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Boehringer-Ingelheim · Jan 27, 2025 · f9e007a · f9e007a
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diff --git a/CHANGELOG.html b/CHANGELOG.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/_images/social_previews/summary_user_guide_templates_45ad33ac.png b/_images/social_previews/summary_user_guide_templates_45ad33ac.png
diff --git a/_images/social_previews/summary_user_guide_templates_fb98484a.png b/_images/social_previews/summary_user_guide_templates_fb98484a.png
diff --git a/_sources/user_guide/templates.md b/_sources/user_guide/templates.md
@@ -1,3 +1,64 @@
 # Project and stage templates
 
-TODO
+DSO provides a templating engine that allows to quickly bootrstap a project (`dso init`), folder, or stages (`dso create`).
+Templates are based on [jinja2](https://jinja.palletsprojects.com/en/stable/templates/).
+
+## Available templates
+
+DSO currently comes with the following templates:
+
+Project templates:
+
+-   [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/init/default) - Default template, with
+    integration of `git`, `dvc`, `uv`, `pre-commit`, and `editorconfig`.
+
+Folder templates:
+
+-   [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/folder/default) - This one is very minimal, just a folder with `dvc.yaml` and `params.in.yaml` files.
+
+Stage templates:
+
+-   [quarto](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in R
+-   [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).
+Templates shipped with DSO are [licensed](https://github.com/Boehringer-Ingelheim/dso/blob/main/src/dso/templates/LICENSE) under the Creative Commons Zero v1.0
+Universal license.
+
+## Using custom template libraries
+
+Currently, dso only supports the internal templates mentioned above. However, we plan to add support to custom
+stage templates soon. This enables some interesting use-cases:
+
+-   Organization-specific templates: Use templates that make it easier to comply with internal processes or apply
+    corporate design.
+-   Best-practice codebases: Start off common analysis types off a predefined template. We believe that some analyses
+    require more flexibility than predefined worflows such as nf-core, but can still benefit from a structured
+    "base" document to get started with.
+
+## Writing templates
+
+Template directories are recursively copied to their destination and files are rendered with [jinja2](https://jinja.palletsprojects.com/en/stable/templates/).
+You can use all features of jinja2 such as `if/else` blocks or loops. Additionally, you have access to the
+following variables:
+
+Available variables for **project** templates:
+
+| variable            | content                                               |
+| ------------------- | ----------------------------------------------------- |
+| project_name        | project/folder name as provided to the `dso init` CLI |
+| project_description | description as provided to the `dso init` CLI         |
+
+Available variables for **folder** templates:
+
+| variable    | content                                                |
+| ----------- | ------------------------------------------------------ |
+| folder_name | folder name as provided to the `dso create folder` CLI |
+
+Available variables for **stage** templates:
+
+| variable          | content                                               |
+| ----------------- | ----------------------------------------------------- |
+| stage_name        | folder name as provided to the `dso create stage` CLI |
+| stage_description | description as provided to the `dso create stage` CLI |
+| stage_path        | Path to the stage relative to the project root        |
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.dev1+gf67c66b',
+    VERSION: '0.1.dev1+g92ce961',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/cli_command_reference.html b/cli_command_reference.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/cli_configuration.html b/cli_configuration.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/cli_installation.html b/cli_installation.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 
@@ -367,7 +367,7 @@ <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+gf67c66b
+dso, version 0.1.dev1+g92ce961
 </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/contributing.html b/contributing.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/faq.html b/faq.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/genindex.html b/genindex.html
@@ -41,7 +41,7 @@
   <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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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>
@@ -52,7 +52,7 @@
     <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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/getting_started.html b/getting_started.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/index.html b/index.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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>
@@ -65,7 +65,7 @@
     <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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/objects.inv b/objects.inv
diff --git a/py-modindex.html b/py-modindex.html
@@ -41,7 +41,7 @@
   <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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
 
     <script>
       DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;

diff --git a/python_api.html b/python_api.html
@@ -51,7 +51,7 @@
   <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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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>
@@ -63,7 +63,7 @@
     <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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/python_usage.html b/python_usage.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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/search.html b/search.html
@@ -40,7 +40,7 @@
   <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=aac195d7"></script>
+    <script src="_static/documentation_options.js?v=282d51b6"></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>
@@ -54,7 +54,7 @@
     <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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/searchindex.js b/searchindex.js
diff --git a/user_guide/accessing_stage_configs.html b/user_guide/accessing_stage_configs.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=aac195d7"></script>
+    <script src="../_static/documentation_options.js?v=282d51b6"></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="prev" title="Params files" href="params_files.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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/user_guide/dvc.html b/user_guide/dvc.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=aac195d7"></script>
+    <script src="../_static/documentation_options.js?v=282d51b6"></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="prev" title="Accessing stage config" href="accessing_stage_configs.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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/user_guide/linting.html b/user_guide/linting.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=aac195d7"></script>
+    <script src="../_static/documentation_options.js?v=282d51b6"></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="prev" title="uv integration" href="uv.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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>
 
 

diff --git a/user_guide/params_files.html b/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=aac195d7"></script>
+    <script src="../_static/documentation_options.js?v=282d51b6"></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="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+gf67c66b" />
+  <meta name="docsearch:version" content="0.1.dev1+g92ce961" />
   </head>