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<div class="content" role="main" v-pre>
<section id="installation-developer-guidelines">
<h1>Installation/Developer Guidelines<a class="headerlink" href="#installation-developer-guidelines" title="Link to this heading">¶</a></h1>
<section id="science-users">
<h2>Science users<a class="headerlink" href="#science-users" title="Link to this heading">¶</a></h2>
<ul>
<li><p>Create and activate a virtual/conda environment with Python 3.11, e.g:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>scope-env<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.11
conda<span class="w"> </span>activate<span class="w"> </span>scope-env
</pre></div>
</div>
</li>
<li><p>Install the latest release of <code class="docutils literal notranslate"><span class="pre">scope-ml</span></code> from PyPI:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>scope-ml
</pre></div>
</div>
</li>
<li><p>In the directory of your choice, run the initialization script. This will create the required directories and copy the necessary files to run the code:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>scope-initialize
</pre></div>
</div>
</li>
<li><p>If using GPU-accelerated period-finding algorithms, install <a class="reference external" href="https://github.com/ZwickyTransientFacility/periodfind">periodfind</a> from the source.</p></li>
<li><p>Change directories to <code class="docutils literal notranslate"><span class="pre">scope</span></code> and modify <code class="docutils literal notranslate"><span class="pre">config.yaml</span></code> to finish the initialization process. This config file is used by default when running all scripts. You can also specify another config file using the <code class="docutils literal notranslate"><span class="pre">--config-path</span></code> argument.</p></li>
</ul>
</section>
<section id="developers-contributors">
<h2>Developers/contributors<a class="headerlink" href="#developers-contributors" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p>Create your own fork the <a class="reference external" href="https://github.com/ZwickyTransientFacility/scope">scope repository</a> by clicking the “fork” button. Then, decide whether you would like to use HTTPS (easier for beginners) or SSH.</p></li>
<li><p>Following one set of instructions below, clone (download) your copy of the repository, and set up a remote called <code class="docutils literal notranslate"><span class="pre">upstream</span></code> that points to the main <code class="docutils literal notranslate"><span class="pre">scope</span></code> repository.</p></li>
</ul>
<section id="https">
<h3>HTTPS:<a class="headerlink" href="#https" title="Link to this heading">¶</a></h3>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/<yourname>/scope.git<span class="w"> </span><span class="o">&&</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>scope
git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/ZwickyTransientFacility/scope.git
</pre></div>
</div>
</section>
<section id="ssh">
<h3>SSH:<a class="headerlink" href="#ssh" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><a class="reference external" href="https://help.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh">Set up SSH authentication with GitHub</a>.</p></li>
</ul>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>git@github.com:<yourname>/scope.git<span class="w"> </span><span class="o">&&</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>scope
git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>git@github.com:ZwickyTransientFacility/scope.git
</pre></div>
</div>
</section>
<section id="setting-up-your-environment-windows-linux-macos">
<h3>Setting up your environment (Windows/Linux/macOS)<a class="headerlink" href="#setting-up-your-environment-windows-linux-macos" title="Link to this heading">¶</a></h3>
<section id="use-a-package-manager-for-installation">
<h4>Use a package manager for installation<a class="headerlink" href="#use-a-package-manager-for-installation" title="Link to this heading">¶</a></h4>
<p>We currently recommend running <code class="docutils literal notranslate"><span class="pre">scope</span></code> with Python 3.11. You may want to begin your installation by creating/activating a virtual environment, for example using conda. We specifically recommend installing miniforge3 (https://github.com/conda-forge/miniforge).</p>
<p>Once you have a package manager installed, run:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>scope-env<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.11
conda<span class="w"> </span>activate<span class="w"> </span>scope-env
</pre></div>
</div>
</section>
<section id="optional-update-your-pythonpath">
<h4>(Optional): Update your <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code><a class="headerlink" href="#optional-update-your-pythonpath" title="Link to this heading">¶</a></h4>
<p>If you plan to import from <code class="docutils literal notranslate"><span class="pre">scope</span></code>, ensure that Python can import from <code class="docutils literal notranslate"><span class="pre">scope</span></code> by modifying the <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code> environment variable. Use a simple text editor like <code class="docutils literal notranslate"><span class="pre">nano</span></code> to modify the appropriate file (depending on which shell you are using). For example, if using bash, run <code class="docutils literal notranslate"><span class="pre">nano</span> <span class="pre">~/.bash_profile</span></code> and add the following line:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYTHONPATH</span><span class="o">=</span><span class="s2">"</span><span class="nv">$PYTHONPATH</span><span class="s2">:</span><span class="nv">$HOME</span><span class="s2">/scope"</span>
</pre></div>
</div>
<p>Save the updated file (<code class="docutils literal notranslate"><span class="pre">Ctrl+O</span></code> in <code class="docutils literal notranslate"><span class="pre">nano</span></code>) and close/reopen your terminal for this change to be recognized. Then <code class="docutils literal notranslate"><span class="pre">cd</span></code> back into scope and activate your <code class="docutils literal notranslate"><span class="pre">scope-env</span></code> again.</p>
</section>
</section>
<section id="install-required-packages">
<h3>Install required packages<a class="headerlink" href="#install-required-packages" title="Link to this heading">¶</a></h3>
<p>Ensure you are in the <code class="docutils literal notranslate"><span class="pre">scope</span></code> directory that contains <code class="docutils literal notranslate"><span class="pre">pyproject.toml</span></code>. Then, install the required python packages by running:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>.
</pre></div>
</div>
<section id="install-dev-requirements-pre-commit-hook">
<h4>Install dev requirements, pre-commit hook<a class="headerlink" href="#install-dev-requirements-pre-commit-hook" title="Link to this heading">¶</a></h4>
<p>We use <code class="docutils literal notranslate"><span class="pre">black</span></code> to format the code and <code class="docutils literal notranslate"><span class="pre">flake8</span></code> to verify that code complies with <a class="reference external" href="https://www.python.org/dev/peps/pep-0008/">PEP8</a>.
Please install our dev requirements and pre-commit hook as follows:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-r<span class="w"> </span>dev-requirements.txt
pre-commit<span class="w"> </span>install
</pre></div>
</div>
<p>This will check your changes before each commit to ensure that they
conform with our code style standards. We use black to reformat Python
code.</p>
<p>The pre-commit hook will lint <em>changes</em> made to the source.</p>
</section>
<section id="create-and-modify-config-yaml">
<h4>Create and modify config.yaml<a class="headerlink" href="#create-and-modify-config-yaml" title="Link to this heading">¶</a></h4>
<p>From the included config.defaults.yaml, make a copy called config.yaml:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>config.defaults.yaml<span class="w"> </span>config.yaml
</pre></div>
</div>
<p>Edit config.yaml to include Kowalski instance and Fritz tokens in the associated empty <code class="docutils literal notranslate"><span class="pre">token:</span></code> fields.</p>
</section>
<section id="optional-install-periodfind">
<h4>(Optional) Install <code class="docutils literal notranslate"><span class="pre">periodfind</span></code><a class="headerlink" href="#optional-install-periodfind" title="Link to this heading">¶</a></h4>
<p>If using GPU-accelerated period-finding algorithms, install <a class="reference external" href="https://github.com/ZwickyTransientFacility/periodfind">periodfind</a> from the source.</p>
</section>
<section id="testing">
<h4>Testing<a class="headerlink" href="#testing" title="Link to this heading">¶</a></h4>
<p>Run <code class="docutils literal notranslate"><span class="pre">scope-test</span></code> to test your installation. Note that for the test to pass, you will need access to the Kowalski database. If you do not have Kowalski access, you can run <code class="docutils literal notranslate"><span class="pre">scope-test-limited</span></code> to run a more limited (but still useful) set of tests.</p>
</section>
</section>
<section id="troubleshooting">
<h3>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Link to this heading">¶</a></h3>
<p>Upon encountering installation/testing errors, manually install the package in question using <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">xxx</span></code> , and remove it from <code class="docutils literal notranslate"><span class="pre">.requirements/dev.txt</span></code>. After that, re-run <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">-r</span> <span class="pre">requirements.txt</span></code> to continue.</p>
<section id="known-issues">
<h4>Known issues<a class="headerlink" href="#known-issues" title="Link to this heading">¶</a></h4>
<ul class="simple">
<li><p>Across all platforms, we are currently aware of <code class="docutils literal notranslate"><span class="pre">scope</span></code> dependency issues with Python 3.12.</p></li>
<li><p>Anaconda may cause problems with environment setup.</p></li>
<li><p>Using <code class="docutils literal notranslate"><span class="pre">pip</span></code> to install <code class="docutils literal notranslate"><span class="pre">healpy</span></code> on an arm64 Mac can raise an error upon import. We recommend including <code class="docutils literal notranslate"><span class="pre">h5py</span></code> as a requirement during the creation of your <code class="docutils literal notranslate"><span class="pre">conda</span></code> environment.</p></li>
<li><p>On Windows machines, <code class="docutils literal notranslate"><span class="pre">healpy</span></code> and <code class="docutils literal notranslate"><span class="pre">cesium</span></code> raise errors upon installation.</p>
<ul>
<li><p>For <code class="docutils literal notranslate"><span class="pre">healpy</span></code>, see <a class="reference external" href="https://healpy.readthedocs.io/en/latest/install.html#installation-on-windows-through-the-windows-subsystem-for-linux">this</a> guide for a potential workaround.</p></li>
<li><p>For <code class="docutils literal notranslate"><span class="pre">cesium</span></code>, try to install from the source (https://cesium-ml.org/docs/install.html#from-source) within <code class="docutils literal notranslate"><span class="pre">scope</span></code>. If you will not be running feature generation, this is not a critical error, but there will be points in the code that fail (e.g. <code class="docutils literal notranslate"><span class="pre">scope.py</span> <span class="pre">test</span></code>, <code class="docutils literal notranslate"><span class="pre">tools/generate_features.py</span></code>)</p></li>
</ul>
</li>
</ul>
<p>If the installation continues to raise errors, update the conda environment and try again.</p>
</section>
</section>
<section id="how-to-contribute">
<h3>How to contribute<a class="headerlink" href="#how-to-contribute" title="Link to this heading">¶</a></h3>
<p>Contributions to <code class="docutils literal notranslate"><span class="pre">scope</span></code> are made through <a class="reference external" href="https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests">GitHub Pull Requests</a>, a set of proposed commits (or patches):</p>
<ol class="arabic">
<li><p>Download the latest version of <code class="docutils literal notranslate"><span class="pre">scope</span></code>, and create a new branch for your work.</p>
<p>Here, let’s say we want to contribute some documentation fixes; we’ll call our branch <code class="docutils literal notranslate"><span class="pre">rewrite-contributor-guide</span></code>.</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>checkout<span class="w"> </span>main
git<span class="w"> </span>pull<span class="w"> </span>upstream<span class="w"> </span>main
git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>rewrite-contributor-guide
</pre></div>
</div>
</li>
<li><p>Make modifications to <code class="docutils literal notranslate"><span class="pre">scope</span></code> and commit your changes using <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">add</span></code> and <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">commit</span></code>.
Each commit message should consist of a summary line and a longer description, e.g.:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Rewrite the contributor guide
While reading through the contributor guide, I noticed several places
in which instructions were out of order. I therefore reorganized all
sections to follow logically, and fixed several grammar mistakes along
the way.
</pre></div>
</div>
</li>
<li><p>When ready, push your branch to GitHub:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>rewrite-contributor-guide
</pre></div>
</div>
<p>Once the branch is uploaded, GitHub should print a URL for turning your branch into a pull request.
Open that URL in your browser, write an informative title and description for your pull request, and submit it.</p>
</li>
<li><p>The team will now review your contribution, and suggest changes.
<em>To simplify review, please limit pull requests to one logical set of changes.</em>
To incorporate changes recommended by the reviewers, commit edits to your branch, and push to the branch again
(there is no need to re-create the pull request, it will automatically track modifications to your branch).</p></li>
<li><p>Sometimes, while you were working on your feature, the <code class="docutils literal notranslate"><span class="pre">main</span></code> branch is updated with new commits, potentially
resulting in conflicts with your feature branch. The are two ways to resolve this situation - merging and rebasing,
please look <a class="reference external" href="https://www.atlassian.com/git/tutorials/merging-vs-rebasing">here</a> for a detailed discussion.
While both ways are acceptable, since we are squashing commits from a PR before merging, we prefer the first option:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>merge<span class="w"> </span>rewrite-contributor-guide<span class="w"> </span>upstream/main
</pre></div>
</div>
</li>
</ol>
<p>Developers may merge <code class="docutils literal notranslate"><span class="pre">main</span></code> into their branch as many times as they want to.</p>
<ol class="arabic simple">
<li><p>Once the pull request has been reviewed and approved by at least one team member, it will be merged into <code class="docutils literal notranslate"><span class="pre">scope</span></code>.</p></li>
</ol>
<section id="releasing-on-pypi">
<h4>Releasing on PyPI<a class="headerlink" href="#releasing-on-pypi" title="Link to this heading">¶</a></h4>
<p>As new features are added to the code, maintainers should occasionally initiate a new release of the <code class="docutils literal notranslate"><span class="pre">scope-ml</span></code> <a class="reference external" href="https://pypi.org/project/scope-ml/">PyPI</a> package. To do this, first bump the version of the package in <code class="docutils literal notranslate"><span class="pre">pyproject.toml</span></code> and <code class="docutils literal notranslate"><span class="pre">scope/__init__.py</span></code> to the intended <code class="docutils literal notranslate"><span class="pre">vX.Y.Z</span></code> format. Then, navigate to “Releases” in the SCoPe GitHub repo and click “Draft a new release”. Enter the version number in “Choose a tag” and click “Generate release notes”. It is also advisable to check the box creating a discussion for the release before clicking “Publish release”.</p>
<p>Upon release, the <code class="docutils literal notranslate"><span class="pre">publish-to-pypi.yml</span></code> workflow will use GitHub Actions to publish a new version of the package to PyPI automatically. <strong>Note that if the version number has not yet been manually updated in <code class="docutils literal notranslate"><span class="pre">pyproject.toml</span></code>, this workflow will fail.</strong></p>
</section>
</section>
<section id="contributing-field-guide-sections">
<h3>Contributing Field Guide sections<a class="headerlink" href="#contributing-field-guide-sections" title="Link to this heading">¶</a></h3>
<p>If you would like to contribute a Field Guide section, please follow the steps below.</p>
<ul class="simple">
<li><p>Make sure to follow the steps described above in the “How to contribute” section!</p></li>
<li><p>Add sections to <code class="docutils literal notranslate"><span class="pre">config.defaults.yaml</span></code> under <code class="docutils literal notranslate"><span class="pre">docs.field_guide.<object_class_type></span></code>.</p>
<ul>
<li><p>Use <code class="docutils literal notranslate"><span class="pre">docs.field_guide.rr_lyr_ab</span></code> as an example. You need to specify the object’s
coordinates and a title for the generated light curve plot. Optionally,
you may specify a period [days] - then a phase-folded light curve will also be rendered.</p></li>
</ul>
</li>
<li><p>Make sure your <code class="docutils literal notranslate"><span class="pre">config.yaml</span></code> file contains a valid Kowalski token.</p>
<ul>
<li><p>See <a class="reference external" href="https://github.com/dmitryduev/penquins">here</a> on how to generate one
(Kowalski account required).</p></li>
<li><p>You can use <code class="docutils literal notranslate"><span class="pre">config.defaults.yaml</span></code> as a template.</p></li>
</ul>
</li>
<li><p>Make sure the structure of your config file is the same as the default,
i.e. you propagated the changes in <code class="docutils literal notranslate"><span class="pre">config.defaults.yaml</span></code>.
(otherwise the <code class="docutils literal notranslate"><span class="pre">scope.py</span></code> utility will later complain and ask you to fix that).</p></li>
<li><p>Add a Markdown file to <code class="docutils literal notranslate"><span class="pre">doc/</span></code> and call it <code class="docutils literal notranslate"><span class="pre">field_guide__<object_class>.md</span></code>.</p>
<ul>
<li><p>Use <a class="reference internal" href="field_guide__rr_lyrae.html"><span class="std std-doc"><code class="docutils literal notranslate"><span class="pre">doc/field_guide__rr_lyrae.md</span></code></span></a> as a template.</p></li>
<li><p>Light curve examples will be generated as <code class="docutils literal notranslate"><span class="pre">data/<object_class_type>.png</span></code> files using the info
you provided in the config.</p></li>
<li><p>Add the following include statements to <a class="reference internal" href="field_guide.html"><span class="std std-doc"><code class="docutils literal notranslate"><span class="pre">doc/field_guide.md</span></code></span></a>:</p></li>
</ul>
</li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">{</span><span class="n">include</span><span class="p">}</span> <span class="o">./</span><span class="n">field_guide__</span><span class="o"><</span><span class="n">object_class</span><span class="o">>.</span><span class="n">md</span>
</pre></div>
</div>
<ul class="simple">
<li><p>If you wish to render a sample Gaia-based HR diagram, you need to create a “Golden” data set
for that class of objects and put it under <code class="docutils literal notranslate"><span class="pre">data/golden</span></code> as <code class="docutils literal notranslate"><span class="pre"><object_class>.csv</span></code></p>
<ul>
<li><p>The <code class="docutils literal notranslate"><span class="pre">csv</span></code> file must follow the same structure as [<code class="docutils literal notranslate"><span class="pre">data/golden/rr_lyr.csv</span></code>].
Please keep the <code class="docutils literal notranslate"><span class="pre">csv</span></code> header (“ra,dec”) and provide object coordinates in degrees.</p></li>
<li><p>The HR diagram will be generated as <code class="docutils literal notranslate"><span class="pre">data/hr__<object_class>.png</span></code></p></li>
</ul>
</li>
<li><p>Run the <code class="docutils literal notranslate"><span class="pre">./scope.py</span> <span class="pre">doc</span></code> command to generate the imagery and build the documentation.</p>
<ul>
<li><p>If the build is successful, you can check the results in
<a class="reference internal" href="#_build/html/index.html"><span class="xref myst"><code class="docutils literal notranslate"><span class="pre">doc/_build/html/index.html</span></code></span></a></p></li>
</ul>
</li>
<li><p>Once you’re happy with the result, commit the changes to a branch on your fork
and open a pull request on GitHub (see the “How to contribute” section above).</p>
<ul>
<li><p>The GitHub Actions CI will run a subset of the testing/deployment pipeline
for each commit you make to your branch -
make sure you get a green checkmark next to the commit hash.</p></li>
<li><p>Once the PR is reviewed, approved, and merged,
the CI will automatically build and deploy the docs to
<a class="reference external" href="https://scope.ztf.dev"><code class="docutils literal notranslate"><span class="pre">https://scope.ztf.dev</span></code></a></p></li>
</ul>
</li>
</ul>
</section>
</section>
</section>
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