sund 2.0.0__tar.gz

sund-2.0.0/LICENSE.md

@@ -0,0 +1,65 @@
+# Licenses
+
+The SUND package is distributed under the MIT License.
+
+Copyright (c) 2025 The SUND toolbox developers.
+
+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.
+
+This package includes code provided under permissive licenses. 
+
+## The SUNDIALS package
+
+SUNDIALS, written by the Lawrence Livermore National Security and Southern Methodist University, is included as a library in this project. SUNDIALS is available at: https://computing.llnl.gov/projects/sundials
+
+## Licenses for included libraries
+<details><summary>SUNDIALS</summary>
+
+Full license available in src/sund/third_party/sundials/LICENSE
+
+BSD 3-Clause License
+
+Copyright (c) 2002-2024, Lawrence Livermore National Security and Southern Methodist University.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+</details>

sund-2.0.0/MANIFEST.in

@@ -0,0 +1,110 @@
+# Include project metadata
+include pyproject.toml
+include README.md
+include LICENSE.md
+
+# Exclude stuff not needed by end users
+prune docs
+prune overrides
+prune tests
+prune dist
+global-exclude .gitlab-ci.yml
+exclude .gitmodules
+exclude pytest.ini
+exclude mkdocs.yml
+exclude .mike.json
+exclude tox.ini
+exclude Dockerfile
+exclude uv.lock
+
+# Include all C/C++ source files and headers
+recursive-include src/_core/_Activity *.cpp *.h
+recursive-include src/_core/_debug *.cpp *.h
+recursive-include src/_core/_Models *.cpp *.h
+recursive-include src/_core/_Simulation *.cpp *.h
+recursive-include src/_core/_StringList *.cpp *.h
+recursive-include src/_core/ExtraFormulas *
+recursive-include src/_core/include *.h
+recursive-include src/_core/sund_sundials *.cpp *.h
+
+recursive-include src/sund/_model_deps *.h *.cpp *.c
+
+# Include Sundials source code, but first remove the 
+#prune src/third_party/sundials
+
+# Include Sundials headers
+recursive-include src/third_party/sundials/include/cvode *.h
+recursive-include src/third_party/sundials/include/ida *.h
+recursive-include src/third_party/sundials/include/sundials *.h
+recursive-include src/third_party/sundials/include/sunlinsol *.h
+recursive-include src/third_party/sundials/include/sunmatrix *.h
+recursive-include src/third_party/sundials/include/sunnonlinsol *.h
+include src/third_party/sundials/include/nvector/nvector_serial.h
+
+# Include Sundials source files
+# CVODE files
+include src/third_party/sundials/src/cvode/cvode.c
+include src/third_party/sundials/src/cvode/cvode_bandpre.c
+include src/third_party/sundials/src/cvode/cvode_bbdpre.c
+include src/third_party/sundials/src/cvode/cvode_diag.c
+include src/third_party/sundials/src/cvode/cvode_fused_stubs.c
+include src/third_party/sundials/src/cvode/cvode_io.c
+include src/third_party/sundials/src/cvode/cvode_ls.c
+include src/third_party/sundials/src/cvode/cvode_nls.c
+include src/third_party/sundials/src/cvode/cvode_proj.c
+recursive-include src/third_party/sundials/src/cvode *.h
+
+# IDA files
+include src/third_party/sundials/src/ida/ida.c
+include src/third_party/sundials/src/ida/ida_bbdpre.c
+include src/third_party/sundials/src/ida/ida_ic.c
+include src/third_party/sundials/src/ida/ida_io.c
+include src/third_party/sundials/src/ida/ida_ls.c
+include src/third_party/sundials/src/ida/ida_nls.c
+recursive-include src/third_party/sundials/src/ida *.h
+
+# NVECTOR files
+include src/third_party/sundials/src/nvector/serial/nvector_serial.c
+
+# SUNDIALS core files
+include src/third_party/sundials/src/sundials/sundials_band.c
+include src/third_party/sundials/src/sundials/sundials_context.c
+include src/third_party/sundials/src/sundials/sundials_dense.c
+include src/third_party/sundials/src/sundials/sundials_direct.c
+include src/third_party/sundials/src/sundials/sundials_errors.c
+include src/third_party/sundials/src/sundials/sundials_hashmap.c
+include src/third_party/sundials/src/sundials/sundials_iterative.c
+include src/third_party/sundials/src/sundials/sundials_linearsolver.c
+include src/third_party/sundials/src/sundials/sundials_logger.c
+include src/third_party/sundials/src/sundials/sundials_math.c
+include src/third_party/sundials/src/sundials/sundials_matrix.c
+include src/third_party/sundials/src/sundials/sundials_nonlinearsolver.c
+include src/third_party/sundials/src/sundials/sundials_nvector.c
+include src/third_party/sundials/src/sundials/sundials_nvector_senswrapper.c
+include src/third_party/sundials/src/sundials/sundials_version.c
+recursive-include src/third_party/sundials/src/sundials *.h
+
+# SUNLINSOL files
+include src/third_party/sundials/src/sunlinsol/band/sunlinsol_band.c
+include src/third_party/sundials/src/sunlinsol/dense/sunlinsol_dense.c
+include src/third_party/sundials/src/sunlinsol/pcg/sunlinsol_pcg.c
+include src/third_party/sundials/src/sunlinsol/spbcgs/sunlinsol_spbcgs.c
+include src/third_party/sundials/src/sunlinsol/spfgmr/sunlinsol_spfgmr.c
+include src/third_party/sundials/src/sunlinsol/spgmr/sunlinsol_spgmr.c
+include src/third_party/sundials/src/sunlinsol/sptfqmr/sunlinsol_sptfqmr.c
+recursive-include src/third_party/sundials/src/sunlinsol *.h
+
+# SUNMATRIX files
+include src/third_party/sundials/src/sunmatrix/band/sunmatrix_band.c
+include src/third_party/sundials/src/sunmatrix/dense/sunmatrix_dense.c
+include src/third_party/sundials/src/sunmatrix/sparse/sunmatrix_sparse.c
+recursive-include src/third_party/sundials/src/sunmatrix *.h
+
+# SUNNONLINSOL files
+include src/third_party/sundials/src/sunnonlinsol/newton/sunnonlinsol_newton.c
+include src/third_party/sundials/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c
+recursive-include src/third_party/sundials/src/sunnonlinsol *.h
+
+# Housekeeping
+exclude .gitignore
+global-exclude *.py[cod] __pycache__ *.so *.dylib *.dll *.DS_Store

sund-2.0.0/PKG-INFO

@@ -0,0 +1,131 @@
+Metadata-Version: 2.4
+Name: sund
+Version: 2.0.0
+Summary: A simulation toolbox for ODE and DAE systems, with focus on systems biology applications.
+Author: ISB group @ Linköping University, Sasan Keshmiri, Gustav Magnusson
+Author-email: William Lövfors <william.lovfors@liu.se>, Henrik Podéus <henrik.podeus.derelov@liu.se>
+Maintainer-email: William Lövfors <william.lovfors@liu.se>, Henrik Podéus <henrik.podeus.derelov@liu.se>
+License-Expression: MIT
+Project-URL: Homepage, https://isbgroup.eu/sund-toolbox
+Project-URL: Repository, https://gitlab.liu.se/ISBgroup/projects/sund
+Keywords: sund,simulation,ODE,DAE,modeling,toolbox,systems biology
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy>=2.0
+Requires-Dist: setuptools>=80.0
+Dynamic: license-file
+
+# SUND toolbox
+
+<img src="./logo/SUND_logo.png"
+     alt="SUND logo"
+     style="max-height:300px;width:100%;width:auto;display:block;margin:0 auto 1rem;" />
+
+SUND (Simulation Using Nonlinear Dynamic models) is a Python package for high‑level, object‑oriented modeling and fast simulation of ODE/DAE systems with complex time‑dependent inputs and hierarchical model structures. Models compile against a SUNDIALS backend for performance and can be seamlessly connected by declaring inputs and outputs.
+
+Supported Python: 3.10–3.14 on Linux (x86_64), Windows (x86_64) and macOS (Intel & ARM).
+
+## Requirements
+
+A C++ compiler (GCC, Clang, or MSVC) is required to install SUND and to compile models for efficient simulations. Pre-built wheels are not provided, as model compilation is performed locally. Ensure your system has a working C++ compiler before installing.
+
+## Install
+
+From PyPI (recommended once published) or local source:
+
+```bash
+pip install sund   # or: uv add sund
+```
+
+### Not on PyPI yet?
+
+While the project is pending publication on PyPI you can install directly from the release archives hosted at:
+
+<https://isbgroup.eu/sund-toolbox/releases/>
+
+Latest build:
+
+```bash
+pip install https://isbgroup.eu/sund-toolbox/releases/sund-latest.tar.gz
+```
+
+Specific version (example):
+
+```bash
+pip install https://isbgroup.eu/sund-toolbox/releases/sund-2.0.0.tar.gz
+```
+
+Install from a built local source distribution (after `uv build --sdist`):
+
+```bash
+pip install dist/sund-<version>.tar.gz
+```
+
+## Quick start
+
+Create, install and simulate a trivial model:
+
+```python
+import sund
+
+# 1. Generate a template model file
+sund.save_model_template("example_model.txt", model_name="Example")
+
+# 2. Install (compiles → C extension module under sund/models)
+sund.install_model("example_model.txt")
+
+# 3. Load an instance
+model = sund.load_model("Example")
+
+# 4. Simulate (time vector in model time unit; default from template is 's')
+sim = sund.Simulation(models=[model], time_vector=[0, 1, 2, 3], time_unit=model.time_unit)
+sim.simulate()
+
+print(sim.feature_values)  # numpy array of outputs/features
+```
+
+See the docs for activities (time‑varying inputs), multiple models, events, validation.
+
+## Documentation
+
+Full user & API docs: <https://isbgroup.eu/sund-toolbox> (versioned; latest alias always points to newest release).
+
+## Model validation (optional)
+
+Validate a model file or content before installing:
+
+```python
+import sund
+results = sund.validate_model_file("example_model.txt", verbose=True)
+```
+
+## Development
+
+Developer & maintainer details (architecture, CI publishing, docs versioning, release steps) live in `DEVELOPMENT.md`.
+
+## History
+
+Origins, milestones, and design context: see `docs/history.md` (versioned site History page). 
+
+## License
+
+MIT License (see `LICENSE.md`). Includes bundled SUNDIALS (BSD 3‑Clause) – see license file for details.
+
+## Citation
+
+If you use SUND in academic work, please cite the project (formal citation text will be added once available).
+
+## Getting help
+
+Open an issue or start a discussion on the project GitLab. Bug reports with a minimal reproducer and model snippet are appreciated.

sund-2.0.0/README.md

@@ -0,0 +1,103 @@
+# SUND toolbox
+
+<img src="./logo/SUND_logo.png"
+     alt="SUND logo"
+     style="max-height:300px;width:100%;width:auto;display:block;margin:0 auto 1rem;" />
+
+SUND (Simulation Using Nonlinear Dynamic models) is a Python package for high‑level, object‑oriented modeling and fast simulation of ODE/DAE systems with complex time‑dependent inputs and hierarchical model structures. Models compile against a SUNDIALS backend for performance and can be seamlessly connected by declaring inputs and outputs.
+
+Supported Python: 3.10–3.14 on Linux (x86_64), Windows (x86_64) and macOS (Intel & ARM).
+
+## Requirements
+
+A C++ compiler (GCC, Clang, or MSVC) is required to install SUND and to compile models for efficient simulations. Pre-built wheels are not provided, as model compilation is performed locally. Ensure your system has a working C++ compiler before installing.
+
+## Install
+
+From PyPI (recommended once published) or local source:
+
+```bash
+pip install sund   # or: uv add sund
+```
+
+### Not on PyPI yet?
+
+While the project is pending publication on PyPI you can install directly from the release archives hosted at:
+
+<https://isbgroup.eu/sund-toolbox/releases/>
+
+Latest build:
+
+```bash
+pip install https://isbgroup.eu/sund-toolbox/releases/sund-latest.tar.gz
+```
+
+Specific version (example):
+
+```bash
+pip install https://isbgroup.eu/sund-toolbox/releases/sund-2.0.0.tar.gz
+```
+
+Install from a built local source distribution (after `uv build --sdist`):
+
+```bash
+pip install dist/sund-<version>.tar.gz
+```
+
+## Quick start
+
+Create, install and simulate a trivial model:
+
+```python
+import sund
+
+# 1. Generate a template model file
+sund.save_model_template("example_model.txt", model_name="Example")
+
+# 2. Install (compiles → C extension module under sund/models)
+sund.install_model("example_model.txt")
+
+# 3. Load an instance
+model = sund.load_model("Example")
+
+# 4. Simulate (time vector in model time unit; default from template is 's')
+sim = sund.Simulation(models=[model], time_vector=[0, 1, 2, 3], time_unit=model.time_unit)
+sim.simulate()
+
+print(sim.feature_values)  # numpy array of outputs/features
+```
+
+See the docs for activities (time‑varying inputs), multiple models, events, validation.
+
+## Documentation
+
+Full user & API docs: <https://isbgroup.eu/sund-toolbox> (versioned; latest alias always points to newest release).
+
+## Model validation (optional)
+
+Validate a model file or content before installing:
+
+```python
+import sund
+results = sund.validate_model_file("example_model.txt", verbose=True)
+```
+
+## Development
+
+Developer & maintainer details (architecture, CI publishing, docs versioning, release steps) live in `DEVELOPMENT.md`.
+
+## History
+
+Origins, milestones, and design context: see `docs/history.md` (versioned site History page). 
+
+## License
+
+MIT License (see `LICENSE.md`). Includes bundled SUNDIALS (BSD 3‑Clause) – see license file for details.
+
+## Citation
+
+If you use SUND in academic work, please cite the project (formal citation text will be added once available).
+
+## Getting help
+
+Open an issue or start a discussion on the project GitLab. Bug reports with a minimal reproducer and model snippet are appreciated.

sund-2.0.0/pyproject.toml

@@ -0,0 +1,161 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "numpy>=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sund"
+version = "2.0.0"
+description = "A simulation toolbox for ODE and DAE systems, with focus on systems biology applications."
+authors = [
+    {name = "ISB group @ Linköping University"},
+    { name = "William Lövfors", email = "william.lovfors@liu.se" },
+    { name = "Henrik Podéus", email = "henrik.podeus.derelov@liu.se"},
+    { name = "Sasan Keshmiri"},
+    { name = "Gustav Magnusson"},
+]
+maintainers = [
+    { name = "William Lövfors", email = "william.lovfors@liu.se" },
+    { name = "Henrik Podéus", email = "henrik.podeus.derelov@liu.se"},
+]
+readme = "README.md"
+requires-python = ">=3.10"
+license = "MIT"
+license-files = ["LICENSE.md"]
+dependencies = [
+    "numpy>=2.0",
+    "setuptools>=80.0",
+]
+keywords = ["sund", "simulation", "ODE", "DAE", "modeling", "toolbox", "systems biology"]
+urls = { Homepage = "https://isbgroup.eu/sund-toolbox", Repository = "https://gitlab.liu.se/ISBgroup/projects/sund"}
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+]
+
+[tool.setuptools]
+packages = ["sund", "sund._model_deps", "sund._model_deps._include", "sund._model_deps._src"] # Setuptools note: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages.
+package-dir = { "" = "src" }
+include-package-data = true
+
+[tool.setuptools.package-data]
+"sund" = ["_model_deps/**/*"]
+
+[project.scripts]
+sund-cleanup = "sund.uninstall_helper:cleanup_package_generated_files"
+
+[dependency-groups]
+dev = [
+    "matplotlib>=3.9.4",
+    "mike>=2.1.3",
+    "mkdocs>=1.5.3",
+    "mkdocs-include-markdown-plugin>=4.0.4",
+    "mkdocs-jupyter>=0.25.1",
+    "mkdocs-material>=9.2.7",
+    "mkdocstrings[python]>=0.29.1",
+    "mkdocstrings-python>=1.1.2",
+    "pytest>=8.3.5",
+    "scipy>=1.13.1",
+    "tox-uv>=1.25.0",
+    "ruff>=0.11.11",
+    "sund",
+    "mkdocs-glightbox>=0.5.1",
+    "twine>=6.2.0",
+    "pre-commit>=4.3.0",
+]
+
+[tool.ruff]
+lint.select = ["ALL"]
+lint.ignore = [
+    "D",       # pydocstyle – don't require docstrings yet
+    "ANN",     # type annotations – skip for now
+    "PLR2004", # magic values in conditionals – too noisy
+    # "T201"     # allow `print()` – useful for quick scripts
+]
+
+# Optional but recommended rule groups
+lint.extend-select = [
+  "I",     # isort – organizes imports
+  "F",     # pyflakes – general error checking
+  "E",     # pycodestyle – PEP8 enforcement
+  "B",     # flake8-bugbear – common bug risks
+  "C4",    # flake8-comprehensions – simplify comprehensions
+  "SIM",   # flake8-simplify – cleaner Python
+  "PERF",  # perflint – performance suggestions
+]
+exclude = [
+    "src/third_party",  # Exclude third-party code
+    "tests/test_remove_comments.py"
+]
+
+# Ruff configuration
+line-length = 100
+target-version = "py314"
+
+# Per-file ignore for test code
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = [
+    "D",    # pydocstyle – don't require docstrings in tests
+    "S101", # Allow `assert` in tests
+    "E501",  # Disable line-length enforcement (we'll control this via formatter)
+    "T201", # Allow `print()` in tests
+    "PLR0913", # Allow many arguments in test functions
+    "C416", # Allow comprehensive list testing
+    "S301", # Allow pickling in tests
+]
+"docs/examples/*" = [
+    "T201", # Allow `print()` in examples
+    "ERA001", # Allow having comments in to explain the code (allows all commented lines)
+    "SIM108", # Allow block if-cases in examples
+]
+"src/sund" = [
+    "ERA001", # Allow having comments in the main code (allows all commented lines)
+]
+ignore = ["COM812"] # trailing comma formatting can conflict with Ruff's own formatter
+
+# Ruff formatter (replaces Black)
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+line-ending = "auto"
+
+[tool.tox]
+requires = ["tox>=4.19", "tox-uv>=1.25.0"] # load tox-uv in tox's own env
+env_list = ["py310", "py311", "py312", "py313", "py314"]
+isolated_build = true
+skip_missing_interpreters = true
+
+[tool.tox.env_run_base]
+description = "Run test with pytest under {base_python}"
+deps = ["pytest>=8.3.5"]
+commands = [
+    ["pytest", "-m", "uninstall"], 
+    ["pytest", "-m", "not performance and not uninstall"],
+]
+
+[tool.tox.env.py310]
+base_python = ["python3.10"]
+
+[tool.tox.env.py311]
+base_python = ["python3.11"]
+
+[tool.tox.env.py312]
+base_python = ["python3.12"]
+
+[tool.tox.env.py313]
+base_python = ["python3.13"]
+
+[tool.tox.env.py314]
+base_python = ["python3.14"]
+
+[tool.uv.sources]
+sund = { workspace = true }
+
+

sund-2.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+