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PTB-MR · Jan 20, 2025 · f4992fb · f4992fb
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diff --git a/.gitignore b/.gitignore
@@ -193,3 +193,4 @@ cython_debug/
 *~
 *.swp
 *.swo
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,6 +7,7 @@ repos:
     hooks:
       - id: check-added-large-files
       - id: check-merge-conflict
+        exclude_types: [rst]
       - id: check-yaml
       - id: check-toml
       - id: check-json
@@ -63,11 +64,22 @@ repos:
           "colab": {"gpuType": "T4","provenance": []},
           "kernelspec": {"display_name": "Python 3 (ipykernel)","language": "python","name": "python3"}
         }'
+        --opt cell_metadata_filter=mystnb,tags,-all
        always_run: true
        pass_filenames: true
        files: ^examples/scripts/.*py
        types_or: [python]
 
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.0
+    hooks:
+    # cleans the .ipynbs (removes outputs, resets all cell-ids to 0..N, cleans steps)
+    # also clean any kernel information left after execution
+    - id: nbstripout
+      name: clean .ipynb output
+      args: [--extra-keys, "metadata.language_info"]
+      files: examples/notebooks
+
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.14.1
     hooks:
@@ -88,6 +100,7 @@ repos:
           - "--index-url=https://download.pytorch.org/whl/cpu"
           - "--extra-index-url=https://pypi.python.org/simple"
 
+
 ci:
   autofix_commit_msg: |
     [pre-commit] auto fixes from pre-commit hooks

diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ MR image reconstruction and processing package specifically developed for PyTorc
 
 ## Awards
 
-- 2024 ISMRM QMRI Study Group Challenge, 2nd prize for Relaxometry (T2* and T1)
+- 2024 ISMRM QMRI Study Group Challenge, 2nd prize for Relaxometry ([T2*](https://github.com/PTB-MR/mrpro/blob/8d2133c4a7ce63ac490798c4eb5a70cc1c543646/examples/qmri_sg_challenge_2024_t2_star.ipynb) and [T1](https://github.com/PTB-MR/mrpro/blob/8d2133c4a7ce63ac490798c4eb5a70cc1c543646/examples/qmri_sg_challenge_2024_t1.ipynb))
 
 ## Main features
 

diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
@@ -7,3 +7,14 @@ html {
 .wy-nav-content {
     max-width: 75% !important;
 }
+
+/* new line after each property */
+dl.py.property {
+    display: block !important;
+}
+
+/* example notebooks outputs */
+.output>.highlight {
+    background: #efefef !important;
+    color: inherit !important;
+}
diff --git a/docs/source/_static/encoded_recon_space.png b/docs/source/_static/encoded_recon_space.png
diff --git a/docs/source/_static/encoded_recon_space.svg b/docs/source/_static/encoded_recon_space.svg
diff --git a/docs/source/_static/favicon.svg b/docs/source/_static/favicon.svg
diff --git a/docs/source/_static/logo_white.svg b/docs/source/_static/logo_white.svg
diff --git a/docs/source/_templates/class_template.rst b/docs/source/_templates/class_template.rst
@@ -4,9 +4,8 @@
 
 .. autoclass:: {{ objname }}
    :members:
+   :special-members: '__init__, __call__, __matmul__, __add__, __mul__, __or__, __and__, __radd__, __rmul__, __rmatmul__, __ror__, __rand__, __truediv__, __eq__, __pow__'
    :inherited-members: Module
    :show-inheritance:
 
-   {% block methods %}
-   .. automethod:: __init__
-   {% endblock %}
+
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -2,57 +2,21 @@ API
 ===
 
 This is the MRpro Application Programming Interface (API) documentation.
+It is designed to assist developers and researchers in understanding and utilizing the core functionalities of MRpro effectively.
+Each module includes detailed descriptions and function signatures to guide you through their usage.
+This documentation is generated from the docstrings, which are also available in your IDE.
 
-MRpro Algorithms
-----------------
+Navigate through the sections below for more information about each module and its capabilities.
 
 .. autosummary::
    :toctree: _autosummary
    :template: module_template.rst
    :recursive:
 
-   mrpro.algorithms
-
-
-MRpro Data
-----------
-
-.. autosummary::
-   :toctree: _autosummary
-   :template: module_template.rst
-   :recursive:
 
+   mrpro.algorithms
    mrpro.data
-
-
-MRpro Operators
----------------
-
-.. autosummary::
-   :toctree: _autosummary
-   :template: module_template.rst
-   :recursive:
-
    mrpro.operators
-
-
-MRpro Phantoms
---------------
-
-.. autosummary::
-   :toctree: _autosummary
-   :template: module_template.rst
-   :recursive:
-
    mrpro.phantoms
-
-
-MRpro Utilities
----------------
-
-.. autosummary::
-   :toctree: _autosummary
-   :template: module_template.rst
-   :recursive:
-
    mrpro.utils
+