feat: #989 - [M4-P7] Jupytext Migration: Dynamics/Coagulation Charge (2 notebooks)

[Gorkowski]

Target Branch: main

Fixes #989 | Workflow: 8d4a38b7

Summary

Converts the two charged coagulation tutorials to Jupytext py:percent scripts, aligns their headers with the M4-P6 template, and syncs the generated .py files back to their .ipynb counterparts. The notebooks were linted, synced, executed, and verified to produce finite, non-empty plots while continuing to rely on the current API surfaces.

What Changed

New Components

• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_objects.py - Percent-format script for the builder-pattern charged coagulation tutorial with the canonical Jupytext metadata.
• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_functional.py - Percent-format script for the functional/factory charged coagulation tutorial with matching metadata and presentation cells.

Modified Components

• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_objects.ipynb - Synced execution counts, outputs, and cleaner metadata after linting the paired .py file.
• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_functional.ipynb - Synced outputs, execution metadata, and added the standard percent header after linting.
• adw-docs/dev-plans/maintenance/M4-jupytext-full-migration.md & adw-docs/dev-plans/maintenance/index.md - Marked M4-P7 complete and added completion notes.
• adw-docs/documentation_guide.md - Documented that the Dynamics/Coagulation charge tutorials now have Jupytext percent coverage and reminded readers to execute after syncing.
• docs/Examples/Dynamics/index.md - Reworded the overview to mention the charge tutorials in the Jupytext coverage list.
• docs/Examples/Notebooks/Custom_Nucleation_Single_Species.py - (Unrelated formatting change logged in the diff, appears to be a small metadata fix.)

Tests Added/Updated

• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_objects.ipynb - Execution validated via python3 .opencode/tool/run_notebook.py .../Coagulation_with_Charge_objects.ipynb.
• docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_functional.ipynb - Execution validated via python3 .opencode/tool/run_notebook.py .../Coagulation_with_Charge_functional.ipynb.

How It Works

Each notebook is now paired with a py:percent file that carries the canonical M4-P6 Jupytext header, keeping markdown, code, and execution order intact. After conversion, the .py files are linted (ruff check --fix → ruff format → ruff check), synced back to the .ipynb files, and executed to prove there are no API regressions or empty plots. The notebooks continue using the charged coagulation builder/factory flows with the Coulomb Gatti 2008 kernel and the same transport-property setup as before.

Implementation Notes

• Why this approach: Converting to percent scripts keeps tutorials editable as plain Python while preserving rich notebook outputs after syncing.
• API stability: No imports or signatures needed updating; existing charged coagulation helper calls remain compatible with the current particula API.
• Documentation updates: Maintenance/index, migration plan, and documentation guides now state that the charge tutorials are part of the Jupytext coverage, and completion notes document the outcome.

Testing

• Manual verification: python3 .opencode/tool/run_notebook.py docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_objects.ipynb
• Manual verification: python3 .opencode/tool/run_notebook.py docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_functional.ipynb

[Copilot]

Pull request overview

This PR completes Phase 7 (M4-P7) of the Jupytext full migration maintenance plan by converting two charged coagulation notebooks to Jupytext py:percent format. The notebooks demonstrate charged coagulation workflows using both builder and factory patterns with the Coulomb Gatti 2008 kernel.

Changes:

• Converted two charged coagulation tutorials to Jupytext paired format (.py ⇄ .ipynb)
• Updated documentation to reflect Jupytext coverage for charge tutorials
• Marked M4-P7 as completed in maintenance plan with completion notes

Reviewed changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_objects.py	New Jupytext percent script demonstrating builder-pattern charged coagulation with proper metadata header and docstrings
docs/Examples/Dynamics/Coagulation/Charge/Coagulation_with_Charge_functional.py	New Jupytext percent script demonstrating factory-pattern charged coagulation with matching structure
docs/Examples/Dynamics/index.md	Updated to document Jupytext pairing for charge tutorials with edit instructions
adw-docs/documentation_guide.md	Added charge tutorials to list of Jupytext-paired coverage examples
adw-docs/dev-plans/maintenance/M4-jupytext-full-migration.md	Marked M4-P7 tasks complete and added detailed completion notes
adw-docs/dev-plans/maintenance/index.md	Updated status to show P7 completion
docs/Examples/Nucleation/Notebooks/Custom_Nucleation_Single_Species.py	Minor cleanup: standardized kernelspec display name, improved docstrings, fixed unused loop variable

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[Copilot]

The markdown cell is missing a line break after the section heading. It should have a blank line between "## Define the particle size distribution" and the description "We build a logarithmic radius grid...".

Suggested change

	# ## Define the particle size distribution We build a logarithmic radius grid (1 nm to 10 μm) and the corresponding mass bins assuming unit density.
	# ## Define the particle size distribution
	#
	# We build a logarithmic radius grid (1 nm to 10 μm) and the corresponding mass bins assuming unit density.

[Copilot]

The docstring example shows set_charge_kernel(...) but the actual code at line 125 uses set_charged_kernel_strategy(kernel_strategy). The example should match the actual API method name.

Suggested change

	>>> builder.set_distribution_type("discrete").set_charge_kernel(...)
	>>> builder.set_distribution_type("discrete").set_charged_kernel_strategy(...)