sbmlsim 0.4.0__tar.gz

sbmlsim-0.4.0/.bumpversion.toml

@@ -0,0 +1,22 @@
+[tool.bumpversion]
+current_version = "0.4.0"
+commit = true
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "./src/sbmlsim/__init__.py"
+
+[[tool.bumpversion.files]]
+filename = "./_docs/_quarto.yml"

sbmlsim-0.4.0/.editorconfig

@@ -0,0 +1,20 @@
+# Editor Configuration (http://editorconfig.org)
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 4
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 88
+
+[*.{json,yml}]
+indent_size = 2
+
+[*.{md,rst}]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

sbmlsim-0.4.0/.github/workflows/main.yml

@@ -0,0 +1,76 @@
+name: CI-CD
+
+on: [push]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest]
+        python-version: ["3.13", "3.14"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install Python dev files (Ubuntu only)
+      run: |
+           if [ "$RUNNER_OS" == "Linux" ]; then
+               sudo add-apt-repository ppa:deadsnakes/ppa && sudo apt-get update && sudo apt-get install -y python${{ matrix.python-version }}-dev
+           fi
+      shell: bash
+
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+
+    - name: Test with tox
+      run:
+        uvx --with tox-uv tox -e py${{ matrix.python-version }}
+
+  release:
+    needs: test
+    if: startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.14"]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/<your-pypi-project-name>
+    permissions:
+      id-token: write
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get tag
+      id: tag
+      run: echo "version=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install hatch twine
+
+    - name: Build package
+      # run: python setup.py sdist bdist_wheel
+      run: hatch build
+    - name: Check the package
+      run: twine check dist/*
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist
+    - name: Create GitHub release
+      uses: softprops/action-gh-release@v1
+      with:
+        body_path: "release-notes/${{ github.ref_name }}.md"
+        draft: false
+        prerelease: false

sbmlsim-0.4.0/.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [push]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3

sbmlsim-0.4.0/.gitignore

@@ -0,0 +1,51 @@
+
+.vscode
+workspace.code-workspace
+.venv
+.idea
+.vscode
+workspace.code-workspace
+uv.lock
+dist
+build
+sbmlsim.egg-info
+cover
+.tox
+.cache
+.coverage
+coverage.xml
+.coverage*
+.benchmark
+*.pyc
+*~
+__pycache__
+src/sbmlsim/comparison/results/amici/
+
+# cached model state
+*.xml.dat
+*.state
+
+.ipynb_checkpoints/
+.pytest_cache
+
+# documentation
+src/sbmlsim/examples/experiments/covid/results/
+src/sbmlsim/examples/experiments/glucose/results/DoseResponseExperiment/DoseResponseExperiment_fig1.svg
+src/sbmlsim/examples/experiments/repressilator/RepressilatorExperiment/RepressilatorExperiment_task_tc.h5
+src/sbmlsim/examples/experiments/midazolam/results/
+src/sbmlsim/examples/experiments/midazolam/results_fit/
+
+# sedml
+src/sbmlsim/combine/examples/results/
+src/sbmlsim/examples/experiments/repressilator/results/
+src/sbmlsim/examples/experiments/covid/results/
+src/sbmlsim/examples/experiments/covid/omex/results/
+src/sbmlsim/examples/experiments/midazolam/results/
+
+src/sbmlsim/combine/results
+src/sbmlsim/combine/examples/l1v4/sbmlsim/
+
+src/sbmlsim/comparison/amicitesting/icg_sd/
+
+/.quarto/
+**/*.quarto_ipynb

sbmlsim-0.4.0/.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+# This is run as a precondition to commits, run manually via `pre-commit run`
+
+# When adding new hooks, it may make sense to once run
+# `pre-commit run --all-files` as by default only changed files are checked
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-yaml
+    description: Check yaml files for parseable syntax
+  - id: check-added-large-files
+    description: Prevent large files from being committed
+  - id: check-merge-conflict
+    description: Check for files that contain merge conflict strings
+  - id: check-symlinks
+    description: Check for symlinks which do not point to anything
+  - id: trailing-whitespace
+    description: Trim trailing whitespaces
+  - id: end-of-file-fixer
+    description: Fix empty lines at ends of files
+  - id: detect-private-key
+    description: Detects the presence of private keys
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.6
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]

sbmlsim-0.4.0/.python-version

@@ -0,0 +1 @@
+3.14

sbmlsim-0.4.0/.quartoignore

@@ -0,0 +1,4 @@
+tests/
+release_notes/
+build/
+**/__pycache__/

sbmlsim-0.4.0/.ruff.toml

@@ -0,0 +1,54 @@
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+target-version = "py313"
+
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = [
+    "F403",   # star imports
+    "F405",   # star imports
+]
+exclude = ["*.ipynb"]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"
+
+[lint.pydocstyle]
+convention = "google"  # Accepts: "google", "numpy", or "pep257".

sbmlsim-0.4.0/.zenodo.json

@@ -0,0 +1,31 @@
+{
+  "upload_type": "software",
+  "title": "sbmlsim: SBML simulation made easy",
+  "creators": [
+    {
+      "orcid": "0000-0003-1725-179X",
+      "affiliation": "Humboldt-University Berlin, Institute for Theoretical Biology, Berlin",
+      "name": "König, Matthias"
+    }
+  ],
+  "description": "<p><code>sbmlsim</code> is a collection of python utilities to simplify simulations with <a href=\"http://www.sbml.org\">SBML</a> models implemented on top of <code><a href=\"http://libroadrunner.org/\">roadrunner</a></code> and other libraries with source code available from <a href=\"https://github.com/matthiaskoenig/sbmlsim\">https://github.com/matthiaskoenig/sbmlsim</a></p>\n<p>Features include among others<ul><li>simulation experiments</li><li>simulation reports</a></li><li>parameter fitting</li></ul></p>\n<p>The documentation is available on <a href=\"https://sbmlsim.readthedocs.io\">https://sbmlsim.readthedocs.io</a></p>\n<p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/sbmlsim/issues\">open an issue</a></p>\n<h2>Funding</h2><p>Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (<strong>LiSyM</strong>, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 <strong><a href=\"https://qualiperf.de\">QuaLiPerF</a></strong> (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)\" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA). Matthias König has received funds from the EOSCsecretariat.eu which has received funding from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.</p>",
+  "access_right": "open",
+  "license": "LGPL-3.0",
+  "keywords": [
+    "modeling",
+    "standardization",
+    "SBML",
+    "SED-ML",
+    "COMBINE"
+  ],
+  "communities": [
+    {
+      "identifier": "eoscsecretariat"
+    }
+  ],
+  "grants": [
+    {
+      "id": "831644"
+    }
+  ]
+}

sbmlsim-0.4.0/LICENSE

@@ -0,0 +1,7 @@
+Copyright (c) 2019-2025 Matthias König
+
+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.

sbmlsim-0.4.0/PKG-INFO

@@ -0,0 +1,116 @@
+Metadata-Version: 2.4
+Name: sbmlsim
+Version: 0.4.0
+Summary: sbmlsim are utilities for the simulation of SBML models.
+Author-email: Matthias König <konigmatt@googlemail.com>
+Maintainer-email: Matthias König <konigmatt@googlemail.com>
+License-File: LICENSE
+Keywords: COMBINE,SBML,modeling,standardization
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.13
+Requires-Dist: altair>=5.5.0
+Requires-Dist: bottleneck>=1.4.2
+Requires-Dist: dill>=0.4.0
+Requires-Dist: jinja2
+Requires-Dist: libroadrunner
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: petab>=0.8.1
+Requires-Dist: pint
+Requires-Dist: pkdb-analysis>=0.3.1
+Requires-Dist: plotly>=6.0.0
+Requires-Dist: psutil>=6.1.1
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: pydoe>=0.3.8
+Requires-Dist: pymetadata>=0.5.10
+Requires-Dist: python-libnuml>=1.1.7
+Requires-Dist: python-libsbml
+Requires-Dist: python-libsedml>=2.0.33
+Requires-Dist: rich
+Requires-Dist: salib>=1.5.2
+Requires-Dist: sbmlutils>=0.9.6
+Requires-Dist: scipy
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: setproctitle>=1.3.4
+Requires-Dist: statsmodels>=0.14.6
+Requires-Dist: sympy
+Requires-Dist: typst>=0.14.5
+Requires-Dist: xarray>=2025.11.0
+Requires-Dist: xmltodict>=0.14.2
+Provides-Extra: dev
+Requires-Dist: bump-my-version>=1.2.4; extra == 'dev'
+Requires-Dist: mypy>=1.18.2; extra == 'dev'
+Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
+Requires-Dist: pytest-cov>=7.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.4.2; extra == 'dev'
+Requires-Dist: quartodoc; extra == 'dev'
+Requires-Dist: ruff>=0.14.0; extra == 'dev'
+Requires-Dist: tox>=4.31.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![](./_docs/images/favicon/sbmlsim-100x100-300dpi.png)
+
+
+# sbmlsim: SBML simulation made easy
+[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg)](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/main.yml)
+[![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
+[![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+
+
+sbmlsim is a collection of python utilities to simplify simulations with
+[SBML](http://www.sbml.org) models implemented on top of
+[roadrunner](http://libroadrunner.org/). Source code is available from
+[https://github.com/matthiaskoenig/sbmlsim](https://github.com/matthiaskoenig/sbmlsim).
+
+Features include among others
+
+- simulation experiments
+- simulation reports
+- parameter fitting
+- sensitivity analysis
+
+Documentation is available from [https://matthiaskoenig.github.io/sbmlsim/](https://matthiaskoenig.github.io/sbmlsim/).
+
+If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
+
+## Installation
+sbmlutils is available from [pypi](https://pypi.python.org/pypi/sbmlsim) and
+can be installed via
+```bash
+pip install sbmlsim
+```
+
+### Develop version
+The latest develop version can be installed via
+```bash
+pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop
+```
+
+## How to cite
+[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+
+## License
+- Source Code: [MIT](https://opensource.org/license/MIT)
+- Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)
+
+## Funding
+Matthias König is supported and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
+"QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection -
+A Systems Medicine Approach)" by grant number 436883643 and by grant number
+465194077 (Priority Programme SPP 2311, Subproject SimLivA).
+
+Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
+within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).
+
+© 2019-2026 Matthias König

sbmlsim-0.4.0/README.md

@@ -0,0 +1,57 @@
+![](./_docs/images/favicon/sbmlsim-100x100-300dpi.png)
+
+
+# sbmlsim: SBML simulation made easy
+[![GitHub Actions CI/CD Status](https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg)](https://github.com/matthiaskoenig/sbmlsim/actions/workflows/main.yml)
+[![Version](https://img.shields.io/pypi/v/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/sbmlsim.svg)](https://pypi.org/project/sbmlsim/)
+[![MIT License](https://img.shields.io/pypi/l/sbmlsim.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+
+
+sbmlsim is a collection of python utilities to simplify simulations with
+[SBML](http://www.sbml.org) models implemented on top of
+[roadrunner](http://libroadrunner.org/). Source code is available from
+[https://github.com/matthiaskoenig/sbmlsim](https://github.com/matthiaskoenig/sbmlsim).
+
+Features include among others
+
+- simulation experiments
+- simulation reports
+- parameter fitting
+- sensitivity analysis
+
+Documentation is available from [https://matthiaskoenig.github.io/sbmlsim/](https://matthiaskoenig.github.io/sbmlsim/).
+
+If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/sbmlsim/issues).
+
+## Installation
+sbmlutils is available from [pypi](https://pypi.python.org/pypi/sbmlsim) and
+can be installed via
+```bash
+pip install sbmlsim
+```
+
+### Develop version
+The latest develop version can be installed via
+```bash
+pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop
+```
+
+## How to cite
+[![DOI](https://zenodo.org/badge/55952847.svg)](https://zenodo.org/badge/latestdoi/55952847)
+
+## License
+- Source Code: [MIT](https://opensource.org/license/MIT)
+- Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)
+
+## Funding
+Matthias König is supported and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
+"QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection -
+A Systems Medicine Approach)" by grant number 436883643 and by grant number
+465194077 (Priority Programme SPP 2311, Subproject SimLivA).
+
+Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
+within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).
+
+© 2019-2026 Matthias König

sbmlsim-0.4.0/RELEASE.md

@@ -0,0 +1,18 @@
+# Release information
+
+## Steps to make a new release
+* update release notes in `release-notes` with commit
+* make sure all tests run (`tox -p`)
+* check formating and linting (`ruff check`)
+* build documentation (`cd _docs | quartodoc build | quatro render`)
+* test bump version (`uvx bump-my-version bump [major|minor|patch] --dry-run -vv`)
+* bump version (`uvx bump-my-version bump [major|minor|patch]`)
+* `git push --tags` (triggers release)
+* `git push`
+
+## Test release
+
+```bash
+uv venv --python 3.14
+uv pip install sbmlsim
+```

sbmlsim-0.4.0/_docs/.gitignore

@@ -0,0 +1,2 @@
+/.quarto/
+**/*.quarto_ipynb

sbmlsim-0.4.0/_docs/README.md

@@ -0,0 +1,18 @@
+# Create documentation
+
+```bash
+cd _docs
+```
+
+quarto add machow/quartodoc
+
+# For deployment
+```bash
+quartodoc build && quarto render
+```
+
+# For development
+```bash
+quartodoc build --watch
+quarto preview
+```

sbmlsim-0.4.0/_docs/_extensions/machow/interlinks/.gitignore

@@ -0,0 +1,3 @@
+*.html
+*.pdf
+*_files/

sbmlsim-0.4.0/_docs/_extensions/machow/interlinks/_extension.yml

@@ -0,0 +1,7 @@
+title: Interlinks
+author: Michael Chow
+version: 1.1.0
+quarto-required: ">=1.2.0"
+contributes:
+  filters:
+    - interlinks.lua