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8 changes: 4 additions & 4 deletions 404.html
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10 changes: 5 additions & 5 deletions commonoptions/index.html
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54 changes: 39 additions & 15 deletions development/index.html
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<meta charset="UTF-8">
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not all of it can be installed as a pure python program using <code v-pre>setuptools</code>.
The build process installs part of Harpy as a pure-python command line program, but
all the extra files Harpy needs to run need to be installed separately. All of
this is handled by <code v-pre>misc/buildlocal.sh</code>. It&#x27;s a little circuitous, but it&#x27;s how
this is handled by <code v-pre>resources/buildlocal.sh</code>. It&#x27;s a little circuitous, but it&#x27;s how
we can keep the source code modular, installable, and have the flexibility of
using non-python code.</p>
<doc-anchor-target id="bioconda-recipe">
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<p>For the ease of installation for end-users, Harpy has a <a href="https://github.com/bioconda/bioconda-recipes/blob/master/recipes/harpy/meta.yaml">recipe</a>
and <a href="https://github.com/bioconda/bioconda-recipes/blob/master/recipes/harpy/build.sh">build script</a> in Bioconda,
which makes it available for download and installation. A copy of the recipe and
build script is also stored in <code v-pre>misc/meta.yml</code> and <code v-pre>misc/build.sh</code>. The yaml file
build script is also stored in <code v-pre>resources/meta.yml</code> and <code v-pre>resources/build.sh</code>. The yaml file
is the metadata of the package, including software deps and their versions. The
build script is how conda will install all of Harpy&#x27;s parts. In order to modify
these files for a new release, you need to fork <code v-pre>bioconda/bioconda-recipes</code>,
create a new branch, modify the Harpy <code v-pre>meta.yml</code> (and possibly <code v-pre>build.sh</code>) files. Bioconda
has an bot that looks for changes to the version number in the <code v-pre>meta.yml</code> file
and will automatically submit a Pull Request when it notices that&#x27;s been changed.</p>
build script is how conda will install all of Harpy&#x27;s parts. Now that Harpy is hosted on
bioconda, when a new version is tagged with a release, Bioconda will automatically create
a pull request (after a delay), typically not requiring any intervention on the development side
for the newest Harpy version to be released for conda installation.</p>
<doc-anchor-target id="the-harpy-repository">
<h2>
<doc-anchor-trigger class="header-anchor-trigger" to="#the-harpy-repository">#</doc-anchor-trigger>
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<li>add and modify code with your typical coding workflow, pushing your changes to your Harpy fork</li>
<li>when it&#x27;s ready for inclusion into Harpy (and testing), create a Pull Request to merge your changes into the Harpy <code v-pre>dev</code> branch</li>
</ol>
<doc-anchor-target id="testing-and-ci">
<doc-anchor-target id="automations">
<h2>
<doc-anchor-trigger class="header-anchor-trigger" to="#testing-and-ci">#</doc-anchor-trigger>
<span>Testing and CI</span>
<doc-anchor-trigger class="header-anchor-trigger" to="#automations">#</doc-anchor-trigger>
<span>Automations</span>
</h2>
</doc-anchor-target>
<doc-anchor-target id="testing">
<h3>
<doc-anchor-trigger class="header-anchor-trigger" to="#testing">#</doc-anchor-trigger>
<span>Testing</span>
</h3>
</doc-anchor-target>
<p>CI (<strong>C</strong>ontinuous <strong>I</strong>ntegration) is a term describing automated actions that do
things to/with your code and are triggered by how you interact with a repository.
Harpy has a series of GitHub Actions triggered by interactions with the <code v-pre>dev</code> branch (in <code v-pre>.github/workflows</code>)
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could not run successfully to completion. These tests do not test for accuracy,
but test for breaking behavior. You&#x27;d be shocked to find out how many errors
crop up this way and require more development so Harpy can be resilient to more use cases.</p>
<doc-anchor-target id="releases">
<h3>
<doc-anchor-trigger class="header-anchor-trigger" to="#releases">#</doc-anchor-trigger>
<span>Releases</span>
</h3>
</doc-anchor-target>
<p>To save on disk space, there is an automation to strip out the unnecessary files and upload a
cleaned tarball to the new release. This is triggered automatically when a new version is tagged.
Tagging is easily accomplished with Git commands in the command line:</p>
<div class="codeblock-wrapper"><doc-codeblock>
<pre class="language-bash"><code v-pre class="language-bash"># make sure you're on the main branch
$ git checkout main

# create the tag locally, where X.X.X is something like 1.7.1
$ git tag X.X.X

# push the new tag to the repository
$ git push origin X.X.X</code></pre>
</doc-codeblock></div>


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8 changes: 4 additions & 4 deletions haplotagdata/index.html
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