Squashed commit of the following:

commit 51d3dda
Author: Felix Zimmermann <[email protected]>
Date:   Sun Jan 12 15:25:48 2025 +0100

    pip install mrpro with notebook option

commit feabab3
Author: Felix Zimmermann <[email protected]>
Date:   Sun Jan 12 15:24:02 2025 +0100

    execute notebooks locally

commit 8a537d4
Author: Felix Zimmermann <[email protected]>
Date:   Sun Jan 12 15:21:48 2025 +0100

    silence jupytext

commit 36785c4
Author: lrlunin <[email protected]>
Date:   Fri Jan 10 13:57:38 2025 +0100

    move cartesion_reconstruction in correct folders

commit d3b0d1b
Author: lrlunin <[email protected]>
Date:   Fri Jan 10 13:54:34 2025 +0100

    run mypy hook as last

commit b66b9b7
Author: Lunin Leonid <[email protected]>
Date:   Thu Jan 9 22:22:38 2025 +0100

    fix notebook_path variable in matrix

commit 8e2cb8e
Merge: f450529 a1873a0
Author: Lunin Leonid <[email protected]>
Date:   Thu Jan 9 22:20:50 2025 +0100

    Merge branch 'main' into notebooks-in-pre-commit

commit f450529
Author: Felix F Zimmermann <[email protected]>
Date:   Thu Jan 9 22:15:20 2025 +0100

    changes to leonids pr (#602)

commit a1873a0
Author: Lunin Leonid <[email protected]>
Date:   Wed Jan 8 09:54:12 2025 +0100

    Add dark and light logo to README (#600)

commit f040c00
Author: Felix F Zimmermann <[email protected]>
Date:   Wed Jan 8 00:07:27 2025 +0100

    Release v0.250107 (#599)

commit 13c4e7e
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 16:24:36 2024 +0100

    fix notebooks_path output

commit 93ef986
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 16:21:23 2024 +0100

    fix matrix element name

commit 7eccf87
Merge: 2d3c3ff 9dc1167
Author: Lunin Leonid <[email protected]>
Date:   Wed Dec 18 16:14:30 2024 +0100

    Merge branch 'main' into notebooks-in-pre-commit

commit 2d3c3ff
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 15:46:10 2024 +0100

    remove space after markdown for colab badge

commit 9a5556d
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 15:45:25 2024 +0100

    add space after markdown for colab badge

commit fba5a6f
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 15:05:55 2024 +0100

    add colab badge for each notebook

commit 159afed
Author: lrlunin <[email protected]>
Date:   Wed Dec 18 14:17:45 2024 +0100

    update jupytext version

commit 34d43f0
Author: lrlunin <[email protected]>
Date:   Tue Dec 10 13:58:43 2024 +0100

    use find for notebook listing in docs

commit f76b236
Author: lrlunin <[email protected]>
Date:   Tue Dec 10 13:23:29 2024 +0100

    one-way conversion from .py to .ipynb, remove preamble from .py representation

commit 865347a
Author: lrlunin <[email protected]>
Date:   Wed Nov 20 22:45:42 2024 +0100

    fixed path for notebooks in examples

commit 1688c70
Author: lrlunin <[email protected]>
Date:   Wed Nov 20 22:44:16 2024 +0100

    fixed trigger for jupytext

commit b9b3a6f
Author: lrlunin <[email protected]>
Date:   Wed Nov 20 22:40:17 2024 +0100

    split scripts and notebooks

commit 279a578
Merge: beddf13 8d24ebb
Author: Lunin Leonid <[email protected]>
Date:   Tue Nov 19 21:10:30 2024 +0100

    Merge branch 'main' into notebooks-in-pre-commit

commit beddf13
Author: lrlunin <[email protected]>
Date:   Tue Nov 19 21:10:03 2024 +0100

    sync .ipynb/.py in pre-commit, add preamble in .py files

commit 0600a53
Author: lrlunin <[email protected]>
Date:   Tue Nov 19 18:42:47 2024 +0100

    moved examples ruff config to examples folder, removed verbose from pre-commit hook

commit 36f3b7a
Author: lrlunin <[email protected]>
Date:   Tue Nov 19 18:25:57 2024 +0100

    fixed missing kernelspec

commit 4d610c6
Author: lrlunin <[email protected]>
Date:   Fri Nov 15 14:23:38 2024 +0100

    also removing metadata.language_info

commit 48e8080
Author: lrlunin <[email protected]>
Date:   Thu Nov 14 22:45:35 2024 +0100

    clean kernel related information from the cells

commit f8aa621
Author: lrlunin <[email protected]>
Date:   Thu Nov 14 20:44:13 2024 +0100

    remove mention of convert steps

commit 534aaa0
Author: lrlunin <[email protected]>
Date:   Thu Nov 14 20:37:43 2024 +0100

    reset cell id

commit 9f5f2da
Merge: 74675d6 38722bf
Author: Lunin Leonid <[email protected]>
Date:   Thu Nov 14 20:36:21 2024 +0100

    Merge branch 'main' into notebooks-in-pre-commit

commit 74675d6
Merge: ae3a613 c268ad2
Author: Lunin Leonid <[email protected]>
Date:   Sun Nov 10 20:50:44 2024 +0100

    Merge branch 'main' into notebooks-in-pre-commit

commit ae3a613
Author: lrlunin <[email protected]>
Date:   Sun Nov 10 20:50:10 2024 +0100

    reset the cells to init states

commit 5d1dba2
Author: lrlunin <[email protected]>
Date:   Fri Nov 8 16:43:47 2024 +0100

    moved notebooks formatting and update to pre-commit

.pre-commit-config.yaml

@@ -42,24 +42,31 @@ repos:
       args: [--extra-keys, "metadata.language_info"]
       files: examples/notebooks
 
-  - repo: https://github.com/mwouts/jupytext
-    rev: v1.16.6
+  - repo: local
     hooks:
      - id: jupytext
        name: convert .py to .ipynb
-       args:
-         - --update
-         - --pipe
-         - "python .precommit/add_notebook_preemble.py {}"
-         - --to
-         - "../notebooks//ipynb"
-         - --update-metadata
-         - '{"accelerator": "GPU","colab": {"gpuType": "T4","provenance": []},"kernelspec": {"display_name": "Python 3 (ipykernel)","language": "python","name": "python3"}}'
-         - -q
-       always_run: false
+       language: python
+
+       additional_dependencies:
+        - jupytext
+       entry: >
+        jupytext
+        --update
+        --pipe
+        "python .precommit/add_notebook_preemble.py {}"
+        --to
+        "../notebooks//ipynb"
+        --update-metadata
+        '{
+          "accelerator": "GPU",
+          "colab": {"gpuType": "T4","provenance": []},
+          "kernelspec": {"display_name": "Python 3 (ipykernel)","language": "python","name": "python3"}
+        }'
+       always_run: true
        pass_filenames: true
        files: ^examples/scripts/.*py
-
+       types_or: [python]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.13.0

.precommit/add_notebook_preemble.py

@@ -16,7 +16,7 @@
 import importlib
 
 if not importlib.util.find_spec('mrpro'):
-    %pip install mrpro
+    %pip install mrpro[notebook]
 """
 
 # the temp files of jupytext have the header which looks like:

docs/source/conf.py

@@ -263,8 +263,10 @@ def replace_patterns_in_markdown(app, docname, source):
 
 
 def sync_notebooks(source_folder, dest_folder):
-    """
-    Synchronize files from the source to the destination folder, copying only new or updated files.
+    """ Sync notebooks from source to destination folder.
+
+    Copy only new or updated files.
+    Set execution mode to 'force' for all copied files.
     """
     dest = Path(dest_folder)
     dest.mkdir(parents=True, exist_ok=True)
@@ -273,7 +275,10 @@ 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}. Setting execution mode to 'force'.")
+        content = nbformat.read(dest_file, as_version=nbformat.NO_CONVERT)
+        content.metadata['mystnb'] = {'execution_mode':'force'}
+        nbformat.write(content, dest_file)
 
 def setup(app):
     app.set_html_assets_policy('always')  # forces mathjax on all pages

examples/notebooks/cartesian_reconstruction.ipynb

@@ -24,7 +24,7 @@
     "import importlib\n",
     "\n",
     "if not importlib.util.find_spec('mrpro'):\n",
-    "    %pip install mrpro"
+    "    %pip install mrpro[notebook]"
    ]
   },
   {
@@ -322,9 +322,7 @@
    "execution_count": null,
    "id": "23",
    "metadata": {
-    "inputHidden": true,
     "lines_to_next_cell": 0,
-    "outputHidden": true,
     "tags": [
      "remove-output"
     ]

examples/notebooks/direct_reconstruction.ipynb

@@ -24,7 +24,7 @@
     "import importlib\n",
     "\n",
     "if not importlib.util.find_spec('mrpro'):\n",
-    "    %pip install mrpro"
+    "    %pip install mrpro[notebook]"
    ]
   },
   {