Update dependencies, workflows, and plotting defaults; replace pip uncomment command with Python script

.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:
 
@@ -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
+          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:

.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
 

.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
@@ -49,8 +49,8 @@ jobs:
 
       - name: Install Python dependencies
         run:
-          python -m pip install 'easydiffraction[charts]' 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: >

.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
+          python tools/nb_uncomment_pip.py ${{ env.NOTEBOOKS_DIR }}/
 
       - name: Run tutorials as Jupyter Notebooks (using src/ as the source dir)
         shell: bash

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

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

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",
@@ -74,7 +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'
 

tools/nb_uncomment_pip.py

@@ -0,0 +1,108 @@
+"""
+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 re
+import sys
+from pathlib import Path
+
+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:
+            # 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:]))

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {

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]'"
    ]
   },
   {