update

docs/source/conf.py

@@ -263,7 +263,7 @@ def sync_notebooks(source_folder, dest_folder):
     """Sync notebooks from source to destination folder.
 
     Copy only new or updated files.
-    Set execution mode to 'cache' for all copied files.
+    Set execution mode to 'force' for all copied files and 'off' for all existing files.
     """
     dest = Path(dest_folder)
     dest.mkdir(parents=True, exist_ok=True)
@@ -272,12 +272,14 @@ def sync_notebooks(source_folder, dest_folder):
             dest_file = dest / src_file.name
             if not dest_file.exists() or src_file.stat().st_mtime > dest_file.stat().st_mtime:
                 shutil.copy2(src_file, dest_file)
-                print(f'Copied {src_file} to {dest_file}')
+                print(f'Copied {src_file} to {dest_file}. Setting execution mode to "force".')
+                mode = 'force'
             else:
                 print(f'Existing {dest_file}. Skipping execution.')
-                content = nbformat.read(dest_file, as_version=nbformat.NO_CONVERT)
-                content.metadata['mystnb'] = {'execution_mode': 'off'}
-                nbformat.write(content, dest_file)
+                mode = 'off'
+            content = nbformat.read(dest_file, as_version=nbformat.NO_CONVERT)
+            content.metadata['mystnb'] = {'execution_mode': mode}
+            nbformat.write(content, dest_file)
 
 
 def setup(app):

docs/source/contributor_guide.rst

@@ -21,7 +21,7 @@ This repository uses a *pyproject.toml* file to specify all the requirements.
     an online repository (e.g. zenodo) such that it can be automatically downloaded.
     Individual cells should be indicated with ``# %%``. For markdown cells use ``# %% [markdown]``.
     The translation from python script to jupyter notebook is done in pre-commit (locally and and on GitHub)
-    using `jupytext <https://jupytext.readthedocs.io/en/latest/>`_ . See their documentation for more details.
+    using `jupytext <https://jupytext.readthedocs.io/en/latest/>`_ . See its documentation for more details.
 
     After translating the scripts to notebooks, the notebooks are run and their output is converted to html and added
     to this documentation in the *Examples* section.

docs/source/index.rst

@@ -12,7 +12,7 @@ MR image reconstruction and processing package for PyTorch
 | **Source code:** `<https://github.com/PTB-MR/mrpro>`_
 | **Bug reports:** `<https://github.com/PTB-MR/mrpro/issues>`_
 | **Try it out:** `Open in Colab <https://colab.research.google.com/github/PTB-MR/mrpro>`_
-| **See our examples: ** :doc:`examples`
+| **See our examples:** :doc:`examples`
 
 Main Features
 -------------

src/mrpro/algorithms/optimizers/cg.py

@@ -42,6 +42,7 @@ def cg(
 
     This implementation assumes that :math:`H` is self-adjoint and does not verify this condition.
 
+    See [Hestenes1952]_, [Nocedal2006]_, and [WikipediaCG]_ for more information.
 
     Parameters
     ----------
@@ -63,6 +64,13 @@ def cg(
     Returns
     -------
         an approximate solution of the linear system :math:`Hx=b`
+
+    References
+    ----------
+    .. [Hestenes1952] Hestenes, M. R., & Stiefel, E. (1952). Methods of conjugate gradients for solving linear systems.
+       *Journal of Research of the National Bureau of Standards*, 49(6), 409-436
+    .. [Nocedal2006] Nocedal, J. (2006). *Numerical Optimization* (2nd ed.). Springer.
+    .. [WikipediaCG] Wikipedia: Conjugate Gradient`<https://en.wikipedia.org/wiki/Conjugate_gradient>_
     """
     if initial_value is not None and (initial_value.shape != right_hand_side.shape):
         raise ValueError(