crn-craft 0.2.0__tar.gz

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crn_craft-0.2.0/Cargo.toml

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+[workspace]
+members = ["crates/crn-craft", "crates/crn-craft-cli", "crates/crn-craft-rules"]
+resolver = "3"
+
+[workspace.package]
+version = "0.2.0"
+edition = "2024"
+rust-version = "1.85"
+license = "MIT"
+repository = "https://github.com/dietmarwo/CRN-craft"
+homepage = "https://github.com/dietmarwo/CRN-craft"
+keywords = ["reaction-network", "gillespie", "ssa", "stochastic", "simulation"]
+categories = ["science", "simulation"]
+
+[workspace.dependencies]
+serde = { version = "=1.0.229", features = ["derive"] }
+# float_roundtrip: decimal literals parse to the correctly rounded double.
+serde_json = { version = "=1.0.154", features = ["float_roundtrip"] }
+serde_path_to_error = "=0.1.20"
+schemars = "=0.8.22"
+sha2 = "=0.10.9"
+libm = "=0.2.15"
+rand_chacha = { version = "=0.3.1", default-features = false, features = ["std"] }
+rand_core = { version = "=0.6.4", default-features = false }
+crn-craft = { path = "crates/crn-craft", version = "0.2.0" }
+crn-craft-rules = { path = "crates/crn-craft-rules", version = "0.2.0" }
+
+[workspace.lints.rust]
+unsafe_code = "forbid"

crn_craft-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Dietmar Wolz
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

crn_craft-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: crn-craft
+Version: 0.2.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Dist: numpy>=1.24,<3
+Requires-Dist: scipy==1.17.0 ; extra == 'fit'
+Requires-Dist: fcmaes-rust==0.2.1 ; extra == 'fit'
+Requires-Dist: sqp-craft==0.17.0 ; extra == 'fit'
+Provides-Extra: fit
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Summary: Reproducible well-mixed reaction network simulation and analysis
+Keywords: chemical reaction networks,stochastic simulation,Gillespie,SSA,systems biology,Rust
+License-Expression: MIT
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Documentation, https://github.com/dietmarwo/CRN-craft/blob/main/docs/tutorial.md
+Project-URL: Issues, https://github.com/dietmarwo/CRN-craft/issues
+Project-URL: Changelog, https://github.com/dietmarwo/CRN-craft/blob/main/CHANGELOG.md
+Project-URL: Optimization ecosystem, https://dietmarwo.github.io/optimization-jobs/
+Project-URL: AI agent guide, https://github.com/dietmarwo/CRN-craft/blob/main/docs/ai-context.md
+Project-URL: Repository, https://github.com/dietmarwo/CRN-craft
+
+# CRN-craft
+
+![CRN-craft: chemical reaction networks in native Rust with stochastic simulation](https://raw.githubusercontent.com/dietmarwo/CRN-craft/main/docs/images/crn-craft-banner.jpg)
+
+Reproducible simulation and analysis of well-mixed chemical reaction networks,
+with a native Rust core. Models, requests and results are versioned JSON
+documents with strict input checks, explicit budgets and replayable seeds.
+
+```bash
+pip install crn-craft
+```
+
+Wheels for CPython 3.10 and newer (stable ABI) on Linux x86_64, Windows x64
+and macOS (x86_64 and arm64); other platforms build from the source
+distribution with a Rust toolchain.
+
+## Example
+
+Immigration–death (birth rate 4, death rate 0.2, starting from zero) has a
+Poisson law with mean `20 (1 - exp(-0.2 t))`: 12.64 at t = 5 and 17.29 at
+t = 10.
+
+```python
+import crn_craft as crn
+
+model = crn.load_example("immigration-death")
+request = crn.ssa_spec(
+    model, end=10.0, save_times=[0.0, 5.0, 10.0], replicates=1000, seed=1
+)
+result = crn.simulate_ssa(model, request)
+print(result["sampler"])
+print(result["statistics"]["mean"], result["statistics"]["mean_standard_error"])
+```
+
+```text
+xoshiro256pp-u53/direct_cr/inverse/fast-1
+[[0.0], [12.618], [17.22500000000001]] [[0.0], [0.10959967193421745], [0.13107843665743252]]
+```
+
+Both means lie within one standard error of the exact values. The same seed
+gives the same result on every run and for every thread count.
+
+## What is included
+
+- Exact stochastic simulation: `direct`, `cached_direct`, `direct_cr`,
+  `sorting_direct` and `rssa_cr`, with inverse or Ziggurat waiting times.
+  `fast` (the default) emulates JumpProcesses.jl; `fast=False` selects the
+  checked policy, which rejects lost increments and channels below the 53-bit
+  selection resolution.
+- Prepared simulations and reusable parameter templates for optimization
+  loops (`crn.prepare_ssa`, `crn.prepare_parameters`).
+- Sparse finite state projection (`crn.fsp`), explicitly approximate Poisson
+  leaping (`crn.tau`), network analysis and conservation checks.
+- Strict SBML and BioNetGen import subsets (`crn-craft-import`) and the
+  `crn-craft` command for archives, verification and export.
+- `pip install "crn-craft[fit]"` adds the pinned SciPy, fcmaes-rust and
+  SQP-craft versions used by the fitting examples.
+
+The rules engine for dynamic, attributed species is in the wheel as
+`crn_craft.rules`: prepared parallel ensembles, trackers, event logs and
+callbacks, and the mtDNA methods; see the
+[mtDNA user manual](https://github.com/dietmarwo/CRN-craft/blob/main/docs/mtdna-user-manual.md).
+Its command-line tools (`rules-check`, `rules`) are in the native CLI
+(`cargo install crn-craft-cli --locked`, crates
+[crn-craft](https://crates.io/crates/crn-craft) and
+[crn-craft-rules](https://crates.io/crates/crn-craft-rules)), which installs a
+`crn-craft` command of the same name as the wheel's. The optional diffsol BDF
+integrator with forward sensitivities and the job worker for
+[optimization-jobs](https://github.com/dietmarwo/optimization-jobs) build from
+the repository and are not part of the wheel.
+
+## Documentation
+
+- [Repository and README](https://github.com/dietmarwo/CRN-craft)
+- [Tutorial](https://github.com/dietmarwo/CRN-craft/blob/main/docs/tutorial.md)
+- [Alternative exact SSA methods and the `fast` switch](https://github.com/dietmarwo/CRN-craft/blob/main/docs/alternative-ssa.md)
+- [Optimization tutorials C1–C4](https://github.com/dietmarwo/CRN-craft/blob/main/tutorials/optimization/README.md)
+- [Agent context](https://github.com/dietmarwo/CRN-craft/blob/main/docs/ai-context.md)
+- [Changelog](https://github.com/dietmarwo/CRN-craft/blob/main/CHANGELOG.md)
+
+A successful numerical run is not biological validation. MIT licensed; see
+[THIRD_PARTY_NOTICES.md](https://github.com/dietmarwo/CRN-craft/blob/main/THIRD_PARTY_NOTICES.md)
+for the Ziggurat tables adapted from Julia.
+

crn_craft-0.2.0/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,48 @@
+# Third-party notices
+
+## Exponential Ziggurat sampler
+
+The exponential tables and algorithm in `crates/crn-craft/src/ssa/ziggurat*`
+are adapted from Julia 1.13.3, `stdlib/Random/src/normal.jl`. The adaptation
+uses CRN-craft random streams, explicit work/cancellation checks, iterative
+rejection and strict positive-wait checks; it does not promise Julia RNG replay.
+
+Upstream: https://github.com/JuliaLang/julia/blob/v1.13.3/stdlib/Random/src/normal.jl
+
+MIT License
+
+Copyright (c) 2009-2025: Jeff Bezanson, Stefan Karpinski, Viral B. Shah, and other contributors: https://github.com/JuliaLang/julia/contributors
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+end of terms and conditions
+
+[Julia's LICENSE.md ends with a pointer to its own THIRDPARTY.md, which
+covers other software in the Julia repository; none of it is used here.]
+
+## Optional parameter-optimization references
+
+The isolated `validation/parameter-optimization/worker` workspace uses rebop
+0.10.0 as an optional benchmark reference. Its generated wrappers invoke the
+upstream macro API; it is not a dependency or implementation of the default
+CRN-craft engine. The upstream MIT notice is preserved in
+`validation/parameter-optimization/REBOP_LICENSE.txt`. Cargo.lock pins its
+reference dependencies. Python fcmaes-rust/rebop dependencies are separately
+listed in that directory's requirements file.