docs: introduce ModeSimulation

[daquinteroflex]

Hi @e-g-melo, we had a conversation about this and thought the best approach is simply to deprecate in the docs for the rc3 release and then update the notebooks separately for 2.10

• rerouting from /api/mode -> /api/mode/index

Greptile Overview

Greptile Summary

This PR restructures the mode documentation to introduce ModeSimulation as the primary interface, deprecating ModeSolver. The changes organize mode-related documentation into a new subdirectory structure with separate files for simulation, specifications, output data, and deprecated components.

Key changes:

• Created new docs/api/mode/ directory with organized sections for simulation, specification, output data, and deprecated classes
• Updated docs/api/simulation.rst to reference ModeSimulation instead of the deprecated ModeSolver
• Converted docs/api/mode.rst to a redirect file that includes the new index for backward compatibility
• Added deprecation notice for ModeSolver and ModeSolverData in favor of ModeSimulation

Issues found:

• Missing version number in the .. deprecated:: directive in deprecated.rst (line 6)
• Missing newlines at end of files in several RST files (style issue)

Confidence Score: 4/5

• This PR is safe to merge with minor documentation fixes recommended
• The documentation restructuring is well-organized and maintains backward compatibility. The main issue is a missing version number in the deprecation directive which is required for proper RST rendering. The missing newlines at EOF are minor style issues that don't affect functionality.
• Pay attention to docs/api/mode/deprecated.rst - the deprecated directive needs a version number to render correctly

Important Files Changed

File Analysis

Filename	Score	Overview
docs/api/mode/index.rst	4/5	New mode section index that organizes simulation, specification, output data, and deprecated content; missing newline at EOF
docs/api/mode/deprecated.rst	3/5	Deprecation notice for ModeSolver in favor of ModeSimulation; missing version number in deprecated directive
docs/api/simulation.rst	5/5	Updated reference from deprecated ModeSolver to new ModeSimulation in the "Other Simulation Types" section

Sequence Diagram

sequenceDiagram
    participant User
    participant DocsIndex as docs/api/index.rst
    participant ModeEntry as docs/api/mode.rst
    participant ModeIndex as docs/api/mode/index.rst
    participant Simulation as mode/simulation.rst
    participant Specification as mode/specification.rst
    participant OutputData as mode/output_data.rst
    participant Deprecated as mode/deprecated.rst
    
    User->>DocsIndex: Navigate to API docs
    DocsIndex->>ModeEntry: Reference mode section
    ModeEntry->>ModeIndex: Include mode/index.rst
    
    Note over ModeIndex: New structured organization
    
    ModeIndex->>Simulation: Include ModeSimulation docs
    ModeIndex->>Specification: Include ModeSpec classes
    ModeIndex->>OutputData: Include data output classes
    ModeIndex->>Deprecated: Include ModeSolver deprecation
    
    Note over Deprecated: ModeSolver → ModeSimulation
    Note over Simulation: New primary interface

Loading

[greptile-apps]

_{8 files reviewed, 4 comments}

_{Edit Code Review Agent Settings | Greptile}

[github-actions]

Diff Coverage

Diff: origin/develop...HEAD, staged and unstaged changes

No lines with coverage information in this diff.

[e-g-melo]

Thanks @daquinteroflex!

Sounds very good!

There is only a typo in: tidy3d.plugins.mode.ModeSolver is will be deprecated in a future version.