Deploy preview for PR 98 🛫

Boehringer-Ingelheim · Jan 30, 2025 · 418ec60 · 418ec60
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diff --git a/pr-preview/pr-98/CHANGELOG.html b/pr-preview/pr-98/CHANGELOG.html
@@ -53,7 +53,7 @@
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 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -67,7 +67,7 @@
     <link rel="prev" title="Configuration" href="cli_configuration.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/_sources/getting_started.md b/pr-preview/pr-98/_sources/getting_started.md
@@ -79,7 +79,8 @@ For more details, please refer to [Configuration files](user_guide/params_files.
 
 ## Implementing a stage
 
-A stage is a single step in your analysis and usually generates some kind of output data from input data. The input data can also be supplied by previous stages. To create a stage, use the `dso create stage` command and select either the _bash_ or _quarto_ template as a starting-point.
+A stage is a single step in your analysis and usually generates some kind of output data from input data. The input data can also be supplied by previous stages. To create a stage, use the `dso create stage` command and select either the _bash_ or one of the _quarto_
+[templates](user_guide/templates.md) as a starting-point.
 
 The essential files of a stage are:
 

diff --git a/pr-preview/pr-98/_sources/user_guide/templates.md b/pr-preview/pr-98/_sources/user_guide/templates.md
@@ -19,7 +19,9 @@ Folder templates:
 
 Stage templates:
 
--   [quarto](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in R
+-   [quarto_r](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in R
+-   [quarto_py](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in Python (quarto markdown (`.qmd`) format)
+-   [quarto_r](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in Python (jupyter notebook (`.ipynb`) format)
 -   [bash](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/bash) - Template for executing a bash snippet
 
 The source code of the templates can be [inspected on GitHub](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates).

diff --git a/pr-preview/pr-98/_static/documentation_options.js b/pr-preview/pr-98/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.dev1+g9166e3c',
+    VERSION: '0.1.dev1+g6481831',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/pr-preview/pr-98/cli_command_reference.html b/pr-preview/pr-98/cli_command_reference.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -67,7 +67,7 @@
     <link rel="prev" title="Installation" href="cli_installation.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/cli_configuration.html b/pr-preview/pr-98/cli_configuration.html
@@ -53,7 +53,7 @@
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 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="Command reference" href="cli_command_reference.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/cli_installation.html b/pr-preview/pr-98/cli_installation.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="FAQ" href="faq.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 
@@ -369,7 +369,7 @@ <h1>Installation<a class="headerlink" href="#installation" title="Link to this h
 </div>
 <p>This command installs the <code class="docutils literal notranslate"><span class="pre">dso</span></code> binary:</p>
 <div class="highlight-ansi-shell-session notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>dso<span class="w"> </span>--version
-dso, version 0.1.dev1+g9166e3c
+dso, version 0.1.dev1+g6481831
 </pre></div>
 </div>
 <p>If you prefer to manage the Python environment yourself, you can use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as usual:</p>

diff --git a/pr-preview/pr-98/contributing.html b/pr-preview/pr-98/contributing.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -67,7 +67,7 @@
     <link rel="prev" title="Changelog" href="CHANGELOG.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
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diff --git a/pr-preview/pr-98/faq.html b/pr-preview/pr-98/faq.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="Quarto integration" href="user_guide/quarto.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/generated/dso._lint.DSO001.html b/pr-preview/pr-98/generated/dso._lint.DSO001.html
@@ -53,7 +53,7 @@
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="../_static/documentation_options.js?v=e35243cb"></script>
+    <script src="../_static/documentation_options.js?v=22a78dfd"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="Linting" href="../user_guide/linting.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
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diff --git a/pr-preview/pr-98/genindex.html b/pr-preview/pr-98/genindex.html
@@ -41,7 +41,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -53,7 +53,7 @@
     <link rel="search" title="Search" href="search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
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diff --git a/pr-preview/pr-98/getting_started.html b/pr-preview/pr-98/getting_started.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -67,7 +67,7 @@
     <link rel="prev" title="DSO: data science operations" href="index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 
@@ -439,7 +439,8 @@ <h2>Configuration files<a class="headerlink" href="#configuration-files" title="
 </section>
 <section id="implementing-a-stage">
 <h2>Implementing a stage<a class="headerlink" href="#implementing-a-stage" title="Link to this heading">#</a></h2>
-<p>A stage is a single step in your analysis and usually generates some kind of output data from input data. The input data can also be supplied by previous stages. To create a stage, use the <code class="docutils literal notranslate"><span class="pre">dso</span> <span class="pre">create</span> <span class="pre">stage</span></code> command and select either the <em>bash</em> or <em>quarto</em> template as a starting-point.</p>
+<p>A stage is a single step in your analysis and usually generates some kind of output data from input data. The input data can also be supplied by previous stages. To create a stage, use the <code class="docutils literal notranslate"><span class="pre">dso</span> <span class="pre">create</span> <span class="pre">stage</span></code> command and select either the <em>bash</em> or one of the <em>quarto</em>
+<a class="reference internal" href="user_guide/templates.html"><span class="std std-doc">templates</span></a> as a starting-point.</p>
 <p>The essential files of a stage are:</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">dvc.yaml</span></code>: The DVC configuration file that defines your data pipelines, dependencies, and outputs.</p></li>

diff --git a/pr-preview/pr-98/index.html b/pr-preview/pr-98/index.html
@@ -53,7 +53,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -66,7 +66,7 @@
     <link rel="next" title="Getting started" href="getting_started.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/objects.inv b/pr-preview/pr-98/objects.inv
@@ -1,5 +1,5 @@
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+# Version: 0.1.dev1+g6481831
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diff --git a/pr-preview/pr-98/py-modindex.html b/pr-preview/pr-98/py-modindex.html
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -54,7 +54,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
 
 
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diff --git a/pr-preview/pr-98/python_api.html b/pr-preview/pr-98/python_api.html
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -64,7 +64,7 @@
     <link rel="prev" title="Usage" href="python_usage.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
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diff --git a/pr-preview/pr-98/python_usage.html b/pr-preview/pr-98/python_usage.html
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="Contributing guide" href="contributing.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>
 
 

diff --git a/pr-preview/pr-98/search.html b/pr-preview/pr-98/search.html
@@ -40,7 +40,7 @@
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-    <script src="_static/documentation_options.js?v=e35243cb"></script>
+    <script src="_static/documentation_options.js?v=22a78dfd"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -55,7 +55,7 @@
     <link rel="search" title="Search" href="#" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
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diff --git a/pr-preview/pr-98/searchindex.js b/pr-preview/pr-98/searchindex.js
diff --git a/pr-preview/pr-98/user_guide/linting.html b/pr-preview/pr-98/user_guide/linting.html
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   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="../_static/documentation_options.js?v=e35243cb"></script>
+    <script src="../_static/documentation_options.js?v=22a78dfd"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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     <link rel="prev" title="uv integration" href="uv.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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diff --git a/pr-preview/pr-98/user_guide/params_files.html b/pr-preview/pr-98/user_guide/params_files.html
@@ -53,7 +53,7 @@
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="../_static/documentation_options.js?v=e35243cb"></script>
+    <script src="../_static/documentation_options.js?v=22a78dfd"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <link rel="prev" title="Project and stage templates" href="templates.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g9166e3c" />
+  <meta name="docsearch:version" content="0.1.dev1+g6481831" />
   </head>