modelbase2 0.1.79__tar.gz → 0.3.0__tar.gz

modelbase2-0.3.0/.flake8

@@ -0,0 +1,10 @@
+[flake8]
+max-line-length = 100
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
+ignore = C901, E203, E266, E402, E501, E741, E722, F401, F403, W503, W605, W291
+
+# C901: too complex
+# E203: whitespace before ':'
+# E741: ambiguous variable name
+# W503: line break before binary operator

modelbase2-0.3.0/.gitattributes

@@ -0,0 +1,5 @@
+# proper line endings
+* text=auto eol=lf
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

modelbase2-0.3.0/.gitchangelog.rc

@@ -0,0 +1,29 @@
+# -*- coding: utf-8; mode: python -*-
+
+ignore_regexps = [
+    r'^dev:\s*(chg|fix|new)\s*:',
+    # r'^bot:\s*(chg|fix|new)\s*:',
+]
+
+section_regexps = [
+    ('New',     [r'^((dev|usr|bot)\s*:\s*new\s*:\s*)([^\n]*)$']),
+    ('Changes', [r'^((dev|usr|bot)\s*:\s*chg\s*:\s*)([^\n]*)$']),
+    ('Fix',     [r'^((dev|usr|bot)\s*:\s*fix\s*:\s*)([^\n]*)$']),
+]
+
+
+body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', r'') | strip
+
+subject_process = (
+    strip 
+    | ReSub(r'^((dev|usr|bot)\s*:\s*)(chg|fix|new)\s*:\s*([^\n@]*)(@[a-z]+\s+)*$', r'\4')
+)
+
+tag_filter_regexp = r'^[0-9]+\.[0-9]+(\.[0-9]+)?$'
+
+unreleased_version_label = "(unreleased)"
+
+output_engine = rest_py
+include_merge = True
+
+revs = []

modelbase2-0.3.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+name: "\U0001F41B Bug report"
+about: "Create a report to help us improve"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Bug report
+
+<!-- Before creating a bug report, check if there is already an open issue about the bug -->
+
+**Describe the bug**
+
+<!-- A clear and concise description of what the bug is. -->
+
+**To Reproduce**
+
+<!-- Steps to reproduce the behavior: -->
+
+**Expected behavior**
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+**Screenshots**
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+**Desktop (please complete the following information):**
+
+- OS, version:
+- Environment:
+
+**Additional context**
+
+<!-- Add any other context about the problem or helpful links here. -->

modelbase2-0.3.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,25 @@
+---
+name: "\U0001F680 Feature Request"
+about: "I have a suggestion (and may want to implement it \U0001F642)!"
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request
+
+<!-- Only create a feature request after discussing on modelbase2 discussion forum. A feature report should only be filled for concise, concrete deliverables. Simple suggestions or general features, like "implementing structural identifiability method" should be addressed on the discussion forum and no feature request should be created. Before creating a feature request, check if there is already an open issue about the feature.-->
+
+**Is your feature request related to a problem/ another issue? Please describe.**
+- [ ] Yes: _Please provide a clear and concise description of what the problem is or to what other issue the feature request is linked. If possible use follow [Github's guidance on linking issues to pull requests](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue) to link issues
+- [ ] No: _Why do you consider this feature to be necessary?
+
+**Describe the the feature**
+A clear and concise description of what you want to happen and to be included. Add any considered drawbacks.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Teachability, Documentation, Adoption, Migration Strategy**
+If you can, explain how users will be able to use this and possibly write out a draft for the docs.

modelbase2-0.3.0/.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: ci
+on:
+  push:
+    branches:
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: uv sync --extra dev --extra torch
+      - run: uv run mkdocs gh-deploy --force

modelbase2-0.3.0/.github/workflows/python-publish.yml

@@ -0,0 +1,51 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Build release distribution
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

modelbase2-0.3.0/.gitignore

@@ -0,0 +1,118 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+.ruff_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# vscode
+.vscode/
+
+# temporary files and folders
+*temp*
+tmp
+# pixi environments
+.pixi
+*.egg-info
+
+# copilot
+.github/copilot-instructions.md

modelbase2-0.3.0/.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/hakancelikdev/unexport
+    rev: 0.4.0
+    hooks:
+      - id: unexport
+        exclude: "tests|__init__.py"
+        args: [--refactor]
+
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        files: \.ipynb$
+        stages: [pre-commit]
+        language: system
+        entry: uvx --from nbconvert jupyter-nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+
+  - repo: https://github.com/aio-libs/sort-all
+    rev: v1.3.0
+    hooks:
+      - id: sort-all
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.1
+    hooks:
+      - id: ruff-format

modelbase2-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,17 @@
+All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome.
+In order to contribute:
+
+1. [Fork the project](https://github.com/Computational-Biology-Aachen/modelbase2)
+2. Improve or extend the project
+3. Create unit tests for your added / improved features in the respective [test directory](https://github.com/Computational-Biology-Aachen/modelbase2/tree/main/tests). The old test suite mostly uses the standard [unittest](https://docs.python.org/3/library/unittest.html) library, however new tests are written with [pytest](https://docs.pytest.org/en/latest/). If you are not familiar with pytest you can still use the unittest interface, as pytest supports both test styles.
+4. Create a [pull request](https://docs.github.com/de/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request)
+
+Your work will then be reviewed as soon as possible (suggestions about some changes, improvements or alternatives may be given).
+
+## Coding standards
+
+In order for your improvements to be accepted, please make sure that you added tests in the respective subfolder of the [test directory](https://github.com/Computational-Biology-Aachen/modelbase2/tree/main/tests). 
+We also ask you to write proper documentation in the [NumPy / SciPy style](https://docs.scipy.org/doc/numpy/docs/howto_document.html) and
+that you name your functions according to [pep8](http://pep8.org/). Further, please use the supplied [pre-commit](https://pre-commit.com/) hook, to make sure that your code passes our guidelines.
+
+Thank you for participating!

modelbase2-0.3.0/PKG-INFO

@@ -0,0 +1,93 @@
+Metadata-Version: 2.4
+Name: modelbase2
+Version: 0.3.0
+Summary: A package to build metabolic models
+Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+License-Expression: GPL-3.0-or-later
+License-File: LICENSE
+Keywords: metabolic,modelling,ode
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: OS Independent
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development
+Requires-Python: >=3.12
+Requires-Dist: dill>=0.3.9
+Requires-Dist: latexify-py>=0.4.4
+Requires-Dist: matplotlib>=3.9.2
+Requires-Dist: more-itertools>=10.5.0
+Requires-Dist: numpy>=2.1.2
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: parameteriser>=0.1.0
+Requires-Dist: pebble>=5.0.7
+Requires-Dist: python-libsbml>=5.20.4
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: sympy>=1.13.1
+Requires-Dist: tabulate>=0.9.0
+Requires-Dist: tqdm>=4.66.6
+Requires-Dist: typing-extensions>=4.12.2
+Provides-Extra: dev
+Requires-Dist: coverage>=7.6.4; extra == 'dev'
+Requires-Dist: jupyter>=1.1.1; extra == 'dev'
+Requires-Dist: mkdocs-jupyter>=0.25.1; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.5.42; extra == 'dev'
+Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
+Requires-Dist: mypy>=1.13.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
+Requires-Dist: pyright>=1.1.387; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.3.3; extra == 'dev'
+Requires-Dist: qtbmodels<0.2,>=0.1.0; extra == 'dev'
+Requires-Dist: requests>=2.32.3; extra == 'dev'
+Requires-Dist: ruff>=0.7.1; extra == 'dev'
+Requires-Dist: ssort>=0.13.0; extra == 'dev'
+Requires-Dist: toml-sort<0.24,>=0.23.1; extra == 'dev'
+Provides-Extra: torch
+Requires-Dist: torch>=2.5.1; extra == 'torch'
+Description-Content-Type: text/markdown
+
+# modelbase
+
+## Installation
+
+You can install modelbase using pip: `pip install modelbase2`
+
+If you want access to the sundials solver suite via the [assimulo](https://jmodelica.org/assimulo/) package, we recommend setting up a virtual environment via [pixi](https://pixi.sh/) or [mamba / conda](https://mamba.readthedocs.io/en/latest/) using the [conda-forge](https://conda-forge.org/) channel.
+
+```bash
+pixi init
+pixi add python assimulo
+pixi add --pypi modelbase2
+```
+
+
+## Development setup
+
+You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge, including assimulo)
+
+### uv
+
+- Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
+- Run `uv sync --extra dev --extra torch` to install dependencies locally
+
+### pixi
+
+- Install `pixi` as described in [the docs](https://pixi.sh/latest/#installation)
+- Run `pixi install --frozen`
+
+
+## Notes
+
+- `uv add $package`
+- `uv add --optional dev $package`

modelbase2-0.3.0/README.md

@@ -0,0 +1,34 @@
+# modelbase
+
+## Installation
+
+You can install modelbase using pip: `pip install modelbase2`
+
+If you want access to the sundials solver suite via the [assimulo](https://jmodelica.org/assimulo/) package, we recommend setting up a virtual environment via [pixi](https://pixi.sh/) or [mamba / conda](https://mamba.readthedocs.io/en/latest/) using the [conda-forge](https://conda-forge.org/) channel.
+
+```bash
+pixi init
+pixi add python assimulo
+pixi add --pypi modelbase2
+```
+
+
+## Development setup
+
+You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge, including assimulo)
+
+### uv
+
+- Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
+- Run `uv sync --extra dev --extra torch` to install dependencies locally
+
+### pixi
+
+- Install `pixi` as described in [the docs](https://pixi.sh/latest/#installation)
+- Run `pixi install --frozen`
+
+
+## Notes
+
+- `uv add $package`
+- `uv add --optional dev $package`

modelbase2-0.3.0/changelog.rst

@@ -0,0 +1,2 @@
+Changelog
+=========

modelbase2-0.3.0/citation.bibtex

@@ -0,0 +1,13 @@
+@article{VanAalst2020,
+abstract = {Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies and disease evolution or transmission. Unfortunately, despite community efforts leading to the development of SBML or the BioModels database, many published models have not been fully exploited, largely due to lack of proper documentation or the dependence on proprietary software. To facilitate synergies within the emerging research fields of systems biology and medicine by reusing and further developing existing models, an open-source toolbox that makes the overall process of model construction more consistent, understandable, transparent and reproducible is desired. Results and Discussion We provide here the update on the development of modelbase, a free expandable Python package for constructing and analysing ordinary differential equation-based mathematical models of dynamic systems. It provides intuitive and unified methods to construct and solve these systems. Significantly expanded visualisation methods allow convenient analyses of structural and dynamic properties of the models. Specifying reaction stoichiometries and rate equations, the system of differential equations is assembled automatically. A newly provided library of common kinetic rate laws highly reduces the repetitiveness of the computer programming code, and provides full SBML compatibility. Previous versions provided functions for automatic construction of networks for isotope labelling studies. Using user-provided label maps, modelbase v1.0 streamlines the expansion of classic models to their isotope-specific versions. Finally, the library of previously published models implemented in modelbase is continuously growing. Ranging from photosynthesis over tumour cell growth to viral infection evolution, all models are available now in a transparent, reusable and unified format using modelbase. Conclusion With the small price of learning a new software package, which is written in Python, currently one of the most popular programming languages, the user can develop new models and actively profit from the work of others, repeating and reproducing models in a consistent, tractable and expandable manner. Moreover, the expansion of models to their label specific versions enables simulating label propagation, thus providing quantitative information regarding network topology and metabolic fluxes.},
+author = {van Aalst, Marvin and Ebenh{\"{o}}h, Oliver and Matuszy{\'{n}}ska, Anna},
+doi = {10.1101/2020.09.30.321380},
+issn = {26928205},
+journal = {bioRxiv},
+keywords = {Biomedical systems,Flux analysis,Isotope tracing,Labelling,Mathematical modelling,Metabolic networks,ODE,Research software,Systems biology,Systems medicine},
+pages = {1--15},
+publisher = {BioMed Central},
+title = {{Constructing and analysing dynamic models with modelbase v1.2.3 - a software update}},
+url = {https://doi.org/10.1186/s12859-021-04122-7},
+year = {2020}
+}

modelbase2-0.3.0/docs/assets/00001-sbml-l3v2.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="_case00001" id="case00001" name="case00001" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

modelbase2-0.3.0/docs/assets/00002-sbml-l3v2.xml

@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="_case00002" id="case00002" name="case00002" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.0015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+      <parameter id="k2" name="k2" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="reaction2" name="reaction2" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> S2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>