mxlpy 0.17.0__py3-none-any.whl → 0.19.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (32) hide show
  1. mxlpy/__init__.py +14 -4
  2. mxlpy/experimental/diff.py +1 -1
  3. mxlpy/fit.py +173 -7
  4. mxlpy/identify.py +7 -1
  5. mxlpy/integrators/int_assimulo.py +10 -3
  6. mxlpy/integrators/int_scipy.py +7 -3
  7. mxlpy/label_map.py +3 -1
  8. mxlpy/meta/codegen_latex.py +1 -1
  9. mxlpy/meta/source_tools.py +1 -1
  10. mxlpy/model.py +146 -87
  11. mxlpy/nn/__init__.py +24 -5
  12. mxlpy/nn/_keras.py +85 -0
  13. mxlpy/nn/_torch.py +76 -15
  14. mxlpy/npe/__init__.py +21 -16
  15. mxlpy/npe/_keras.py +326 -0
  16. mxlpy/npe/_torch.py +73 -148
  17. mxlpy/plot.py +196 -52
  18. mxlpy/sbml/_export.py +8 -1
  19. mxlpy/surrogates/__init__.py +25 -17
  20. mxlpy/surrogates/_keras.py +137 -0
  21. mxlpy/surrogates/_poly.py +19 -8
  22. mxlpy/surrogates/_qss.py +31 -0
  23. mxlpy/surrogates/_torch.py +51 -127
  24. mxlpy/symbolic/symbolic_model.py +2 -2
  25. mxlpy/types.py +57 -114
  26. {mxlpy-0.17.0.dist-info → mxlpy-0.19.0.dist-info}/METADATA +27 -28
  27. mxlpy-0.19.0.dist-info/RECORD +54 -0
  28. mxlpy-0.19.0.dist-info/licenses/LICENSE +21 -0
  29. mxlpy/nn/_tensorflow.py +0 -0
  30. mxlpy-0.17.0.dist-info/RECORD +0 -51
  31. mxlpy-0.17.0.dist-info/licenses/LICENSE +0 -674
  32. {mxlpy-0.17.0.dist-info → mxlpy-0.19.0.dist-info}/WHEEL +0 -0
{mxlpy-0.17.0.dist-info → mxlpy-0.19.0.dist-info}/METADATA RENAMED
@@ -1,17 +1,17 @@
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  Metadata-Version: 2.4
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  Name: mxlpy
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- Version: 0.17.0
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+ Version: 0.19.0
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  Summary: A package to build metabolic models
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  Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
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  Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
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- License-Expression: GPL-3.0-or-later
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+ License-Expression: MIT
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  License-File: LICENSE
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  Keywords: metabolic,modelling,ode
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  Classifier: Development Status :: 5 - Production/Stable
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  Classifier: Environment :: Console
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  Classifier: Intended Audience :: Developers
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  Classifier: Intended Audience :: Science/Research
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- Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
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+ Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: MacOS
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  Classifier: Operating System :: Microsoft :: Windows
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  Classifier: Operating System :: OS Independent
@@ -24,6 +24,7 @@ Classifier: Topic :: Software Development
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  Requires-Python: >=3.12
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  Requires-Dist: dill>=0.3.9
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  Requires-Dist: latexify-py>=0.4.4
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+ Requires-Dist: lazy-import>=0.2.2
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  Requires-Dist: matplotlib>=3.9.2
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  Requires-Dist: mike>=2.1.3
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  Requires-Dist: more-itertools>=10.5.0
@@ -41,20 +42,10 @@ Requires-Dist: tabulate>=0.9.0
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  Requires-Dist: toml>=0.10.2
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  Requires-Dist: tqdm>=4.66.6
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  Requires-Dist: typing-extensions>=4.12.2
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- Provides-Extra: dev
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- Requires-Dist: coverage>=7.6.4; extra == 'dev'
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- Requires-Dist: jupyter>=1.1.1; extra == 'dev'
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- Requires-Dist: mkdocs-jupyter>=0.25.1; extra == 'dev'
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- Requires-Dist: mkdocs-material>=9.5.42; extra == 'dev'
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- Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
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- Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
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- Requires-Dist: pyright>=1.1.387; extra == 'dev'
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- Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
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- Requires-Dist: pytest>=8.3.3; extra == 'dev'
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- Requires-Dist: requests>=2.32.3; extra == 'dev'
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- Requires-Dist: ruff>=0.7.1; extra == 'dev'
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- Requires-Dist: ssort>=0.13.0; extra == 'dev'
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- Requires-Dist: toml-sort<0.24,>=0.23.1; extra == 'dev'
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+ Provides-Extra: keras
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+ Requires-Dist: keras>=3.9.2; extra == 'keras'
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+ Provides-Extra: tensorflow
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+ Requires-Dist: tensorflow>=2.19.0; extra == 'tensorflow'
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  Provides-Extra: torch
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  Requires-Dist: torch>=2.5.1; extra == 'torch'
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  Description-Content-Type: text/markdown
@@ -67,7 +58,7 @@ Description-Content-Type: text/markdown
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  [![pypi](https://img.shields.io/pypi/v/mxlpy.svg)](https://pypi.python.org/pypi/mxlpy)
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  [![docs][docs-badge]][docs]
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- ![License](https://img.shields.io/badge/license-GPL--3.0-blue?style=flat-square)
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+ ![License](https://img.shields.io/badge/license-MIT-blue?style=flat-square)
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  ![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fgist.github.com%2Fmarvinvanaalst%2F98ab3ce1db511de42f9871e91d85e4cd%2Fraw%2Fcoverage.json&query=%24.message&label=Coverage&color=%24.color&suffix=%20%25)
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  [![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)
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  [![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
@@ -78,22 +69,34 @@ Description-Content-Type: text/markdown
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  ## Installation
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- You can install mxlpy using pip: `pip install mxlpy`
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+ You can install mxlpy using pip: `pip install mxlpy`.
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+
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+ Due to their sizes, the machine learning are optional dependencies. You cann install them using
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+
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+ ```shell
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+ # One of them respectively
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+ pip install mxlpy[torch]
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+ pip install mxlpy[tensorflow]
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+ pip install mxlpy[keras]
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+
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+ # together
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+ pip install mxlpy[torch, tensorflow, keras]
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+ ```
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  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.
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  ```bash
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  pixi init
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  pixi add python assimulo
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- pixi add --pypi mxlpy[torch]
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+ pixi add --pypi mxlpy
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  ```
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  ## How to cite
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- If you use this software in your scientific work, please cite [this article](...):
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+ If you use this software in your scientific work, please cite [this article](https://doi.org/10.1101/2025.05.06.652335):
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- - [doi](https://doi.org/)
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- - [bibtex file](https://fillme.out)
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+ - [doi](https://doi.org/10.1101/2025.05.06.652335)
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+ - [bibtex file](https://github.com/Computational-Biology-Aachen/MxlPy/citation.bibtex)
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  ## Development setup
@@ -103,7 +106,7 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
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  ### uv
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  - Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
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- - Run `uv sync --extra dev --extra torch` to install dependencies locally
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+ - Run `uv sync --all-extras --all-groups` to install dependencies locally
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  ### pixi
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@@ -111,7 +114,3 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
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  - Run `pixi install --frozen`
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- ## Notes
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-
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- - `uv add $package`
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- - `uv add --optional dev $package`
mxlpy-0.19.0.dist-info/RECORD ADDED
@@ -0,0 +1,54 @@
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+ mxlpy/__init__.py,sha256=ODndmfAX0zFTSqK1kVQN2s4W3FDqxuu5Mvf1pnv0IdE,4421
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+ mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
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+ mxlpy/fit.py,sha256=WNg98wW47xkd4gNEgj3t8eNNTqfVpHEJTbXMRQBe22o,12457
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+ mxlpy/fns.py,sha256=VxDDyEdtGD7fEoT5LiiEaRqFk-0fIunRXHr1dCMpCdE,14002
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+ mxlpy/identify.py,sha256=veYYCjTDAlzibrWtciX2egfEWWgosOpqgLBgbfVj42g,2130
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+ mxlpy/label_map.py,sha256=_bStQJtQ4RlmTQyrW34W62pyXFF_XFVbTXv-ybdly0s,17816
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+ mxlpy/linear_label_map.py,sha256=DqzN_akacPccZwzYAR3ANIdzAU_GU6Xe6gWV9DHAAWU,10282
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+ mxlpy/mc.py,sha256=oYd8a3ycyZLyh-ZxTYUjDRNfsCcwSQaLWssxv0yC5Cc,17399
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+ mxlpy/mca.py,sha256=1_qBX9lHI6svXSebtwvMldAMwPlLqMylAPmxMbMQdWw,9359
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+ mxlpy/model.py,sha256=ykdFmh7AejqN8qJUXddc9tFVhDWED4CZ8QgRyyCrmK0,60784
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+ mxlpy/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
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+ mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
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+ mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
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+ mxlpy/plot.py,sha256=MiV2Oi5kvI04VjjWiiVbAzRCGaZWue58_hQIRGzS4ik,28879
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+ mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ mxlpy/report.py,sha256=ZwnjquPAvo4A8UqK-BT19SZFSEUOy1FALqoh7uTmbAI,7793
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+ mxlpy/scan.py,sha256=FBPpjv66v4IWZ5OwG_EWUdrucLWR9gq_XEsLFC-otaw,18969
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+ mxlpy/simulator.py,sha256=9Ne4P5Jrwgx4oAlljPvCqSCCy98_5Lv1B87y1AkbI4c,21041
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+ mxlpy/types.py,sha256=swhRTCRNbmI8-2Z3Y0YA9QkxrTxwzYJlMz2qFcfpRsA,12698
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+ mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
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+ mxlpy/experimental/diff.py,sha256=cxr3GkZOkhUaWDj1eXHbjKSVKciGIp_IUf7Jkh0FdEE,8968
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+ mxlpy/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
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+ mxlpy/integrators/int_assimulo.py,sha256=H092idSPeFkPKAOVbr8M8iGdDpfc-MlPeDvh3-tP4rY,5013
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+ mxlpy/integrators/int_scipy.py,sha256=87nAVMY0DLQ_RAIDNa7pN6Xw8NFv5ifyZd8EmPT9rgY,4649
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+ mxlpy/meta/__init__.py,sha256=Jyy4063fZy6iT4LSwjPyEAVr4N_3xxcLc8wDBoDPyKc,278
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+ mxlpy/meta/codegen_latex.py,sha256=OjDgfRRvibs9Bg75J_FSl9fh_MTs8Vqu4Wm9L2JTOCk,19982
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+ mxlpy/meta/codegen_modebase.py,sha256=_ZAW4NvXhKwJQLGz5hkwwZpL2JMAJlfG-GUWkYIiNvw,3124
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+ mxlpy/meta/codegen_py.py,sha256=xSdeuEGPGc-QKRMgJO4VSPGMlxCPEV5prkKjNQ2D2hg,3483
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+ mxlpy/meta/source_tools.py,sha256=GSSFgH2lZ24e6eQxJ-lx4WSwawoPYdIwj_klt5Kr0h8,13464
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+ mxlpy/nn/__init__.py,sha256=Qjr-ERsY2lbD75sFBOhCUwEasQDSJKcpBn_kReLZ6oA,633
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+ mxlpy/nn/_keras.py,sha256=wffBYvQDNGp5me6x2yW4EwpKsnMojCJbXHfKE156a-w,2175
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+ mxlpy/nn/_torch.py,sha256=Omq7iMx2kbUXht2It-egiIYT2DzLGPbkpTCX-h17teI,5752
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+ mxlpy/npe/__init__.py,sha256=hBHCUD2JYDBBGS2kTY8mTCfWB3u1R7m5l--wUupZt6o,1270
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+ mxlpy/npe/_keras.py,sha256=ytvXMPK9KUCGOzTQm08_SgafiMb-MOIUdZQV7JjAO40,9721
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+ mxlpy/npe/_torch.py,sha256=v3joh6lFJJxvYJj--wzmKXL9UMTaIN3h6hPNq0uX9NU,11250
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+ mxlpy/sbml/__init__.py,sha256=AS7IwrBzBgN8coUZkyBEtiYa9ICWyY1wzp1ujVm5ItA,226
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+ mxlpy/sbml/_data.py,sha256=XwT1sSxn6KLTXYMbk4ORbEAEgZhQDBfoyrjMBDAoY_s,1135
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+ mxlpy/sbml/_export.py,sha256=4tU3SVxfEvl0E1urZWHyphkiAeH5HeRO1cODvvrczAQ,20342
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+ mxlpy/sbml/_import.py,sha256=5odQBdpD93mQJp2bVIabmPo6NK60nxqrdSVB8fEsF_A,22099
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+ mxlpy/sbml/_mathml.py,sha256=bNk9RQ_NQFDhY1R354p-gwqqHaIiyAwZ1xLPHHhiguQ,24436
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+ mxlpy/sbml/_name_conversion.py,sha256=XK9DEyzhrD0GBBwwjK9RA0yORrDX5c-Uvx0VtKMR5rA,1325
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+ mxlpy/sbml/_unit_conversion.py,sha256=dW_I6_Ou09ccwnp6LIdrPriIQnQUK5lJcjzM2Fawm6U,1927
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+ mxlpy/surrogates/__init__.py,sha256=cz9qr0ToYSutIK45IvKrMe1mPP7Lj0I_V0HYGixfpZU,916
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+ mxlpy/surrogates/_keras.py,sha256=y4nW626Nr4OQrTdZneDf-Ox2sKmqKmGmEbjpuQMEl10,3816
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+ mxlpy/surrogates/_poly.py,sha256=qhwiWMQsQGq6qBEzagR-riM7Yp33FilsudMkGZ7mkEU,3598
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+ mxlpy/surrogates/_qss.py,sha256=q-CoULIntdXclArm7eHGHlZpgBKQmJrZ0ZaG2Q3B_Pg,712
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+ mxlpy/surrogates/_torch.py,sha256=lGKjLgHmUsD0iAbKzQUeKfN8C88ChQPg1pqidiYucWg,6315
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+ mxlpy/symbolic/__init__.py,sha256=3hQjCMw8-6iOxeUdfnCg8449fF_BRF2u6lCM1GPpkRY,222
49
+ mxlpy/symbolic/strikepy.py,sha256=UMx2LMRwCkASKjdCYEvh9tKlW9dk3nDoWM9NNJXWL_8,19960
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+ mxlpy/symbolic/symbolic_model.py,sha256=lxkDW7L00Og_8Rwf7j0Gek0nQxRu7kyboioY4ZUqfx0,2435
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+ mxlpy-0.19.0.dist-info/METADATA,sha256=YValpHti39pA32FnMfkI0zLgmD7yVG8M_WGWNytSrm8,4307
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+ mxlpy-0.19.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
53
+ mxlpy-0.19.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
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+ mxlpy-0.19.0.dist-info/RECORD,,
mxlpy-0.19.0.dist-info/licenses/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ MIT License
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+
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+ Copyright (c) [2025] [Marvin van Aalst, Anna Matuszyńska]
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
mxlpy/nn/_tensorflow.py DELETED
File without changes
mxlpy-0.17.0.dist-info/RECORD DELETED
@@ -1,51 +0,0 @@
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- mxlpy/__init__.py,sha256=lGo7XQTVuR1p8rW1J6gZsgdQWRqfYa9AWbvZQwT8oLQ,4236
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- mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
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- mxlpy/fit.py,sha256=LwSoLfNVrqSlTtuUApwH36LjzGU0HLs4C_2qqTTjXFE,7859
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- mxlpy/fns.py,sha256=VxDDyEdtGD7fEoT5LiiEaRqFk-0fIunRXHr1dCMpCdE,14002
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- mxlpy/identify.py,sha256=af52SCG4nlY9sSw22goaIheuvXR09QYK4ksCT24QHWI,1946
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- mxlpy/label_map.py,sha256=urv-QTb0MUEKjwWvKtJSB8H2kvhLn1EKfRIH7awQQ8Y,17769
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- mxlpy/linear_label_map.py,sha256=DqzN_akacPccZwzYAR3ANIdzAU_GU6Xe6gWV9DHAAWU,10282
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- mxlpy/mc.py,sha256=oYd8a3ycyZLyh-ZxTYUjDRNfsCcwSQaLWssxv0yC5Cc,17399
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- mxlpy/mca.py,sha256=1_qBX9lHI6svXSebtwvMldAMwPlLqMylAPmxMbMQdWw,9359
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- mxlpy/model.py,sha256=H1rAKaB5pAQcMuBh5GnXuBReADTx5IDa1x0CdUZ6VlI,58411
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- mxlpy/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
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- mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
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- mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
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- mxlpy/plot.py,sha256=4uu-6d8LH-GWX-sG_TlSpkSsnikv1DLTtnjJzA7nuRA,24670
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- mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- mxlpy/report.py,sha256=ZwnjquPAvo4A8UqK-BT19SZFSEUOy1FALqoh7uTmbAI,7793
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- mxlpy/scan.py,sha256=FBPpjv66v4IWZ5OwG_EWUdrucLWR9gq_XEsLFC-otaw,18969
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- mxlpy/simulator.py,sha256=9Ne4P5Jrwgx4oAlljPvCqSCCy98_5Lv1B87y1AkbI4c,21041
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- mxlpy/types.py,sha256=fB8-oTJkIpkGP0affoVx1ak2zOuTpT6xH-w62oSJxiU,14814
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- mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
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- mxlpy/experimental/diff.py,sha256=4bztagJzFMsQJM7dlun_kv-WrWssM8CIw7gcL63hFf8,8952
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- mxlpy/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
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- mxlpy/integrators/int_assimulo.py,sha256=TCBWQd558ZeRdBba1jCNsFyLBOssKvm8dXK36Aqg4_k,4817
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- mxlpy/integrators/int_scipy.py,sha256=dFHlYTeb2zX97f3VuNdMJdI7WEYshF4JAIgprKKk2z4,4581
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- mxlpy/meta/__init__.py,sha256=Jyy4063fZy6iT4LSwjPyEAVr4N_3xxcLc8wDBoDPyKc,278
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