Abstract We present \code{WGQED1D}, a lightweight, validated Python toolkit for microscopic simulation of single-photon scattering by
N two-level atoms in a one-dimensional bidirectional waveguide. The toolkit implements the standard non-Hermitian effective Hamiltonian on the single-excitation manifold, with bidirectional dipole--dipole interactions mediated by retarded photon exchange, together with the input--output relation needed to reconstruct the output field. A careful microscopic calibration
β=OD/(2N) between optical depth and per-atom waveguide-coupling efficiency is required for quantitative agreement with the free-space Beer--Lambert limit; we verify this calibration to better than
0.1% on a representative range of optical depths. The implementation is deterministic in the single-excitation subspace, runs in
O(N2) memory and
O(N2) operations per timestep, and produces converged results for realistic atomic ensembles (
N∼200--
1000) in seconds to minutes on a laptop. We document the model, implementation, and three validations: (i) pulse-averaged Beer--Lambert transmission across $\OD\in[0.25,3]$; (ii) the Wiseman--Steinberg weak-value formula $\tauT = \langle\tauG\rangle_{\rm post}$ for the post-selected atomic excitation time; and (iii) direct comparison with recent experimental data from the Angulo et al.\ measurement of negative atomic excitation time [Phys.\ Rev.\ Lett.\ \textbf{136}, 153601 (2026)]. The toolkit provides a reproducible numerical platform for studies of weak measurement, anomalous dispersion, group delay, and post-selected observables in single-photon transmission through optically thick atomic clouds. The source code is openly available under the MIT license.