CHANGES.rst

v0.9.0 (2024-04-24)

• Fractional stoichiometries are now officially supported in parser (e.g. Fe2O3.14)
• Complexes/crystal water should now be delimited with '..' (fix by @jeremyagray)
• Unicode printing of subscript decimal point should now work (gh-223, fix by @jeremyagray)
• Substance class now has a __hash__ function (fix by @DNIIBOY)
• Unit per100eV now has correct repr (fix by @daankoning)
• Passing results from balance_stoichiometry into Reaction now works (gh-218, thanks @montmorill)

v0.8.4 (2024-04-24)

• Reverted parsing behavior for crystal water. Use this release to convert to new syntax: NaSO4..10H2O from chempy-0.9+ the following syntax is supported: Fe2O3.14 v0.8.3 had a regression in this respect, see gh-223

v0.8.3

• Fixes for latest version of quantities.
• Build python wheel as part of release script.

v0.8.2

• changed version of dependency "pyodesys"

v0.8.1

• package "jupyter" was listed as formal dependency, now removed.

v0.8.0

• Some minor fixes.
• Updated lowest support versions of a few dependencies.
• Dropped pytest-pep8 for now (unmaintained).

v0.7.12

• Update some heavy elements Uuo -> Og, etc.
• Fix PuLP warning in solve stoichiometry

v0.7.11

• Support for newer version of PuLP when running test suite.

v0.7.10

• Added support for newer SymPy version.

v0.7.9

• Fixed regression in balance_stoichiometry
• More robust expression handling.
• Fixed SyntaxWarning for upcoming CPython 3.8

v0.7.8

• Reaction __init__ got a new kwarg: dont_check
• Fixes to check logic
• Fixes to pretty printing
• ArrheniusParam got a new convenience classmethod: from_rateconst_at_T
• ReactionSystem got a new method: concatenate
• New submodule for template rendering: .util.rendering

v0.7.7

• Fixed a bug in chempy.kinetics.ode._validate
• balance_stoichiometry now is even more allowing with "allow_duplicates"

v0.7.6

• balance_stoichiometry got a new keyword argument "allow_duplicates" (see gh-120)

v0.7.5

• Made chempy.units.to_unitless more strict

v0.7.4

• Fixed bug with quantities.constants when used with Arrhenius class

v0.7.3

• Fixed an issue with PuLP under FreeBSD (gh-109)

v0.7.2

• Fixed bug in Reaction.precipitate_stoich
• Changed Python-3-only syntax to support Python 2
• Python < 3.5 is now deprecated for ChemPy <0.7

v0.7.1

• Updated requirements on upstream packages

v0.7.0

• Drop official support for Python 2.7

v0.6.10

• Fixed bug in Reaction.precipitate_stoich
• Changed Python-3-only syntax to support Python 2

v0.6.8

• Fix use of numpy.linalg.lstsq
• Upper limit on pyodesys (<0.12), chempy 0.7.x will use pyodesys>=0.12

v0.6.7

• Updated manuscript for JOSS.

v0.6.6

• Support for containers in chempy.units.unit_of.
• balance_stoichiometry now correctly find the canonical solution when underdetermined=None is passed.
• chempy.kinetics.integrated was refactored to have more approachable API.

v0.6.5

• Fix assertion firing

v0.6.4

• Enhancements for .units.is_unitless & .units.get_physical_quantity
• New functions in chempy.units: compare_equality & uniform.

v0.6.3

• Fix bug in Reaction.check_consistent_units

v0.6.2

• More relaxed tests with respect to 3rd party programs

v0.6.1

• Extensive test suite in conda package no longer require graphviz & latex

v0.6.0

• balance_stoichiometry now accepts either of True, False, None as underdetermined.
• NameSpace and AttributeContainer are now public in .util.pyutil.
• New printers in chempy.printing, allows user to subclass printers.
• Jupyter Notebook representation of ReactionSystem is now interactive (JavaScript/CSS)
• More data from the literature: water viscosity (chempy.properties.water_viscosity_korson_1969).
• New methods for ReactionSystem: - split: splits reaction-system into disjoint parts - categorize_substances: e.g. "nonparticipating", "unaffected".
• Better documentation throughout.

v0.5.7

• New option in .kinetics._native.get_native: conc_roots

v0.5.6

• New method: ReactionSystem.sort_substances_inplace()
• New patched NumPy "module": .units.patched_numpy
• Updated .util.bkh.integration_with_sliders to be compatible with latest bokeh.

v0.5.5

• Fix non-deterministic ordering of dictionary in get_odesys().

v0.5.4

• Fix to bokeh interface (chempy.util.bkh).

v0.5.3

• Fixes balance_stoichiometry
• Documentation fixes
• More k_fmt & landscape options in .util.table.rsys2pdf_table

v0.5.2

• Fix balance_reacions (non-deterministic ordering could cause endless loop)
• Fix unit scaling of .kinetics.rates.Eyring

v0.5.1

• Moved ReactionSystem to .reactionsystem, (import directly from chempy).
• Steady state analysis
• now in default_units: molar, milli-, micro- & nano-
• CSTR kinetics
• Minor fixes, new notebooks

v0.5.0

• .electrochemistry.nernst_formula - thanks to Adel Qalieh (@adelq)
• moved .util.parsing.number_to_scientific_* to .printing(.numbers)
• Number formatting now handles uncertainties.
• refereence in reimplementations now a dict
• Fixes to .kinetics.ode.get_odesys (refactored)

v0.4.1

• Fixes for enhanced robustness: - .kinetics.ode.get_odesys - .chemistry.as_per_substance_array
• Minor changes.

v0.4.0

• Multiple fixes throughout
• Refactored .equilibria
• .core and .debye_huckel was merged into .electrolytes
• New functions: balance_stoichiometry, mass_fractions
• kwargs one=, exp=, ln= changed throughout to use backend=None (backen=math)
• .chemistry.ArrheniusRate moved (and changed) to .arrhenius.ArrheniusParam
• Equilibrium got a new method: cancel and a new staticmethod: eliminate
• Reaction now raises ValueError if the Reaction has a zero net effect.
• It is now possible to use (parts of) chempy even when only Python stdlib is available
• Substance got a new method: molar_mass, and a two new attributes: unicode_name, html_name
• .util.parsing.to_latex was renamed to formula_to_latex.
• New functions in util.parsing: formula_to_unicode, formula_to_html
• Parsing of crystal water now supported.
• ReactionSystem.__init__ got a new kwarg: substance_factory
• ReactionSystem raises ValueError if it contains duplicate instances of Reaction
• ReactionSystem got new methods: - as_per_substance_dict (inverse of as_per_substance_array) - unimolecular_html_table - bimolecular_html_table
• .kinetics.ode.law_of_mass_action_rates was updated to handle RateExpr
• fix in .properties.sulfuric_acid_density_myhre_1998.density_from_concentration for input with units
• enhancements to .util.deprecation.Deprecation
• .util.stoich.decompose_yields now takes iterable of Reaction instances as second arg.
• .util.table.rsys2tablines now pretty-prints ref={'doi': 'abc123'} too.
• chempy.util.stoich.decompose_yields now takes reactions instead of iterable of dicts (backward incompatible change).

v0.3.5

• More robust setup.py

v0.3.3

• chempy.units.allclose now handles iterables with disparate units.

v0.3.2

• Substance.from_formula now prefers e.g. Fe+3 over Fe/3+, latter deprecated

v0.3.1

• chemistry.Solute deprecated, will be removed in v0.4.0, use chemistry.Species instead
• ReactionSystem now handles "substances" argument more robustely.

v0.3.0

• Signature of chempy.chemistry.Substance changed
• New module chempy.util.parsing, (drop dependency on periodictable)
• EqSystem.root and EqSystem.roots got new kwarg: neqsys_type
• chemistry.Equilibrium learned to handle inactive reactants/products
• chemistry.Reaction dropped kwarg 'k' (deprecated since v0.2.0)

v0.2.0

• Signature of chempy.equilibria.roots, changed.
• Added two new modules: chempy.util.table, chempy.util.graph
• chempy.einstein_smoluchowski added
• Reaction, ReactionSystems now expects stoichs etc. to be given wrt to Substance names.
• Added chempy.chemistry.ArrheniusRate
• EqSystemLog, EqSystemLin -> EqSystem, (NumSysLog, NumSysLin)
• Support for solid phases in equilibria
• Submodules for water properties moved to chempy.properties
• Moved class Equilibrium from .equilibria to .chemistry
• Renamed Reaction.params to Reaction.param
• Added method: Reaction.order()
• Added chempy.properties.sulfuric_acid_density_myhre_1998

v0.1.0

• Initial release