mxlpy 0.22.0__py3-none-any.whl → 0.24.0__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 (34) hide show
  1. mxlpy/__init__.py +13 -6
  2. mxlpy/carousel.py +52 -5
  3. mxlpy/compare.py +15 -2
  4. mxlpy/experimental/diff.py +14 -0
  5. mxlpy/fit.py +20 -1
  6. mxlpy/integrators/__init__.py +4 -0
  7. mxlpy/integrators/int_assimulo.py +3 -3
  8. mxlpy/integrators/int_diffrax.py +119 -0
  9. mxlpy/integrators/int_scipy.py +12 -6
  10. mxlpy/label_map.py +1 -2
  11. mxlpy/mc.py +85 -24
  12. mxlpy/mca.py +8 -4
  13. mxlpy/meta/__init__.py +6 -1
  14. mxlpy/meta/codegen_latex.py +9 -0
  15. mxlpy/meta/codegen_model.py +55 -12
  16. mxlpy/meta/codegen_mxlpy.py +215 -58
  17. mxlpy/meta/source_tools.py +129 -80
  18. mxlpy/meta/sympy_tools.py +12 -6
  19. mxlpy/model.py +314 -96
  20. mxlpy/plot.py +60 -29
  21. mxlpy/sbml/_data.py +34 -0
  22. mxlpy/sbml/_export.py +17 -8
  23. mxlpy/sbml/_import.py +68 -547
  24. mxlpy/scan.py +163 -249
  25. mxlpy/simulator.py +9 -359
  26. mxlpy/types.py +723 -80
  27. mxlpy/units.py +5 -0
  28. {mxlpy-0.22.0.dist-info → mxlpy-0.24.0.dist-info}/METADATA +7 -1
  29. mxlpy-0.24.0.dist-info/RECORD +57 -0
  30. mxlpy/sbml/_mathml.py +0 -692
  31. mxlpy/sbml/_unit_conversion.py +0 -74
  32. mxlpy-0.22.0.dist-info/RECORD +0 -58
  33. {mxlpy-0.22.0.dist-info → mxlpy-0.24.0.dist-info}/WHEEL +0 -0
  34. {mxlpy-0.22.0.dist-info → mxlpy-0.24.0.dist-info}/licenses/LICENSE +0 -0
mxlpy/units.py CHANGED
@@ -36,6 +36,7 @@ from sympy.physics.units import (
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  watt,
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  weber,
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  )
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+ from sympy.physics.units.quantities import Quantity
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  __all__ = [
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  "ampere",
@@ -126,3 +127,7 @@ sievert = joule / kilogram # type: ignore
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  lumen = candela * steradian # type: ignore
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  dimensionless = None
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  item = 1 # pseudounit for one thing
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+
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+ # Plant units
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+ mol_chl = Quantity("mol_chl", abbrev="mol_chl")
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+ mmol_mol_chl = mmol / mol_chl
{mxlpy-0.22.0.dist-info → mxlpy-0.24.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mxlpy
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- Version: 0.22.0
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+ Version: 0.24.0
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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>
@@ -22,6 +22,7 @@ Classifier: Programming Language :: Python :: 3.11
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  Classifier: Topic :: Scientific/Engineering
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  Classifier: Topic :: Software Development
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  Requires-Python: >=3.12
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+ Requires-Dist: diffrax>=0.7.0
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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
@@ -32,6 +33,7 @@ Requires-Dist: numpy>=2.1.2
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  Requires-Dist: pandas>=2.2.3
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  Requires-Dist: parameteriser>=0.1.0
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  Requires-Dist: pebble>=5.0.7
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+ Requires-Dist: pysbml>=0.3.0
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  Requires-Dist: python-libsbml>=5.20.4
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  Requires-Dist: salib>=1.5.1
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  Requires-Dist: scipy>=1.14.1
@@ -42,6 +44,7 @@ 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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+ Requires-Dist: wadler-lindig>=0.1.7
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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
@@ -118,3 +121,6 @@ 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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+ ## LLMs
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+
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+ We support the [llms.txt](https://llmstxt.org/) convention for making documentation available to large language models and the applications that make use of them. It is located at [docs/llms.txt](https://github.com/Computational-Biology-Aachen/MxlPy/tree/main/docs/llms.txt)
mxlpy-0.24.0.dist-info/RECORD ADDED
@@ -0,0 +1,57 @@
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+ mxlpy/__init__.py,sha256=MzR_lZLel95RyWISsF16mDLscGoaw79oD976MFo5_TI,4453
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+ mxlpy/carousel.py,sha256=3M2rqi2bx87y8D-oqEKTKZ6Q_clDQHbdLNdVjLJeO7c,6013
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+ mxlpy/compare.py,sha256=rJPOXc-aX6I1EC3ERAAW5Jn04kMwrlqUqdBgbZa6LA4,8098
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+ mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
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+ mxlpy/fit.py,sha256=UTNvbUcL9mg7NuH5qq3syqpXXqynT_lXmKQudxwWcsE,22880
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+ mxlpy/fns.py,sha256=NLxYwa3ylS7SkISBjw_TgQSKEm7WnkZF9wPigX_ZCAM,13915
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+ mxlpy/identify.py,sha256=G-Zyr_l-K2mDtIV1xGrQ52QJxoBYqRoNA5RW6GpbNjs,2213
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+ mxlpy/label_map.py,sha256=PwYanfg07hC0ayyOOP72RFlCQNvhCTbpOhW6kZZ2GUU,17826
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+ mxlpy/linear_label_map.py,sha256=6Ye6IziWGKkYD_5z3FmTVwnJ2T9SvVGN3U4CfXjXseo,10320
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+ mxlpy/mc.py,sha256=uMHknTNHmK5b4REM3PtCpCjEr9LoSIBsGsCNU4_yHpg,18639
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+ mxlpy/mca.py,sha256=IoOHJbjPnAEDqKk64OjFjgRPX5K_aE9D4RrCJ1xFIkw,9457
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+ mxlpy/model.py,sha256=kjZTQo8yM62JX2GedwTCfxtTQpdprg8vJzgJvp_5XCI,79643
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+ mxlpy/parallel.py,sha256=yLQLw5O4vnPVp_Zmtw1UhPWtB3483foimxQB-TwFKPg,5016
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+ mxlpy/parameterise.py,sha256=IgbvfEnkmaqVq_5GgFjHqApGUN9CJrsVD3Fr7pg9iFA,758
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+ mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
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+ mxlpy/plot.py,sha256=Dng9tyga8xagINQO_OZvjLRoaYGFR8crMljDHrzwEF8,33603
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+ mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ mxlpy/report.py,sha256=v597yzKecgtoNmlNZ_nVhBCa3czNw0tksOK5mLtAQvE,10631
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+ mxlpy/scan.py,sha256=KXFdeWwgUBqJBCiOGDdMAGU5nS3PRVn7Cg0ISpzzK1U,17160
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+ mxlpy/simulator.py,sha256=-jsSP1fEnJnHj1hcj37cAPUyyP57mP_ow2cL-xd9iw8,16699
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+ mxlpy/types.py,sha256=Vg3ekCkhbH8HjqdDTA7vaAdFp9Diney3ARZZfbq0MoA,33475
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+ mxlpy/units.py,sha256=4bKXkCYsONUVWRdzV7aVcWFQSA6sxilebgXXFUEKw_c,2091
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+ mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
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+ mxlpy/experimental/diff.py,sha256=fmsM53lH86TD2iglQILK-XeZnIAtwHAcGC3Afs8V-tc,9457
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+ mxlpy/integrators/__init__.py,sha256=TKo2dkJqdW3_n7YrmF6k3kEjr8_kr3-7MDaLu-zFWRg,533
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+ mxlpy/integrators/int_assimulo.py,sha256=1cvR8cOBdrl_DQs9v0o7wItSG5iyYqwZVh7EO0fg3ro,5021
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+ mxlpy/integrators/int_diffrax.py,sha256=q_8NZgIZ6T-SRRcI8kSjEb6l-DbXqPv6rjj9KApkQac,3326
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+ mxlpy/integrators/int_scipy.py,sha256=xKyisVN1jW5hxmVD2K_RpoQ2MwNrMxSGODsAEgEt6_I,4922
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+ mxlpy/meta/__init__.py,sha256=8-UPZan2pT6RSuN65KC4vV9WPJiAzm2ZsXz3Zu_rmww,475
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+ mxlpy/meta/codegen_latex.py,sha256=Owj5GKDFkiqks2mIDQIXV3M_5TysGwAZgKSq8C3KBIg,23461
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+ mxlpy/meta/codegen_model.py,sha256=FkVrAS7HOyTQPNTItgyo8jjDEylkbETGnxJgRTBDAP4,6722
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+ mxlpy/meta/codegen_mxlpy.py,sha256=FjBw37IqziB4dv5VBAvKenFODfxjJXdW6rQqx9CqYUk,8433
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+ mxlpy/meta/source_tools.py,sha256=e6ufIsBjgde3QuQ9OsAYES0Lib4WALw4E-0wH_2cF6Y,22442
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+ mxlpy/meta/sympy_tools.py,sha256=mWVn63OMeiTmVlV586pXxDa3l-_Pc1VcP1G39vYRGS4,3203
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+ mxlpy/nn/__init__.py,sha256=Qjr-ERsY2lbD75sFBOhCUwEasQDSJKcpBn_kReLZ6oA,633
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+ mxlpy/nn/_keras.py,sha256=-5zjHRu8OjSiZeuBSIZFyB63uBsNNH5o9y4kBcPnhx8,2263
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+ mxlpy/nn/_torch.py,sha256=GUJmLU282VU4O-fs3Sz90SEaAnfuXN2MPlBr_tHmvn4,5775
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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=Mt97CddpLi3wIrA1b_5cagLmDdNxAVF_S7QV57Pzw8s,226
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+ mxlpy/sbml/_data.py,sha256=98w5vyhdOHilD5zjy21XFzam0FlvcW_cb1XRTsIgD_M,2019
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+ mxlpy/sbml/_export.py,sha256=leKf7dFqpoYxO3xFu4j_mM5eAgo-lq__ywADXsmamRU,21008
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+ mxlpy/sbml/_import.py,sha256=_4MR54YyVkIh9eVAiSMd7yijhHC_ds-3v7M_C4Zn8BY,3565
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+ mxlpy/sbml/_name_conversion.py,sha256=93muW47M7qJoE227HKHmThWpPeWsXDN9eM8cRH2pqPs,1340
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+ mxlpy/surrogates/__init__.py,sha256=cz9qr0ToYSutIK45IvKrMe1mPP7Lj0I_V0HYGixfpZU,916
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+ mxlpy/surrogates/_keras.py,sha256=r2pR3iTJOaMqtATbsCm5CF94TYG9b-9cKljc8kMOplQ,3852
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+ mxlpy/surrogates/_poly.py,sha256=z2g3JTdVyQJ8dIiXP4BOun_yMZOrlYpPNvQ0wmFYDTk,3672
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+ mxlpy/surrogates/_qss.py,sha256=9w-hPPhdcwybkyaSX0sIfYfvcKu1U5j4HHj4SlgZcYQ,723
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+ mxlpy/surrogates/_torch.py,sha256=gU0secuRBYgewhNqZmSo6_Xf804dSzwWwIYmdKA7y60,6389
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+ mxlpy/symbolic/__init__.py,sha256=_vM5YM5I6OH0QDbFt9uGYKO8Z5Vly0wbGuvUScVrPRU,258
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+ mxlpy/symbolic/strikepy.py,sha256=tzo3uvPpXLDex09hWTuitVzuTNwbgl7jWGjD8g6a8iI,20033
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+ mxlpy/symbolic/symbolic_model.py,sha256=cKfWoktvFmXjuo8egE7gXKrKBq2iBUiy_BcIKIvvz8A,3026
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+ mxlpy-0.24.0.dist-info/METADATA,sha256=Hqld-ntG-lfZey_b-aHgJo-T8KYylrC-iSf9CxMs-XA,4980
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+ mxlpy-0.24.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ mxlpy-0.24.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
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+ mxlpy-0.24.0.dist-info/RECORD,,