Update to v0.7.3

Added type hinting and mypy testing

Update to v0.7.1

MANTIS 0.7.1 introduces official Sphinx and Read the Docs documentation integration alongside comprehensive docstring cleanups across the codebase. This release reorganizes the tutorial suite into two modular guides (Tutorial_1 for fundamentals and setup, and Tutorial_2 for advanced multi-element isotopes and carbonate chemistry), adds $^{13}\text{C}$ carbon isotope tracking to the calcite dissolution benchmark model, updates CI actions to v6, and includes full regression benchmark datasets and tests for the Luff & Wallmann (2003) model.

Update to v0.7.0

MANTIS 0.7.0 introduces multi-element isotope tracking with automated element grouping (derive_isotope_species_maps), allowing concurrent tracking of multi-isotope systems (e.g., $^{13}\text{C}$ and $^{34}\text{S}$) within combined reaction cascades. This release replaces iterative fixed-point speciation with a vectorized 1D Newton-Raphson solver in $\ln([\text{H}^+])$ for robust and rapid carbonate speciation convergence, adds explicit zero-, first-, and second-order reaction kinetic support, and expands declarative plotting with composite species evaluation (e.g. $\text{CaCO}_3$ and $\text{POC}$) and custom styling for measured benchmark data (measured_data_as). Furthermore, MANTIS 0.7.0 adds the Luff & Wallmann (2003) carbonate dissolution benchmark, coupled C–S isotope models, and updates core dependencies with scipy >= 1.18.1 and official Python 3.15 CI support.

Update to 0.6.0

MANTIS 0.6.0 introduces mixed-phase sorption modeling with dynamic partitioning ($f_{\text{dis}}$) across solid, dissolved, and bio-irrigated pools, alongside sediment age-dependent reaction rate scaling. This release significantly expands declarative plotting capabilities with automated Pint-based unit conversions for concentrations, reaction rates, and solid-phase metrics ($\text{wt}%$ and $\mu\text{mol}/\text{g}_{\text{dry}}$), as well as unit-mapped measured data comparison. It also delivers numerical stability enhancements to carbonate and sulfide speciation loops via under-relaxation, adds the new SimpleFe diagenesis benchmark model (Du et al., 2023) and irrigation examples with regression tests, and includes a rewritten comprehensive tutorial (docs/Tutorial_new.md).

Update to 0.5.0

MANTIS 0.5.0 streamlines model setup with automatic reaction isotope species mapping (derive_isotope_species_map), removing the need to manually declare isotope dictionaries in reaction files. This release centralizes and automates rate constant unit conversions in diff_lib via pint with clear filename and line-number error reporting. Additionally, it introduces full support for reaction-free, purely diffusive simulations (reactions=None) with context-aware pH validation, equilibrium isotope fractionation in declarative speciation blocks, a new mantis_create_examples CLI scaffolding command, a minimal basic_transport_and_reaction starter template, and enhanced depth-scale customization in declarative plotting.

Update to v0.4.0

MANTIS 0.4.0 introduces a fully declarative plotting layout engine with automatic shared color palettes and solid weight-percent conversions, a unified speciation framework and strict schema validator (species_parser.py) supporting flexible alkalinity contributions (include_in_TA), and a multi-section spatial grid generator (grid_setup). This release also brings steady-state sediment age modeling (compute_sediment_age()), exponential biodiffusion profiles, Free vs. Total pH scale conversions, fractional trust-region Newton step limiting with line search safeguards.

maintenance release to 0.3.1

Fixed CI issues

v0.3.0

MANTIS 0.3.0 Release Notes

MANTIS 0.3.0 introduces preliminary support marine carbonate equilibrium chemistry calculations, species-agnostic equation and analytical SymPy Jacobian generation, multi-isotope companion cross-derivatives, and calcite precipitation/dissolution dynamics.

Highlights

• Marine Carbonate Equilibrium Chemistry (seawater_carbonate.py):
  • Implements consensus oceanographic formulations (Lueker et al. 2000, Mucci 1983, Millero 1995, Ingle 1975, UNESCO 1981 density) calculating stoichiometric constants ($K_1^, K_2^, K_{\text{sp}}'$) and calcite saturation state ($\Omega$) as functions of temperature, salinity, and pressure.
  • Complete thermodynamic speciation ($[\text{CO}_2^*], [\text{HCO}_3^-], [\text{CO}_3^{2-}]$) from any parameter pair: pH & DIC, pH & TA, or DIC & TA.
  • Automatic boundary condition checking and porewater equilibrium initialization (adjust_omega=True) with solid calcite ($\text{CaCO}_3$).
  • Gated behind carbonate_equilibrium_chemistry in model.configure() to keep non-carbonate models isolated from side effects.
• Species-Agnostic SymPy Analytical Jacobian Generator:
  • Replaced hardcoded species logic with generalized phase permutations (liquid_to_liquid, solid_to_liquid, liquid_to_solid, solid_transformation) and automated SymPy differentiation for chemical Jacobians.
  • Speciation factors and equilibrium partitioning are now dynamically inferred from species.py metadata.
• Multi-Isotope Cross-Derivatives & Coupling:
  • Full analytical cross-derivatives for companion isotope species scaled by reactant isotope ratios, preventing numerical ratio divergence at sharp fronts across all isotope systems (S, C, N, O).
  • Added multi-species pooled delta calculations via get_total_delta().
• Calcite Reactions & Diagnostics:
  • Added dedicated calcite precipitation and dissolution kinetics with smooth saturation transitions, coupled to TA and DIC in the chemical Jacobian.
  • Added prefill=True species option to initialize porewater profiles directly from boundary concentrations.
• Smart Timestamp-Aware Equation Rebuilding:
  • Automatic cache invalidation and equation regeneration when any core MANTIS library source file is updated.