Replace GLFW and nativefiledialog with SDL3 + Create layered renderer architecture with GPU API

[Copilot]

Consolidates windowing and file dialog dependencies from GLFW + nativefiledialog into SDL3, reducing dependency footprint and leveraging SDL3's native cross-platform file dialogs. Additionally refactors all rendering code into a layered renderer architecture with a standalone low-level GPU API to prepare for future SDL-GPU transition.

Changes

Dependency Management

• Added SDL3 as submodule (main branch)
• Removed GLFW and nativefiledialog submodules
• Updated CMakeLists.txt: static SDL3 build with optional X11 features disabled

Core Migration (src/app/application.cpp)

• Window/GL context: glfwCreateWindow → SDL_CreateWindow, glfwMakeContextCurrent → SDL_GL_MakeCurrent
• Event loop: glfwPollEvents → SDL_PollEvent with native SDL event handling
• File dialogs: NFD_OpenDialog/SaveDialog → SDL_ShowOpenFileDialog/ShowSaveFileDialog with async callbacks
• Timing: glfwGetTime → SDL_GetTicks

ImGui Backend

• Added imgui_impl_sdl3.{cpp,h} from ImGui 1.90.5, patched for SDL3 API changes:
  • Keyboard events: keysym struct → flat key/scancode/mod fields
  • Constants: SDLK_a → SDLK_A, SDL_SYSTEM_CURSOR_ARROW → SDL_SYSTEM_CURSOR_DEFAULT
  • Text input: SDL_SetTextInputRect → SDL_SetTextInputArea(window, rect, cursor)
• Updated for ImGui 1.92.5 compatibility: SetPlatformImeDataFn → platform_io.Platform_SetImeDataFn
• Removed imgui_impl_glfw.{cpp,h}

Layered Renderer Architecture

Low-Level GPU API (src/gfx/gpu.{h,cpp})

NEW: Created abstraction layer for all GPU operations:

• Texture Management: create_texture_2d/3d(), update_texture(), destroy_texture(), bind_texture()
• Shader Management: create_shader(), destroy_shader(), use_shader(), set_uniform() (multiple type overloads)
• Framebuffer Management: create_framebuffer(), destroy_framebuffer(), bind_framebuffer(), attach_texture_to_framebuffer()
• VAO Management: create_vertex_array(), destroy_vertex_array(), bind_vertex_array()
• Rendering State: set_viewport(), set_scissor(), enable_blend(), enable_depth_test(), enable_cull_face(), set_depth_mask(), set_color_mask(), clear_color(), clear()
• Draw Operations: draw_arrays(), draw_elements()

High-Level Renderer Module (src/gfx/renderer.{h,cpp})

• Moved ~578 lines of rendering code from main.cpp to renderer module
• Functions migrated:
  • fill_gbuffer() - Molecular representation rendering to GBuffer
  • apply_postprocessing() - All post-processing effects (SSAO, TAA, DoF, etc.)
  • draw_representations_opaque() - Opaque molecular rendering
  • draw_representations_transparent() - Volume rendering (orbitals, electron density)
  • draw_representations_opaque_lean_and_mean() - Optimized rendering for selections/highlights
• Clean API: main.cpp now uses renderer::*() calls instead of direct OpenGL
• Uses GPU API: Renderer layer uses low-level GPU API for all OpenGL operations

Component Refactoring

NEW: Started migrating components to use GPU API:

• Ramachandran Component: Refactored texture creation/destruction to use gpu::create_texture_2d() and gpu::destroy_texture()
• Replaced glGenFramebuffers/glGenVertexArrays with gpu::create_framebuffer() and gpu::create_vertex_array()
• Uses glTexStorage2D via GPU API for immutable texture storage

File Dialog Implementation

// Before: Synchronous NFD with manual filter parsing
nfdchar_t* out_path = NULL;
nfdresult_t result = NFD_OpenDialog("jpg,png,bmp", NULL, &out_path);
if (result == NFD_OKAY) { /* use out_path */ }

// After: Async SDL3 with callback and proper cleanup
struct DialogState { const char* result_path; bool completed; };
DialogState state = {NULL, false};
SDL_ShowOpenFileDialog(callback, &state, NULL, filters, count, NULL, false);
while (!state.completed) { SDL_WaitEventTimeout(&event, 10); }

Security & Quality

• Fixed race condition: changed dialog state from static to local
• Added buffer overflow protection in filter extension parsing (validate length before allocation)
• Improved responsiveness: SDL_Delay(10) → SDL_WaitEventTimeout(&event, 10)

Architecture Improvement

The new layered architecture provides clean separation of concerns:

Components (ramachandran, veloxchem, etc.)
   ↓
High-level Renderer (renderer.h/cpp)
   ├─> renderer::fill_gbuffer()
   ├─> renderer::apply_postprocessing()
   └─> renderer::clear_gbuffer()
          ↓
Low-level GPU API (gpu.h/cpp)
   ├─> gpu::create_texture()
   ├─> gpu::create_shader()
   ├─> gpu::bind_framebuffer()
   ├─> gpu::set_viewport()
   └─> gpu::draw_arrays()
          ↓
OpenGL

Benefits:

• All OpenGL calls isolated in GPU API layer
• Components use GPU API instead of direct OpenGL
• High-level renderer focuses on rendering logic, not OpenGL details
• Easy to swap OpenGL for SDL-GPU in future by reimplementing GPU API
• MDlib rendering code (md_gl_draw()) remains unchanged as requested

Progress

• ✅ Low-level GPU API layer complete
• ✅ High-level renderer using GPU API
• ✅ Ramachandran component partially migrated to GPU API
• 🔄 Remaining: Complete component migration (ramachandran rendering, veloxchem, etc.)

Notes

• Manual testing recommended on Windows/macOS to verify native file dialogs and platform-specific behavior
• Layered renderer architecture ready for future SDL-GPU migration
• MDlib rendering code remains unchanged as requested

Original prompt

Create a PR that introduces SDL3 as a new dependency. This should replace the existing dependencies on glfw and native file dialogue.

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[scanberg]

@copilot I have updated imgui and implot in the current version.
The overarching goal of this branch is to transition all rendering code of VIAMD and MDLIB into SDL-GPU. However, the current state of the codebase is not really ready for that transition yet. And in the first phase, one should stick to OpenGL and use SDL for window management.

I want you to investigate and transition all of the rendering code within the codebase and move it into a stand alone renderer such that no OpenGL calls are made from within main.cpp or any other portion of the code base and all of it occurs within this renderer. This includes rendering molecular representations and immediate 2D drawing.

MDlib is still in charge of rendering molecules and is using OpenGL. That can remain so for now. Only make changes within viamd for now.

[Copilot]

@copilot I have updated imgui and implot in the current version.
The overarching goal of this branch is to transition all rendering code of VIAMD and MDLIB into SDL-GPU. However, the current state of ...

I'll create a standalone renderer module to encapsulate all rendering code. This will move OpenGL calls out of main.cpp into a dedicated renderer that handles molecular representations, immediate 2D drawing, and post-processing.

I'll create:

• src/gfx/renderer.h/cpp - Main renderer interface
• Abstract rendering operations through the renderer API
• Keep mdlib's OpenGL rendering unchanged as requested

Working on this now...

[scanberg]

@copilot I updated the backends to the officially provided backends from ImGui.
I want you to move all of the rendering code (OpenGL) or gl abstractions within all of the components used in VIAMD into renderer.
There might need to separate this into a renderer which does high level rendering operations (such as molecule drawing, immediate mode, postprocessing) and then a lower-level API 'gpu' which handles the actual interfacing with the underlying GPU, i.e. creating and handling textures, volumes, shaders.

[Copilot]

@copilot I updated the backends to the officially provided backends from ImGui.
I want you to move all of the rendering code (OpenGL) or gl abstractions within all of the components used in VIAMD int...

I'll extend the renderer architecture to move all OpenGL code from components into the renderer, and create a layered architecture:

High-level renderer (renderer.h/cpp): Molecule drawing, immediate mode, postprocessing operations
Low-level GPU API (gpu.h/cpp): Texture management, shader programs, framebuffers, VAOs

I'll refactor:

• Ramachandran component (texture generation, shader programs, rendering)
• Veloxchem component (rendering operations)
• Remaining OpenGL calls in main.cpp

Working on this now...