PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.3.4

• Removed self-dependency in pyproject.toml.

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.3.3

• Numpy version restriction to <2 removed, as Autograd incompatibility has been resolved.

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.3.2

• Numpy version restricted to <2 to work around Autograd incompatibility (removal of msort function).

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.3

New features

• Added "dlnfCO2_dT" and "dlnpCO2_dT" results, the theoretical effect of temperature on the natural log of ƒCO₂ and pCO₂.
• Added the PLR18 parameterisation of the carbonic acid constants for sea-ice brines.

Default options

• Reverted default opt_k_carbonic to 10 (i.e., LDK00) for consistency with the best practice guide.

Bug fixes

• Updated pyco2.equilibria.p1atm.kH2CO3_NBS_MCHP73 (used for opt_k_carbonic options 6 and 7) to update any salinity values less than 10^–16 to be 10^–16, because zero salinities give a NaN for K₂, which causes problems for Autograd. This should not make any practical difference, because the parameterisation is only valid for salinities above 19.
• Added opt_pressured_kCO2 to results dict and incorporated it correctly into the uncertainty propagation functions.

Technical

• Updated from building with setup.py to pyproject.toml.

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.2

New features

• Added opt_pressured_kCO2 to enable pressure corrections for the fugacity factor and CO₂ solubility constant following W74. These have been added to CO2SYS-MATLAB by Jon Sharp at the same time with consistent results (differences less than 10⁻⁴ %). These pressure corrections are not enabled by default, for consistency with previous versions.

Bug fixes

• Fixed logicals in solve.core() that had meant no results were returned for parameter type combinations 7, 10, 7, 11, 8, 10 and 8, 11.
• Updated Autograd version for compatibility with Python 3.11.

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.1

Breaking changes

• For consistency with other settings, buffers_mode kwarg key changed to opt_buffers_mode and its values are now integers rather than strings.

New features

• Adds new par1_type / par2_type options 10 and 11 for saturation states with respect to calcite and aragonite.
• Adds KSK18 parameterisation for estimating total borate from salinity.

Dependencies

• Switched to Autograd v1.4.

PyCO2SYS: marine carbonate system calculations in Python

Changes in v1.8.0

New features

• Adds pressure_atmosphere and pressure_atmosphere_out arguments, rather than assuming 1 atm total barometric pressure.

Behind-the-scenes improvements

• Adds additional constraint to the initial pH estimate for more robust results for the alkalinity-CO₂ fugacity parameter pair.
• Difference derivatives for uncertainties now have a fixed step size for each argument, instead of scaling depending on arguments, for more reproducible results.

PyCO2SYS: marine carbonate system calculations in Python

PyCO2SYS is a Python toolbox for solving the marine carbonate system and calculating related seawater properties. Its core is a Python implementation of CO2SYS for MATLAB. Documentation is available at PyCO2SYS.readthedocs.io.

Changes in v1.7.1

Bug fixes

• Improved handling of zero-valued inputs.
• Adjusted CO2SYS_wrap to work with latest pandas release.

PyCO2SYS: marine carbonate system calculations in Python

PyCO2SYS is a Python toolbox for solving the marine carbonate system and calculating related seawater properties. Its core is a Python implementation of CO2SYS for MATLAB. Documentation is available at PyCO2SYS.readthedocs.io.

Changes in v1.7.0

New features

• Can now run pyco2.sys with no carbonate system parameter arguments provided, to just return all the equilibrium constants etc. under the specified conditions.
• Can also run pyco2.sys with only one carbonate system parameter argument. This does not solve the carbonate system, but does calculate all that can be calculated with that parameter.
• Added carbonic acid constants parameterisation of SB21.
• Added bisulfate dissociation constant parameterisation of WM13/WMW14.
• Added spreadsheet-to-spreadsheet function pyco2.ezio (with thanks to Daniel Sandborn).
• Integrated uncertainty propagation into the main pyco2.sys function and expanded its capabilities.

Internal updates

• Switched default first-guess pH for solving from the alkalinity-carbonate ion parameter pair at low alkalinity from 10 to 3.
• Renamed various internal functions and variables for better consistency with the Pythonic pyco2.sys i/o syntax.
• Removed the PyCO2SYS.test module, instead defining the round-robin test functions it contained directly in the test suite.
• Added various internal settings for testing and validation against older CO2SYS-MATLAB versions.
• Adjust aqueous CO₂ calculation for better consistency with CO2SYS-MATLAB (but negligible changes in the results).
• Can now use PyCO2SYS.hello() to find version number and credits (alias for PyCO2SYS.say_hello()).
• The final component of DIC (or DIC itself) to be calculated is now always computed by difference from the known components.
• Various functions in convert module renamed.

Validation

• Rigorous validation against various CO2SYS-MATLAB versions performed, as described in forthcoming PyCO2SYS manuscript (Humphreys et al., in prep.).

Bug fixes

• par1, par2, par1_type and par2_type arguments now always get broadcasted to the maximum size, even if they are scalar.
• Erroneous "k_phosphate_*" keys corrected to "k_phosphoric_".
• Override values for equilibrium constants under output conditions now assigned correctly.
• Fixed minor errors in initial pH estimates when solving from alkalinity and either DIC or [CO$_2$(aq)].

PyCO2SYS: marine carbonate system calculations in Python

PyCO2SYS is a Python toolbox for solving the marine carbonate system and calculating related seawater properties. Its core is a Python implementation of CO2SYS for MATLAB. Documentation is available at PyCO2SYS.rtfd.io.

Changes in v1.6.0

Bug fixes

• Updates the total alkalinity equation to fix minor error in pH scale conversions inherited from CO2SYS-MATLAB (see related note in v1.5.0 release notes).

New inputs and outputs

• Enables inputting total molalities and equilibrium constants for up to two additional contributors to total alkalinity.
• Full chemical speciation returned in the output dict of pyco2.sys, not just the alkalinity components as before.

New syntax

• Adds sys as an alias for CO2SYS_nd at the top level. Recommended Python-style syntax is thus now pyco2.sys.