pysbml 0.1.0__tar.gz

pysbml-0.1.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: "\U0001F41B Bug report"
+about: "Create a report to help us improve"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Bug report

pysbml-0.1.0/.github/ISSUE_TEMPLATE/discussion

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+---
+name: "\U0001F5E8 Discussion"
+about: "Create a discussion"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Discussion

pysbml-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: "I have a suggestion (and may want to implement it \U0001F642)!"
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request

pysbml-0.1.0/.github/copilot-instructions.md

@@ -0,0 +1,9 @@
+Write documentation without type annotations and examples.
+
+Assume that the reader of the documentation has a mathematical background.
+
+Add the type annotation that tests return `None` for generated tests.
+
+Don't comment the code.
+
+Don't give default values in function documentation.

pysbml-0.1.0/.github/pull_request_template.md

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+<!--
+     For Work In Progress Pull Requests, please use the Draft PR feature,
+     see https://github.blog/2019-02-14-introducing-draft-pull-requests/ for further details.
+
+     Before submitting a Pull Request, please ensure you've done the following:
+     - 📖 Read the contribution guideline: https://github.com/Computational-Biology-Aachen/modelbase2/blob/main/CONTRIBUTING.md
+     - 👷‍♀️ Create small PRs. In most cases this will be possible.
+     - ✅ If applicable provide tests for your changes.
+     - 📝 Use descriptive commit messages.
+     - 📗 Update any related documentation and include any relevant screenshots.
+-->
+
+## What type of PR is this? (check all applicable)
+
+- [ ] Refactor
+- [ ] Feature
+- [ ] Bug Fix
+- [ ] Optimization
+- [ ] Documentation Update
+
+## Description
+
+_Please replace this line with a comprehensive description of what changes have been done.
+
+## Related Tickets & Documents
+
+<!--
+For pull requests that relate or close an issue, please include them
+below.  We 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).
+
+For example having the text: "closes #1234" would connect the current pull
+request to issue 1234.  And when we merge the pull request, Github will
+automatically close the issue.
+-->
+
+- Related Issue #
+- Closes #
+
+## QA Instructions, Screenshots, Recordings
+
+_Please replace this line with instructions on how to test your changes.
+
+## Added/updated tests?
+_We encourage you to keep the code coverage percentage at 80% and above._
+
+- [ ] Yes
+- [ ] No, and this is why: _please replace this line with details on why tests
+      have not been included_
+- [ ] I need help with writing tests
+
+## Added/updated documentation
+
+- [ ] Yes
+- [ ] No, and this is why: _please replace this line with details on why documentation has not been updated
+- [ ] I need help with writing documentation
+
+## Checked Coding standard
+- [ ] Named functions according to [pep8](http://pep8.org/)
+- [ ] Used pre-commit [pre-commit](https://pre-commit.com/)
+  
+
+
+

pysbml-0.1.0/.github/workflows/docs.yml

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+name: documentation
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+
+permissions:
+  contents: write
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+
+      - 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 3.12
+
+      - 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 --all-extras --all-groups
+      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV
+      - run: uv run mike deploy --update-aliases --push ${{ env.VERSION }} latest
+      - run: uv run mike set-default --push latest

pysbml-0.1.0/.github/workflows/python-publish.yml

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+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+
+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 3.12
+
+      - 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/

pysbml-0.1.0/.github/workflows/tests.yml

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+name: ci
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  default-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up environment
+        run: uv sync --all-extras --all-groups
+
+      - name: Run tests
+        run: uv run pytest --disable-warnings --cov --cov-report json tests/
+
+      - name: Get coverage value
+        run: python -c "import json; print('COVERAGE={}'.format(json.load(open('coverage.json'))['totals']['percent_covered_display']))" >> $GITHUB_ENV
+
+      - name: Coverage badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: b518d017c83b8938be27036ee04df0e3
+          filename: coverage.json
+          label: Coverage
+          message: ${{ env.COVERAGE }}
+          valColorRange: ${{ env.COVERAGE }}
+          maxColorRange: 100
+          minColorRange: 0

pysbml-0.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# User stuff
+tmp/
+temp/
+*tmp.ipynb
+*temp.ipynb

pysbml-0.1.0/.pre-commit-config.yaml

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+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/astral-sh/uv-pre-commit
+    rev: 0.7.2
+    hooks:
+      - id: uv-lock
+        name: uv-lock
+        stages: [pre-commit]
+        always_run: True
+
+  - 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: v0.11.6
+    hooks:
+      - id: ruff
+        types_or: [python, pyi] # don't fix notebooks
+        args: [--fix]
+      - id: ruff-format

pysbml-0.1.0/.python-version

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+3.12

pysbml-0.1.0/.vscode/settings.json

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+{
+    "python.defaultInterpreterPath": ".venv/bin/python",
+    // "python.defaultInterpreterPath": ".pixi/envs/default/bin/python",
+    "[python]": {
+        "editor.rulers": [
+            88
+        ]
+    },
+    "notebook.output.textLineLimit": 50,
+    "files.exclude": {
+        "**/*.bbl": true,
+        "**/*.blg": true,
+        "**/*.dvi": true,
+        "**/*.fdb_latexmk": true,
+        "**/*.fls": true,
+        "**/*.aux": true,
+        "**/*.synctex.gz": true,
+        "**/*.log": true,
+        "**/*.out": true,
+        "**/*.toc": true,
+        "**/*.lof": true,
+        "**/*.lot": true,
+        "**/*.glsdefs": true,
+        "**/_minted-main": true,
+        "**/*synctex(busy)": true,
+        "**/*.run.xml": true,
+        "**/*.bcf": true,
+        "**/*.mypy_cache": true,
+        "**/*.pytest_cache": true,
+        "**/*.ruff_cache": true,
+        "**/__pycache__": true,
+        "**/*.egg-info": true,
+        // envs
+        "**/*.venv": true,
+        "**/*.pixi": true,
+    },
+}

pysbml-0.1.0/CONTRIBUTING.md

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+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/pysbml)
+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/pysbml/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/mxlpy/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!

pysbml-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) [2025] [Marvin van Aalst]
+
+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.

pysbml-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pysbml
+Version: 0.1.0
+Summary: Add your description here
+Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: python-libsbml>=5.20.4
+Requires-Dist: sympy>=1.14.0
+Description-Content-Type: text/markdown
+
+# pySBML
+
+[![pypi](https://img.shields.io/pypi/v/pysbml.svg)](https://pypi.python.org/pypi/pysbml)
+[![docs][docs-badge]][docs]
+![License](https://img.shields.io/badge/license-MIT-blue?style=flat-square)
+![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fgist.githubusercontent.com%2Fmarvinvanaalst%2Fb518d017c83b8938be27036ee04df0e3%2Fraw%2F77de2288523103b449f89df15b627431bbfdf403%2Fcoverage.json&query=%24.message&label=Coverage&color=%24.color&suffix=%20%25)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
+[![PyPI Downloads](https://static.pepy.tech/badge/pysbml)](https://pepy.tech/projects/pysbml)
+
+[docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
+[docs]: https://computational-biology-aachen.github.io/pysbml/
+
+
+`pySBML` takes SBML models and makes them simpler :heart:
+
+## Installation
+
+Installation is as easy as `pip install pysbml`.
+
+
+## Transform this
+
+**Compartments**
+
+| name | size | is_constant |
+| ---- | ---- | ----------- |
+| C    | 1.0  | True        |
+
+**Variables**
+
+| name | amount | conc    | constant | substance_units | compartment | only_substance_units | boundary_condition |
+| ---- | ------ | ------- | -------- | --------------- | ----------- | -------------------- | ------------------ |
+| S1   | None   | 0.00015 | False    | substance       | C           | False                | False              |
+| S2   | None   | 0.0     | False    | substance       | C           | False                | False              |
+
+**Parameters**
+
+| name | value | is_constant | unit |
+| ---- | ----- | ----------- | ---- |
+| k1   | 1.0   | True        |      |
+
+**Reactions**
+
+| name      | body        | args        | stoichiometry           | local pars |
+| --------- | ----------- | ----------- | ----------------------- | ---------- |
+| reaction1 | C * k1 * S1 | [C, k1, S1] | {'S1': -1.0, 'S2': 1.0} | {}         |
+
+## Into this
+
+
+**Parameters**
+
+| name | value | unit |
+| ---- | ----- | ---- |
+| k1   | 1.0   | None |
+| C    | 1.0   | None |
+
+**Variables**
+
+| name | value   | unit |
+| ---- | ------- | ---- |
+| S1   | 0.00015 | None |
+| S2   | 0.0     | None |
+
+**Reactions**
+
+| name      | fn    | stoichiometry           |
+| --------- | ----- | ----------------------- |
+| reaction1 | S1*k1 | {'S1': -1.0, 'S2': 1.0} |
+
+
+
+## Development setup
+
+We recommend using `uv`
+
+### uv
+
+- Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
+- Run `uv sync --all-extras --all-groups` to install dependencies locally

pysbml-0.1.0/README.md

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+# pySBML
+
+[![pypi](https://img.shields.io/pypi/v/pysbml.svg)](https://pypi.python.org/pypi/pysbml)
+[![docs][docs-badge]][docs]
+![License](https://img.shields.io/badge/license-MIT-blue?style=flat-square)
+![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fgist.githubusercontent.com%2Fmarvinvanaalst%2Fb518d017c83b8938be27036ee04df0e3%2Fraw%2F77de2288523103b449f89df15b627431bbfdf403%2Fcoverage.json&query=%24.message&label=Coverage&color=%24.color&suffix=%20%25)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
+[![PyPI Downloads](https://static.pepy.tech/badge/pysbml)](https://pepy.tech/projects/pysbml)
+
+[docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
+[docs]: https://computational-biology-aachen.github.io/pysbml/
+
+
+`pySBML` takes SBML models and makes them simpler :heart:
+
+## Installation
+
+Installation is as easy as `pip install pysbml`.
+
+
+## Transform this
+
+**Compartments**
+
+| name | size | is_constant |
+| ---- | ---- | ----------- |
+| C    | 1.0  | True        |
+
+**Variables**
+
+| name | amount | conc    | constant | substance_units | compartment | only_substance_units | boundary_condition |
+| ---- | ------ | ------- | -------- | --------------- | ----------- | -------------------- | ------------------ |
+| S1   | None   | 0.00015 | False    | substance       | C           | False                | False              |
+| S2   | None   | 0.0     | False    | substance       | C           | False                | False              |
+
+**Parameters**
+
+| name | value | is_constant | unit |
+| ---- | ----- | ----------- | ---- |
+| k1   | 1.0   | True        |      |
+
+**Reactions**
+
+| name      | body        | args        | stoichiometry           | local pars |
+| --------- | ----------- | ----------- | ----------------------- | ---------- |
+| reaction1 | C * k1 * S1 | [C, k1, S1] | {'S1': -1.0, 'S2': 1.0} | {}         |
+
+## Into this
+
+
+**Parameters**
+
+| name | value | unit |
+| ---- | ----- | ---- |
+| k1   | 1.0   | None |
+| C    | 1.0   | None |
+
+**Variables**
+
+| name | value   | unit |
+| ---- | ------- | ---- |
+| S1   | 0.00015 | None |
+| S2   | 0.0     | None |
+
+**Reactions**
+
+| name      | fn    | stoichiometry           |
+| --------- | ----- | ----------------------- |
+| reaction1 | S1*k1 | {'S1': -1.0, 'S2': 1.0} |
+
+
+
+## Development setup
+
+We recommend using `uv`
+
+### uv
+
+- Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
+- Run `uv sync --all-extras --all-groups` to install dependencies locally

pysbml-0.1.0/docs/assets/00462.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="_case00462" id="case00462" name="case00462" 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="C" name="C" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="C" initialConcentration="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="C" initialConcentration="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> C </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>