Merge branch 'bugfix' of https://github.com/KingsburyLab/pyEQL into b…

…ugfix

.github/workflows/post-process.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Run tests
         run: |
           pytest -n auto --cov=src/pyEQL --cov-report=xml
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.github/workflows/release.yml

@@ -57,4 +57,4 @@ jobs:
           tox -e clean,build
 
       - name: Upload to PyPi
-        uses: pypa/gh-action-pypi-publish@v1.10.2
+        uses: pypa/gh-action-pypi-publish@v1.12.2

.github/workflows/testing.yaml

@@ -61,7 +61,7 @@ jobs:
       - name: Run tests
         run: |
           pytest -n auto --cov=src/pyEQL --cov-report=xml
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

docs/class_solution.md

@@ -10,7 +10,7 @@ This page contains detailed information on each of the methods, attributes, and
 .. autoclass:: pyEQL.Solution
    :members:
    :inherited-members:
-   :private-members: _get_property
+   :private-members: _get_property, _get_diffusion_coefficient, _get_molar_conductivity, _get_mobility
    :special-members: __init__
    :member-order: bysource
 ```

docs/tutorials.md

@@ -9,10 +9,19 @@ browser using Binder by clicking the respective links below.
 [View Notebook on GitHub](https://github.com/KingsburyLab/pyEQL/tree/main/docs/examples/pyeql_demo.ipynb) | Try Interactive Notebook on Binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/KingsburyLab/pyEQL/main?labpath=docs%2Fexamples%2Fpyeql_demo.ipynb)
 
 ```{toctree}
-:maxdepth: 1
+:maxdepth: 2
 examples/pyeql_demo
 ```
 
+## Overview of Activity Coefficient Methods
+
+[View Notebook on GitHub](https://github.com/KingsburyLab/pyEQL/tree/main/docs/examples/pyeql_tutorial_activity.ipynb) | Try Interactive Notebook on Binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/KingsburyLab/pyEQL/main?labpath=docs%2Fexamples%2Fpyeql_tutorial_activity.ipynb)
+
+```{toctree}
+:maxdepth: 2
+examples/pyeql_tutorial_activity
+```
+
 ## Calculating Osmotic Pressure
 
 [View Notebook on GitHub](https://github.com/KingsburyLab/pyEQL/tree/main/docs/examples/pyeql_tutorial_osmotic_pressure.ipynb) | Try Interactive Notebook on Binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/KingsburyLab/pyEQL/main?labpath=docs%2Fexamples%2Fpyeql_tutorial_osmotic_pressure.ipynb)
@@ -26,7 +35,20 @@ examples/pyeql_tutorial_osmotic_pressure
 
 [View Notebook on GitHub](https://github.com/KingsburyLab/pyEQL/tree/main/docs/examples/pyeql_tutorial_database.ipynb) | Try Interactive Notebook on Binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/KingsburyLab/pyEQL/main?labpath=docs%2Fexamples%2Fpyeql_tutorial_osmotic_pressure.ipynb)
 
+
+
 ```{toctree}
 :maxdepth: 2
 examples/pyeql_tutorial_database
 ```
+
+## Modeling Carbonate Equilibrium
+
+[View Notebook on GitHub](https://github.com/KingsburyLab/pyEQL/tree/main/docs/examples/pyeql_tutorial_carbonate.ipynb) | Try Interactive Notebook on Binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/KingsburyLab/pyEQL/main?labpath=docs%2Fexamples%2Fpyeql_tutorial_carbonate.ipynb)
+
+```{toctree}
+:maxdepth: 2
+examples/pyeql_tutorial_carbonate
+```
+
+

requirements/macos-latest_py3.10.txt

@@ -4,52 +4,50 @@
 #
 #    pip-compile --output-file=requirements/macos-latest_py3.10.txt
 #
-aioitertools==0.11.0
+aioitertools==0.12.0
     # via maggma
 annotated-types==0.7.0
     # via pydantic
-appdirs==1.4.4
-    # via pint
 attrs==24.2.0
     # via
     #   jsonlines
     #   jsonschema
     #   referencing
 bcrypt==4.2.0
     # via paramiko
-boto3==1.34.158
+boto3==1.35.57
     # via maggma
-botocore==1.34.158
+botocore==1.35.57
     # via
     #   boto3
     #   s3transfer
-certifi==2024.7.4
+certifi==2024.8.30
     # via requests
-cffi==1.17.0
+cffi==1.17.1
     # via
     #   cryptography
     #   pynacl
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
-contourpy==1.2.1
+contourpy==1.3.0
     # via matplotlib
-cryptography==43.0.1
+cryptography==43.0.3
     # via paramiko
 cycler==0.12.1
     # via matplotlib
-dnspython==2.6.1
+dnspython==2.7.0
     # via
     #   maggma
     #   pymongo
 flexcache==0.3
     # via pint
-flexparser==0.3.1
+flexparser==0.4
     # via pint
-fonttools==4.53.1
+fonttools==4.54.1
     # via matplotlib
 iapws==1.5.4
     # via pyEQL (setup.py)
-idna==3.7
+idna==3.10
     # via requests
 jmespath==1.0.1
     # via
@@ -61,86 +59,89 @@ jsonlines==4.0.0
     # via maggma
 jsonschema==4.23.0
     # via maggma
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
-maggma==0.69.1
+maggma==0.70.0
     # via pyEQL (setup.py)
-matplotlib==3.9.1.post1
+matplotlib==3.9.2
     # via pymatgen
-mongomock==4.1.2
+mongomock==4.2.0.post1
     # via maggma
-monty==2024.7.30
+monty==2024.10.21
     # via
     #   maggma
     #   pyEQL (setup.py)
     #   pymatgen
 mpmath==1.3.0
     # via sympy
-msgpack==1.0.8
+msgpack==1.1.0
     # via maggma
-networkx==3.3
+networkx==3.4.2
     # via pymatgen
 numpy==1.26.4
     # via
     #   contourpy
     #   maggma
     #   matplotlib
+    #   monty
     #   pandas
     #   periodictable
     #   pyEQL (setup.py)
     #   pymatgen
     #   scipy
     #   spglib
-orjson==3.10.7
+orjson==3.10.11
     # via maggma
-packaging==24.1
+packaging==24.2
     # via
     #   matplotlib
     #   mongomock
     #   plotly
 palettable==3.3.3
     # via pymatgen
-pandas==2.2.2
+pandas==2.2.3
     # via
     #   maggma
     #   pymatgen
-paramiko==3.4.0
+paramiko==3.5.0
     # via sshtunnel
 periodictable==1.7.1
     # via phreeqpython
 phreeqpython==1.5.2
     # via pyEQL (setup.py)
-pillow==10.4.0
+pillow==11.0.0
     # via matplotlib
-pint==0.24.3
+pint==0.24.4
     # via pyEQL (setup.py)
-plotly==5.23.0
+platformdirs==4.3.6
+    # via pint
+plotly==5.24.1
     # via pymatgen
 pybtex==0.24.0
     # via pymatgen
 pycparser==2.22
     # via cffi
-pydantic==2.8.2
+pydantic==2.9.2
     # via
     #   maggma
     #   pydantic-settings
-pydantic-core==2.20.1
+pydantic-core==2.23.4
     # via pydantic
-pydantic-settings==2.4.0
+pydantic-settings==2.6.1
     # via maggma
-pydash==8.0.3
+pydash==8.0.4
     # via maggma
-pymatgen==2024.5.1
+pymatgen==2024.10.29
     # via pyEQL (setup.py)
-pymongo==4.8.0
+pymongo==4.10.1
     # via maggma
 pynacl==1.5.0
     # via paramiko
-pyparsing==3.1.2
+pyparsing==3.2.0
     # via
     #   matplotlib
     #   periodictable
@@ -152,31 +153,34 @@ python-dateutil==2.9.0.post0
     #   pandas
 python-dotenv==1.0.1
     # via pydantic-settings
-pytz==2024.1
-    # via pandas
+pytz==2024.2
+    # via
+    #   mongomock
+    #   pandas
 pyyaml==6.0.2
     # via pybtex
-pyzmq==26.1.0
+pyzmq==26.2.0
     # via maggma
 referencing==0.35.1
     # via
     #   jsonschema
     #   jsonschema-specifications
 requests==2.32.3
     # via pymatgen
-rpds-py==0.20.0
+rpds-py==0.21.0
     # via
     #   jsonschema
     #   referencing
 ruamel-yaml==0.18.6
     # via
     #   maggma
+    #   monty
     #   pymatgen
-ruamel-yaml-clib==0.2.8
+ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
-s3transfer==0.10.2
+s3transfer==0.10.3
     # via boto3
-scipy==1.14.0
+scipy==1.14.1
     # via
     #   iapws
     #   phreeqpython
@@ -192,13 +196,13 @@ spglib==2.5.0
     # via pymatgen
 sshtunnel==0.4.0
     # via maggma
-sympy==1.13.1
+sympy==1.13.3
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
 tenacity==9.0.0
     # via plotly
-tqdm==4.66.5
+tqdm==4.67.0
     # via
     #   maggma
     #   pymatgen
@@ -210,11 +214,11 @@ typing-extensions==4.12.2
     #   pydantic
     #   pydantic-core
     #   pydash
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
 uncertainties==3.2.2
     # via pymatgen
-urllib3==2.2.2
+urllib3==2.2.3
     # via
     #   botocore
     #   requests