patchsim 0.1.0__tar.gz

patchsim-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
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+*.vscode
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+# C extensions
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+.installed.cfg
+*.egg
+MANIFEST
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+pytest_cache/
+
+# Translations
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+# Django stuff:
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+# Environments
+.env
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+env.bak/
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+# Data file types
+*.csv
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+*.xlsx
+output/**
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+# Keep package template scaffold files tracked
+!src/patchsim/templates/project/data/
+!src/patchsim/templates/project/data/networks/
+!src/patchsim/templates/project/data/networks/*.csv
+!src/patchsim/templates/project/data/patch/
+!src/patchsim/templates/project/data/patch/*.csv
+!src/patchsim/templates/project/data/seeds/
+!src/patchsim/templates/project/data/seeds/*.csv
+!src/patchsim/templates/project/output/.gitkeep
+
+# Additions for GeoJSON, .zip files, and shapefiles
+*.geojson
+*.zip
+*.shp
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+*.prj
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+.pdm-build/
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+# Exception for .png files in assets/
+!assets/*.png
+
+# Allow tracked data CSVs
+!data/
+!data/networks/
+!data/networks/*.csv
+
+!data/patch/
+!data/patch/*.csv
+
+!data/seeds/
+!data/seeds/*.csv

patchsim-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.1.0] - 2026-08-22
+
+### Added
+
+- Configuration-selectable adaptive ODE and deterministic explicit-Euler solvers that
+  share reporting grids and derivative logic.
+- Validated distance- and gravity-based spatial contact generation with explicit units,
+  normalization settings, and a physical-validation report.
+- Generic within-patch group stratification using modeller-supplied interaction matrices.
+- Seeded first-order and total-order Sobol sensitivity studies with verified artifact
+  reuse and compact provenance.
+- Bounded multi-start least-squares calibration for prepared observations, including
+  optional population-conserving fitted initial states and local diagnostics.
+- A side-effect-free `patchsim.simulate()` API for external analysis and fitting code.
+- SIS model template, complete workflow documentation, and the JOSS manuscript source.
+
+### Changed
+
+- SALib is available through the optional `analysis` dependency group rather than the
+  base simulation installation.
+- Run artifacts identify the selected solver, and the CLI exposes validation, contact
+  generation, sensitivity, and calibration workflows.
+- Documentation now states the implemented network orientation, transition semantics,
+  solver behavior, validation limits, and artifact contracts.
+- **Breaking:** `NetworkModel.simulate_discrete()` uses each interval's width and rejects
+  invalid time grids or divergent steps instead of assuming unit spacing.
+- **Breaking:** transition expressions reject floor division and modulo because they
+  introduce discontinuities into rate arithmetic.
+
+### Security
+
+- Transition rate expressions are now parsed and evaluated against an arithmetic-only
+  allowlist instead of `eval`. Expressions come from user-supplied YAML, and configs are
+  shared as self-contained project directories, so a config could previously execute
+  arbitrary code when a simulation was run.
+
+### Fixed
+
+- Rate expressions that overflow, divide by zero, or produce a complex value are now
+  rejected instead of returning `inf` or a complex number into the simulation.
+- Rate expressions accept numpy scalars of any dtype; previously only `float64` worked,
+  because it is the one numpy type that subclasses Python's `float`.
+- Patch-specific parameter overrides now affect CLI ODE runs instead of being parsed
+  and ignored.
+- Model validation rejects global or patch-specific parameter names that duplicate a
+  compartment name.
+- Explicit-Euler roundoff checks scale with each compartment update rather than unrelated
+  population magnitudes.
+
+## 0.1.0b1 - 2026-04-08
+
+### Added
+- Config-relative path resolution for `PatchFile`, `SeedFile`, `NetworkFile`, and `OutputDir`.
+- Built-in YAML model templates for `sir`, `seir`, and `sirs` under package templates.
+- `list-models` now reports both Python reference models and YAML templates.
+
+### Changed
+- Validation now checks transition source/target compartments explicitly.
+- Validation now checks transition expression identifiers against `compartments ∪ Parameters`.
+- Compartment source-of-truth reconciled: when `compartments` is provided in config, it must match `SeedFile` columns.
+- Package metadata updated to `Development Status :: 4 - Beta`.
+- Runtime dependencies now include conservative minimum version floors.
+
+### Removed
+- Removed unused `patchsim.utils.loader` module and its documentation reference.

patchsim-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use PatchSim, please cite the software using this metadata."
+type: software
+title: "PatchSim: a modular simulation framework for patch-based metapopulation epidemiology"
+version: 0.1.0
+abstract: >-
+  PatchSim is a Python framework for simulating compartmental infectious disease
+  dynamics across spatial patches and optional population groups.
+authors:
+  - family-names: Illikkal
+    given-names: Adish Assain
+    orcid: "https://orcid.org/0009-0001-1009-4560"
+    affiliation: "AI and Robotics Technology Park (ARTPARK), Indian Institute of Science, Bengaluru, India"
+  - family-names: Mukherjee
+    given-names: Shreya
+    orcid: "https://orcid.org/0009-0008-3629-0376"
+    affiliation: "AI and Robotics Technology Park (ARTPARK), Indian Institute of Science, Bengaluru, India"
+  - family-names: S
+    given-names: Sneha
+    orcid: "https://orcid.org/0009-0009-1854-6443"
+    affiliation: "AI and Robotics Technology Park (ARTPARK), Indian Institute of Science, Bengaluru, India"
+repository-code: "https://github.com/dsih-artpark/patchsim"
+url: "https://patchsim.readthedocs.io/"
+license: GPL-3.0-only
+keywords:
+  - epidemiology
+  - metapopulation
+  - compartmental models
+  - spatial networks