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leoschwarz committed Aug 9, 2024
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<h1 id="contribute">Contribute</h1>
<p>This page describes some information relevant for contruibuting to bfabricPy.</p>
<h2 id="development-install">Development install</h2>
<p>You should install the <code>dev</code> group as it contains some extra packages for running the tests.</p>
<pre><code class="language-bash">pip install -e &quot;.[dev]&quot;
</code></pre>
<h2 id="running-tests">Running tests</h2>
<p>With <code>nox</code> and <code>uv</code> installed, it is as simple as running <code>nox</code> in the project root without any arguments.</p>
<h2 id="integration-tests">Integration tests</h2>
<p>Note that integration tests have been moved to a separate repository. Please contact us if you are interested.</p>
<h2 id="documentation">Documentation</h2>
<p>We currently do not have a versioning solution for the documentation, but we can add that later once it is more mature.</p>
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<li class="nav-item">
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<li class="nav-item">
<a href="../contribute/" class="nav-link">Contribute</a>
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Expand Down Expand Up @@ -99,7 +102,7 @@ <h3 id="key-features">Key Features</h3>
<li><strong>No Circular Imports</strong>: Ensure there are no circular dependencies between entities by deferring imports of other entities inside modules until all relevant modules are processed.</li>
</ul>
<h3 id="entity">Entity</h3>
<p>Each entity has to provide the name of its B-Fabric of its class name as <code>ENDPOINT</code>.
<p>Each entity has to provide the name of its B-Fabric entity classname as <code>ENDPOINT</code>.
An entity is defined uniquely by its <code>classname</code> and <code>id</code>.</p>
<p>Entities are initialized with the full result structure obtained from a <code>read</code> operation on its particular endpoint.
A <code>return_id_only</code> result is generally not supposed to be used to initialize an entity instance and behavior is undefined as of now.
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<li class="nav-item">
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Expand Down Expand Up @@ -100,44 +103,23 @@ <h1 id="home">Home</h1>
<p>This package connects the <a href="https://fgcz-bfabric.uzh.ch/bfabric/">bfabric</a> system to the <a href="https://www.python.org/">python</a> and <a href="https://cran.r-project.org/">R</a> world while providing a JSON and REST interface using <a href="https://www.fullstackpython.com">Flask</a>.
The <a href="https://github.com/cpanse/bfabricShiny">bfabricShiny</a> R package is an extension and provides code snippets and sample implementation for a seamless R shiny bfabric integration.
For more advanced users the <em>bfabricPy</em> package also provides a powerful query interface on the command-line though using the provided scripts.</p>
<p>Please see below for how to install bfabricPy.</p>
<h2 id="installation">Installation</h2>
<p>The package can be installed like any other Python package, so if you are familiar you might not need to read this section.
Currently, it's only available from GitHub.</p>
<p>The best way to install the package depends on your use case, i.e. whether you want to:</p>
<ol>
<li>Use the command line scripts</li>
<li>Use the Python API</li>
<li>Develop on the package</li>
</ol>
<p>The command line scripts are currently included in all cases.</p>
<h3 id="command-line-scripts">Command line scripts</h3>
<p>To use the command line scripts, it's recommended to install <code>bfabricPy</code> with <a href="https://pipx.pypa.io/">pipx</a>.
If you don't have <code>pipx</code> installed, refer to the <a href="https://pipx.pypa.io/stable/installation/">pipx documentation</a> for instructions.</p>
<p>You can execute a command using a specific version of <code>bfabricPy</code> with the <code>pipx run</code> command.
This command handles the dependencies of multiple concurrent installations:</p>
<pre><code class="language-bash">pipx run --spec &quot;git+https://github.com/fgcz/bfabricPy.git@stable&quot; bfabric_read.py --help
</code></pre>
<p>To install a specific version of bfabricPy on your system and make the command available without <code>pipx run</code> prefix, use the following command:</p>
<p>The package is not available on PyPI as of now, but can be installed directly from GitHub and a <code>stable</code> branch is available for your convenience.</p>
<p>If you are only interested in running the command line scripts, installation with <code>pipx</code> is recommended as it will create a separate virtual environment for bfabricPy and make it possible to upgrade your installation later easily.</p>
<pre><code class="language-bash">pipx install &quot;git+https://github.com/fgcz/bfabricPy.git@stable&quot;
bfabric_read.py --help
</code></pre>
<h3 id="python-api">Python API</h3>
<p>If you're interested in using the Python API of <code>bfabricPy</code>, you have two options:</p>
<h4 id="1-configure-it-in-your-pyprojecttoml-file">1. Configure it in your <code>pyproject.toml</code> file.</h4>
<p>Note that <code>pipx</code> is also useful in scripts, if you want to run a particular version without forcing the global installation of that version (simply replace "stable" with a tag of your chosing):</p>
<pre><code class="language-bash">pipx run --spec &quot;git+https://github.com/fgcz/bfabricPy.git@stable&quot; bfabric_read.py --help
</code></pre>
<p>If you want to add it to a <code>pyproject.toml</code> the syntax for specifying a git dependency is as follows:</p>
<pre><code class="language-toml">[project]
dependencies = [
&quot;bfabricPy @ git+https://github.com/fgcz/bfabricPy.git@stable&quot;
]
</code></pre>
<h4 id="2-install-the-bfabricpy-package-directly-using-pip">2. Install the <code>bfabricPy</code> package directly using pip.</h4>
<pre><code class="language-bash">pip install git+https://github.com/fgcz/bfabricPy.git
</code></pre>
<h3 id="development">Development</h3>
<p>As a bfabricPy developer: (i.e. an editable install)</p>
<pre><code>pip install -e &quot;.[dev]&quot;
</code></pre>
<h2 id="configuration">Configuration</h2>
<p>Create a file as follows: (note: the password is not your login password, but the web service password)</p>
<p>Create a file as follows: (note: the password is not your login password, but the web service password available on your profile page)</p>
<pre><code># ~/.bfabricpy.yml

GENERAL:
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