pyEQL 1.1.5__tar.gz → 1.1.6__tar.gz

{pyeql-1.1.5 → pyeql-1.1.6}/.github/workflows/post-process.yml

@@ -33,26 +33,32 @@ jobs:
     strategy:
       max-parallel: 6
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        version:
+          - { python: "3.9", resolution: highest, extras: testing }
+          - { python: "3.10", resolution: lowest-direct, extras: testing }
+          - { python: "3.11", resolution: highest, extras: testing }
+          - { python: "3.12", resolution: lowest-direct, extras: testing }
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
           - macos-14
         exclude:
-          - os: macos-14
-            python-version: "3.9"
+          - {version: {
+               python: "3.9" },
+            os: macos-14 }
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+          python-version: ${{ matrix.version.python }}
       - name: Install test requirements
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[testing]"
+          pip install uv
+          uv pip install '.[${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
       - name: Run tests
         run: |
           pytest -n auto --cov=src/pyEQL --cov-report=xml

{pyeql-1.1.5 → pyeql-1.1.6}/.github/workflows/release.yml

@@ -57,4 +57,4 @@ jobs:
           tox -e clean,build
 
       - name: Upload to PyPi
-        uses: pypa/gh-action-pypi-publish@v1.8.14
+        uses: pypa/gh-action-pypi-publish@v1.10.0

{pyeql-1.1.5 → pyeql-1.1.6}/AUTHORS.md

@@ -5,9 +5,12 @@ developed and maintained by the Kingsbury Lab at Princeton University.
 
 Other contributors, listed alphabetically, are:
 
-* Kirill Pushkarev (@kirill-push)
-* Dhruv Duseja (@DhruvDuseja)
-* Andrew Rosen (@arosen93)
-* Hernan Grecco (@hgrecco)
+- Arpit Bhardwaj (@abhardwaj73)
+- Dhruv Duseja (@DhruvDuseja)
+- Hernan Grecco (@hgrecco)
+- Jaebeom Park (@Jaebeom-P)
+- Kirill Pushkarev (@kirill-push)
+- Andrew Rosen (@arosen93)
+- Sui Xiong Tay (@SuixiongTay)
 
 (If you think that your name belongs here, please let the maintainer know)

{pyeql-1.1.5 → pyeql-1.1.6}/CHANGELOG.md

@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.6] - 2024-09-01
+
+### Fixed
+
+- `Solution.get_total_amount`: Bugfix that caused an error when called on certain elements
+  without specifying an oxidation state. For example, `get_total_amount('N')` could raise
+  an exception in a solution containing `Na` (but no `N`) due to a flaw in a logical
+  test.
+- `Solution._adjust_charge_balance`: Removed a misleading and redundant log message (#162, @SuixiongTay)
+
+### Added
+
+- `gibbs_mix`: A new keyword argument `activity_correction` was added to `gibbs_mix`. It defaults
+  to `True` (no change from prior behavior), but can be set to `False` in order to calculate the
+  ideal mixing energy, which is equivalent to only considering entropic effects. (#178, @Jaebeom-P)
+- `standardize_formula`: Improve formatting of ammonium sulfate salts. Aqueous ammonium sulfate previously
+  standardized to `H8S(NO2)2(aq)`, now it will display as `(NH4)2SO4(aq)`.
+
+### Changed
+
+- **BREAKING** `entropy_mix` now returns the ideal mixing _entropy_ in units of J/K rather than the mixing
+  _energy_ in J. This was done to improve clarity with respect to the function name. An `activity_correction`
+  kwarg was added to `gibbs_mix` so that you can still calculate the ideal mixing energy by setting it to `False`.
+  (#178, @Jaebeom-P)
+- Revise documentation of `gibbs_mix`, `entropy_mix`, and `donnan_eql`. (#178, @Jaebeom-P)
+- CI: Improve comprehensiveness of CI dependency testing. (#163, #164, @abhardwaj73)
+
 ## [1.1.5] - 2024-07-28
 
 ### Fixed

{pyeql-1.1.5/src/pyEQL.egg-info → pyeql-1.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.1.5
+Version: 1.1.6
 Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
 Project-URL: Docs, https://pyeql.readthedocs.io/
@@ -21,22 +21,22 @@ License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
 Requires-Dist: pint>=0.19
-Requires-Dist: numpy<2
-Requires-Dist: scipy
+Requires-Dist: numpy<2,>1.26
+Requires-Dist: scipy>=1.12
 Requires-Dist: pymatgen==2024.5.1
-Requires-Dist: iapws
+Requires-Dist: iapws>=1.5.3
 Requires-Dist: monty>=2024.7.12
 Requires-Dist: maggma>=0.67.0
-Requires-Dist: phreeqpython
+Requires-Dist: phreeqpython>=1.5.2
 Provides-Extra: testing
-Requires-Dist: setuptools; extra == "testing"
-Requires-Dist: pre-commit; extra == "testing"
-Requires-Dist: pytest; extra == "testing"
-Requires-Dist: pytest-cov; extra == "testing"
-Requires-Dist: pytest-xdist; 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; extra == "testing"
-Requires-Dist: ruff; 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"

{pyeql-1.1.5 → pyeql-1.1.6}/docs/authors.md

@@ -5,9 +5,12 @@ developed and maintained by the Kingsbury Lab at Princeton University.
 
 Other contributors, listed alphabetically, are:
 
-* Kirill Pushkarev (@kirill-push)
-* Dhruv Duseja (@DhruvDuseja)
-* Andrew Rosen (@arosen93)
-* Hernan Grecco (@hgrecco)
+- Arpit Bhardwaj (@abhardwaj73)
+- Dhruv Duseja (@DhruvDuseja)
+- Hernan Grecco (@hgrecco)
+- Jaebeom Park (@Jaebeom-P)
+- Kirill Pushkarev (@kirill-push)
+- Andrew Rosen (@arosen93)
+- Sui Xiong Tay (@SuixiongTay)
 
 (If you think that your name belongs here, please let the maintainer know)

{pyeql-1.1.5 → pyeql-1.1.6}/docs/changelog.md

@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.6] - 2024-09-01
+
+### Fixed
+
+- `Solution.get_total_amount`: Bugfix that caused an error when called on certain elements
+  without specifying an oxidation state. For example, `get_total_amount('N')` could raise
+  an exception in a solution containing `Na` (but no `N`) due to a flaw in a logical
+  test.
+- `Solution._adjust_charge_balance`: Removed a misleading and redundant log message (#162, @SuixiongTay)
+
+### Added
+
+- `gibbs_mix`: A new keyword argument `activity_correction` was added to `gibbs_mix`. It defaults
+  to `True` (no change from prior behavior), but can be set to `False` in order to calculate the
+  ideal mixing energy, which is equivalent to only considering entropic effects. (#178, @Jaebeom-P)
+- `standardize_formula`: Improve formatting of ammonium sulfate salts. Aqueous ammonium sulfate previously
+  standardized to `H8S(NO2)2(aq)`, now it will display as `(NH4)2SO4(aq)`.
+
+### Changed
+
+- **BREAKING** `entropy_mix` now returns the ideal mixing _entropy_ in units of J/K rather than the mixing
+  _energy_ in J. This was done to improve clarity with respect to the function name. An `activity_correction`
+  kwarg was added to `gibbs_mix` so that you can still calculate the ideal mixing energy by setting it to `False`.
+  (#178, @Jaebeom-P)
+- Revise documentation of `gibbs_mix`, `entropy_mix`, and `donnan_eql`. (#178, @Jaebeom-P)
+- CI: Improve comprehensiveness of CI dependency testing. (#163, #164, @abhardwaj73)
+
 ## [1.1.5] - 2024-07-28
 
 ### Fixed

{pyeql-1.1.5 → pyeql-1.1.6}/pyproject.toml

@@ -21,13 +21,13 @@ license = {file = "LICENSE"}
 requires-python = ">=3.9"
 dependencies = [
         "pint>=0.19",
-        "numpy<2",
-        "scipy",
+        "numpy>1.26,<2",
+        "scipy>=1.12",
         "pymatgen==2024.5.1",
-        "iapws",
+        "iapws>=1.5.3",
         "monty>=2024.7.12",
         "maggma>=0.67.0",
-        "phreeqpython",
+        "phreeqpython>=1.5.2",
     ]
 
 [project.urls]
@@ -38,14 +38,14 @@ Package = "https://pypi.org/project/pyEQL"
 
 [project.optional-dependencies]
 testing = [
-    "setuptools",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-    "pytest-xdist",
+    "setuptools>=68",
+    "pre-commit>=2",
+    "pytest>=7",
+    "pytest-cov>=2.11",
+    "pytest-xdist>2",
     "black",
-    "mypy",
-    "ruff",
+    "mypy>1",
+    "ruff>0.0.100",
     "tox<4",
     ]
 docs = [

{pyeql-1.1.5 → pyeql-1.1.6}/requirements/macos-latest_py3.10.txt

@@ -10,22 +10,22 @@ annotated-types==0.7.0
     # via pydantic
 appdirs==1.4.4
     # via pint
-attrs==23.2.0
+attrs==24.2.0
     # via
     #   jsonlines
     #   jsonschema
     #   referencing
-bcrypt==4.1.3
+bcrypt==4.2.0
     # via paramiko
-boto3==1.34.142
+boto3==1.34.158
     # via maggma
-botocore==1.34.142
+botocore==1.34.158
     # via
     #   boto3
     #   s3transfer
 certifi==2024.7.4
     # via requests
-cffi==1.16.0
+cffi==1.17.0
     # via
     #   cryptography
     #   pynacl
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==42.0.8
+cryptography==43.0.0
     # via paramiko
 cycler==0.12.1
     # via matplotlib
@@ -67,13 +67,13 @@ kiwisolver==1.4.5
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
-maggma==0.69.0
+maggma==0.69.1
     # via pyEQL (setup.py)
-matplotlib==3.9.1
+matplotlib==3.9.1.post1
     # via pymatgen
 mongomock==4.1.2
     # via maggma
-monty==2024.5.24
+monty==2024.7.30
     # via
     #   maggma
     #   pyEQL (setup.py)
@@ -95,7 +95,7 @@ numpy==1.26.4
     #   pymatgen
     #   scipy
     #   spglib
-orjson==3.10.6
+orjson==3.10.7
     # via maggma
 packaging==24.1
     # via
@@ -116,9 +116,9 @@ phreeqpython==1.5.2
     # via pyEQL (setup.py)
 pillow==10.4.0
     # via matplotlib
-pint==0.24.1
+pint==0.24.3
     # via pyEQL (setup.py)
-plotly==5.22.0
+plotly==5.23.0
     # via pymatgen
 pybtex==0.24.0
     # via pymatgen
@@ -130,9 +130,9 @@ pydantic==2.8.2
     #   pydantic-settings
 pydantic-core==2.20.1
     # via pydantic
-pydantic-settings==2.3.4
+pydantic-settings==2.4.0
     # via maggma
-pydash==8.0.1
+pydash==8.0.3
     # via maggma
 pymatgen==2024.5.1
     # via pyEQL (setup.py)
@@ -154,9 +154,9 @@ python-dotenv==1.0.1
     # via pydantic-settings
 pytz==2024.1
     # via pandas
-pyyaml==6.0.1
+pyyaml==6.0.2
     # via pybtex
-pyzmq==26.0.3
+pyzmq==26.1.0
     # via maggma
 referencing==0.35.1
     # via
@@ -164,7 +164,7 @@ referencing==0.35.1
     #   jsonschema-specifications
 requests==2.32.3
     # via pymatgen
-rpds-py==0.19.0
+rpds-py==0.20.0
     # via
     #   jsonschema
     #   referencing
@@ -188,17 +188,17 @@ six==1.16.0
     # via
     #   pybtex
     #   python-dateutil
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sshtunnel==0.4.0
     # via maggma
-sympy==1.13.0
+sympy==1.13.1
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
-tenacity==8.5.0
+tenacity==9.0.0
     # via plotly
-tqdm==4.66.4
+tqdm==4.66.5
     # via
     #   maggma
     #   pymatgen

{pyeql-1.1.5 → pyeql-1.1.6}/requirements/macos-latest_py3.10_extras.txt

@@ -12,26 +12,26 @@ annotated-types==0.7.0
     # via pydantic
 appdirs==1.4.4
     # via pint
-attrs==23.2.0
+attrs==24.2.0
     # via
     #   jsonlines
     #   jsonschema
     #   referencing
-babel==2.15.0
+babel==2.16.0
     # via sphinx
-bcrypt==4.1.3
+bcrypt==4.2.0
     # via paramiko
-black==24.4.2
+black==24.8.0
     # via pyEQL (setup.py)
-boto3==1.34.142
+boto3==1.34.158
     # via maggma
-botocore==1.34.142
+botocore==1.34.158
     # via
     #   boto3
     #   s3transfer
 certifi==2024.7.4
     # via requests
-cffi==1.16.0
+cffi==1.17.0
     # via
     #   cryptography
     #   pynacl
@@ -43,9 +43,9 @@ click==8.1.7
     # via black
 contourpy==1.2.1
     # via matplotlib
-coverage[toml]==7.5.4
+coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==42.0.8
+cryptography==43.0.0
     # via paramiko
 cycler==0.12.1
     # via matplotlib
@@ -60,7 +60,7 @@ docutils==0.20.1
     #   myst-parser
     #   sphinx
     #   sphinx-rtd-theme
-exceptiongroup==1.2.1
+exceptiongroup==1.2.2
     # via pytest
 execnet==2.1.1
     # via pytest-xdist
@@ -106,7 +106,7 @@ latexcodec==3.0.0
     # via pybtex
 linkify-it-py==2.0.3
     # via myst-parser
-maggma==0.69.0
+maggma==0.69.1
     # via pyEQL (setup.py)
 markdown-it-py==3.0.0
     # via
@@ -115,7 +115,7 @@ markdown-it-py==3.0.0
     #   rich
 markupsafe==2.1.5
     # via jinja2
-matplotlib==3.9.1
+matplotlib==3.9.1.post1
     # via pymatgen
 mdit-py-plugins==0.4.1
     # via myst-parser
@@ -123,7 +123,7 @@ mdurl==0.1.2
     # via markdown-it-py
 mongomock==4.1.2
     # via maggma
-monty==2024.5.24
+monty==2024.7.30
     # via
     #   maggma
     #   pyEQL (setup.py)
@@ -132,13 +132,13 @@ mpmath==1.3.0
     # via sympy
 msgpack==1.0.8
     # via maggma
-mypy==1.10.1
+mypy==1.11.1
     # via pyEQL (setup.py)
 mypy-extensions==1.0.0
     # via
     #   black
     #   mypy
-myst-parser[linkify]==3.0.1
+myst-parser[linkify]==4.0.0
     # via pyEQL (setup.py)
 networkx==3.3
     # via pymatgen
@@ -155,7 +155,7 @@ numpy==1.26.4
     #   pymatgen
     #   scipy
     #   spglib
-orjson==3.10.6
+orjson==3.10.7
     # via maggma
 packaging==24.1
     # via
@@ -182,19 +182,19 @@ phreeqpython==1.5.2
     # via pyEQL (setup.py)
 pillow==10.4.0
     # via matplotlib
-pint==0.24.1
+pint==0.24.3
     # via pyEQL (setup.py)
 platformdirs==4.2.2
     # via
     #   black
     #   virtualenv
-plotly==5.22.0
+plotly==5.23.0
     # via pymatgen
 pluggy==1.5.0
     # via
     #   pytest
     #   tox
-pre-commit==3.7.1
+pre-commit==3.8.0
     # via pyEQL (setup.py)
 py==1.11.0
     # via tox
@@ -208,9 +208,9 @@ pydantic==2.8.2
     #   pydantic-settings
 pydantic-core==2.20.1
     # via pydantic
-pydantic-settings==2.3.4
+pydantic-settings==2.4.0
     # via maggma
-pydash==8.0.1
+pydash==8.0.3
     # via maggma
 pygments==2.18.0
     # via
@@ -226,7 +226,7 @@ pyparsing==3.1.2
     # via
     #   matplotlib
     #   periodictable
-pytest==8.2.2
+pytest==8.3.2
     # via
     #   pyEQL (setup.py)
     #   pytest-cov
@@ -245,12 +245,12 @@ python-dotenv==1.0.1
     # via pydantic-settings
 pytz==2024.1
     # via pandas
-pyyaml==6.0.1
+pyyaml==6.0.2
     # via
     #   myst-parser
     #   pre-commit
     #   pybtex
-pyzmq==26.0.3
+pyzmq==26.1.0
     # via maggma
 referencing==0.35.1
     # via
@@ -262,7 +262,7 @@ requests==2.32.3
     #   sphinx
 rich==13.7.1
     # via pyEQL (setup.py)
-rpds-py==0.19.0
+rpds-py==0.20.0
     # via
     #   jsonschema
     #   referencing
@@ -272,7 +272,7 @@ ruamel-yaml==0.18.6
     #   pymatgen
 ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
-ruff==0.5.1
+ruff==0.5.7
     # via pyEQL (setup.py)
 s3transfer==0.10.2
     # via boto3
@@ -291,9 +291,9 @@ six==1.16.0
     #   tox
 snowballstemmer==2.2.0
     # via sphinx
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
-sphinx==7.3.7
+sphinx==7.4.7
     # via
     #   myst-parser
     #   pyEQL (setup.py)
@@ -301,27 +301,27 @@ sphinx==7.3.7
     #   sphinxcontrib-jquery
 sphinx-rtd-theme==2.0.0
     # via pyEQL (setup.py)
-sphinxcontrib-applehelp==1.0.8
+sphinxcontrib-applehelp==2.0.0
     # via sphinx
-sphinxcontrib-devhelp==1.0.6
+sphinxcontrib-devhelp==2.0.0
     # via sphinx
-sphinxcontrib-htmlhelp==2.0.5
+sphinxcontrib-htmlhelp==2.1.0
     # via sphinx
 sphinxcontrib-jquery==4.1
     # via sphinx-rtd-theme
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
-sphinxcontrib-qthelp==1.0.7
+sphinxcontrib-qthelp==2.0.0
     # via sphinx
-sphinxcontrib-serializinghtml==1.1.10
+sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 sshtunnel==0.4.0
     # via maggma
-sympy==1.13.0
+sympy==1.13.1
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
-tenacity==8.5.0
+tenacity==9.0.0
     # via plotly
 tomli==2.0.1
     # via
@@ -333,7 +333,7 @@ tomli==2.0.1
     #   tox
 tox==3.28.0
     # via pyEQL (setup.py)
-tqdm==4.66.4
+tqdm==4.66.5
     # via
     #   maggma
     #   pymatgen