code, but as the name of a newly created R variable holding the corresponding vector data, converted via the Java conversion layer.</p>
<div class="sourceClojure">
<div class="sourceCode" id="cb99"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb99-1"><a href="#cb99-1" aria-hidden="true" tabindex="-1"></a>(-&gt;code (<span class="kw">range</span> <span class="dv">10000</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb100"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb100-1"><a href="#cb100-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x2b388d53f7f945bb"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb100"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb100-1"><a href="#cb100-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$xc9e606e4a89f4816"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="sourceClojure">
<div class="sourceCode" id="cb101"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb101-1"><a href="#cb101-1" aria-hidden="true" tabindex="-1"></a>(<span class="kw">-&gt;</span> (<span class="kw">conj</span> (<span class="kw">range</span> <span class="dv">10000</span>) :!string)</span>
Expand Down Expand Up @@ -729,7 +729,7 @@ <h3 data-number="3.3.3" class="anchored" data-anchor-id="maps"><span class="head
<span id="cb109-2"><a href="#cb109-2" aria-hidden="true" tabindex="-1"></a> (<span class="kw">range</span> <span class="dv">1000</span> <span class="dv">1100</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb110"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb110-1"><a href="#cb110-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x988d4207df794d5e"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb110"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb110-1"><a href="#cb110-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x3c9aa6a0f6964e50"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="sourceClojure">
<div class="sourceCode" id="cb111"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb111-1"><a href="#cb111-1" aria-hidden="true" tabindex="-1"></a>(<span class="kw">-&gt;</span> (r (<span class="kw">zipmap</span> (<span class="kw">map</span> #(<span class="kw">str</span> <span class="st">"key"</span> <span class="va">%</span>) (<span class="kw">range</span> <span class="dv">100</span>))</span>
Expand Down Expand Up @@ -786,7 +786,7 @@ <h3 data-number="3.3.4" class="anchored" data-anchor-id="calls-operators-and-spe
<span id="cb123-2"><a href="#cb123-2" aria-hidden="true" tabindex="-1"></a> -&gt;code)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="printedClojure">
<div class="sourceCode" id="cb124"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb124-1"><a href="#cb124-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$xe77736ea02c64fd9(c(1L,2L,4L))"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb124"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb124-1"><a href="#cb124-1" aria-hidden="true" tabindex="-1"></a><span class="st">".MEM$x052d9553b4e84d0b(c(1L,2L,4L))"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="sourceClojure">
<div class="sourceCode" id="cb125"><pre class="sourceCode clojure code-with-copy"><code class="sourceCode clojure"><span id="cb125-1"><a href="#cb125-1" aria-hidden="true" tabindex="-1"></a>(<span class="kw">-&gt;</span> (<span class="kw">list</span> (r <span class="at">'median</span>) [<span class="dv">1</span> <span class="dv">2</span> <span class="dv">4</span>])</span>
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