From 998a81d66d00f3fe270ea5d505cc992b2e9e5a21 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:01:13 +0100
Subject: [PATCH 01/33] Updated pre-commit hooks

---
 .pre-commit-config.yaml | 33 ++++++++++++++++++++++-----------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af67085..e99afec 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,15 +1,26 @@
+---
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0  # Use the latest stable version
-    hooks:
-      - id: check-added-large-files # Prevent giant files from being committed.
-        args: ["--maxkb=1000"]     
-      - id: check-merge-conflict    # Check for files that contain merge conflict strings.
-      - id: check-toml              # Attempts to load all TOML files to verify syntax.
-      - id: check-yaml              # Attempts to load all yaml files to verify syntax.
-        args: ["--unsafe"]
-
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files  # Prevent giant files from being committed.
+        args: [--maxkb=500]
+      - id: check-merge-conflict  # Check for files that contain merge conflict strings.
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
+    rev: 0.8.2
+    hooks:
+      - id: nbstripout  # strip jupyter noteook output
+  - repo: https://github.com/psf/black
+    rev: 25.12.0
+    hooks:
+      - id: black
+        # args: [--line-length=88]
+        # language_version: python3.12
+  - repo: https://github.com/pycqa/isort
+    rev: 7.0.0
     hooks:
-      - id: nbstripout # remove jupyter notebook cell output
+      - id: isort
+        name: isort (python)

From 908180b8aee63dbe182de2a4d8fba96c4fd838b0 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:03:48 +0100
Subject: [PATCH 02/33] Updated pre commit hooks

---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e99afec..ea8483f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,11 +10,11 @@ repos:
         args: [--maxkb=500]
       - id: check-merge-conflict  # Check for files that contain merge conflict strings.
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.2
+    rev: 0.9.0
     hooks:
       - id: nbstripout  # strip jupyter noteook output
   - repo: https://github.com/psf/black
-    rev: 25.12.0
+    rev: 26.1.0
     hooks:
       - id: black
         # args: [--line-length=88]

From a4dca0b7ae76be322fa906f84f119bbd646a837f Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:04:59 +0100
Subject: [PATCH 03/33] isort before black

---
 .pre-commit-config.yaml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ea8483f..33e477f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,14 +13,12 @@ repos:
     rev: 0.9.0
     hooks:
       - id: nbstripout  # strip jupyter noteook output
-  - repo: https://github.com/psf/black
-    rev: 26.1.0
-    hooks:
-      - id: black
-        # args: [--line-length=88]
-        # language_version: python3.12
   - repo: https://github.com/pycqa/isort
     rev: 7.0.0
     hooks:
       - id: isort
         name: isort (python)
+  - repo: https://github.com/psf/black
+    rev: 26.1.0
+    hooks:
+      - id: black

From cffa0821b1c4380c08a9c10f552af53e77cf2a4c Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:06:10 +0100
Subject: [PATCH 04/33] Updated python versions

---
 pyproject.toml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index ee0af26..1a57f17 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,16 +11,12 @@ readme = "README.md"
 keywords = [ "python" ]
 license = { file = "LICENSE.txt" }
 authors = [ { name = "Max" } ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 classifiers = [
   "Development Status :: 3 - Alpha",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
-  "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
   "numpy",
@@ -53,4 +49,3 @@ where = [ "src" ]
 
 [tool.isort]
 profile = "black"
-

From 80e9ebb1eead46632d1f24446bcc3a22d12f793a Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:13:01 +0100
Subject: [PATCH 05/33] Moved tests into the src

---
 {tests => src/app/tests}/unit/__init__.py | 0
 {tests => src/app/tests}/unit/test_app.py | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename {tests => src/app/tests}/unit/__init__.py (100%)
 rename {tests => src/app/tests}/unit/test_app.py (100%)

diff --git a/tests/unit/__init__.py b/src/app/tests/unit/__init__.py
similarity index 100%
rename from tests/unit/__init__.py
rename to src/app/tests/unit/__init__.py
diff --git a/tests/unit/test_app.py b/src/app/tests/unit/test_app.py
similarity index 100%
rename from tests/unit/test_app.py
rename to src/app/tests/unit/test_app.py

From 23e2f8db1cac78accd2726f1229ab41fd4cef18f Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:14:25 +0100
Subject: [PATCH 06/33] Added script for setting up project

---
 setup_project.sh | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 setup_project.sh

diff --git a/setup_project.sh b/setup_project.sh
new file mode 100644
index 0000000..5a26113
--- /dev/null
+++ b/setup_project.sh
@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ $# -ne 1 ]]; then
+  echo "Usage: $0 <app-name>"
+  exit 1
+fi
+
+APPNAME="$1"
+APPNAME_UNDERSCORE="${APPNAME//-/_}"
+
+# 1. Find and replace "testproject" with app name
+grep -rl "testproject" . | while IFS= read -r file; do
+  LC_ALL=C sed -i.bak "s/testproject/${APPNAME}/g" "$file"
+  rm -f "${file}.bak"
+done
+
+# 2. Move src/app to src/<appname_with_underscores>
+if [[ -d "src/app" ]]; then
+  mv src/app "src/${APPNAME_UNDERSCORE}"
+else
+  echo "Error: src/app does not exist"
+  exit 1
+fi
+
+echo "Done:"
+echo "  Replaced 'testproject' → '${APPNAME}'"
+echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"

From 22db63e61b67aaf50a58026c8c9546a753256c03 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:18:56 +0100
Subject: [PATCH 07/33] Rename the import

---
 setup_project.sh | 11 +++++++++++
 1 file changed, 11 insertions(+)
 mode change 100644 => 100755 setup_project.sh

diff --git a/setup_project.sh b/setup_project.sh
old mode 100644
new mode 100755
index 5a26113..380bdd6
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -23,6 +23,17 @@ else
   exit 1
 fi
 
+# 3. Replace import in src/**/*.py
+# from app.main import main -> from <appname_with_underscores>.main import main
+
+find src -type f -name "*.py" -print0 | while IFS= read -r -d '' file; do
+  LC_ALL=C sed -i.bak \
+    "s/from app\.main import main/from ${APPNAME_UNDERSCORE}.main import main/g" \
+    "$file"
+  rm -f "${file}.bak"
+done
+
+
 echo "Done:"
 echo "  Replaced 'testproject' → '${APPNAME}'"
 echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"

From fc469d9ba2ec77c4bcab27cccdd3bb8b8485f8a8 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:19:55 +0100
Subject: [PATCH 08/33] Updated prints

---
 setup_project.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup_project.sh b/setup_project.sh
index 380bdd6..436ca50 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -37,3 +37,4 @@ done
 echo "Done:"
 echo "  Replaced 'testproject' → '${APPNAME}'"
 echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"
+echo "  Replaced import statements in src/**/*.py"

From 7c92571b0389a6a42b83bc37573ec709ee189255 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:27:53 +0100
Subject: [PATCH 09/33] Added more deps

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 1a57f17..b27f9e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,10 +35,13 @@ optional-dependencies.docs = [
   "nbconvert",
   "nbsphinx",
   "jupyterlab",
+  "linkify-it-py",
   "pre-commit",
   "pyproject-fmt",
   "sphinx",
   "sphinx-book-theme",
+  "sphinxcontrib-mermaid",
+  "sphinx-design",
 ]
 optional-dependencies.test = [ "coverage", "pytest" ]
 urls."Source" = "https://github.com/max-models/template-python"

From 98fc575f228080785f9e0f8b0a560fb2705f739c Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:30:36 +0100
Subject: [PATCH 10/33] Added _static

---
 docs/_static/custom.css | 93 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 docs/_static/custom.css

diff --git a/docs/_static/custom.css b/docs/_static/custom.css
new file mode 100644
index 0000000..a9aa047
--- /dev/null
+++ b/docs/_static/custom.css
@@ -0,0 +1,93 @@
+/* Improved toctree styling */
+
+/* Main page toctree container */
+.toctree-wrapper {
+    margin: 2rem 0;
+}
+
+/* Toctree list styling */
+.toctree-wrapper ul {
+    padding-left: 0;
+    list-style: none;
+}
+
+/* Toctree list items */
+.toctree-wrapper li {
+    margin: 0.4rem 0;
+    padding: 0.6rem 1rem;
+    border-bottom: 1.5px solid #c5d1e0;
+    border-left: 3px solid transparent;
+    transition: all 0.2s ease;
+}
+
+.toctree-wrapper li:hover {
+    border-left-color: #4f46e5;
+    background: rgba(79, 70, 229, 0.03);
+}
+
+.toctree-wrapper li:last-child {
+    border-bottom: 1.5px solid #c5d1e0;
+}
+
+/* Toctree links */
+.toctree-wrapper a.reference {
+    font-size: 1.1rem;
+    font-weight: 500;
+    color: #1a365d;
+    text-decoration: none;
+    display: inline-block;
+    transition: all 0.2s ease;
+    padding: 0.25rem 0;
+}
+
+.toctree-wrapper a.reference:hover {
+    color: #2563eb;
+    transform: translateX(5px);
+}
+
+/* Nested toctree items */
+.toctree-wrapper ul ul {
+    padding-left: 1.5rem;
+    margin-top: 0.3rem;
+}
+
+.toctree-wrapper ul ul li {
+    margin: 0.25rem 0;
+    padding: 0.4rem 0.8rem;
+    border-bottom: 1px solid #dce4f0;
+    border-left: 2px solid transparent;
+}
+
+.toctree-wrapper ul ul li:hover {
+    border-left-color: #6366f1;
+    background: rgba(99, 102, 241, 0.03);
+}
+
+.toctree-wrapper ul ul a.reference {
+    font-size: 1rem;
+    font-weight: 400;
+    color: #4a5568;
+}
+
+.toctree-wrapper ul ul a.reference:hover {
+    color: #4f46e5;
+}
+
+/* Toctree caption */
+.toctree-wrapper p.caption {
+    font-size: 1.3rem;
+    font-weight: 600;
+    color: #1e3a5f;
+    margin-bottom: 1rem;
+    padding-bottom: 0.5rem;
+    border-bottom: 3px solid #4f46e5;
+}
+
+/* Improve spacing on main page */
+div.section > .toctree-wrapper {
+    background: linear-gradient(135deg, #f0f4f8 0%, #e8eef5 100%);
+    padding: 1.5rem;
+    border-radius: 12px;
+    box-shadow: 0 4px 6px rgba(79, 70, 229, 0.08);
+    border: 1px solid #dce4f0;
+}

From 4787fc55d502d43141144e050ce1cbf26a7f2fba Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:41:13 +0100
Subject: [PATCH 11/33] Moved custom.css

---
 docs/{ => source}/_static/custom.css | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename docs/{ => source}/_static/custom.css (100%)

diff --git a/docs/_static/custom.css b/docs/source/_static/custom.css
similarity index 100%
rename from docs/_static/custom.css
rename to docs/source/_static/custom.css

From c9d68e8ec9172d30d86dcd2210f36df03ab260b6 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 12:53:19 +0100
Subject: [PATCH 12/33] Rewrote the docs a bit

---
 docs/source/api.md                          |  6 --
 docs/source/api/all_classes.rst             |  9 +++
 docs/source/api/index.rst                   | 10 +++
 docs/source/conf.py                         | 88 ++++++++++++---------
 docs/source/getting_started.rst             | 11 +++
 docs/source/guides/install.rst              | 30 +++++++
 docs/source/guides/quickstart.rst           |  6 ++
 docs/source/index.md                        | 11 ---
 docs/source/index.rst                       | 14 ++++
 docs/source/quickstart.md                   | 38 ---------
 docs/source/{tutorials.md => tutorials.rst} |  2 +-
 11 files changed, 130 insertions(+), 95 deletions(-)
 delete mode 100644 docs/source/api.md
 create mode 100644 docs/source/api/all_classes.rst
 create mode 100644 docs/source/api/index.rst
 create mode 100644 docs/source/getting_started.rst
 create mode 100644 docs/source/guides/install.rst
 create mode 100644 docs/source/guides/quickstart.rst
 delete mode 100644 docs/source/index.md
 create mode 100644 docs/source/index.rst
 delete mode 100644 docs/source/quickstart.md
 rename docs/source/{tutorials.md => tutorials.rst} (89%)

diff --git a/docs/source/api.md b/docs/source/api.md
deleted file mode 100644
index a1c08b6..0000000
--- a/docs/source/api.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# API
-
-Description of the API
-
-```{toctree}
-:maxdepth: 1
\ No newline at end of file
diff --git a/docs/source/api/all_classes.rst b/docs/source/api/all_classes.rst
new file mode 100644
index 0000000..9936e69
--- /dev/null
+++ b/docs/source/api/all_classes.rst
@@ -0,0 +1,9 @@
+Full Class Index
+================
+
+All Classes and Functions
+--------------------------
+
+This page contains the complete API reference for all SAPIC classes and functions.
+
+.. doxygenindex::
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
new file mode 100644
index 0000000..6cdd41d
--- /dev/null
+++ b/docs/source/api/index.rst
@@ -0,0 +1,10 @@
+API Reference
+=============
+
+This section contains the automatically generated C++ API reference.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Full API Index
+
+   all_classes
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 85ee72f..d9c3b85 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -2,26 +2,10 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-
 import os
-import shutil
-
-
-def copy_tutorials(app):
-    src = os.path.abspath("../tutorials")
-    dst = os.path.abspath("source/tutorials")
-
-    # Remove existing target directory if it exists
-    if os.path.exists(dst):
-        shutil.rmtree(dst)
+import sys
 
-    shutil.copytree(src, dst)
-
-
-def setup(app):
-    app.connect("builder-inited", copy_tutorials)
-    # app.add_stylesheet("my-styles.css")
-    app.add_css_file("custom.css")
+sys.path.insert(0, os.path.abspath("../src"))
 
 
 # -- Project information -----------------------------------------------------
@@ -32,46 +16,72 @@ def setup(app):
 author = "Max"
 
 # -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
 extensions = [
-    "nbsphinx",
-    "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
-    "myst_parser",  # enable Markdown support
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.mermaid",
+    "sphinx_design",
+    "myst_parser",
 ]
 
-exclude_patterns = []
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-# Recognize both .rst and .md
-source_suffix = {
-    ".rst": "restructuredtext",
-    ".md": "markdown",
-}
 
 # -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# Activate the theme.
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
 html_theme = "sphinx_book_theme"
 
-
-html_static_path = ["_static"]
-templates_path = ["_templates"]
-
-
-# html_sidebars = {"**": []}
-
 html_theme_options = {
     "repository_branch": "devel",
-    "show_toc_level": 3,
+    "show_toc_level": 2,
     "secondary_sidebar_items": ["page-toc"],
+    "use_sidenotes": True,
+    "home_page_in_toc": True,
+    "collapse_navigation": False,
+    "navigation_depth": 2,
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/max-models/template-python",
+            "url": "https://github.com/max-models/template-projects/",
             "icon": "fab fa-github",
             "type": "fontawesome",
         },
+        {
+            "name": "⭐ Star us!",
+            "url": "https://github.com/max-models/template-projects/",
+            "icon": "fas fa-star",
+            "type": "fontawesome",
+        },
     ],
 }
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+breathe_separate_member_pages = False
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+html_css_files = ["custom.css"]
+
+autosummary_generate = True
+
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": False,
+    "show-inheritance": True,
+}
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
new file mode 100644
index 0000000..4890f2d
--- /dev/null
+++ b/docs/source/getting_started.rst
@@ -0,0 +1,11 @@
+Getting Started
+===============
+
+Learn how to install and use `template-python`.
+
+.. toctree::
+   :maxdepth: 1
+
+   guides/install
+   guides/quickstart
+   tutorials
diff --git a/docs/source/guides/install.rst b/docs/source/guides/install.rst
new file mode 100644
index 0000000..04922ba
--- /dev/null
+++ b/docs/source/guides/install.rst
@@ -0,0 +1,30 @@
+Installation
+============
+
+Create and activate python environment::
+
+   python -m venv env
+   source env/bin/activate
+   pip install --upgrade pip
+
+Install the code and requirements with pip::
+
+   pip install -e .
+
+Run the code with::
+
+   template-python
+
+
+Build docs
+==========
+
+::
+
+   make html
+   cd ../
+   open docs/_build/html/index.html
+
+
+.. toctree::
+   :maxdepth: 1
diff --git a/docs/source/guides/quickstart.rst b/docs/source/guides/quickstart.rst
new file mode 100644
index 0000000..d219ff4
--- /dev/null
+++ b/docs/source/guides/quickstart.rst
@@ -0,0 +1,6 @@
+# Quickstart
+
+First, ensure that `template-python` is installed on your system.
+
+```{toctree}
+:maxdepth: 1
diff --git a/docs/source/index.md b/docs/source/index.md
deleted file mode 100644
index d082474..0000000
--- a/docs/source/index.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# Welcome
-
-Write the documentation of your python package here
-
-```{toctree}
-:maxdepth: 2
-:caption: Contents
-
-quickstart.md
-tutorials.md
-api.md
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..4ed8623
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,14 @@
+template-python Documentation
+=============================
+
+Write the documentation of your python package here
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Documentation
+
+   getting_started
+   tutorials
+   code_overview
+   development
+   api/index
diff --git a/docs/source/quickstart.md b/docs/source/quickstart.md
deleted file mode 100644
index a2d6ec8..0000000
--- a/docs/source/quickstart.md
+++ /dev/null
@@ -1,38 +0,0 @@
-# Quickstart
-
-Clone the repo
-
-```
-git clone ...
-```
-
-Create and activate python environment
-
-```
-python -m venv env
-source env/bin/activate
-pip install --upgrade pip
-```
-
-Install the code and requirements with pip
-
-```
-pip install -e .
-```
-
-Run the code with
-
-```
-template-python
-```
-
-# Build docs
-
-```
-make html
-cd ../
-open docs/_build/html/index.html
-```
-
-```{toctree}
-:maxdepth: 1
\ No newline at end of file
diff --git a/docs/source/tutorials.md b/docs/source/tutorials.rst
similarity index 89%
rename from docs/source/tutorials.md
rename to docs/source/tutorials.rst
index 84e10de..a6b12f4 100644
--- a/docs/source/tutorials.md
+++ b/docs/source/tutorials.rst
@@ -6,4 +6,4 @@ Here are a few tutorials to help you get started.
 :maxdepth: 1
 :glob:
 
-tutorials/*
\ No newline at end of file
+tutorials/*

From a9f08b5b0219471b5bb35d8ef62f2e7a0645d1c8 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:05:36 +0100
Subject: [PATCH 13/33] Updated the docs

---
 docs/source/api/all_classes.rst   |  9 ---------
 docs/source/api/index.rst         | 13 ++++++++-----
 docs/source/conf.py               |  2 +-
 docs/source/guides/quickstart.rst | 18 ++++++++++++++----
 docs/source/index.rst             |  5 +----
 docs/source/tutorials.rst         | 10 +++++-----
 6 files changed, 29 insertions(+), 28 deletions(-)
 delete mode 100644 docs/source/api/all_classes.rst

diff --git a/docs/source/api/all_classes.rst b/docs/source/api/all_classes.rst
deleted file mode 100644
index 9936e69..0000000
--- a/docs/source/api/all_classes.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-Full Class Index
-================
-
-All Classes and Functions
---------------------------
-
-This page contains the complete API reference for all SAPIC classes and functions.
-
-.. doxygenindex::
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
index 6cdd41d..d1bd8af 100644
--- a/docs/source/api/index.rst
+++ b/docs/source/api/index.rst
@@ -1,10 +1,13 @@
 API Reference
 =============
 
-This section contains the automatically generated C++ API reference.
+This section contains the automatically generated Python API reference.
 
-.. toctree::
-   :maxdepth: 1
-   :caption: Full API Index
+Modules
+-------
 
-   all_classes
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   app
diff --git a/docs/source/conf.py b/docs/source/conf.py
index d9c3b85..86d1fd8 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -27,7 +27,7 @@
     "sphinx.ext.napoleon",
     "sphinxcontrib.mermaid",
     "sphinx_design",
-    "myst_parser",
+    "nbsphinx",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
diff --git a/docs/source/guides/quickstart.rst b/docs/source/guides/quickstart.rst
index d219ff4..4bea978 100644
--- a/docs/source/guides/quickstart.rst
+++ b/docs/source/guides/quickstart.rst
@@ -1,6 +1,16 @@
-# Quickstart
+Quickstart
+==========
 
-First, ensure that `template-python` is installed on your system.
+First, ensure that ``template-python`` is installed on your system.
 
-```{toctree}
-:maxdepth: 1
+Basic Usage
+-----------
+
+After installation, you can run the application with::
+
+   template-python
+
+For more details, see the :doc:`install` guide.
+
+.. toctree::
+   :maxdepth: 1
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 4ed8623..85109c7 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,14 +1,11 @@
 template-python Documentation
 =============================
 
-Write the documentation of your python package here
+Write the documentation of your python package here.
 
 .. toctree::
    :maxdepth: 1
    :caption: Documentation
 
    getting_started
-   tutorials
-   code_overview
-   development
    api/index
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index a6b12f4..4848767 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -1,9 +1,9 @@
-# Tutorials
+Tutorials
+=========
 
 Here are a few tutorials to help you get started.
 
-```{toctree}
-:maxdepth: 1
-:glob:
+.. toctree::
+   :maxdepth: 1
 
-tutorials/*
+   tutorials/example_tutorial

From d4437e7bbad5017fed6cf9a0835ae627c8f44c1f Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:06:31 +0100
Subject: [PATCH 14/33] Autosummary to gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index eaf73dd..6548c34 100644
--- a/.gitignore
+++ b/.gitignore
@@ -172,3 +172,4 @@ cython_debug/
 
 # Unit test output
 junit/
+docs/source/api/_autosummary/

From e54c1ea5f3f87592a8ba67d1180622224fdcca16 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:11:12 +0100
Subject: [PATCH 15/33] Added ruff to pre-commit

---
 .github/workflows/static_analysis.yml | 77 +++++++--------------------
 .pre-commit-config.yaml               |  6 +++
 2 files changed, 24 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/static_analysis.yml b/.github/workflows/static_analysis.yml
index 61b3cb6..dd976df 100644
--- a/.github/workflows/static_analysis.yml
+++ b/.github/workflows/static_analysis.yml
@@ -15,42 +15,32 @@ defaults:
     shell: bash
 
 jobs:
-  cloc:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      - name: Download and run cloc
-        run: |
-          curl -s https://raw.githubusercontent.com/AlDanial/cloc/master/cloc > cloc
-          chmod +x cloc
-          ./cloc --version
-          ./cloc $(git ls-files)
-
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
 
-      - name: Code formatting with black
-        run: |
-          pip install black "black[jupyter]"
-          black --check src/
-          black --check tutorials/
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.1
 
-  isort:
+  cloc:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      - name: Code formatting with isort
+      - name: Download and run cloc
         run: |
-          pip install isort
-          isort --check src/
-          isort --check tutorials/
+          curl -s https://raw.githubusercontent.com/AlDanial/cloc/master/cloc > cloc
+          chmod +x cloc
+          ./cloc --version
+          ./cloc $(git ls-files)
 
   mypy:
     runs-on: ubuntu-latest
@@ -59,43 +49,12 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v4
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
       - name: Type checking with mypy
         run: |
           pip install mypy
           mypy src/ || true
-
-  prospector:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Code analysis with prospector
-        run: |
-          pip install prospector
-          prospector src/ || true
-
-  ruff:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Linting with ruff
-        run: |
-          pip install ruff
-          ruff check src/ || true
-
-  pylint:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Linting with pylint
-        run: |
-          pip install pylint
-          pylint src/ || true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 33e477f..b70aead 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -22,3 +22,9 @@ repos:
     rev: 26.1.0
     hooks:
       - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

From 6e514f9b65a67b24713f3ae1d40b1a7d78a904ce Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:14:31 +0100
Subject: [PATCH 16/33] Added test_docs_job

---
 .github/workflows/docs.yml      |  2 +-
 .github/workflows/test_docs.yml | 50 +++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/test_docs.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index c59b8ea..5c9d160 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -2,7 +2,7 @@ name: Deploy docs to GitHub Pages
 
 on:
   push:
-    branches: ["devel", "main"] # TODO: Set to main only after release
+    branches: ["devel"]
   workflow_dispatch:
 
 permissions:
diff --git a/.github/workflows/test_docs.yml b/.github/workflows/test_docs.yml
new file mode 100644
index 0000000..bce688f
--- /dev/null
+++ b/.github/workflows/test_docs.yml
@@ -0,0 +1,50 @@
+name: Test Documentation Build
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install pandoc
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[docs]"
+
+      - name: Build Sphinx docs
+        run: |
+          cd docs
+          sphinx-build -b html -W --keep-going source build/html
+
+      - name: Upload docs artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: documentation
+          path: docs/build/html/
+          retention-days: 7

From 911daddc96b598f29afc4d5f5b9aaa7d1effde3b Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:17:37 +0100
Subject: [PATCH 17/33] Adde test_docs

---
 .github/actions/build-docs/action.yml         | 40 +++++++++++++++++++
 .../workflows/{docs.yml => publish_docs.yml}  | 19 +++------
 .../{publish.yml => publish_pypi.yml}         |  1 -
 .github/workflows/test_docs.yml               | 20 ++--------
 4 files changed, 48 insertions(+), 32 deletions(-)
 create mode 100644 .github/actions/build-docs/action.yml
 rename .github/workflows/{docs.yml => publish_docs.yml} (68%)
 rename .github/workflows/{publish.yml => publish_pypi.yml} (99%)

diff --git a/.github/actions/build-docs/action.yml b/.github/actions/build-docs/action.yml
new file mode 100644
index 0000000..7795498
--- /dev/null
+++ b/.github/actions/build-docs/action.yml
@@ -0,0 +1,40 @@
+name: 'Build Documentation'
+description: 'Build Sphinx documentation'
+inputs:
+  python-version:
+    description: 'Python version to use'
+    required: false
+    default: '3.10'
+  treat-warnings-as-errors:
+    description: 'Treat warnings as errors (-W flag)'
+    required: false
+    default: 'false'
+runs:
+  using: 'composite'
+  steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install pandoc
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y pandoc
+
+    - name: Install Python dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install ".[docs]"
+
+    - name: Build Sphinx docs
+      shell: bash
+      run: |
+        cd docs
+        if [ "${{ inputs.treat-warnings-as-errors }}" = "true" ]; then
+          sphinx-build -b html -W --keep-going source build/html
+        else
+          sphinx-build -b html source build/html
+        fi
diff --git a/.github/workflows/docs.yml b/.github/workflows/publish_docs.yml
similarity index 68%
rename from .github/workflows/docs.yml
rename to .github/workflows/publish_docs.yml
index 5c9d160..553243a 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/publish_docs.yml
@@ -25,20 +25,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install pandoc
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y pandoc
-
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ".[docs]"
-
-      - name: Build Sphinx docs
-        run: |
-          cd docs
-          make html
+      - name: Build documentation
+        uses: ./.github/actions/build-docs
+        with:
+          python-version: '3.10'
+          treat-warnings-as-errors: 'false'
 
       - name: Setup Pages
         uses: actions/configure-pages@v5
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish_pypi.yml
similarity index 99%
rename from .github/workflows/publish.yml
rename to .github/workflows/publish_pypi.yml
index d91ffc6..6a4ba69 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -32,4 +32,3 @@ jobs:
       #    TWINE_USERNAME: __token__  # Use API token
       #    TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       #  run: twine upload dist/*
-
diff --git a/.github/workflows/test_docs.yml b/.github/workflows/test_docs.yml
index bce688f..ffe898d 100644
--- a/.github/workflows/test_docs.yml
+++ b/.github/workflows/test_docs.yml
@@ -21,25 +21,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Build documentation
+        uses: ./.github/actions/build-docs
         with:
           python-version: '3.10'
-
-      - name: Install pandoc
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y pandoc
-
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ".[docs]"
-
-      - name: Build Sphinx docs
-        run: |
-          cd docs
-          sphinx-build -b html -W --keep-going source build/html
+          treat-warnings-as-errors: 'true'
 
       - name: Upload docs artifact
         uses: actions/upload-artifact@v4

From 56d7981a67b7750d64997b84cf373e2193386fc8 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:23:35 +0100
Subject: [PATCH 18/33] isort,black --> ruff

---
 .pre-commit-config.yaml | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b70aead..b96501a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,18 +13,9 @@ repos:
     rev: 0.9.0
     hooks:
       - id: nbstripout  # strip jupyter noteook output
-  - repo: https://github.com/pycqa/isort
-    rev: 7.0.0
-    hooks:
-      - id: isort
-        name: isort (python)
-  - repo: https://github.com/psf/black
-    rev: 26.1.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.9.1
     hooks:
       - id: ruff
-        args: [--fix]
+        args: [--fix, --select, I]
       - id: ruff-format

From 82a0fff8067ade8bbae1d69a7b0c360119be2765 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:26:09 +0100
Subject: [PATCH 19/33] Added rm

---
 setup_project.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup_project.sh b/setup_project.sh
index 436ca50..63ab141 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -38,3 +38,4 @@ echo "Done:"
 echo "  Replaced 'testproject' → '${APPNAME}'"
 echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"
 echo "  Replaced import statements in src/**/*.py"
+echo "You can now remove this script with: rm setup_project.sh"

From c89a708fb2645d65954183dc7eff4d0750745189 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:28:48 +0100
Subject: [PATCH 20/33] Test setup script

---
 .github/workflows/test_setup_script.yml | 67 +++++++++++++++++++++++++
 .github/workflows/testing.yml           |  6 +--
 2 files changed, 68 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/test_setup_script.yml

diff --git a/.github/workflows/test_setup_script.yml b/.github/workflows/test_setup_script.yml
new file mode 100644
index 0000000..6422326
--- /dev/null
+++ b/.github/workflows/test_setup_script.yml
@@ -0,0 +1,67 @@
+name: Test Setup Script
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test-setup-script:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Run setup script
+        run: |
+          bash setup_project.sh my-test-app
+
+      - name: Verify changes
+        run: |
+          # Check that src/app was moved to src/my_test_app
+          if [ ! -d "src/my_test_app" ]; then
+            echo "Error: src/my_test_app does not exist"
+            exit 1
+          fi
+
+          # Check that src/app no longer exists
+          if [ -d "src/app" ]; then
+            echo "Error: src/app still exists"
+            exit 1
+          fi
+
+          # Check that testproject was replaced in pyproject.toml
+          if grep -q "testproject" pyproject.toml; then
+            echo "Error: 'testproject' still found in pyproject.toml"
+            exit 1
+          fi
+
+          if ! grep -q "my-test-app" pyproject.toml; then
+            echo "Error: 'my-test-app' not found in pyproject.toml"
+            exit 1
+          fi
+
+          echo "✓ All checks passed!"
+
+      - name: Install project with new name
+        run: |
+          pip install --upgrade pip
+          pip install -e .
+
+      - name: Test renamed command works
+        run: |
+          my-test-app
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index f84e48c..634eac4 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -44,10 +44,6 @@ jobs:
           pip install --upgrade pip
           pip install ".[dev]"
 
-      - name: Check installation
-        run: |
-          template-python
-
       - name: Run tests
         run: |
           pytest .
@@ -63,4 +59,4 @@ jobs:
           make clean
           make html
           cd ..
-          ls docs/build/html/index.html
\ No newline at end of file
+          ls docs/build/html/index.html

From 9df0568f69fa4d93db85f5b8cf79518f19ddb68c Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:30:11 +0100
Subject: [PATCH 21/33] Fixes

---
 .gitattributes                   |  2 +-
 .gitlab-ci.yml                   |  1 -
 pytest.ini                       |  2 +-
 tutorials/example_tutorial.ipynb | 16 ++++------------
 4 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/.gitattributes b/.gitattributes
index 2f41707..8425c58 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1 @@
-*.ipynb filter=strip-notebook-output  
+*.ipynb filter=strip-notebook-output
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7de373c..d0b7c87 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,4 +54,3 @@ deploy:
   stage: deploy
   script: echo "Define your deployment script!"
   environment: production
-
diff --git a/pytest.ini b/pytest.ini
index fa4a21d..fcccae1 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,2 +1,2 @@
-[pytest]  
+[pytest]
 pythonpath = src
diff --git a/tutorials/example_tutorial.ipynb b/tutorials/example_tutorial.ipynb
index 4f568bb..da4e6f7 100644
--- a/tutorials/example_tutorial.ipynb
+++ b/tutorials/example_tutorial.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "efb79425-958b-412c-afa9-055e27a69baa",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Tutorial 1"
@@ -10,18 +10,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "id": "68ad1562-4953-444c-96c7-9026bcc54cc7",
+   "execution_count": null,
+   "id": "1",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Example tutorial which will be published in the docs!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\"Example tutorial which will be published in the docs!\")"
    ]

From e8062b42f13d228bb9a1c0cd6ce05100cf4c5cc8 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:33:22 +0100
Subject: [PATCH 22/33] Renaming

---
 .github/workflows/{testing.yml => test.yml} | 9 ---------
 1 file changed, 9 deletions(-)
 rename .github/workflows/{testing.yml => test.yml} (85%)

diff --git a/.github/workflows/testing.yml b/.github/workflows/test.yml
similarity index 85%
rename from .github/workflows/testing.yml
rename to .github/workflows/test.yml
index 634eac4..fbc55a1 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/test.yml
@@ -51,12 +51,3 @@ jobs:
       - name: Test tutorials
         run: |
           jupyter nbconvert --to notebook --execute tutorials/*.ipynb --output-dir=/tmp --ExecutePreprocessor.timeout=300
-
-      - name: Test docs build
-        run: |
-          pip install ".[docs]"
-          cd docs
-          make clean
-          make html
-          cd ..
-          ls docs/build/html/index.html

From 0dba336a8e95f991d400c86bb1e3737d78b92cfc Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:35:23 +0100
Subject: [PATCH 23/33] Separate tutorial and pytest

---
 .github/workflows/test.yml           | 26 +++++-----------
 .github/workflows/test_pytest.yml    | 41 +++++++++++++++++++++++++
 .github/workflows/test_tutorials.yml | 46 ++++++++++++++++++++++++++++
 3 files changed, 94 insertions(+), 19 deletions(-)
 create mode 100644 .github/workflows/test_pytest.yml
 create mode 100644 .github/workflows/test_tutorials.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fbc55a1..42b12d9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-name: Tests
+name: Test Pytest
 
 on:
   push:
@@ -11,43 +11,31 @@ on:
       - devel
 
 jobs:
-  build:
+  pytest:
     runs-on: ubuntu-latest
 
     steps:
-      # Checkout the repository
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      # Set up Python
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'  # Adjust as needed
+          python-version: '3.10'
 
-      # Cache pip dependencies
       - name: Cache pip
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-
 
-      - name: Install dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y pandoc
-
       - name: Install project
         run: |
           pip install --upgrade pip
-          pip install ".[dev]"
+          pip install ".[test]"
 
       - name: Run tests
         run: |
           pytest .
-
-      - name: Test tutorials
-        run: |
-          jupyter nbconvert --to notebook --execute tutorials/*.ipynb --output-dir=/tmp --ExecutePreprocessor.timeout=300
diff --git a/.github/workflows/test_pytest.yml b/.github/workflows/test_pytest.yml
new file mode 100644
index 0000000..42b12d9
--- /dev/null
+++ b/.github/workflows/test_pytest.yml
@@ -0,0 +1,41 @@
+name: Test Pytest
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install project
+        run: |
+          pip install --upgrade pip
+          pip install ".[test]"
+
+      - name: Run tests
+        run: |
+          pytest .
diff --git a/.github/workflows/test_tutorials.yml b/.github/workflows/test_tutorials.yml
new file mode 100644
index 0000000..599aa81
--- /dev/null
+++ b/.github/workflows/test_tutorials.yml
@@ -0,0 +1,46 @@
+name: Test Tutorials
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+jobs:
+  tutorials:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install project
+        run: |
+          pip install --upgrade pip
+          pip install ".[dev]"
+
+      - name: Execute tutorials
+        run: |
+          jupyter nbconvert --to notebook --execute tutorials/*.ipynb --output-dir=/tmp --ExecutePreprocessor.timeout=300

From 821c50157bc21a49d2417a84f20854be5a5413e1 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:30:24 +0100
Subject: [PATCH 24/33] Fixed setup_project.sh

---
 .github/workflows/test_setup_script.yml | 20 +++-----------------
 setup_project.sh                        | 15 +++++++++++----
 2 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/test_setup_script.yml b/.github/workflows/test_setup_script.yml
index 6422326..50e455f 100644
--- a/.github/workflows/test_setup_script.yml
+++ b/.github/workflows/test_setup_script.yml
@@ -44,23 +44,9 @@ jobs:
             exit 1
           fi
 
-          # Check that testproject was replaced in pyproject.toml
-          if grep -q "testproject" pyproject.toml; then
-            echo "Error: 'testproject' still found in pyproject.toml"
-            exit 1
-          fi
-
-          if ! grep -q "my-test-app" pyproject.toml; then
-            echo "Error: 'my-test-app' not found in pyproject.toml"
-            exit 1
-          fi
-
-          echo "✓ All checks passed!"
-
-      - name: Install project with new name
-        run: |
-          pip install --upgrade pip
-          pip install -e .
+          # Check that template-python was replaced in pyproject.toml
+          if grep -q "template-python" pyproject.toml; then
+            echo "Error: 'template-python' still found in pyproject.toml"
 
       - name: Test renamed command works
         run: |
diff --git a/setup_project.sh b/setup_project.sh
index 63ab141..b3a53e1 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -9,9 +9,15 @@ fi
 APPNAME="$1"
 APPNAME_UNDERSCORE="${APPNAME//-/_}"
 
-# 1. Find and replace "testproject" with app name
-grep -rl "testproject" . | while IFS= read -r file; do
-  LC_ALL=C sed -i.bak "s/testproject/${APPNAME}/g" "$file"
+# 1. Find and replace "template-python" with app name
+grep -rl "template-python" . --exclude-dir=.git --exclude-dir=docs/build | while IFS= read -r file; do
+  LC_ALL=C sed -i.bak "s/template-python/${APPNAME}/g" "$file"
+  rm -f "${file}.bak"
+done
+
+# Also replace template_python with appname_underscore
+grep -rl "template_python" . --exclude-dir=.git --exclude-dir=docs/build | while IFS= read -r file; do
+  LC_ALL=C sed -i.bak "s/template_python/${APPNAME_UNDERSCORE}/g" "$file"
   rm -f "${file}.bak"
 done
 
@@ -35,7 +41,8 @@ done
 
 
 echo "Done:"
-echo "  Replaced 'testproject' → '${APPNAME}'"
+echo "  Replaced 'template-python' → '${APPNAME}'"
+echo "  Replaced 'template_python' → '${APPNAME_UNDERSCORE}'"
 echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"
 echo "  Replaced import statements in src/**/*.py"
 echo "You can now remove this script with: rm setup_project.sh"

From b77cf124ee933024f020549c06089be35c01cef0 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:37:59 +0100
Subject: [PATCH 25/33] Test

---
 .github/workflows/test_setup_script.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/test_setup_script.yml b/.github/workflows/test_setup_script.yml
index 50e455f..db1637e 100644
--- a/.github/workflows/test_setup_script.yml
+++ b/.github/workflows/test_setup_script.yml
@@ -47,6 +47,20 @@ jobs:
           # Check that template-python was replaced in pyproject.toml
           if grep -q "template-python" pyproject.toml; then
             echo "Error: 'template-python' still found in pyproject.toml"
+            exit 1
+          fi
+
+          if ! grep -q "my-test-app" pyproject.toml; then
+            echo "Error: 'my-test-app' not found in pyproject.toml"
+            exit 1
+          fi
+
+          echo "✓ All checks passed!"
+
+      - name: Install project with new name
+        run: |
+          pip install --upgrade pip
+          pip install -e .
 
       - name: Test renamed command works
         run: |

From 9d41ebac54ef41270d14dd08d1e8dbd679e025eb Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:47:16 +0100
Subject: [PATCH 26/33] Fixed setup_project.sh

---
 setup_project.sh | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/setup_project.sh b/setup_project.sh
index b3a53e1..2533997 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -29,8 +29,9 @@ else
   exit 1
 fi
 
-# 3. Replace import in src/**/*.py
+# 3. Replace import in src/**/*.py and entry points
 # from app.main import main -> from <appname_with_underscores>.main import main
+# Also replace "app.main:main" -> "<appname_with_underscores>.main:main" in pyproject.toml
 
 find src -type f -name "*.py" -print0 | while IFS= read -r -d '' file; do
   LC_ALL=C sed -i.bak \
@@ -39,6 +40,12 @@ find src -type f -name "*.py" -print0 | while IFS= read -r -d '' file; do
   rm -f "${file}.bak"
 done
 
+# Replace app.main:main entry point in pyproject.toml
+if [[ -f "pyproject.toml" ]]; then
+  LC_ALL=C sed -i.bak "s/app\.main:main/${APPNAME_UNDERSCORE}.main:main/g" "pyproject.toml"
+  rm -f "pyproject.toml.bak"
+fiand entry points
+
 
 echo "Done:"
 echo "  Replaced 'template-python' → '${APPNAME}'"

From fdd3848de4bba4ad42dbc299b5d19790f8251a67 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:50:16 +0100
Subject: [PATCH 27/33] Remove the test file in the script

---
 setup_project.sh | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/setup_project.sh b/setup_project.sh
index 2533997..0caeb7a 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -44,12 +44,18 @@ done
 if [[ -f "pyproject.toml" ]]; then
   LC_ALL=C sed -i.bak "s/app\.main:main/${APPNAME_UNDERSCORE}.main:main/g" "pyproject.toml"
   rm -f "pyproject.toml.bak"
-fiand entry points
+fi
+
+# 4. Remove the test_setup_script.yml workflow since it's no longer needed
+if [[ -f ".github/workflows/test_setup_script.yml" ]]; then
+  rm -f ".github/workflows/test_setup_script.yml"
+fi
 
 
 echo "Done:"
 echo "  Replaced 'template-python' → '${APPNAME}'"
 echo "  Replaced 'template_python' → '${APPNAME_UNDERSCORE}'"
 echo "  Moved src/app → src/${APPNAME_UNDERSCORE}"
-echo "  Replaced import statements in src/**/*.py"
+echo "  Replaced import statements and entry points"
+echo "  Removed .github/workflows/test_setup_script.yml"
 echo "You can now remove this script with: rm setup_project.sh"

From 8e1b100ecbf8ef905f3e4cd0a1c1762516ff2a12 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:50:46 +0100
Subject: [PATCH 28/33] Run everything relative to the script directory

---
 setup_project.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/setup_project.sh b/setup_project.sh
index 0caeb7a..3d40f0b 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -1,6 +1,10 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
+# Get the directory where this script is located
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$SCRIPT_DIR"
+
 if [[ $# -ne 1 ]]; then
   echo "Usage: $0 <app-name>"
   exit 1

From 359cca94caae57a0d532f37afde5e33ac8e66f11 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:03:44 +0100
Subject: [PATCH 29/33] Fixed docs build

---
 docs/source/conf.py       | 5 ++++-
 docs/source/tutorials.rst | 2 +-
 setup_project.sh          | 8 +++++++-
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 86d1fd8..af7ddd2 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -36,7 +36,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**/.ipynb_checkpoints"]
+
+# nbsphinx configuration
+nbsphinx_execute = "never"  # Don't execute notebooks during build
 
 
 # -- Options for HTML output -------------------------------------------------
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index 4848767..4b448a9 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -6,4 +6,4 @@ Here are a few tutorials to help you get started.
 .. toctree::
    :maxdepth: 1
 
-   tutorials/example_tutorial
+   tutorials/example_tutorial.ipynb
diff --git a/setup_project.sh b/setup_project.sh
index 3d40f0b..a245bd0 100755
--- a/setup_project.sh
+++ b/setup_project.sh
@@ -50,7 +50,13 @@ if [[ -f "pyproject.toml" ]]; then
   rm -f "pyproject.toml.bak"
 fi
 
-# 4. Remove the test_setup_script.yml workflow since it's no longer needed
+# 4. Update docs/source/api/index.rst to reference the new module name
+if [[ -f "docs/source/api/index.rst" ]]; then
+  LC_ALL=C sed -i.bak "s/^   app$/   ${APPNAME_UNDERSCORE}/" "docs/source/api/index.rst"
+  rm -f "docs/source/api/index.rst.bak"
+fi
+
+# 5. Remove the test_setup_script.yml workflow since it's no longer needed
 if [[ -f ".github/workflows/test_setup_script.yml" ]]; then
   rm -f ".github/workflows/test_setup_script.yml"
 fi

From 9cd1392d596ac9d90af265f720900d66a5a5c141 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:06:14 +0100
Subject: [PATCH 30/33] Removed .github/workflows/test.yml

---
 .github/workflows/test.yml | 41 --------------------------------------
 1 file changed, 41 deletions(-)
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 42b12d9..0000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-name: Test Pytest
-
-on:
-  push:
-    branches:
-      - main
-      - devel
-  pull_request:
-    branches:
-      - main
-      - devel
-
-jobs:
-  pytest:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install project
-        run: |
-          pip install --upgrade pip
-          pip install ".[test]"
-
-      - name: Run tests
-        run: |
-          pytest .

From bd11a74df802c4e968ab3072ae3ff99a56f118e1 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:09:24 +0100
Subject: [PATCH 31/33] copy tutorials

---
 docs/source/conf.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index af7ddd2..a687be3 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -3,10 +3,21 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
+import shutil
 import sys
+from pathlib import Path
 
 sys.path.insert(0, os.path.abspath("../src"))
 
+# Copy tutorial notebooks from project root to docs/source/tutorials/
+tutorials_source = Path(__file__).parent.parent.parent / "tutorials"
+tutorials_dest = Path(__file__).parent / "tutorials"
+
+if tutorials_source.exists():
+    tutorials_dest.mkdir(exist_ok=True)
+    for notebook in tutorials_source.glob("*.ipynb"):
+        shutil.copy2(notebook, tutorials_dest / notebook.name)
+
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

From 378605e4d2ec556809bfbd0d11ee519f1de08640 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:14:53 +0100
Subject: [PATCH 32/33] Fix publishing to pypi

---
 .github/workflows/publish_pypi.yml | 16 +++++++------
 README.md                          | 37 ++++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 6a4ba69..cf03ba3 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -8,6 +8,12 @@ on:
 jobs:
   build-and-publish:
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/template-python/
+    permissions:
+      id-token: write
+      contents: read
 
     steps:
       - name: Checkout repository
@@ -21,14 +27,10 @@ jobs:
       - name: Install build tools
         run: |
           python -m pip install --upgrade pip
-          pip install build twine
+          pip install build
 
       - name: Build the package
         run: python -m build
 
-      # Uncomment to publish on pypi
-      #- name: Publish to PyPI
-      #  env:
-      #    TWINE_USERNAME: __token__  # Use API token
-      #    TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      #  run: twine upload dist/*
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/README.md b/README.md
index 8ca65e2..3cb7f82 100644
--- a/README.md
+++ b/README.md
@@ -34,3 +34,40 @@ make html
 cd ../
 open docs/_build/html/index.html
 ```
+
+# Publishing on PyPI
+
+This project is configured to automatically publish to PyPI using GitHub Actions with trusted publishing (OIDC).
+
+## Setup (One-time configuration)
+
+### 1. Create PyPI Account and Project
+
+1. Create an account on [PyPI](https://pypi.org/)
+2. Create a new project or claim your project name
+
+### 2. Configure Trusted Publishing on PyPI
+
+1. Go to your PyPI project settings
+2. Navigate to "Publishing" → "Add a new publisher"
+3. Configure the trusted publisher with these details:
+   - **PyPI Project Name**: `template-python` (or your project name)
+   - **Owner**: Your GitHub username/organization
+   - **Repository name**: `template-python`
+   - **Workflow name**: `publish_pypi.yml`
+   - **Environment name**: `pypi`
+
+### 3. Configure GitHub Environment (Optional but Recommended)
+
+1. Go to your GitHub repository → Settings → Environments
+2. Create an environment named `pypi`
+3. Add protection rules:
+   - Deployment branches: Only `main` branch
+
+## Publishing Process
+
+Once configured, publishing is automatic:
+
+1. **Merge to main branch**: Any push to the `main` branch triggers the workflow
+2. **Automatic build**: The workflow builds the Python package
+3. **Automatic publish**: The package is automatically published to PyPI using trusted publishing

From 555ae61992b5e5a79c2f1f3a212ed0cd679edfd1 Mon Sep 17 00:00:00 2001
From: Max <max.lindqvist@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:16:21 +0100
Subject: [PATCH 33/33] Formatting with prettier

---
 .github/actions/build-docs/action.yml   | 14 ++--
 .github/workflows/publish_docs.yml      |  4 +-
 .github/workflows/static_analysis.yml   |  4 +-
 .github/workflows/test_docs.yml         |  4 +-
 .github/workflows/test_pytest.yml       |  2 +-
 .github/workflows/test_setup_script.yml |  2 +-
 .github/workflows/test_tutorials.yml    |  2 +-
 .gitlab-ci.yml                          |  4 +-
 .pre-commit-config.yaml                 |  6 +-
 README.md                               |  1 -
 docs/source/_static/custom.css          | 86 ++++++++++++-------------
 rules/devel_rules.json                  | 10 +--
 rules/main_rules.json                   |  9 +--
 13 files changed, 68 insertions(+), 80 deletions(-)

diff --git a/.github/actions/build-docs/action.yml b/.github/actions/build-docs/action.yml
index 7795498..ca4822e 100644
--- a/.github/actions/build-docs/action.yml
+++ b/.github/actions/build-docs/action.yml
@@ -1,16 +1,16 @@
-name: 'Build Documentation'
-description: 'Build Sphinx documentation'
+name: "Build Documentation"
+description: "Build Sphinx documentation"
 inputs:
   python-version:
-    description: 'Python version to use'
+    description: "Python version to use"
     required: false
-    default: '3.10'
+    default: "3.10"
   treat-warnings-as-errors:
-    description: 'Treat warnings as errors (-W flag)'
+    description: "Treat warnings as errors (-W flag)"
     required: false
-    default: 'false'
+    default: "false"
 runs:
-  using: 'composite'
+  using: "composite"
   steps:
     - name: Set up Python
       uses: actions/setup-python@v5
diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml
index 553243a..88833dd 100644
--- a/.github/workflows/publish_docs.yml
+++ b/.github/workflows/publish_docs.yml
@@ -28,8 +28,8 @@ jobs:
       - name: Build documentation
         uses: ./.github/actions/build-docs
         with:
-          python-version: '3.10'
-          treat-warnings-as-errors: 'false'
+          python-version: "3.10"
+          treat-warnings-as-errors: "false"
 
       - name: Setup Pages
         uses: actions/configure-pages@v5
diff --git a/.github/workflows/static_analysis.yml b/.github/workflows/static_analysis.yml
index dd976df..fce5a85 100644
--- a/.github/workflows/static_analysis.yml
+++ b/.github/workflows/static_analysis.yml
@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Run pre-commit
         uses: pre-commit/action@v3.0.1
@@ -52,7 +52,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Type checking with mypy
         run: |
diff --git a/.github/workflows/test_docs.yml b/.github/workflows/test_docs.yml
index ffe898d..dce6436 100644
--- a/.github/workflows/test_docs.yml
+++ b/.github/workflows/test_docs.yml
@@ -24,8 +24,8 @@ jobs:
       - name: Build documentation
         uses: ./.github/actions/build-docs
         with:
-          python-version: '3.10'
-          treat-warnings-as-errors: 'true'
+          python-version: "3.10"
+          treat-warnings-as-errors: "true"
 
       - name: Upload docs artifact
         uses: actions/upload-artifact@v4
diff --git a/.github/workflows/test_pytest.yml b/.github/workflows/test_pytest.yml
index 42b12d9..57c03cc 100644
--- a/.github/workflows/test_pytest.yml
+++ b/.github/workflows/test_pytest.yml
@@ -21,7 +21,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Cache pip
         uses: actions/cache@v4
diff --git a/.github/workflows/test_setup_script.yml b/.github/workflows/test_setup_script.yml
index db1637e..c1e9e4c 100644
--- a/.github/workflows/test_setup_script.yml
+++ b/.github/workflows/test_setup_script.yml
@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Run setup script
         run: |
diff --git a/.github/workflows/test_tutorials.yml b/.github/workflows/test_tutorials.yml
index 599aa81..58a7e81 100644
--- a/.github/workflows/test_tutorials.yml
+++ b/.github/workflows/test_tutorials.yml
@@ -21,7 +21,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Cache pip
         uses: actions/cache@v4
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d0b7c87..bbbbcf4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,14 +19,14 @@ cache:
     - .cache/pip
 
 before_script:
-  - python --version ; pip --version  # For debugging
+  - python --version ; pip --version # For debugging
   - pip install virtualenv
   - virtualenv venv
   - source venv/bin/activate
 
 test:
   script:
-    - pip install ruff tox  # you can also use tox
+    - pip install ruff tox # you can also use tox
     - pip install --editable ".[test]"
     - tox -e py,ruff
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b96501a..61316d0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,13 +6,13 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: check-added-large-files  # Prevent giant files from being committed.
+      - id: check-added-large-files # Prevent giant files from being committed.
         args: [--maxkb=500]
-      - id: check-merge-conflict  # Check for files that contain merge conflict strings.
+      - id: check-merge-conflict # Check for files that contain merge conflict strings.
   - repo: https://github.com/kynan/nbstripout
     rev: 0.9.0
     hooks:
-      - id: nbstripout  # strip jupyter noteook output
+      - id: nbstripout # strip jupyter noteook output
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.9.1
     hooks:
diff --git a/README.md b/README.md
index 3cb7f82..8f49086 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,6 @@ template-python
 
 # Build docs
 
-
 ```
 make html
 cd ../
diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
index a9aa047..fb0ac08 100644
--- a/docs/source/_static/custom.css
+++ b/docs/source/_static/custom.css
@@ -2,92 +2,92 @@
 
 /* Main page toctree container */
 .toctree-wrapper {
-    margin: 2rem 0;
+  margin: 2rem 0;
 }
 
 /* Toctree list styling */
 .toctree-wrapper ul {
-    padding-left: 0;
-    list-style: none;
+  padding-left: 0;
+  list-style: none;
 }
 
 /* Toctree list items */
 .toctree-wrapper li {
-    margin: 0.4rem 0;
-    padding: 0.6rem 1rem;
-    border-bottom: 1.5px solid #c5d1e0;
-    border-left: 3px solid transparent;
-    transition: all 0.2s ease;
+  margin: 0.4rem 0;
+  padding: 0.6rem 1rem;
+  border-bottom: 1.5px solid #c5d1e0;
+  border-left: 3px solid transparent;
+  transition: all 0.2s ease;
 }
 
 .toctree-wrapper li:hover {
-    border-left-color: #4f46e5;
-    background: rgba(79, 70, 229, 0.03);
+  border-left-color: #4f46e5;
+  background: rgba(79, 70, 229, 0.03);
 }
 
 .toctree-wrapper li:last-child {
-    border-bottom: 1.5px solid #c5d1e0;
+  border-bottom: 1.5px solid #c5d1e0;
 }
 
 /* Toctree links */
 .toctree-wrapper a.reference {
-    font-size: 1.1rem;
-    font-weight: 500;
-    color: #1a365d;
-    text-decoration: none;
-    display: inline-block;
-    transition: all 0.2s ease;
-    padding: 0.25rem 0;
+  font-size: 1.1rem;
+  font-weight: 500;
+  color: #1a365d;
+  text-decoration: none;
+  display: inline-block;
+  transition: all 0.2s ease;
+  padding: 0.25rem 0;
 }
 
 .toctree-wrapper a.reference:hover {
-    color: #2563eb;
-    transform: translateX(5px);
+  color: #2563eb;
+  transform: translateX(5px);
 }
 
 /* Nested toctree items */
 .toctree-wrapper ul ul {
-    padding-left: 1.5rem;
-    margin-top: 0.3rem;
+  padding-left: 1.5rem;
+  margin-top: 0.3rem;
 }
 
 .toctree-wrapper ul ul li {
-    margin: 0.25rem 0;
-    padding: 0.4rem 0.8rem;
-    border-bottom: 1px solid #dce4f0;
-    border-left: 2px solid transparent;
+  margin: 0.25rem 0;
+  padding: 0.4rem 0.8rem;
+  border-bottom: 1px solid #dce4f0;
+  border-left: 2px solid transparent;
 }
 
 .toctree-wrapper ul ul li:hover {
-    border-left-color: #6366f1;
-    background: rgba(99, 102, 241, 0.03);
+  border-left-color: #6366f1;
+  background: rgba(99, 102, 241, 0.03);
 }
 
 .toctree-wrapper ul ul a.reference {
-    font-size: 1rem;
-    font-weight: 400;
-    color: #4a5568;
+  font-size: 1rem;
+  font-weight: 400;
+  color: #4a5568;
 }
 
 .toctree-wrapper ul ul a.reference:hover {
-    color: #4f46e5;
+  color: #4f46e5;
 }
 
 /* Toctree caption */
 .toctree-wrapper p.caption {
-    font-size: 1.3rem;
-    font-weight: 600;
-    color: #1e3a5f;
-    margin-bottom: 1rem;
-    padding-bottom: 0.5rem;
-    border-bottom: 3px solid #4f46e5;
+  font-size: 1.3rem;
+  font-weight: 600;
+  color: #1e3a5f;
+  margin-bottom: 1rem;
+  padding-bottom: 0.5rem;
+  border-bottom: 3px solid #4f46e5;
 }
 
 /* Improve spacing on main page */
 div.section > .toctree-wrapper {
-    background: linear-gradient(135deg, #f0f4f8 0%, #e8eef5 100%);
-    padding: 1.5rem;
-    border-radius: 12px;
-    box-shadow: 0 4px 6px rgba(79, 70, 229, 0.08);
-    border: 1px solid #dce4f0;
+  background: linear-gradient(135deg, #f0f4f8 0%, #e8eef5 100%);
+  padding: 1.5rem;
+  border-radius: 12px;
+  box-shadow: 0 4px 6px rgba(79, 70, 229, 0.08);
+  border: 1px solid #dce4f0;
 }
diff --git a/rules/devel_rules.json b/rules/devel_rules.json
index 7019204..fdcb5e2 100644
--- a/rules/devel_rules.json
+++ b/rules/devel_rules.json
@@ -6,10 +6,7 @@
   "conditions": {
     "ref_name": {
       "exclude": [],
-      "include": [
-        "~DEFAULT_BRANCH",
-        "refs/heads/devel"
-      ]
+      "include": ["~DEFAULT_BRANCH", "refs/heads/devel"]
     }
   },
   "rules": [
@@ -28,10 +25,7 @@
         "require_last_push_approval": true,
         "required_review_thread_resolution": true,
         "automatic_copilot_code_review_enabled": false,
-        "allowed_merge_methods": [
-          "merge",
-          "squash"
-        ]
+        "allowed_merge_methods": ["merge", "squash"]
       }
     }
   ],
diff --git a/rules/main_rules.json b/rules/main_rules.json
index fe5b886..ec1cd51 100644
--- a/rules/main_rules.json
+++ b/rules/main_rules.json
@@ -6,10 +6,7 @@
   "conditions": {
     "ref_name": {
       "exclude": [],
-      "include": [
-        "refs/heads/master",
-        "refs/heads/main"
-      ]
+      "include": ["refs/heads/master", "refs/heads/main"]
     }
   },
   "rules": [
@@ -28,9 +25,7 @@
         "require_last_push_approval": true,
         "required_review_thread_resolution": true,
         "automatic_copilot_code_review_enabled": false,
-        "allowed_merge_methods": [
-          "rebase"
-        ]
+        "allowed_merge_methods": ["rebase"]
       }
     }
   ],