pyEQL 1.1.6__tar.gz → 1.3.0__tar.gz

{pyeql-1.1.6 → pyeql-1.3.0}/.github/workflows/post-process.yml

@@ -34,19 +34,15 @@ jobs:
       max-parallel: 6
       matrix:
         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 }
+          - { python: "3.13", resolution: highest, extras: testing }
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
           - macos-14
-        exclude:
-          - {version: {
-               python: "3.9" },
-            os: macos-14 }
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -61,8 +57,8 @@ jobs:
           uv pip install '.[${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
       - name: Run tests
         run: |
-          pytest -n auto --cov=src/pyEQL --cov-report=xml
-      - uses: codecov/codecov-action@v4
+          pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

{pyeql-1.1.6 → pyeql-1.3.0}/.github/workflows/release.yml

@@ -57,4 +57,4 @@ jobs:
           tox -e clean,build
 
       - name: Upload to PyPi
-        uses: pypa/gh-action-pypi-publish@v1.10.0
+        uses: pypa/gh-action-pypi-publish@v1.12.4

{pyeql-1.1.6 → pyeql-1.3.0}/.github/workflows/testing.yaml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - main
+      - pourbaix
     paths-ignore:
       - CHANGELOG.md
 
@@ -23,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: "3.11"
           cache: pip
       - name: Run pre-commit
         run: |
@@ -36,21 +37,17 @@ jobs:
       max-parallel: 6
       matrix:
         # for most PRs, test the min and max supported python on every platform, test all python on ubuntu
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.12","3.13"]
         os:
           - ubuntu-latest
           - macos-latest
           - macos-14
           - windows-latest
         include:
-          - os: ubuntu-latest
-            python-version: "3.10"
           - os: ubuntu-latest
             python-version: "3.11"
-        # no python 3.9 on the macos-14 runner
-        exclude:
-          - os: macos-14
-            python-version: "3.9"
+          - os: ubuntu-latest
+            python-version: "3.12"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -64,8 +61,8 @@ jobs:
           pip install -e ".[testing]"
       - name: Run tests
         run: |
-          pytest -n auto --cov=src/pyEQL --cov-report=xml
-      - uses: codecov/codecov-action@v4
+          pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -77,10 +74,12 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: Install tox
         run: |
           python -m pip install tox
       - uses: r-lib/actions/setup-pandoc@v2
       - name: Build docs
         run: tox -e docs
+      - name: Check links
+        run: tox -e links

{pyeql-1.1.6 → pyeql-1.3.0}/.github/workflows/upgrade_dependencies.yml

@@ -6,7 +6,7 @@ on:
   workflow_dispatch: # Allow running on-demand
   schedule:
     # Runs on the 10th day of every month at 8:00 UTC (4:00 Eastern)
-    - cron: '0 8 10 * *'
+    - cron: "0 8 10 * *"
 
 jobs:
   upgrade:
@@ -14,9 +14,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         package: ["."]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -24,7 +24,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
+          cache: "pip"
       - name: Upgrade Python dependencies
         shell: bash
         run: |

{pyeql-1.1.6 → pyeql-1.3.0}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 exclude: "^docs/conf.py"
 
-default_stages: [commit]
+default_stages: [pre-commit]
 
 default_install_hook_types: [pre-commit, commit-msg]
 
@@ -12,26 +12,30 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.5
+    rev: v0.12.7
     hooks:
-      - id: ruff
-        args: [--fix, --ignore, "D,E501", "--show-fixes"]
+      # Run the linter. filters are to exclude .ipynb files
+      - id: ruff-check
+        types_or: [ python, pyi ]
+        args: [--fix, --ignore, "D,E501", --show-fixes]
+      # Run the formatter. This WILL run on .ipynb files
+      - id: ruff-format
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
+        stages: [pre-commit, commit-msg]
         exclude_types: [html, svg]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -41,8 +45,8 @@ repos:
         exclude_types: [svg]
       - id: trailing-whitespace
         exclude_types: [svg]
-
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
-    hooks:
-      - id: prettier
+      - id: check-yaml
+      - id: check-json
+      - id: pretty-format-json
+        exclude_types: [jupyter]
+        args: [--autofix, --indent=4]

{pyeql-1.1.6 → pyeql-1.3.0}/.readthedocs.yml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

pyeql-1.3.0/.zenodo.json

@@ -0,0 +1,25 @@
+{
+    "creators": [
+        {
+            "affiliation": "Princeton University",
+            "name": "Kingsbury, Ryan",
+            "orcid": "0000-0002-7168-3967"
+        }
+    ],
+    "rights": [
+        {
+            "description": {
+                "en": ""
+            },
+            "id": "lgpl-3.0-only",
+            "props": {
+                "scheme": "spdx",
+                "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
+            },
+            "title": {
+                "en": "GNU Lesser General Public License v3.0 only"
+            }
+        }
+    ],
+    "title": "pyEQL: A python library for water chemistry"
+}

{pyeql-1.1.6 → pyeql-1.3.0}/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 → pyeql-1.3.0}/CHANGELOG.md

@@ -5,6 +5,91 @@ 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).
 
+## [1.3.0] - 2025-08-08
+
+### Fixed
+
+- `Solution.__add__`: engine, solvent, database were not inherited by the sum of `Solution`
+  objects (#258, @ugognw)
+- `Solution.get_activity_coefficient`: Fixed bugs where incorrect Pitzer scaling parameters $\alpha_1$
+  and $\alpha_2$ parameters were used to calculate activity coefficients and solute molar volumes for salts with multivalent ions (#258, @ugognw)
+- `Solution.get_salt_dict`: fixed errors in the calculation of concentrations for salts
+  containing polyvalent cations (#258, @ugognw)
+- `Solution.get_salt_dict` now respects the `cutoff` parameter. Note that `cutoff`
+  is now interpreted in units of moles per kilogram of solution (#258, @ugognw)
+- `Solution.get_salt_dict` always returns a salt dictionary sorted in order of decreasing salt concentration (#258, @ugognw)
+- `Solution.__init__`: Raise `ValueError` if a user sets inconsistent `H[+1]` in `solutes` and
+  `pH` keyword arguments (#270, @gnuhpdiem, @rkingsbury). Previously, if the user set `H[+1]` in `solutes`, it's value would silently override the `pH` kwarg. Now, you will get a `ValueError`
+  if the two are inconsistent, unless the `pH` kwarg is kept at the default value. In that case,
+  a warning will be logged.
+- `standardize_formula`: properly interpret ambiguous dash / hyphen characters as "minus" (#264, @rkingsbury)
+- Ensure `Solution.p()` always returns a regular `float` and returns `np.nan` if the
+  concentration is zero or negative (#269, @rkingsbury)
+- `Solution.get_diffusion_coefficient`: prevent diffusion coefficient adjustment when temperature
+  is within 1 degree of the the reference value (#215, @YitongPan1)
+- Tests: literature data used in `test_mixed_electrolyte_activity.py` was updated to reflect
+  corrected we recently became aware of. (#271, @Ouriel-N, @rkingsbury)
+- Docs: Sphinx warnings are cleared (#255, ugognw)
+- Docs: Minor fixes for private / cached methods (#197, @githubalexliu)
+- Docs: Edit documentation of `debye_parameter_B` (#196, @YitongPan1)
+
+### Added
+
+- Docs/CI: sphinx linkcheck job and tox environment/command (`tox -e links`) (#255, @ugognw)
+- Docs: add carbonate system tutorial (#204, @NikhilDhruv)
+
+### Changed
+
+- **BREAKING** - the return value of `Solution.get_salt_dict` now includes `Salt` objects instead of keys corresponding
+  to `cation` and `anion`. See the example in the docstring for how to adapt existing code to accommodate this
+  change. (#258, @ugognw)
+- **BREAKING** - `Solution.get_salt_dict` no longer returns an entry for water (#258, @ugognw)
+- **BREAKING** - `Solution.get_salt` will not return water and may return `None` if no salt is present.
+  Previously, `Solution.get_salt` would have returned a `Salt` representing water. (#258, @ugognw)
+- Ensure more consistent column formatting in `Solution.print()` (#269, @rkingsbury)
+- Switch `math.log10` to `np.log10` in `Solution.p()` (#269, @rkingsbury)
+- update pre-commit configuration (#269, @rkingsbury)
+- use [`--dist loadscope`](https://pytest-xdist.readthedocs.io/en/latest/distribution.html) in parallelized CI tests. Closes #170. (#269, @rkingsbury)
+- update license specification in `pyproject.toml` to conform to [latest packaging standards](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license). Closes #233. (#269, @rkingsbury)
+- add `py.typed` to report type checking to other libraries. Closes #179. (#269, @rkingsbury)
+- Support `numpy>2.0`
+- Bump `pint` to `0.24.4` for `numpy` `v2.0` compatibility and to mitigate CI issues (#239, @SuixiongTay, @rkingsbury)
+- CI: add `python` `v3.13` to post-merge unit tests
+- Docs: `tox -e docs` command configured to fail on warning (#255, @ugognw)
+- Docs: ReadTheDocs built with Python 3.11 (#255, ugognw)
+- Use `importlib` to locate test files (#241, @SuixiongTay)
+- Support `numpy>2.0`
+- Bump `pint` to `0.24.4` for `numpy` `v2.0` compatibility and to mitigate CI issues (#239, @SuixiongTay, @rkingsbury)
+- CI: add `python` `v3.13` to post-merge unit tests
+- bump `pymatgen` to `v2025.1.9`
+- bump `maggma` to `v0.71.4`
+
+### Removed
+
+- **BREAKING** Methods previously marked for deprecation - `list_solutes`, `list_activities`,
+  `list_concentrations`, `list_salts` have been removed.
+- `Solution.add_solvent` has been marked for deprecation and will be removed in a future
+  release. Use `add_solute` instead.
+- Python 3.9 version classifier in pyproject.toml (#247, @ugognw)
+- `Solution.list_salts` (use `Solution.get_salt_dict()` instead) (#258)
+
+## [1.2.0] - 2024-09-24
+
+### Fixed
+
+- Database: removed several erroneous species (such as `CO32-` which was really `CO3[-2]`),
+  corrected other parsing errors, and updated formula syntax for consistency with recent
+  `standardize_formula` changes (e.g., `H4NCl -> NH4Cl`) (#190, @rkingsbury)
+
+### Changed
+
+- Bump `pymatgen` to `v2024.9.10` for additional upstream formula fixes. (#188, @abhardwaj73)
+
+### Removed
+
+- **BREAKING** - dropped python 3.9 support, in accordance with numpy deprecation policy.
+  (#188, @abhardwaj73)
+
 ## [1.1.6] - 2024-09-01
 
 ### Fixed

{pyeql-1.1.6 → pyeql-1.3.0}/CITATION.cff

@@ -1,16 +1,16 @@
 cff-version: "1.2.0"
 authors:
-- family-names: Kingsbury
-  given-names: Ryan
-  orcid: "https://orcid.org/0000-0002-7168-3967"
+  - family-names: Kingsbury
+    given-names: Ryan
+    orcid: "https://orcid.org/0000-0002-7168-3967"
 doi: 10.5281/zenodo.8332915
 message: If you use this software, please cite our article in the
   Journal of Open Source Software.
 preferred-citation:
   authors:
-  - family-names: Kingsbury
-    given-names: Ryan
-    orcid: "https://orcid.org/0000-0002-7168-3967"
+    - family-names: Kingsbury
+      given-names: Ryan
+      orcid: "https://orcid.org/0000-0002-7168-3967"
   date-published: 2024-03-25
   doi: 10.21105/joss.06295
   issn: 2475-9066

{pyeql-1.1.6/src/pyEQL.egg-info → pyeql-1.3.0}/PKG-INFO

@@ -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
@@ -15,18 +15,17 @@ 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: pint>=0.24.4
+Requires-Dist: numpy>1.26
 Requires-Dist: scipy>=1.12
-Requires-Dist: pymatgen==2024.5.1
+Requires-Dist: pymatgen>=2025.1.9
 Requires-Dist: iapws>=1.5.3
-Requires-Dist: monty>=2024.7.12
-Requires-Dist: maggma>=0.67.0
+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"
@@ -44,11 +43,12 @@ Requires-Dist: sphinx-rtd-theme; extra == "docs"
 Requires-Dist: myst-parser[linkify]; extra == "docs"
 Provides-Extra: full
 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-1.1.6 → pyeql-1.3.0}/README.md

@@ -1,7 +1,7 @@
 [![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)
@@ -65,7 +65,7 @@ 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-1.1.6 → pyeql-1.3.0}/docs/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 → pyeql-1.3.0}/docs/changelog.md

@@ -5,6 +5,91 @@ 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).
 
+## [1.3.0] - 2025-08-08
+
+### Fixed
+
+- `Solution.__add__`: engine, solvent, database were not inherited by the sum of `Solution`
+  objects (#258, @ugognw)
+- `Solution.get_activity_coefficient`: Fixed bugs where incorrect Pitzer scaling parameters $\alpha_1$
+  and $\alpha_2$ parameters were used to calculate activity coefficients and solute molar volumes for salts with multivalent ions (#258, @ugognw)
+- `Solution.get_salt_dict`: fixed errors in the calculation of concentrations for salts
+  containing polyvalent cations (#258, @ugognw)
+- `Solution.get_salt_dict` now respects the `cutoff` parameter. Note that `cutoff`
+  is now interpreted in units of moles per kilogram of solution (#258, @ugognw)
+- `Solution.get_salt_dict` always returns a salt dictionary sorted in order of decreasing salt concentration (#258, @ugognw)
+- `Solution.__init__`: Raise `ValueError` if a user sets inconsistent `H[+1]` in `solutes` and
+  `pH` keyword arguments (#270, @gnuhpdiem, @rkingsbury). Previously, if the user set `H[+1]` in `solutes`, it's value would silently override the `pH` kwarg. Now, you will get a `ValueError`
+  if the two are inconsistent, unless the `pH` kwarg is kept at the default value. In that case,
+  a warning will be logged.
+- `standardize_formula`: properly interpret ambiguous dash / hyphen characters as "minus" (#264, @rkingsbury)
+- Ensure `Solution.p()` always returns a regular `float` and returns `np.nan` if the
+  concentration is zero or negative (#269, @rkingsbury)
+- `Solution.get_diffusion_coefficient`: prevent diffusion coefficient adjustment when temperature
+  is within 1 degree of the the reference value (#215, @YitongPan1)
+- Tests: literature data used in `test_mixed_electrolyte_activity.py` was updated to reflect
+  corrected we recently became aware of. (#271, @Ouriel-N, @rkingsbury)
+- Docs: Sphinx warnings are cleared (#255, ugognw)
+- Docs: Minor fixes for private / cached methods (#197, @githubalexliu)
+- Docs: Edit documentation of `debye_parameter_B` (#196, @YitongPan1)
+
+### Added
+
+- Docs/CI: sphinx linkcheck job and tox environment/command (`tox -e links`) (#255, @ugognw)
+- Docs: add carbonate system tutorial (#204, @NikhilDhruv)
+
+### Changed
+
+- **BREAKING** - the return value of `Solution.get_salt_dict` now includes `Salt` objects instead of keys corresponding
+  to `cation` and `anion`. See the example in the docstring for how to adapt existing code to accommodate this
+  change. (#258, @ugognw)
+- **BREAKING** - `Solution.get_salt_dict` no longer returns an entry for water (#258, @ugognw)
+- **BREAKING** - `Solution.get_salt` will not return water and may return `None` if no salt is present.
+  Previously, `Solution.get_salt` would have returned a `Salt` representing water. (#258, @ugognw)
+- Ensure more consistent column formatting in `Solution.print()` (#269, @rkingsbury)
+- Switch `math.log10` to `np.log10` in `Solution.p()` (#269, @rkingsbury)
+- update pre-commit configuration (#269, @rkingsbury)
+- use [`--dist loadscope`](https://pytest-xdist.readthedocs.io/en/latest/distribution.html) in parallelized CI tests. Closes #170. (#269, @rkingsbury)
+- update license specification in `pyproject.toml` to conform to [latest packaging standards](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license). Closes #233. (#269, @rkingsbury)
+- add `py.typed` to report type checking to other libraries. Closes #179. (#269, @rkingsbury)
+- Support `numpy>2.0`
+- Bump `pint` to `0.24.4` for `numpy` `v2.0` compatibility and to mitigate CI issues (#239, @SuixiongTay, @rkingsbury)
+- CI: add `python` `v3.13` to post-merge unit tests
+- Docs: `tox -e docs` command configured to fail on warning (#255, @ugognw)
+- Docs: ReadTheDocs built with Python 3.11 (#255, ugognw)
+- Use `importlib` to locate test files (#241, @SuixiongTay)
+- Support `numpy>2.0`
+- Bump `pint` to `0.24.4` for `numpy` `v2.0` compatibility and to mitigate CI issues (#239, @SuixiongTay, @rkingsbury)
+- CI: add `python` `v3.13` to post-merge unit tests
+- bump `pymatgen` to `v2025.1.9`
+- bump `maggma` to `v0.71.4`
+
+### Removed
+
+- **BREAKING** Methods previously marked for deprecation - `list_solutes`, `list_activities`,
+  `list_concentrations`, `list_salts` have been removed.
+- `Solution.add_solvent` has been marked for deprecation and will be removed in a future
+  release. Use `add_solute` instead.
+- Python 3.9 version classifier in pyproject.toml (#247, @ugognw)
+- `Solution.list_salts` (use `Solution.get_salt_dict()` instead) (#258)
+
+## [1.2.0] - 2024-09-24
+
+### Fixed
+
+- Database: removed several erroneous species (such as `CO32-` which was really `CO3[-2]`),
+  corrected other parsing errors, and updated formula syntax for consistency with recent
+  `standardize_formula` changes (e.g., `H4NCl -> NH4Cl`) (#190, @rkingsbury)
+
+### Changed
+
+- Bump `pymatgen` to `v2024.9.10` for additional upstream formula fixes. (#188, @abhardwaj73)
+
+### Removed
+
+- **BREAKING** - dropped python 3.9 support, in accordance with numpy deprecation policy.
+  (#188, @abhardwaj73)
+
 ## [1.1.6] - 2024-09-01
 
 ### Fixed

{pyeql-1.1.6 → pyeql-1.3.0}/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
 ```