mf6pqc 1.0.0__tar.gz

mf6pqc-1.0.0/CHANGELOG.md

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+# Changelog
+
+## 1.0.0
+
+- Provide SNIA, SIA and Strang coupling with optional porosity, hydraulic
+  conductivity, diffusion and density feedback, and an opt-in thermal pathway.
+
+- Require modflowapi 1.0.1 or a compatible 1.x release.
+- Standard Python logging with opt-in progress messages for library users.
+- Single-source versioning, explicit package contents, build checks and CI.
+- Consistent example layout, portable paths, isolated native verification,
+  import-safe drivers and clean plotting notebooks.
+- Strict integer, schedule, mask, initial-condition and tolerance validation.
+- Native PhreeqcRM status failures become actionable Python exceptions;
+  failures finalize resources and closed instances cannot be reused.
+- Correct geometric TDIS expansion for multipliers close to one; reject
+  unsupported time units and ATS before native initialization.
+- Honor configured chemistry print masks and initial user density.
+- Read calculated density independently of selected output, preserving all columns.
+- Validate serialized metadata and physical fields before writing; write the
+  manifest last and include provenance and explicit time-axis semantics.
+- Retain historical class, constructor, coupling-method and updater imports.
+
+The recorded E13 pH/Ca comparison exceeds its acceptance thresholds; see
+[verification history](docs/release-readiness.md). Version 1.0.0 packaging
+preparation does not constitute a new numerical validation of the examples.
+
+## 0.1.0 — 2026-03-01
+
+- Initial archived release on [Zenodo](https://doi.org/10.5281/zenodo.18822578).

mf6pqc-1.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use MF6PQC, cite the software and the original MODFLOW 6 and PhreeqcRM publications."
+title: "MF6PQC: A Reactive Transport Framework Coupling MODFLOW 6 and PhreeqcRM"
+type: software
+version: 1.0.0
+authors:
+  - family-names: Wang
+    given-names: Zitao
+repository-code: "https://github.com/wangzitao21/mf6pqc"
+license: GPL-3.0-only

mf6pqc-1.0.0/CONTRIBUTING.md

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+# Contributing
+
+Install `python -m pip install -e ".[dev,examples]"` in an isolated environment.
+Run unittest, Ruff lint/format checks, and `python scripts/check_examples.py`
+before submitting changes. Use an appropriate short native case when changing
+numerical behavior; do not launch expensive benchmarks automatically.
+
+Keep the runtime independent of individual case names, repository paths and
+plotting dependencies. Add a regression test for a demonstrated numerical or
+lifecycle failure. State units, array ordering, timestep semantics and state
+ownership whenever an interface changes. Preserve reference inputs and acceptance
+thresholds during refactoring; a changed benchmark definition requires evidence
+and explicit documentation.
+
+Examples follow the shared layout described in `examples/README.md`. Put model
+construction and scientific constants in `modflow_model.py`, orchestration in
+`run.py`, and figures in `plot.ipynb` or `plot.py`. Importing a script must not
+run a simulation or read generated outputs. Clear notebook outputs before commit.
+Generated output and workspaces are never committed.
+
+A pull request should describe the problem, resulting behavior, relevant tests,
+quantitative before/after comparisons, and any unresolved scientific limitation.
+Do not present unrun cases as newly validated. For research use, report both solver
+convergence and comparison against independent evidence.