From 0342d7b1507b5f705e367f68176e2e925472c3ba Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 12:24:15 +0200
Subject: [PATCH 1/9] Updates 'easydiffraction' dependency to 'visualization'
 extras

---
 .github/workflows/test-tutorials-colab.yaml |  2 +-
 docs/installation-and-setup/index.md        | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-tutorials-colab.yaml b/.github/workflows/test-tutorials-colab.yaml
index 3327b37a..0c322352 100644
--- a/.github/workflows/test-tutorials-colab.yaml
+++ b/.github/workflows/test-tutorials-colab.yaml
@@ -49,7 +49,7 @@ jobs:
 
       - name: Install Python dependencies
         run:
-          python -m pip install 'easydiffraction[charts]' nbconvert nbmake
+          python -m pip install 'easydiffraction[visualization]' nbconvert nbmake
           pytest pytest-xdist
 
       - name: Check if Jupyter Notebooks run without errors
diff --git a/docs/installation-and-setup/index.md b/docs/installation-and-setup/index.md
index bb7c6c78..965eca69 100644
--- a/docs/installation-and-setup/index.md
+++ b/docs/installation-and-setup/index.md
@@ -83,13 +83,13 @@ installed using `pip`. We strongly recommend installing it within a virtual
 environment, as described in the [Environment Setup](#environment-setup)
 section.
 
-We recommend installing the latest release of EasyDiffraction with the `charts`
-extras, which include optional dependencies used for simplified visualization of
-charts and tables. This can be especially useful for running the Jupyter
-Notebook examples. To do so, use the following command:
+We recommend installing the latest release of EasyDiffraction with the 
+`visualization` extras, which include optional dependencies used for simplified 
+visualization of charts and tables. This can be especially useful for running 
+the Jupyter Notebook examples. To do so, use the following command:
 
 ```console
-pip install 'easydiffraction[charts]'
+pip install 'easydiffraction[visualization]'
 ```
 
 If only the core functionality is needed, the library can be installed simply
@@ -128,10 +128,10 @@ To install EasyDiffraction from, e.g., the `develop` branch of GitHub:
 pip install git+https://github.com/easyscience/diffraction-lib@develop
 ```
 
-To include extra dependencies (e.g., charts):
+To include extra dependencies (e.g., visualization):
 
 ```console
-pip install 'easydiffraction[charts] @ git+https://github.com/easyscience/diffraction-lib@develop'
+pip install 'easydiffraction[visualization] @ git+https://github.com/easyscience/diffraction-lib@develop'
 ```
 
 ## How to Run Tutorials

From 4023fb69c1199a54017112b44dfb0fe3b0517ded Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 12:24:41 +0200
Subject: [PATCH 2/9] Removes Python 3.10 support

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ea48009e..0d80e0c3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,6 @@ classifiers = [
   'Operating System :: OS Independent',
   'Programming Language :: Python :: 3 :: Only',
   'Programming Language :: Python :: 3',
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",

From f7271b8c232a9a62a196e2c8b900096e6d7ef99e Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 14:27:37 +0200
Subject: [PATCH 3/9] Update workflows and notebooks

---
 .github/workflows/build-docs.yml                            | 3 ++-
 .github/workflows/test-tutorials-colab.yaml                 | 4 ++--
 .github/workflows/test-tutorials.yaml                       | 2 ++
 docs/installation-and-setup/index.md                        | 6 +++---
 tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb   | 2 +-
 tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb      | 2 +-
 tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb         | 2 +-
 tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb            | 2 +-
 tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb            | 2 +-
 .../cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb      | 2 +-
 ...cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb | 2 +-
 ...msc-summer-school-2025_analysis-powder-diffraction.ipynb | 2 +-
 tutorials/pdf_pd-neut-cwl_Ni.ipynb                          | 2 +-
 tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb                    | 2 +-
 tutorials/pdf_pd-xray_NaCl.ipynb                            | 2 +-
 tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb      | 2 +-
 16 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index c104a841..1c7313fe 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -104,7 +104,7 @@ jobs:
           cp ../assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg
 
       # Convert python scripts in the notebooks directory to Jupyter notebooks
-      # Strip output from the notebooks and simpify cell ids
+      # Strip output from the notebooks, simpify cell ids and replace '# !pip' with '!pip'
       # The notebooks are used to generate the documentation
       - name:
           Convert ${{ env.NOTEBOOKS_DIR }}/*.py to docs/${{env.NOTEBOOKS_DIR
@@ -113,6 +113,7 @@ jobs:
           cp -R ${{ env.NOTEBOOKS_DIR }}/data docs/${{ env.NOTEBOOKS_DIR }}/
           jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb
           nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb
+          sed -i '' 's/# !pip/!pip/g' ${{ env.NOTEBOOKS_DIR }}/*.ipynb
           mv ${{ env.NOTEBOOKS_DIR }}/*.ipynb docs/${{ env.NOTEBOOKS_DIR }}/
 
       # The following step is needed to avoid the following message during the build:
diff --git a/.github/workflows/test-tutorials-colab.yaml b/.github/workflows/test-tutorials-colab.yaml
index 0c322352..02640df2 100644
--- a/.github/workflows/test-tutorials-colab.yaml
+++ b/.github/workflows/test-tutorials-colab.yaml
@@ -49,8 +49,8 @@ jobs:
 
       - name: Install Python dependencies
         run:
-          python -m pip install 'easydiffraction[visualization]' nbconvert nbmake
-          pytest pytest-xdist
+          python -m pip install 'easydiffraction[visualization]' nbconvert
+          nbmake pytest pytest-xdist
 
       - name: Check if Jupyter Notebooks run without errors
         run: >
diff --git a/.github/workflows/test-tutorials.yaml b/.github/workflows/test-tutorials.yaml
index 496b400d..df3acb2a 100644
--- a/.github/workflows/test-tutorials.yaml
+++ b/.github/workflows/test-tutorials.yaml
@@ -142,6 +142,7 @@ jobs:
       # Check if tutorials as Jupyter Notebooks run without errors
       # Convert all Python scripts in the folder tutorials/ to Jupyter Notebooks
       # Strip output from Jupyter Notebooks and rename cell ids
+      # Replace '# !pip' with '!pip' in Jupyter Notebooks
       # Run all Jupyter Notebooks in the folder tutorials/ in parallel
       # -n auto: run as many in parallel as you have cores (auto mode)
       # --nbmake-timeout=600: set timeout to 600 seconds
@@ -150,6 +151,7 @@ jobs:
         run: |
           jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb
           nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb
+          sed -i '' 's/# !pip/!pip/g' ${{ env.NOTEBOOKS_DIR }}/*.ipynb
 
       - name: Run tutorials as Jupyter Notebooks (using src/ as the source dir)
         shell: bash
diff --git a/docs/installation-and-setup/index.md b/docs/installation-and-setup/index.md
index 965eca69..25220f91 100644
--- a/docs/installation-and-setup/index.md
+++ b/docs/installation-and-setup/index.md
@@ -83,9 +83,9 @@ installed using `pip`. We strongly recommend installing it within a virtual
 environment, as described in the [Environment Setup](#environment-setup)
 section.
 
-We recommend installing the latest release of EasyDiffraction with the 
-`visualization` extras, which include optional dependencies used for simplified 
-visualization of charts and tables. This can be especially useful for running 
+We recommend installing the latest release of EasyDiffraction with the
+`visualization` extras, which include optional dependencies used for simplified
+visualization of charts and tables. This can be especially useful for running
 the Jupyter Notebook examples. To do so, use the following command:
 
 ```console
diff --git a/tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb b/tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb
index 5534d395..81adb316 100644
--- a/tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb
+++ b/tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb
@@ -45,7 +45,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb b/tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
index 1f262e1b..1362eb58 100644
--- a/tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
+++ b/tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
@@ -51,7 +51,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb b/tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb
index f493bc93..90776439 100644
--- a/tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb
+++ b/tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb
@@ -39,7 +39,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb b/tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb
index 8a07be6f..5a3445e8 100644
--- a/tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb
+++ b/tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb
@@ -39,7 +39,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb b/tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb
index 74787584..ee9f64b0 100644
--- a/tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb
+++ b/tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb
@@ -39,7 +39,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb b/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb
index 1823e82f..5ca083c0 100644
--- a/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb
+++ b/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb
@@ -42,7 +42,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb b/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb
index 36f14857..e4fa9b1c 100644
--- a/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb
+++ b/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb
@@ -40,7 +40,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
index fb94399c..40ae4b17 100644
--- a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
+++ b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
@@ -45,7 +45,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/pdf_pd-neut-cwl_Ni.ipynb b/tutorials/pdf_pd-neut-cwl_Ni.ipynb
index 454227ab..57416ff9 100644
--- a/tutorials/pdf_pd-neut-cwl_Ni.ipynb
+++ b/tutorials/pdf_pd-neut-cwl_Ni.ipynb
@@ -43,7 +43,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb b/tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb
index f11ab0f7..854c8183 100644
--- a/tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb
+++ b/tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb
@@ -40,7 +40,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/pdf_pd-xray_NaCl.ipynb b/tutorials/pdf_pd-xray_NaCl.ipynb
index c2dd4fd7..be876d10 100644
--- a/tutorials/pdf_pd-xray_NaCl.ipynb
+++ b/tutorials/pdf_pd-xray_NaCl.ipynb
@@ -42,7 +42,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {
diff --git a/tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb b/tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
index bfe5281d..09ab7e0f 100644
--- a/tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
+++ b/tutorials/quick_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
@@ -51,7 +51,7 @@
     "if hasattr(builtins, '__IPYTHON__'):\n",
     "    if importlib.util.find_spec('easydiffraction') is None:\n",
     "        print('Installing the easydiffraction library...')\n",
-    "        # !pip install 'easydiffraction[visualization]'"
+    "        !pip install 'easydiffraction[visualization]'"
    ]
   },
   {

From 3066483dec02f321b35169bbf261d9375fc0fe68 Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 14:59:14 +0200
Subject: [PATCH 4/9] Updates workflow to trigger on 'patch' branch

---
 .github/workflows/build-docs.yml | 2 +-
 docs/mkdocs.yml                  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 1c7313fe..8cb2c63a 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -4,7 +4,7 @@ on:
   # Trigger the workflow on push
   push:
     # Selected branches
-    branches: [develop, master, docs]
+    branches: [develop, master, docs, patch]
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 5e2528cf..d713a5f8 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -4,10 +4,10 @@
 
 # Project information
 site_name: EasyDiffraction Library
-site_url: https://docs.easydiffraction.org/lib
+site_url: https://docs.easydiffraction.org/lib/
 
 # Repository
-repo_url: https://github.com/easyscience/diffraction-lib
+repo_url: https://github.com/easyscience/diffraction-lib/
 edit_uri: edit/develop/docs/
 
 # Copyright

From 68ca6a00f5c7d45bdafe8004fe7e64fc628a064f Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 15:27:39 +0200
Subject: [PATCH 5/9] Update documentation URLs for EasyDiffraction

---
 pyproject.toml                                                | 2 +-
 .../dmsc-summer-school-2025_analysis-powder-diffraction.ipynb | 4 ++--
 .../dmsc-summer-school-2025_analysis-powder-diffraction.py    | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0d80e0c3..f156cfb0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,7 +73,7 @@ visualization = [
 
 [project.urls]
 homepage = 'https://easydiffraction.org'
-documentation = 'https://easyscience.github.io/diffraction-lib'
+documentation = 'https://docs.easydiffraction.org/lib'
 source = 'https://github.com/easyscience/diffraction-lib'
 tracker = 'https://github.com/easyscience/diffraction-lib/issues'
 
diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
index 40ae4b17..0ade4a5a 100644
--- a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
+++ b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
@@ -62,7 +62,7 @@
     "This tutorial is self-contained and designed for hands-on learning.\n",
     "However, if you're interested in exploring more advanced features or learning\n",
     "about additional capabilities of the EasyDiffraction library, please refer to\n",
-    "the official documentation: https://easyscience.github.io/diffraction-lib\n",
+    "the official documentation: https://docs.easydiffraction.org/lib/tutorials/\n",
     "\n",
     "Depending on your requirements, you may choose to import only specific\n",
     "classes. However, for the sake of simplicity in this tutorial, we will import\n",
@@ -1915,7 +1915,7 @@
     "To continue learning and exploring more features of\n",
     "the EasyDiffraction library, you can visit the official tutorial page\n",
     "and select one of the many available tutorials:\n",
-    "https://easyscience.github.io/diffraction-lib/tutorials/"
+    "https://docs.easydiffraction.org/lib/tutorials/"
    ]
   }
  ],
diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
index 8ce98927..9e61e4bd 100644
--- a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
+++ b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
@@ -31,7 +31,7 @@
 # This tutorial is self-contained and designed for hands-on learning.
 # However, if you're interested in exploring more advanced features or learning
 # about additional capabilities of the EasyDiffraction library, please refer to
-# the official documentation: https://easyscience.github.io/diffraction-lib
+# the official documentation: https://docs.easydiffraction.org/lib/tutorials/
 #
 # Depending on your requirements, you may choose to import only specific
 # classes. However, for the sake of simplicity in this tutorial, we will import
@@ -1121,4 +1121,4 @@
 # To continue learning and exploring more features of
 # the EasyDiffraction library, you can visit the official tutorial page
 # and select one of the many available tutorials:
-# https://easyscience.github.io/diffraction-lib/tutorials/
+# https://docs.easydiffraction.org/lib/tutorials/

From ed967ba9a3dc5544ca5b1aa0d70e818a5f5793a1 Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 15:40:39 +0200
Subject: [PATCH 6/9] Replaces sed pip uncomment command with Python script

---
 .github/workflows/build-docs.yml            |   2 +-
 .github/workflows/test-tutorials-colab.yaml |   2 +-
 .github/workflows/test-tutorials.yaml       |   2 +-
 tools/nb_uncomment_pip.py                   | 111 ++++++++++++++++++++
 4 files changed, 114 insertions(+), 3 deletions(-)
 create mode 100644 tools/nb_uncomment_pip.py

diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 8cb2c63a..f18f6e4c 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -113,7 +113,7 @@ jobs:
           cp -R ${{ env.NOTEBOOKS_DIR }}/data docs/${{ env.NOTEBOOKS_DIR }}/
           jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb
           nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb
-          sed -i '' 's/# !pip/!pip/g' ${{ env.NOTEBOOKS_DIR }}/*.ipynb
+          python tools/nb_uncomment_pip.py ${{ env.NOTEBOOKS_DIR }}/
           mv ${{ env.NOTEBOOKS_DIR }}/*.ipynb docs/${{ env.NOTEBOOKS_DIR }}/
 
       # The following step is needed to avoid the following message during the build:
diff --git a/.github/workflows/test-tutorials-colab.yaml b/.github/workflows/test-tutorials-colab.yaml
index 02640df2..6cfa6d76 100644
--- a/.github/workflows/test-tutorials-colab.yaml
+++ b/.github/workflows/test-tutorials-colab.yaml
@@ -1,4 +1,4 @@
-name: Testing tutorials on Colab
+name: Test tutorials on Colab
 
 on:
   # Trigger the workflow on push
diff --git a/.github/workflows/test-tutorials.yaml b/.github/workflows/test-tutorials.yaml
index df3acb2a..529aea24 100644
--- a/.github/workflows/test-tutorials.yaml
+++ b/.github/workflows/test-tutorials.yaml
@@ -151,7 +151,7 @@ jobs:
         run: |
           jupytext ${{ env.NOTEBOOKS_DIR }}/*.py --from py:percent --to ipynb
           nbstripout ${{ env.NOTEBOOKS_DIR }}/*.ipynb
-          sed -i '' 's/# !pip/!pip/g' ${{ env.NOTEBOOKS_DIR }}/*.ipynb
+          python tools/nb_uncomment_pip.py ${{ env.NOTEBOOKS_DIR }}/
 
       - name: Run tutorials as Jupyter Notebooks (using src/ as the source dir)
         shell: bash
diff --git a/tools/nb_uncomment_pip.py b/tools/nb_uncomment_pip.py
new file mode 100644
index 00000000..206845d3
--- /dev/null
+++ b/tools/nb_uncomment_pip.py
@@ -0,0 +1,111 @@
+"""
+Uncomment `# !pip ...` lines in Jupyter notebooks so they become `!pip ...`.
+
+- Operates only on code cells (does not touch outputs/metadata/markdown).
+- Matches lines that start with optional whitespace, then `# !pip` (e.g., "  # !pip install ...").
+- Rewrites to keep the original indentation and replace the leading "# !pip" with "!pip".
+- Processes one or more paths (files or directories) given as CLI args, recursively for directories.
+"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+import re
+
+import nbformat
+
+# Regex: beginning-of-line, capture leading whitespace, then "#", spaces, then "!pip"
+_PATTERN = re.compile(r"^(\s*)#\s*!pip\b")
+
+
+def fix_cell_source(src: str) -> tuple[str, int]:
+    """
+    Replace lines starting with optional whitespace + '# !pip' with '!pip'.
+    Returns the updated source and number of replacements performed.
+    """
+    changed = 0
+    new_lines: list[str] = []
+    for line in src.splitlines(keepends=False):
+        m = _PATTERN.match(line)
+        if m:
+            indent = m.group(1)
+            # Replace only the first '# !pip' at the beginning, preserve the rest of the line
+            # e.g., "  # !pip install foo" -> "  !pip install foo"
+            new_line = _PATTERN.sub(r"\1!pip", line, count=1)
+            if new_line != line:
+                changed += 1
+            new_lines.append(new_line)
+        else:
+            new_lines.append(line)
+    return ("\n".join(new_lines), changed)
+
+
+def process_notebook(path: Path) -> int:
+    """
+    Process a single .ipynb file. Returns number of lines changed.
+    """
+    nb = nbformat.read(path, as_version=4)
+    total_changes = 0
+    for cell in nb.cells:
+        if cell.cell_type != "code":
+            continue
+        new_src, changes = fix_cell_source(cell.source or "")
+        if changes:
+            cell.source = new_src
+            total_changes += changes
+    if total_changes:
+        nbformat.write(nb, path)
+    return total_changes
+
+
+def iter_notebooks(paths: list[Path]):
+    for p in paths:
+        if p.is_dir():
+            yield from (q for q in p.rglob("*.ipynb") if q.is_file())
+        elif p.is_file() and p.suffix == ".ipynb":
+            yield p
+
+
+def main(argv: list[str]) -> int:
+    ap = argparse.ArgumentParser(
+        description="Uncomment '# !pip ...' to '!pip ...' in code cells of .ipynb notebooks."
+    )
+    ap.add_argument("paths", nargs="+", help="Notebook files or directories to process")
+    ap.add_argument("--dry-run", action="store_true", help="Report changes without writing files")
+    args = ap.parse_args(argv)
+
+    targets = list(iter_notebooks([Path(p) for p in args.paths]))
+    if not targets:
+        print("No .ipynb files found.", file=sys.stderr)
+        return 1
+
+    total_files = 0
+    total_changes = 0
+    for nb_path in targets:
+        changes = process_notebook(nb_path) if not args.dry_run else 0
+        if args.dry_run:
+            # For dry-run, compute changes without writing
+            nb = nbformat.read(nb_path, as_version=4)
+            changes = 0
+            for cell in nb.cells:
+                if cell.cell_type != "code":
+                    continue
+                _, c = fix_cell_source(cell.source or "")
+                changes += c
+        if changes:
+            action = "UPDATED" if not args.dry_run else "WOULD UPDATE"
+            print(f"{action}: {nb_path} ({changes} line(s))")
+            total_files += 1
+            total_changes += changes
+
+    if total_files == 0:
+        print("No changes needed.")
+    else:
+        print(f"Done. Files changed: {total_files}, lines changed: {total_changes}")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main(sys.argv[1:]))
\ No newline at end of file

From b8621b90b3e6e134828890fa49337d520af62463 Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 15:45:32 +0200
Subject: [PATCH 7/9] Sets Plotly as the plotting engine

---
 ...ool-2025_analysis-powder-diffraction.ipynb | 244 +++++++++---------
 ...school-2025_analysis-powder-diffraction.py |   7 +
 2 files changed, 136 insertions(+), 115 deletions(-)

diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
index 0ade4a5a..affa9299 100644
--- a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
+++ b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
@@ -231,7 +231,10 @@
     "columns: TOF, intensity, and intensity error (if available).\n",
     "\n",
     "The `plot_meas` method of the project enables us to visualize the measured\n",
-    "diffraction pattern."
+    "diffraction pattern.\n",
+    "\n",
+    "Before plotting, we set the plotting engine to 'plotly', which provides\n",
+    "interactive visualizations."
    ]
   },
   {
@@ -240,13 +243,23 @@
    "id": "16",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "project_1.plotter.engine = 'plotly'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "project_1.plot_meas(expt_name='sim_si')"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "18",
    "metadata": {},
    "source": [
     "If you zoom in on the highest TOF peak (around 120,000 μs), you will notice\n",
@@ -261,7 +274,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,7 +284,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "19",
+   "id": "20",
    "metadata": {},
    "source": [
     "To visualize the effect of excluding the high TOF region, we can plot\n",
@@ -282,7 +295,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -291,7 +304,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "21",
+   "id": "22",
    "metadata": {},
    "source": [
     "#### Set Instrument Parameters\n",
@@ -314,7 +327,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -324,7 +337,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "source": [
     "Every parameters is an object, which has different attributes, such as\n",
@@ -337,7 +350,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -346,7 +359,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "25",
+   "id": "26",
    "metadata": {},
    "source": [
     "The `value` attribute represents the current value of the parameter as a float.\n",
@@ -360,7 +373,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -369,7 +382,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27",
+   "id": "28",
    "metadata": {},
    "source": [
     "Note that to set the value of the parameter, you can simply assign a new value\n",
@@ -378,7 +391,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "28",
+   "id": "29",
    "metadata": {},
    "source": [
     "#### Set Peak Profile Parameters\n",
@@ -402,7 +415,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -418,7 +431,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "30",
+   "id": "31",
    "metadata": {},
    "source": [
     "#### Set Background\n",
@@ -452,7 +465,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -468,7 +481,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "32",
+   "id": "33",
    "metadata": {},
    "source": [
     "### 🧩 Create a Sample Model – Si\n",
@@ -510,7 +523,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "33",
+   "id": "34",
    "metadata": {},
    "source": [
     "```\n",
@@ -542,7 +555,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34",
+   "id": "35",
    "metadata": {},
    "source": [
     "\n",
@@ -556,7 +569,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -565,7 +578,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "36",
+   "id": "37",
    "metadata": {},
    "source": [
     "#### Set Space Group"
@@ -574,7 +587,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37",
+   "id": "38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -584,7 +597,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "38",
+   "id": "39",
    "metadata": {},
    "source": [
     "#### Set Lattice Parameters"
@@ -593,7 +606,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39",
+   "id": "40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -602,7 +615,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "40",
+   "id": "41",
    "metadata": {},
    "source": [
     "#### Set Atom Sites"
@@ -611,7 +624,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "41",
+   "id": "42",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -628,7 +641,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "42",
+   "id": "43",
    "metadata": {},
    "source": [
     "### 🔗 Assign Sample Model to Experiment\n",
@@ -642,7 +655,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43",
+   "id": "44",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -651,7 +664,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "44",
+   "id": "45",
    "metadata": {},
    "source": [
     "### 🚀 Analyze and Fit the Data\n",
@@ -683,7 +696,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -703,7 +716,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "46",
+   "id": "47",
    "metadata": {},
    "source": [
     "#### Show Free Parameters\n",
@@ -715,7 +728,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47",
+   "id": "48",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -724,7 +737,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "48",
+   "id": "49",
    "metadata": {},
    "source": [
     "#### Visualize Diffraction Patterns\n",
@@ -740,7 +753,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "49",
+   "id": "50",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -749,7 +762,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "50",
+   "id": "51",
    "metadata": {},
    "source": [
     "#### Run Fitting\n",
@@ -761,7 +774,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "51",
+   "id": "52",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -770,7 +783,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "52",
+   "id": "53",
    "metadata": {},
    "source": [
     "#### Check Fit Results\n",
@@ -788,7 +801,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "53",
+   "id": "54",
    "metadata": {},
    "source": [
     "#### Visualize Fit Results\n",
@@ -802,7 +815,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "54",
+   "id": "55",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -811,7 +824,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "55",
+   "id": "56",
    "metadata": {},
    "source": [
     "#### TOF vs d-spacing\n",
@@ -830,7 +843,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "56",
+   "id": "57",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -839,7 +852,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "57",
+   "id": "58",
    "metadata": {},
    "source": [
     "As you can see, the calculated diffraction pattern now matches the measured\n",
@@ -874,7 +887,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "58",
+   "id": "59",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -885,7 +898,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "59",
+   "id": "60",
    "metadata": {},
    "source": [
     "### 🔬 Exercise 2: Define an Experiment\n",
@@ -904,7 +917,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "60",
+   "id": "61",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -914,7 +927,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "61",
+   "id": "62",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -924,7 +937,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "62",
+   "id": "63",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -939,7 +952,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "63",
+   "id": "64",
    "metadata": {},
    "source": [
     "#### Exercise 2.1: Inspect Measured Data\n",
@@ -959,17 +972,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "64",
+   "id": "65",
    "metadata": {},
    "outputs": [],
    "source": [
+    "project_2.plotter.engine = 'plotly'\n",
     "project_2.plot_meas(expt_name='sim_lbco')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "65",
+   "id": "66",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -980,7 +994,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "66",
+   "id": "67",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -989,7 +1003,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "67",
+   "id": "68",
    "metadata": {},
    "source": [
     "#### Exercise 2.2: Set Instrument Parameters\n",
@@ -1005,7 +1019,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "68",
+   "id": "69",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1015,7 +1029,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "69",
+   "id": "70",
    "metadata": {},
    "source": [
     "#### Exercise 2.3: Set Peak Profile Parameters\n",
@@ -1033,7 +1047,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "70",
+   "id": "71",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1049,7 +1063,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "71",
+   "id": "72",
    "metadata": {},
    "source": [
     "#### Exercise 2.4: Set Background\n",
@@ -1068,7 +1082,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "72",
+   "id": "73",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1084,7 +1098,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "73",
+   "id": "74",
    "metadata": {},
    "source": [
     "### 🧩 Exercise 3: Define a Sample Model – LBCO\n",
@@ -1100,7 +1114,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "74",
+   "id": "75",
    "metadata": {},
    "source": [
     "```\n",
@@ -1135,7 +1149,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "75",
+   "id": "76",
    "metadata": {},
    "source": [
     "#### Exercise 3.1: Create Sample Model\n",
@@ -1151,7 +1165,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "76",
+   "id": "77",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1160,7 +1174,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "77",
+   "id": "78",
    "metadata": {},
    "source": [
     "#### Exercise 3.2: Set Space Group\n",
@@ -1175,7 +1189,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "78",
+   "id": "79",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1185,7 +1199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "79",
+   "id": "80",
    "metadata": {},
    "source": [
     "#### Exercise 3.3: Set Lattice Parameters\n",
@@ -1200,7 +1214,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "80",
+   "id": "81",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1209,7 +1223,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "81",
+   "id": "82",
    "metadata": {},
    "source": [
     "#### Exercise 3.4: Set Atom Sites\n",
@@ -1226,7 +1240,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "82",
+   "id": "83",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1272,7 +1286,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "83",
+   "id": "84",
    "metadata": {},
    "source": [
     "### 🔗 Exercise 4: Assign Sample Model to Experiment\n",
@@ -1287,7 +1301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "84",
+   "id": "85",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1296,7 +1310,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "85",
+   "id": "86",
    "metadata": {},
    "source": [
     "### 🚀 Exercise 5: Analyze and Fit the Data\n",
@@ -1316,7 +1330,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86",
+   "id": "87",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1328,7 +1342,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "87",
+   "id": "88",
    "metadata": {},
    "source": [
     "#### Exercise 5.2: Run Fitting\n",
@@ -1347,7 +1361,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "88",
+   "id": "89",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1357,7 +1371,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "89",
+   "id": "90",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1366,7 +1380,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "90",
+   "id": "91",
    "metadata": {},
    "source": [
     "#### Exercise 5.3: Find the Misfit in the Fit\n",
@@ -1401,7 +1415,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "91",
+   "id": "92",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1410,7 +1424,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "92",
+   "id": "93",
    "metadata": {},
    "source": [
     "#### Exercise 5.4: Refine the LBCO Lattice Parameter\n",
@@ -1426,7 +1440,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "93",
+   "id": "94",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1436,7 +1450,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "94",
+   "id": "95",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1446,7 +1460,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95",
+   "id": "96",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1455,7 +1469,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "96",
+   "id": "97",
    "metadata": {},
    "source": [
     "One of the main goals of this study was to refine the lattice parameter of\n",
@@ -1467,7 +1481,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "97",
+   "id": "98",
    "metadata": {},
    "source": [
     "#### Exercise 5.5: Visualize the Fit Results in d-spacing\n",
@@ -1483,7 +1497,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "98",
+   "id": "99",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1492,7 +1506,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "99",
+   "id": "100",
    "metadata": {},
    "source": [
     "#### Exercise 5.6: Refine the Peak Profile Parameters\n",
@@ -1511,7 +1525,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "100",
+   "id": "101",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1520,7 +1534,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "101",
+   "id": "102",
    "metadata": {},
    "source": [
     "The peak profile parameters are determined based on both the instrument\n",
@@ -1540,7 +1554,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "102",
+   "id": "103",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1556,7 +1570,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "103",
+   "id": "104",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1566,7 +1580,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "104",
+   "id": "105",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1575,7 +1589,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "105",
+   "id": "106",
    "metadata": {},
    "source": [
     "#### Exercise 5.7: Find Undefined Features\n",
@@ -1596,7 +1610,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "106",
+   "id": "107",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1605,7 +1619,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "107",
+   "id": "108",
    "metadata": {},
    "source": [
     "#### Exercise 5.8: Identify the Cause of the Unexplained Peaks\n",
@@ -1631,7 +1645,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "108",
+   "id": "109",
    "metadata": {},
    "source": [
     "#### Exercise 5.9: Identify the impurity phase\n",
@@ -1653,7 +1667,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "109",
+   "id": "110",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1663,7 +1677,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "110",
+   "id": "111",
    "metadata": {},
    "source": [
     "#### Exercise 5.10: Create a Second Sample Model – Si as Impurity\n",
@@ -1681,7 +1695,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "111",
+   "id": "112",
    "metadata": {},
    "source": [
     "**Set Space Group**"
@@ -1690,7 +1704,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "112",
+   "id": "113",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1700,7 +1714,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "113",
+   "id": "114",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1710,7 +1724,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "114",
+   "id": "115",
    "metadata": {},
    "source": [
     "**Set Lattice Parameters**"
@@ -1719,7 +1733,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "115",
+   "id": "116",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1728,7 +1742,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "116",
+   "id": "117",
    "metadata": {},
    "source": [
     "**Set Atom Sites**"
@@ -1737,7 +1751,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "117",
+   "id": "118",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1754,7 +1768,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "118",
+   "id": "119",
    "metadata": {},
    "source": [
     "**🔗 Assign Sample Model to Experiment**"
@@ -1763,7 +1777,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "119",
+   "id": "120",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1772,7 +1786,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "120",
+   "id": "121",
    "metadata": {},
    "source": [
     "#### Exercise 5.11: Refine the Scale of the Si Phase\n",
@@ -1798,7 +1812,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "121",
+   "id": "122",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1807,7 +1821,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "122",
+   "id": "123",
    "metadata": {},
    "source": [
     "As you can see, the calculated pattern is now the sum of both phases,\n",
@@ -1820,7 +1834,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "123",
+   "id": "124",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1829,7 +1843,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "124",
+   "id": "125",
    "metadata": {},
    "source": [
     "**Run Fitting**\n",
@@ -1840,7 +1854,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "125",
+   "id": "126",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1849,7 +1863,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "126",
+   "id": "127",
    "metadata": {},
    "source": [
     "**Visualize Fit Results**\n",
@@ -1863,7 +1877,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "127",
+   "id": "128",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1873,7 +1887,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "128",
+   "id": "129",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1882,7 +1896,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "129",
+   "id": "130",
    "metadata": {},
    "source": [
     "All previously unexplained peaks are now accounted for in the pattern, and the\n",
@@ -1903,7 +1917,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "130",
+   "id": "131",
    "metadata": {},
    "source": [
     "## 🎁 Bonus\n",
diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
index 9e61e4bd..68dcadc1 100644
--- a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
+++ b/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py
@@ -129,6 +129,12 @@
 #
 # The `plot_meas` method of the project enables us to visualize the measured
 # diffraction pattern.
+#
+# Before plotting, we set the plotting engine to 'plotly', which provides
+# interactive visualizations.
+
+# %%
+project_1.plotter.engine = 'plotly'
 
 # %%
 project_1.plot_meas(expt_name='sim_si')
@@ -567,6 +573,7 @@
 # **Solution:**
 
 # %%
+project_2.plotter.engine = 'plotly'
 project_2.plot_meas(expt_name='sim_lbco')
 
 # %%

From 3a3034510b2058137f376bff25b82731eb731587 Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 15:51:06 +0200
Subject: [PATCH 8/9] Standardizes single quotes in Python script

---
 tools/nb_uncomment_pip.py | 43 ++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 23 deletions(-)

diff --git a/tools/nb_uncomment_pip.py b/tools/nb_uncomment_pip.py
index 206845d3..8d2a2ff4 100644
--- a/tools/nb_uncomment_pip.py
+++ b/tools/nb_uncomment_pip.py
@@ -10,14 +10,14 @@
 from __future__ import annotations
 
 import argparse
+import re
 import sys
 from pathlib import Path
-import re
 
 import nbformat
 
 # Regex: beginning-of-line, capture leading whitespace, then "#", spaces, then "!pip"
-_PATTERN = re.compile(r"^(\s*)#\s*!pip\b")
+_PATTERN = re.compile(r'^(\s*)#\s*!pip\b')
 
 
 def fix_cell_source(src: str) -> tuple[str, int]:
@@ -30,16 +30,15 @@ def fix_cell_source(src: str) -> tuple[str, int]:
     for line in src.splitlines(keepends=False):
         m = _PATTERN.match(line)
         if m:
-            indent = m.group(1)
             # Replace only the first '# !pip' at the beginning, preserve the rest of the line
             # e.g., "  # !pip install foo" -> "  !pip install foo"
-            new_line = _PATTERN.sub(r"\1!pip", line, count=1)
+            new_line = _PATTERN.sub(r'\1!pip', line, count=1)
             if new_line != line:
                 changed += 1
             new_lines.append(new_line)
         else:
             new_lines.append(line)
-    return ("\n".join(new_lines), changed)
+    return ('\n'.join(new_lines), changed)
 
 
 def process_notebook(path: Path) -> int:
@@ -49,9 +48,9 @@ def process_notebook(path: Path) -> int:
     nb = nbformat.read(path, as_version=4)
     total_changes = 0
     for cell in nb.cells:
-        if cell.cell_type != "code":
+        if cell.cell_type != 'code':
             continue
-        new_src, changes = fix_cell_source(cell.source or "")
+        new_src, changes = fix_cell_source(cell.source or '')
         if changes:
             cell.source = new_src
             total_changes += changes
@@ -63,22 +62,20 @@ def process_notebook(path: Path) -> int:
 def iter_notebooks(paths: list[Path]):
     for p in paths:
         if p.is_dir():
-            yield from (q for q in p.rglob("*.ipynb") if q.is_file())
-        elif p.is_file() and p.suffix == ".ipynb":
+            yield from (q for q in p.rglob('*.ipynb') if q.is_file())
+        elif p.is_file() and p.suffix == '.ipynb':
             yield p
 
 
 def main(argv: list[str]) -> int:
-    ap = argparse.ArgumentParser(
-        description="Uncomment '# !pip ...' to '!pip ...' in code cells of .ipynb notebooks."
-    )
-    ap.add_argument("paths", nargs="+", help="Notebook files or directories to process")
-    ap.add_argument("--dry-run", action="store_true", help="Report changes without writing files")
+    ap = argparse.ArgumentParser(description="Uncomment '# !pip ...' to '!pip ...' in code cells of .ipynb notebooks.")
+    ap.add_argument('paths', nargs='+', help='Notebook files or directories to process')
+    ap.add_argument('--dry-run', action='store_true', help='Report changes without writing files')
     args = ap.parse_args(argv)
 
     targets = list(iter_notebooks([Path(p) for p in args.paths]))
     if not targets:
-        print("No .ipynb files found.", file=sys.stderr)
+        print('No .ipynb files found.', file=sys.stderr)
         return 1
 
     total_files = 0
@@ -90,22 +87,22 @@ def main(argv: list[str]) -> int:
             nb = nbformat.read(nb_path, as_version=4)
             changes = 0
             for cell in nb.cells:
-                if cell.cell_type != "code":
+                if cell.cell_type != 'code':
                     continue
-                _, c = fix_cell_source(cell.source or "")
+                _, c = fix_cell_source(cell.source or '')
                 changes += c
         if changes:
-            action = "UPDATED" if not args.dry_run else "WOULD UPDATE"
-            print(f"{action}: {nb_path} ({changes} line(s))")
+            action = 'UPDATED' if not args.dry_run else 'WOULD UPDATE'
+            print(f'{action}: {nb_path} ({changes} line(s))')
             total_files += 1
             total_changes += changes
 
     if total_files == 0:
-        print("No changes needed.")
+        print('No changes needed.')
     else:
-        print(f"Done. Files changed: {total_files}, lines changed: {total_changes}")
+        print(f'Done. Files changed: {total_files}, lines changed: {total_changes}')
     return 0
 
 
-if __name__ == "__main__":
-    raise SystemExit(main(sys.argv[1:]))
\ No newline at end of file
+if __name__ == '__main__':
+    raise SystemExit(main(sys.argv[1:]))

From f029bbafc51b784c64d484e2fc8cd0d42dac511f Mon Sep 17 00:00:00 2001
From: Andrew Sazonov <andrew.sazonov@icloud.com>
Date: Mon, 11 Aug 2025 15:55:13 +0200
Subject: [PATCH 9/9] Removes dev dependencies installation step

---
 .github/workflows/publish-pypi.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
index c4e702f7..76ee6261 100644
--- a/.github/workflows/publish-pypi.yml
+++ b/.github/workflows/publish-pypi.yml
@@ -29,9 +29,6 @@ jobs:
       - name: Upgrade package installer for Python
         run: pip install --upgrade pip
 
-      - name: Install Python dependencies
-        run: pip install '.[dev]'
-
       - name: Create Python package
         run: python -m build