mxlpy 0.22.0__py3-none-any.whl → 0.23.0__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 (28) hide show
  1. mxlpy/__init__.py +11 -2
  2. mxlpy/carousel.py +6 -4
  3. mxlpy/compare.py +2 -2
  4. mxlpy/integrators/__init__.py +4 -0
  5. mxlpy/integrators/int_assimulo.py +3 -3
  6. mxlpy/integrators/int_diffrax.py +119 -0
  7. mxlpy/integrators/int_scipy.py +12 -6
  8. mxlpy/label_map.py +1 -2
  9. mxlpy/mc.py +22 -22
  10. mxlpy/mca.py +8 -4
  11. mxlpy/meta/codegen_model.py +2 -1
  12. mxlpy/meta/codegen_mxlpy.py +194 -58
  13. mxlpy/meta/source_tools.py +124 -80
  14. mxlpy/meta/sympy_tools.py +5 -5
  15. mxlpy/model.py +288 -91
  16. mxlpy/plot.py +16 -14
  17. mxlpy/sbml/_export.py +13 -5
  18. mxlpy/sbml/_import.py +68 -547
  19. mxlpy/scan.py +38 -242
  20. mxlpy/simulator.py +4 -359
  21. mxlpy/types.py +655 -83
  22. mxlpy/units.py +5 -0
  23. {mxlpy-0.22.0.dist-info → mxlpy-0.23.0.dist-info}/METADATA +4 -1
  24. {mxlpy-0.22.0.dist-info → mxlpy-0.23.0.dist-info}/RECORD +26 -27
  25. mxlpy/sbml/_mathml.py +0 -692
  26. mxlpy/sbml/_unit_conversion.py +0 -74
  27. {mxlpy-0.22.0.dist-info → mxlpy-0.23.0.dist-info}/WHEEL +0 -0
  28. {mxlpy-0.22.0.dist-info → mxlpy-0.23.0.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-0.23.0.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: 0.23.0
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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>=0.2.0
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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
{mxlpy-0.22.0.dist-info → mxlpy-0.23.0.dist-info}/RECORD RENAMED
@@ -1,36 +1,37 @@
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- mxlpy/__init__.py,sha256=GlBZ-WmSoMgVIeAyVqtEJiRe_jLar84bjbg_FlAr2vw,4477
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- mxlpy/carousel.py,sha256=o72YKzfPCDhT5oHhow4oNvIShG-i3-Z0UMEQLt2iE5A,4699
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- mxlpy/compare.py,sha256=PJbb_R9GTGrkcEpGNpUfwZpZbUmZHNjsMQ_5qPAxVNo,7746
1
+ mxlpy/__init__.py,sha256=XQc1WNOxUzRbM8s7hO4p6r7dFsru0BCcedJITawqIo0,4574
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+ mxlpy/carousel.py,sha256=nYWEdxDd7lm5INfZjpwaEhYqysg9e4EH9Ubcl6bPca8,4721
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+ mxlpy/compare.py,sha256=o-tUxHJrzzVsQkiKPCFD_4bpqsWrvBMyOPoBQ1Dl420,7746
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  mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
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  mxlpy/fit.py,sha256=3hGUqJ2tOOToZLMMaJw5M9b6_UlUJwT_MhUvfPmRBd8,22355
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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=kNzqDVp5X6T4uod-y79d6cItOd7_9jmpojDA1TSPRoE,17872
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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=AvvnyNIEvaB9gJyd0RtaFs_uVhZ7Xh2FpljHH04YRkc,17217
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- mxlpy/mca.py,sha256=BRNbisYijT2SUT6VdIpIh3Id3VgL3NTtycn0VARDWlE,9375
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- mxlpy/model.py,sha256=GD1FGppxDJwvEx4ehcQeOx3qkqr8PxDTQ0TwoixBvKI,71617
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+ mxlpy/mc.py,sha256=6n6VAuSVcXinqcWxNJAioMYpBmSAB40WItPloK1vmBM,17017
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+ mxlpy/mca.py,sha256=IoOHJbjPnAEDqKk64OjFjgRPX5K_aE9D4RrCJ1xFIkw,9457
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+ mxlpy/model.py,sha256=tAz_Rbe_S1Ho-k_14gBxmE9RMYo2xJUWYkdLYUyMKHg,79072
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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=PA7tAmy2XXACxBLtdnfpxKUFRzi-lnCQjr7gw_nzxKU,32544
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+ mxlpy/plot.py,sha256=oZq8NqycdiJwqEm7FVpNTBkjGYgPBEbqDqZxbrvUtDI,32662
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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=WARFQgFwOsO2PzC1d2rGDfgDjYV8cYwc196IB2rzrzY,19416
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- mxlpy/simulator.py,sha256=so7Dax42EKppeBUTxWWKxYhdAFKS2jAgWzS04fXuFpY,27751
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- mxlpy/types.py,sha256=Z697aAiJ3Dp2nvMvdm60Z8rEhQjKKgrYHa1riZpY-QE,12994
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- mxlpy/units.py,sha256=WHtP9s90VR8rUpPLsQ_eQeiW3wMPEryMvLpsDfu0tEo,1946
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+ mxlpy/scan.py,sha256=DI5R_xKEUV28FTXqxYz41lQFkAXHE41R_S-ztHPeCoM,13676
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+ mxlpy/simulator.py,sha256=NaD0UxvEqiRUp8dZqW4su1Xc9QzHwa9XqGGAIgGV6D0,16559
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+ mxlpy/types.py,sha256=FpNZT5ZkhFHYSVA1LS7eZ3ljpzK0_fHo5h48nregR6w,31440
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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=g5hKvFsEUdEk5OGQ_aQuCxLAnenD_jG4G__EcVfKsx4,9104
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- mxlpy/integrators/__init__.py,sha256=OLdcNCDIOiD1Z2LO143YtD47cMadNJt0app41nLAx5o,456
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- mxlpy/integrators/int_assimulo.py,sha256=8gLR1D4zJ-TnJ9DTkfkqA2uVE0H2w_npZhZ8RoWZOX8,5013
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- mxlpy/integrators/int_scipy.py,sha256=82nU6cN4PjPoTEXSK5GuFxG89EnnKBHbjG8A9YDPKnc,4749
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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=_Bec5aPJ6YyAkxUXlsQtAy_2VzX0tPGVSj-eGACqrXc,404
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  mxlpy/meta/codegen_latex.py,sha256=i4tPvk2-toAYqtf4TynuE9sfUSHUp21AMUgjgFEB0uo,23215
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- mxlpy/meta/codegen_model.py,sha256=LT767mzniKgAAtMTbejGcl6YmivNa3J1wZjEsH6iX9M,5067
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- mxlpy/meta/codegen_mxlpy.py,sha256=Yx6GtsHUup4bIrEyMw9FYE60Y35xAK81IC-r0EdZDEM,3576
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- mxlpy/meta/source_tools.py,sha256=imdNbGfDjmEEI7gLWm3BFUfB1xwhW4Lt6mhKvE0PhLw,20735
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- mxlpy/meta/sympy_tools.py,sha256=TJSCFK9yuxwNrUHbZrcayo_g1UQWmiUiw4Z5V_pUye4,2853
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+ mxlpy/meta/codegen_model.py,sha256=mRpK7pTPYTIMmJAqno7TA6vg5poSQThGWP43_zHU7as,5124
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+ mxlpy/meta/codegen_mxlpy.py,sha256=asXGAY0fr5sUSRw7LlBUoFgTkXcJt9M6LZtVqsiF4RU,7869
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+ mxlpy/meta/source_tools.py,sha256=dqP2dP8OLloBY8pLPuQl2uVB6GfDDn52u8vhPOTei1M,22302
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+ mxlpy/meta/sympy_tools.py,sha256=XaRXdyXiiiOHBXatxoRTRKwy7BaM9I0lL6PE5HP33wE,3016
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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
@@ -39,11 +40,9 @@ 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=yYli7ZQ1_pnH9kt5EmcuHM0moQoa43rrFVdrseXlG0o,1136
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- mxlpy/sbml/_export.py,sha256=DibzxWLsHQeI4rmvhpV0AfbDmud3lIcfcdm5BV51-PE,20538
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- mxlpy/sbml/_import.py,sha256=aCxNKEO6qaZRc7XWFwzOLE1PV0hXFstJbD-SkLjef2k,22082
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- mxlpy/sbml/_mathml.py,sha256=oaU9q5yb9jvDGxDJrqOkbOiurCB1Vv_P99oUwJ7v1VE,24437
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+ mxlpy/sbml/_export.py,sha256=0R34btB5COKD1gsWisdlWdEbJ-BUrjb78s6sWnm5Ph4,20945
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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/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=r2pR3iTJOaMqtATbsCm5CF94TYG9b-9cKljc8kMOplQ,3852
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  mxlpy/surrogates/_poly.py,sha256=z2g3JTdVyQJ8dIiXP4BOun_yMZOrlYpPNvQ0wmFYDTk,3672
@@ -52,7 +51,7 @@ mxlpy/surrogates/_torch.py,sha256=gU0secuRBYgewhNqZmSo6_Xf804dSzwWwIYmdKA7y60,63
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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-0.22.0.dist-info/METADATA,sha256=LsEH4wwslk1cTqQzL_JvkHvPlk5zdfnNebzUzPPhHeY,4601
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- mxlpy-0.22.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- mxlpy-0.22.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
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- mxlpy-0.22.0.dist-info/RECORD,,
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+ mxlpy-0.23.0.dist-info/METADATA,sha256=80ODNl3NCffUmuu_mJmvUmld7uNm390vMtlhNx2Soes,4696
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+ mxlpy-0.23.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ mxlpy-0.23.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
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+ mxlpy-0.23.0.dist-info/RECORD,,