refactor(io): Deprecate LAMMPS Writer and Streamline I/O Module

[TKanX]

Summary:

Removed the LAMMPS writer implementation (src/io/lammps/) and associated configuration types from the library and CLI. This change streamlines the project's focus on structure parameterization and BGF export, reducing maintenance overhead for legacy formats. The LammpsData and LammpsSettings output formats have been removed from the public API and CLI options.

Changes:

• Removed LAMMPS Writer:

  • Deleted src/io/lammps/ module and LammpsConfig struct.
  • Removed write_lammps_package, write_lammps_data, and write_settings_file functions.
  • Updated src/io/mod.rs to remove re-exports and module references.

• Updated CLI:

  • Removed LammpsOptions struct and associated flags (--lmp-*) from cli.rs.
  • Removed LammpsData and LammpsSettings variants from BioOutputFormat and ChemOutputFormat.
  • Updated commands/bio.rs and commands/chem.rs to remove LAMMPS writing logic.
  • Removed config/lammps.rs builder.

• Cleaned Up Dependencies & Docs:

  • Updated MANUAL.md to remove LAMMPS command references and options.
  • Updated README.md examples to use BGF export instead of LAMMPS.
  • Updated ARCHITECTURE.md diagrams and descriptions to reflect the removal of the LAMMPS writer.
  • Removed sample outputs (.data, .settings) from documentation examples.

• Refactored Examples:

  • Deleted drug molecule examples (Acetaminophen.sdf, etc.) that were primarily used for LAMMPS testing.
  • Updated examples/basic/README.md to showcase BGF and MOL2/SDF workflows.

[Copilot]

Pull request overview

This PR removes the deprecated LAMMPS writer (library + CLI surface area) and updates documentation/examples to focus on structure processing and BGF export.

Changes:

• Removed src/io/lammps and all public API/CLI options related to LAMMPS output (config types, format variants, CLI flags).
• Updated dforge commands to drop LAMMPS write paths and adjust stdout default formats (bio→BGF, chem→MOL2).
• Cleaned up docs and examples by removing LAMMPS references and sample drug datasets/assets.

Reviewed changes

Copilot reviewed 19 out of 37 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/lib.rs	Updates crate-level docs to remove LAMMPS export claims.
src/io/mod.rs	Removes LAMMPS module wiring, exports, and Format variants.
src/io/lammps/writer.rs	Deletes the LAMMPS writer implementation (data/settings/package generation).
src/io/lammps/mod.rs	Deletes the LAMMPS submodule entry point.
src/bin/dforge/util/convert.rs	Removes CLI→library conversions for removed LAMMPS formats/boundary types.
src/bin/dforge/io/infer.rs	Removes .data/.lammps/.settings output inference for LAMMPS formats.
src/bin/dforge/display/error.rs	Updates user hints to remove LAMMPS from supported output formats and parsing hint branches.
src/bin/dforge/config/mod.rs	Removes the LAMMPS config builder module export.
src/bin/dforge/config/lammps.rs	Deletes the LAMMPS config builder.
src/bin/dforge/commands/chem.rs	Removes LAMMPS writing/config handling; defaults stdout output to MOL2.
src/bin/dforge/commands/bio.rs	Removes LAMMPS writing/config handling; defaults stdout output to BGF.
src/bin/dforge/cli.rs	Removes LAMMPS CLI flags/options and output format variants.
examples/drugs/images/penicillin-g-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/morphine-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/methamphetamine-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/metformin-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/mdma-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/ketamine-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/ibuprofen-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/cocaine-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/aspirin-structure.svg	Removes legacy drug example image asset.
examples/drugs/images/acetaminophen-structure.svg	Removes legacy drug example image asset.
examples/drugs/README.md	Removes LAMMPS-focused drug example documentation.
examples/drugs/Penicillin-G.sdf	Removes legacy drug example input.
examples/drugs/Morphine.sdf	Removes legacy drug example input.
examples/drugs/Methamphetamine.sdf	Removes legacy drug example input.
examples/drugs/Metformin.sdf	Removes legacy drug example input.
examples/drugs/MDMA.sdf	Removes legacy drug example input.
examples/drugs/Ketamine.sdf	Removes legacy drug example input.
examples/drugs/Ibuprofen.sdf	Removes legacy drug example input.
examples/drugs/Cocaine.sdf	Removes legacy drug example input.
examples/drugs/Aspirin.sdf	Removes legacy drug example input.
examples/drugs/Acetaminophen.sdf	Removes legacy drug example input.
examples/basic/README.md	Updates basic examples to remove LAMMPS outputs from commands/outputs.
README.md	Updates README narrative and code example to use BGF export instead of LAMMPS.
MANUAL.md	Updates CLI manual to remove LAMMPS formats/options and adjust output rules.
ARCHITECTURE.md	Updates architecture docs/diagrams to remove the LAMMPS writer component.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.