//! Input/Output and data schema module
//!
//! This module handles reading and writing various file formats including
//! HDF5, JSON, fchk, and molden files for molecular data and results.
//!
//! # Features
//!
//! - **HDF5 I/O**: Optimized storage with chunking and compression for large datasets
//! - **JSON I/O**: Human-readable format for configuration and small datasets
//! - **Schema definitions**: Complete data structures for GW/BSE calculations
//! - **Checkpoint management**: Save/restore calculation state
//! - **File format readers**: Support for fchk (Gaussian) and molden formats

// Module inherits clippy settings from lib.rs

use crate::common::Result;
use ndarray::{Array1, Array2};
use serde::{Deserialize, Serialize};
use std::path::Path;

// Schema definitions
pub mod df_tensors;
pub mod hdf5_io;
pub mod schema;

// Re-export main schema types
pub use df_tensors::{DFMetadata, DFTensorsS24};
pub use hdf5_io::{read_hdf5, write_hdf5};
pub use schema::{
    BSEParams, BasisSetData, CalculationParams, CalculationResults, CalculationType, GWParams,
    Metadata, MoleculeInput, QuasixData,
};

/// Molecular system data.
///
/// Contains basic molecular structure information including geometry,
/// charge, and basis set details.
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct MolecularData {
    /// Molecule name/identifier
    pub name: String,
    /// Number of atoms
    pub natoms: usize,
    /// Number of electrons
    pub nelec: usize,
    /// Number of basis functions
    pub nbasis: usize,
    /// Atomic coordinates (natoms x 3)
    pub coords: Vec<[f64; 3]>,
    /// Atomic numbers
    pub atomic_numbers: Vec<u32>,
    /// Basis set name
    pub basis_set: String,
}

impl MolecularData {
    /// Create new molecular data.
    ///
    /// # Arguments
    ///
    /// * `natoms` - Number of atoms in the molecule
    /// * `nelec` - Total number of electrons
    /// * `nbasis` - Number of basis functions
    #[must_use]
    pub fn new(natoms: usize, nelec: usize, nbasis: usize) -> Self {
        Self {
            name: String::new(),
            natoms,
            nelec,
            nbasis,
            coords: vec![[0.0; 3]; natoms],
            atomic_numbers: vec![0; natoms],
            basis_set: String::new(),
        }
    }

    /// Load molecular data from JSON file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the JSON file
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be read or parsed
    pub fn from_json(_path: &Path) -> Result<Self> {
        todo!("Implement JSON loading")
    }

    /// Save molecular data to JSON file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path where the JSON file will be saved
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be written
    pub fn to_json(&self, _path: &Path) -> Result<()> {
        todo!("Implement JSON saving")
    }
}

/// GW calculation results.
///
/// Contains quasiparticle energies, Z-factors, and convergence information
/// from a GW calculation.
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct GWResults {
    /// Quasiparticle energies
    pub qp_energies: Vec<f64>,
    /// Z-factors (renormalization)
    pub z_factors: Vec<f64>,
    /// Number of occupied orbitals
    pub n_occ: usize,
    /// Spectral functions
    pub spectral_functions: Option<Vec<Vec<f64>>>,
    /// Quality metrics (NOTE: QualityMetrics moved to benchmarks module)
    pub quality_metrics: crate::benchmarks::QualityMetrics,
    /// Convergence achieved
    pub converged: bool,
    /// Number of iterations
    pub iterations: usize,
}

impl GWResults {
    /// Create new GW results with specified number of states.
    ///
    /// # Arguments
    ///
    /// * `nstates` - Number of states to store results for
    #[must_use]
    pub fn new(nstates: usize) -> Self {
        Self {
            qp_energies: vec![0.0; nstates],
            z_factors: vec![0.0; nstates],
            n_occ: 0,
            spectral_functions: None,
            quality_metrics: crate::benchmarks::QualityMetrics::default(),
            converged: false,
            iterations: 0,
        }
    }

    /// Save GW results to HDF5 file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the HDF5 file
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be written
    pub fn to_hdf5(&self, _path: &Path) -> Result<()> {
        todo!("Implement HDF5 writing")
    }

    /// Load GW results from HDF5 file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the HDF5 file
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be read or parsed
    pub fn from_hdf5(_path: &Path) -> Result<Self> {
        todo!("Implement HDF5 reading")
    }
}

/// BSE calculation results.
///
/// Contains excitation energies, oscillator strengths, and transition
/// dipole moments from a Bethe-Salpeter equation calculation.
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct BSEResults {
    /// Excitation energies
    pub excitation_energies: Vec<f64>,
    /// Oscillator strengths
    pub oscillator_strengths: Vec<f64>,
    /// Transition dipole moments
    pub dipole_moments: Vec<[f64; 3]>,
    /// Dominant configurations
    pub configurations: Vec<Vec<(usize, usize, f64)>>,
}

impl BSEResults {
    /// Create new BSE results with specified number of excitations.
    ///
    /// # Arguments
    ///
    /// * `nexcitations` - Number of excitations to store
    #[must_use]
    pub fn new(nexcitations: usize) -> Self {
        Self {
            excitation_energies: vec![0.0; nexcitations],
            oscillator_strengths: vec![0.0; nexcitations],
            dipole_moments: vec![[0.0; 3]; nexcitations],
            configurations: vec![Vec::new(); nexcitations],
        }
    }
}

/// Checkpoint file handler for saving and restoring calculation state.
///
/// Enables restart capability for long-running calculations by periodically
/// saving the current state to disk.
#[derive(Debug)]
pub struct CheckpointManager {
    /// Base directory for checkpoints
    pub checkpoint_dir: String,
    /// Checkpoint frequency (iterations)
    pub frequency: usize,
}

impl CheckpointManager {
    /// Create new checkpoint manager.
    ///
    /// # Arguments
    ///
    /// * `checkpoint_dir` - Directory where checkpoint files will be stored
    #[must_use]
    pub fn new(checkpoint_dir: String) -> Self {
        Self {
            checkpoint_dir,
            frequency: 10,
        }
    }

    /// Save checkpoint to disk.
    ///
    /// # Arguments
    ///
    /// * `iteration` - Current iteration number
    /// * `data` - GW results to save
    ///
    /// # Errors
    ///
    /// Returns an error if the checkpoint cannot be written
    pub fn save_checkpoint(&self, _iteration: usize, _data: &GWResults) -> Result<()> {
        todo!("Implement checkpoint saving")
    }

    /// Load the most recent checkpoint from disk.
    ///
    /// # Returns
    ///
    /// A tuple containing the iteration number and GW results
    ///
    /// # Errors
    ///
    /// Returns an error if no checkpoint exists or cannot be read
    pub fn load_checkpoint(&self) -> Result<(usize, GWResults)> {
        todo!("Implement checkpoint loading")
    }

    /// Clean up old checkpoint files, keeping only the most recent ones.
    ///
    /// # Arguments
    ///
    /// * `keep_last` - Number of most recent checkpoints to keep
    ///
    /// # Errors
    ///
    /// Returns an error if files cannot be deleted
    pub fn cleanup_old(&self, _keep_last: usize) -> Result<()> {
        todo!("Implement checkpoint cleanup")
    }
}

/// Fchk file reader for Gaussian formatted checkpoint files.
///
/// Provides utilities to extract molecular data, orbital coefficients,
/// and energies from Gaussian fchk files.
#[derive(Debug)]
pub struct FchkReader;

impl FchkReader {
    /// Read molecular data from fchk file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the fchk file
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be read or parsed
    pub fn read_molecular_data(_path: &Path) -> Result<MolecularData> {
        todo!("Implement fchk reader")
    }

    /// Read molecular orbital coefficients from fchk file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the fchk file
    ///
    /// # Returns
    ///
    /// A 2D array of MO coefficients (nbasis x norbitals)
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be read or parsed
    pub fn read_mo_coefficients(_path: &Path) -> Result<Array2<f64>> {
        todo!("Implement MO coefficient reading")
    }

    /// Read orbital energies from fchk file.
    ///
    /// # Arguments
    ///
    /// * `path` - Path to the fchk file
    ///
    /// # Returns
    ///
    /// A 1D array of orbital energies
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be read or parsed
    pub fn read_orbital_energies(_path: &Path) -> Result<Array1<f64>> {
        todo!("Implement orbital energy reading")
    }
}

/// Molden file writer for visualization.
///
/// Creates molden format files that can be visualized in molecular
/// visualization software like VMD or Jmol.
#[derive(Debug)]
pub struct MoldenWriter;

impl MoldenWriter {
    /// Write molden file with molecular orbitals.
    ///
    /// # Arguments
    ///
    /// * `path` - Path where the molden file will be saved
    /// * `mol_data` - Molecular structure and basis information
    /// * `mo_coeffs` - Molecular orbital coefficients
    ///
    /// # Errors
    ///
    /// Returns an error if the file cannot be written
    pub fn write(_path: &Path, _mol_data: &MolecularData, _mo_coeffs: &Array2<f64>) -> Result<()> {
        todo!("Implement molden writer")
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_molecular_data_creation() {
        let mol_data = MolecularData::new(3, 10, 30);
        assert_eq!(mol_data.natoms, 3);
        assert_eq!(mol_data.nelec, 10);
        assert_eq!(mol_data.nbasis, 30);
    }

    #[test]
    fn test_gw_results_creation() {
        let results = GWResults::new(10);
        assert_eq!(results.qp_energies.len(), 10);
        assert_eq!(results.z_factors.len(), 10);
        assert!(!results.converged);
    }

    #[test]
    fn test_bse_results_creation() {
        let results = BSEResults::new(5);
        assert_eq!(results.excitation_energies.len(), 5);
        assert_eq!(results.oscillator_strengths.len(), 5);
    }

    #[test]
    fn test_checkpoint_manager_creation() {
        let manager = CheckpointManager::new("/tmp/checkpoints".to_string());
        assert_eq!(manager.checkpoint_dir, "/tmp/checkpoints");
        assert_eq!(manager.frequency, 10);
    }
}
