pyEQL 1.1.6__py3-none-any.whl → 1.3.0__py3-none-any.whl

pyEQL/utils.py

@@ -61,17 +61,21 @@ def standardize_formula(formula: str):
         'Na+1', and 'Na[+]' will all standardize to "Na[+1]"
     """
     # fix permuted sign and charge number (e.g. Co2+)
-    for str, rep in zip(["²⁺", "³⁺", "⁴⁺", "²⁻", "³⁻", "⁴⁻"], ["+2", "+3", "+4", "-2", "-3", "-4"]):
+    for str, rep in zip(["²⁺", "³⁺", "⁴⁺", "²⁻", "³⁻", "⁴⁻"], ["+2", "+3", "+4", "-2", "-3", "-4"], strict=False):
         formula = formula.replace(str, rep)
 
     # replace superscripts with non superscripts
-    for char, rep in zip("⁻⁺⁰¹²³⁴⁵⁶⁷⁸⁹", "-+0123456789"):
+    for char, rep in zip("⁻⁺⁰¹²³⁴⁵⁶⁷⁸⁹", "-+0123456789", strict=False):
         formula = formula.replace(char, rep)
 
     # replace subscripts with non subscripts
-    for char, rep in zip("₀₁₂₃₄₅₆₇₈₉", "0123456789"):
+    for char, rep in zip("₀₁₂₃₄₅₆₇₈₉", "0123456789", strict=False):
         formula = formula.replace(char, rep)
 
+    # replace different types of dashes with a minus sign
+    for char in [r"‑", r"‐", r"‒", r"–", r"—", r"−"]:  # noqa: RUF001
+        formula = formula.replace(char, "-")
+
     sform = Ion.from_formula(formula).reduced_formula
 
     # TODO - manual formula adjustments. May be implemented upstream in pymatgen in the future
@@ -81,18 +85,24 @@ def standardize_formula(formula: str):
     # ammonia
     if sform == "H4N[+1]":
         sform = "NH4[+1]"
+    elif "H4NCl" in sform:
+        sform = sform.replace("H4NCl", "NH4Cl")
+    elif sform == "SO3[-1]":
+        sform = "S2O6[-2]"
+    elif sform == "SO4[-1]":
+        sform = "S2O8[-2]"
     elif sform == "H3N(aq)":
         sform = "NH3(aq)"
     # phosphoric acid system
     elif sform == "PH3O4(aq)":
         sform = "H3PO4(aq)"
-    elif sform == "PHO4[-2]":
-        sform = "HPO4[-2]"
-    elif sform == "P(HO2)2[-1]":
-        sform = "H2PO4[-1]"
+    elif "PHO4" in sform:
+        sform = sform.replace("PHO4", "HPO4")
+    elif "P(HO2)2" in sform:
+        sform = sform.replace("P(HO2)2", "H2PO4")
     # thiocyanate
-    elif sform == "CSN[-1]":
-        sform = "SCN[-1]"
+    elif "CSN" in sform:
+        sform = sform.replace("CSN", "SCN")
     # triiodide, nitride, an phosphide
     elif sform == "I[-0.33333333]":
         sform = "I3[-1]"
@@ -137,6 +147,9 @@ def standardize_formula(formula: str):
     elif sform == "C2I2ClO2[-1]":
         sform = "CI2ClCOO[-1]"
 
+    # ammonium nitrate salts
+    elif sform == "H4N2O3(aq)":
+        sform = "NH4NO3(aq)"
     # ammonium sulfate salts
     elif sform == "H8S(NO2)2(aq)":
         sform = "(NH4)2SO4(aq)"

{pyEQL-1.1.6.dist-info → pyeql-1.3.0.dist-info}/METADATA

@@ -1,13 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pyEQL
-Version: 1.1.6
+Version: 1.3.0
 Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
+License-Expression: LGPL-3.0-or-later
 Project-URL: Docs, https://pyeql.readthedocs.io/
 Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
 Project-URL: Package, https://pypi.org/project/pyEQL
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -15,40 +15,40 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-License-File: COPYING
 License-File: AUTHORS.md
-Requires-Dist: pint >=0.19
-Requires-Dist: numpy <2,>1.26
-Requires-Dist: scipy >=1.12
-Requires-Dist: pymatgen ==2024.5.1
-Requires-Dist: iapws >=1.5.3
-Requires-Dist: monty >=2024.7.12
-Requires-Dist: maggma >=0.67.0
-Requires-Dist: phreeqpython >=1.5.2
+Requires-Dist: pint>=0.24.4
+Requires-Dist: numpy>1.26
+Requires-Dist: scipy>=1.12
+Requires-Dist: pymatgen>=2025.1.9
+Requires-Dist: iapws>=1.5.3
+Requires-Dist: monty>=2024.12.10
+Requires-Dist: maggma>=0.71.4
+Requires-Dist: phreeqpython>=1.5.2
+Provides-Extra: testing
+Requires-Dist: setuptools>=68; extra == "testing"
+Requires-Dist: pre-commit>=2; extra == "testing"
+Requires-Dist: pytest>=7; extra == "testing"
+Requires-Dist: pytest-cov>=2.11; extra == "testing"
+Requires-Dist: pytest-xdist>2; extra == "testing"
+Requires-Dist: black; extra == "testing"
+Requires-Dist: mypy>1; extra == "testing"
+Requires-Dist: ruff>0.0.100; extra == "testing"
+Requires-Dist: tox<4; extra == "testing"
 Provides-Extra: docs
-Requires-Dist: sphinx >=3.2.1 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
-Requires-Dist: myst-parser[linkify] ; extra == 'docs'
+Requires-Dist: sphinx>=3.2.1; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: myst-parser[linkify]; extra == "docs"
 Provides-Extra: full
-Requires-Dist: rich ; extra == 'full'
-Provides-Extra: testing
-Requires-Dist: setuptools >=68 ; extra == 'testing'
-Requires-Dist: pre-commit >=2 ; extra == 'testing'
-Requires-Dist: pytest >=7 ; extra == 'testing'
-Requires-Dist: pytest-cov >=2.11 ; extra == 'testing'
-Requires-Dist: pytest-xdist >2 ; extra == 'testing'
-Requires-Dist: black ; extra == 'testing'
-Requires-Dist: mypy >1 ; extra == 'testing'
-Requires-Dist: ruff >0.0.100 ; extra == 'testing'
-Requires-Dist: tox <4 ; extra == 'testing'
+Requires-Dist: rich; extra == "full"
+Dynamic: license-file
 
 [![Read the Docs](https://img.shields.io/readthedocs/pyeql)](https://pyeql.readthedocs.io/en/latest/)
 [![testing](https://github.com/KingsburyLab/pyeql/workflows/testing/badge.svg)](https://github.com/KingsburyLab/pyeql/actions?query=workflow%3Atesting)
 [![codecov](https://codecov.io/gh/KingsburyLab/pyeql/branch/main/graph/badge.svg?token=I7RP0QML6S)](https://codecov.io/gh/KingsburyLab/pyeql)
-![Supported python versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)
+![Supported python versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8332915.svg)](https://doi.org/10.5281/zenodo.8332915)
 [![PyPI version](https://badge.fury.io/py/pyEQL.svg)](https://badge.fury.io/py/pyEQL)
 [![status](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6/status.svg)](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6)
@@ -112,7 +112,7 @@ Detailed documentation is available at [https://pyeql.readthedocs.io/](https://p
 
 ### Dependencies
 
-- Python 3.9+. This project will attempt to adhere to NumPy's
+- Python 3.10+. This project will attempt to adhere to NumPy's
   [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html) deprecation policy
   for older version of Python.
 - [pint](https://github.com/hgrecco/pint) - for units-aware calculations

pyeql-1.3.0.dist-info/RECORD

@@ -0,0 +1,26 @@
+pyEQL/__init__.py,sha256=yqblN0G2ussRNrcq1Icf0CjgBtbG2T5a0nwbXxrttCM,2009
+pyEQL/activity_correction.py,sha256=P8fYWE4OJh41JMg2JEfzP9fYWpXuprRcw5kbkWQILMw,37172
+pyEQL/engines.py,sha256=D7FQsi9GA9G-RQmGeBPmECWsARRR5wokcFb5gM_mWmU,34445
+pyEQL/equilibrium.py,sha256=YZdc3zKj96Fpn-KyHwBZNwwUfeGP_pB11ImkmWlrHWg,8428
+pyEQL/functions.py,sha256=xevJri40Boi_k6JMgzL-HY3ExztbI2uto0soS9OV5ko,11451
+pyEQL/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyEQL/salt_ion_match.py,sha256=r60dsgBjfhzUCM2BvUIQTF6C37XTpuM5JI2F1t3Dc5A,4074
+pyEQL/solute.py,sha256=no00Rc3tRfHmyht4wm2UXA1KZhKC45tWMO5QEkZY6yg,5140
+pyEQL/solution.py,sha256=qP9w_bXRm3sjFksMPo4XqAcJH2FufmmlrIir7hUpnkM,112869
+pyEQL/utils.py,sha256=dMkLhFFgvL2zUgGvEZ-gtJ8ZtVO7JB2JtEnFM839ELU,7380
+pyEQL/database/geothermal.dat,sha256=kksnfcBtWdOTpNn4CLXU1Mz16cwas2WuVKpuMU8CaVI,234230
+pyEQL/database/llnl.dat,sha256=jN-a0kfUFbQlYMn2shTVRg1JX_ZhLa-tJ0lLw2YSpLU,751462
+pyEQL/database/phreeqc_license.txt,sha256=8W1r8VxC2kVptIMSU9sDFNASYqN7MdwKEtIWWfjTQuM,2906
+pyEQL/database/pyeql_db.json,sha256=0hj_RLERTPyYbhAridUZv2ttzSe6tlyTotiJoAQfg04,1079003
+pyEQL/presets/Ringers lactate.yaml,sha256=kaGiBbg_JFrmOm8xZqb_EMVqeQYxll7pOOvXcmxAJ5I,413
+pyEQL/presets/normal saline.yaml,sha256=eT5MZKgc0uW-TrQOiX87ZoTwlMO-OEhTvQyQAXoIa80,318
+pyEQL/presets/rainwater.yaml,sha256=QG3aol2Z5HwLj-s6frN7hYNQr01qw_HR2h5f4BdAvVc,337
+pyEQL/presets/seawater.yaml,sha256=Kts0vAmXSPvPzy_PJpx0RR2uSt40izxp-687Qi02oro,843
+pyEQL/presets/urine.yaml,sha256=Zpcr2Dp7xZrlLqzYk4UcMyWXlNrd2AFUexWpb8k9FEg,679
+pyEQL/presets/wastewater.yaml,sha256=zJcpp9Ye4hIw6iInsdV5bgjTNuJ8oAUVimsUgZXlG-w,502
+pyeql-1.3.0.dist-info/licenses/AUTHORS.md,sha256=vm40bLDv3LLqNiY0QrMfs7j8eBFg6x-5OPcu5cH4G3o,633
+pyeql-1.3.0.dist-info/licenses/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
+pyeql-1.3.0.dist-info/METADATA,sha256=JlfgJBpRaUHufqtTY4Tgjd8LEQwED7nuX7vzjTJs4To,6108
+pyeql-1.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pyeql-1.3.0.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
+pyeql-1.3.0.dist-info/RECORD,,

{pyEQL-1.1.6.dist-info → pyeql-1.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.0.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{pyEQL-1.1.6.dist-info → pyeql-1.3.0.dist-info/licenses}/AUTHORS.md

@@ -6,8 +6,13 @@ developed and maintained by the Kingsbury Lab at Princeton University.
 Other contributors, listed alphabetically, are:
 
 - Arpit Bhardwaj (@abhardwaj73)
+- Nikhil Dhruv (@NikhilDhruv)
 - Dhruv Duseja (@DhruvDuseja)
+- @githubalexliu
 - Hernan Grecco (@hgrecco)
+- @Ouriel Ndalamba (@Ouriel-N)
+- Ugo Nwosu (@ugognw)
+- Yitong Pan (@YitongPan1)
 - Jaebeom Park (@Jaebeom-P)
 - Kirill Pushkarev (@kirill-push)
 - Andrew Rosen (@arosen93)

pyEQL-1.1.6.dist-info/COPYING

@@ -1,165 +0,0 @@
-                 GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-
-  This version of the GNU Lesser General Public License incorporates
-the terms and conditions of version 3 of the GNU General Public
-License, supplemented by the additional permissions listed below.
-
-  0. Additional Definitions.
-
-  As used herein, "this License" refers to version 3 of the GNU Lesser
-General Public License, and the "GNU GPL" refers to version 3 of the GNU
-General Public License.
-
-  "The Library" refers to a covered work governed by this License,
-other than an Application or a Combined Work as defined below.
-
-  An "Application" is any work that makes use of an interface provided
-by the Library, but which is not otherwise based on the Library.
-Defining a subclass of a class defined by the Library is deemed a mode
-of using an interface provided by the Library.
-
-  A "Combined Work" is a work produced by combining or linking an
-Application with the Library.  The particular version of the Library
-with which the Combined Work was made is also called the "Linked
-Version".
-
-  The "Minimal Corresponding Source" for a Combined Work means the
-Corresponding Source for the Combined Work, excluding any source code
-for portions of the Combined Work that, considered in isolation, are
-based on the Application, and not on the Linked Version.
-
-  The "Corresponding Application Code" for a Combined Work means the
-object code and/or source code for the Application, including any data
-and utility programs needed for reproducing the Combined Work from the
-Application, but excluding the System Libraries of the Combined Work.
-
-  1. Exception to Section 3 of the GNU GPL.
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-  You may convey a covered work under sections 3 and 4 of this License
-without being bound by section 3 of the GNU GPL.
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-  2. Conveying Modified Versions.
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-  If you modify a copy of the Library, and, in your modifications, a
-facility refers to a function or data to be supplied by an Application
-that uses the facility (other than as an argument passed when the
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-   function or data, the facility still operates, and performs
-   whatever part of its purpose remains meaningful, or
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-   b) under the GNU GPL, with none of the additional permissions of
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-  3. Object Code Incorporating Material from Library Header Files.
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-facilities that are not Applications and are not covered by this
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-choice, if you do both of the following:
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-   a) Accompany the combined library with a copy of the same work based
-   on the Library, uncombined with any other library facilities,
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-   is a work based on the Library, and explaining where to find the
-   accompanying uncombined form of the same work.
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-  6. Revised Versions of the GNU Lesser General Public License.
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-  The Free Software Foundation may publish revised and/or new versions
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-Library.

pyEQL-1.1.6.dist-info/RECORD

@@ -1,26 +0,0 @@
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-pyEQL-1.1.6.dist-info/RECORD,,