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<section id="tips-for-developers">
<h1>Tips for developers<a class="headerlink" href="#tips-for-developers" title="Link to this heading"></a></h1>
<p>It is recommended to run the project with python 3.11.</p>
<section id="start-service">
<h2>Start service<a class="headerlink" href="#start-service" title="Link to this heading"></a></h2>
<p>The different notebooks in <code class="docutils literal notranslate"><span class="pre">./notebooks</span></code> provide more complete documentation regarding the set up and administration of the server.</p>
<section id="on-local-machine">
<h3>On local machine<a class="headerlink" href="#on-local-machine" title="Link to this heading"></a></h3>
<p>To start the container on a local machine, first create a mondodb volume
with <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">volume</span> <span class="pre">create</span> <span class="pre">mongodata</span></code>, then go to <code class="docutils literal notranslate"><span class="pre">lomas/server/</span></code> and run <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">compose</span> <span class="pre">up</span></code>.
If you encounter any issue, you might want to run <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">compose</span> <span class="pre">down</span></code> first.</p>
<section id="additional-services">
<h4>Additional services<a class="headerlink" href="#additional-services" title="Link to this heading"></a></h4>
<p>Running <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">compose</span> <span class="pre">up</span></code> will also start two additional services automatically:</p>
<ul class="simple">
<li><p>a jupyter notebook environment that will be available at the address http://127.0.0.1:8888/ to interact as a user with the server</p></li>
<li><p>a streamlit application that will be available at the address http://localhost:8501/ to interact with the server and the administration database as an administrator.</p></li>
</ul>
</section>
</section>
<section id="on-a-kubernetes-cluster">
<h3>On a kubernetes cluster<a class="headerlink" href="#on-a-kubernetes-cluster" title="Link to this heading"></a></h3>
<p>To start the server on a kubernetes cluster, first add the repo with:
<code class="docutils literal notranslate"><span class="pre">helm</span> <span class="pre">repo</span> <span class="pre">add</span> <span class="pre">lomas</span> <span class="pre">https://dscc-admin-ch.github.io/helm-charts</span></code>
and then install the chart with:
<code class="docutils literal notranslate"><span class="pre">helm</span> <span class="pre">install</span> <span class="pre">lomas-sever</span> <span class="pre">lomas/lomas-server</span></code></p>
</section>
<section id="on-onyxia">
<h3>On Onyxia<a class="headerlink" href="#on-onyxia" title="Link to this heading"></a></h3>
<p>To start the server on Onyxia, select the <code class="docutils literal notranslate"><span class="pre">lomas</span> </code>service, (optionnally adapt the administration and runtime parameters) and click on ‘Lancer’.</p>
</section>
</section>
<section id="tests">
<h2>Tests<a class="headerlink" href="#tests" title="Link to this heading"></a></h2>
<p>It is possible to test the server with standard tests or integration tests (for the mongodb).
The <code class="docutils literal notranslate"><span class="pre">run_integration_tests.sh</span></code> script runs the integration tests, make sure to have an activated python venv in a linux environment with the server requirements installed for it to work.</p>
<p>Local tests (except for those using the mongodb_admin) can be run with a simple <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">-m</span> <span class="pre">unittest</span> <span class="pre">discover</span> <span class="pre">-s</span> <span class="pre">.</span> </code> from the <code class="docutils literal notranslate"><span class="pre">lomas_server</span></code> directory. The tests will be based on the config in <code class="docutils literal notranslate"><span class="pre">lomas/server/lomas_server/tests/test_configs/test_config.yaml</span></code> and be executed with the AdminYamlDatabase.
For local tests on the mongodb_admin, first get in the container with <code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">exec</span> <span class="pre">-it</span> <span class="pre">lomas_server_dev</span> <span class="pre">bash</span></code> and then run the tests.</p>
<p>A github workflow is configured to run the integration tests script for pull requests on the develop and master branches.</p>
</section>
<section id="linting-and-other-checks">
<h2>Linting and other checks<a class="headerlink" href="#linting-and-other-checks" title="Link to this heading"></a></h2>
<p>Here is a list of the checks performed:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>- Use black to automatically format the code: `black .`
- Use flake to verify formating and performing a static code analysis: `flake8 .`
- Use mypy for static type checking: `mypy .`
- Use pylint for further static analysis: `pylint --disable=E0401 --disable=C0114 --disable=R0903 --disable=E0611 --disable=W0511 --disable=duplicate-code tests/ .`

- `--disable=E0401` to ignore import-error
- `--disable=C0114` to ignore missing-module-docstring
- `--disable=R0903` to ignore too-few-public-methods
- `--disable=E0611` to ignore no-name-in-module
- `--disable=W0511` to ignore fixme (TODOs)
- `--disable=duplicate-code tests/` to ignore duplicate-code statements related to the tests
</pre></div>
</div>
<p>We rely on a github workflow to automatically run the checks on pull requests.</p>
</section>
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Link to this heading"></a></h2>
<p>Documentation is automatically generated from the code docstrings with sphinx, as well as the resulting html pages.
The process goes in two steps
- <code class="docutils literal notranslate"><span class="pre">sphinx-apidoc</span> <span class="pre">-o</span> <span class="pre">./docs/source</span> <span class="pre">./lomas_server</span></code> for generating the .rst files.
- <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">html</span></code> from the <code class="docutils literal notranslate"><span class="pre">./docs</span></code> folder to generate the webpages.</p>
<p>We do not check the documentation files into the repo, but rather rely on a github workflow to generate and publish it
on a dedicated repo’s github pages for easy access from the web.</p>
</section>
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