Merge branch 'main' into dev

KingsburyLab · Sep 18, 2024 · df8d693 · df8d693
2 parents d7ec1a0 + 95dcffd
commit df8d693
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diff --git a/.github/workflows/post-process.yml b/.github/workflows/post-process.yml
@@ -34,7 +34,6 @@ 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 }
@@ -43,10 +42,6 @@ jobs:
           - macos-latest
           - windows-latest
           - macos-14
-        exclude:
-          - {version: {
-               python: "3.9" },
-            os: macos-14 }
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -57,4 +57,4 @@ jobs:
           tox -e clean,build
 
       - name: Upload to PyPi
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.1
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -23,7 +23,7 @@ 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: |
@@ -36,7 +36,7 @@ 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"]
         os:
           - ubuntu-latest
           - macos-latest
@@ -47,10 +47,6 @@ jobs:
             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"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -77,7 +73,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Install tox
         run: |
           python -m pip install tox

diff --git a/.github/workflows/upgrade_dependencies.yml b/.github/workflows/upgrade_dependencies.yml
@@ -6,25 +6,25 @@ 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:
     name: ${{ matrix.package }} (${{ matrix.os }}/py${{ matrix.python-version }})
     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:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
+          cache: "pip"
       - name: Upgrade Python dependencies
         shell: bash
         run: |

diff --git a/AUTHORS.md b/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)
diff --git a/CHANGELOG.md b/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

diff --git a/README.md b/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

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -4,7 +4,7 @@
 pint>=0.19
 numpy
 scipy
-pymatgen>=2023.10.11
+pymatgen>=2024.9.10
 iapws
 monty
 maggma

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,12 +18,12 @@ classifiers=[
         "Topic :: Scientific/Engineering",
     ]
 license = {file = "LICENSE"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
         "pint>=0.19",
         "numpy>1.26,<2",
         "scipy>=1.12",
-        "pymatgen==2024.5.1",
+        "pymatgen>=2024.9.10",
         "iapws>=1.5.3",
         "monty>=2024.7.29",
         "maggma>=0.67.0",

diff --git a/requirements/macos-latest_py3.10.txt b/requirements/macos-latest_py3.10.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.10_extras.txt b/requirements/macos-latest_py3.10_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.11.txt b/requirements/macos-latest_py3.11.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.11_extras.txt b/requirements/macos-latest_py3.11_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.12.txt b/requirements/macos-latest_py3.12.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.12_extras.txt b/requirements/macos-latest_py3.12_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.9.txt b/requirements/macos-latest_py3.9.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/macos-latest_py3.9_extras.txt b/requirements/macos-latest_py3.9_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.10_extras.txt b/requirements/ubuntu-latest_py3.10_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.11_extras.txt b/requirements/ubuntu-latest_py3.11_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.12.txt b/requirements/ubuntu-latest_py3.12.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.12_extras.txt b/requirements/ubuntu-latest_py3.12_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/ubuntu-latest_py3.9_extras.txt b/requirements/ubuntu-latest_py3.9_extras.txt
@@ -45,7 +45,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.10.txt b/requirements/windows-latest_py3.10.txt
@@ -35,7 +35,7 @@ colorama==0.4.6
     # via tqdm
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.10_extras.txt b/requirements/windows-latest_py3.10_extras.txt
@@ -52,7 +52,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.11.txt b/requirements/windows-latest_py3.11.txt
@@ -35,7 +35,7 @@ colorama==0.4.6
     # via tqdm
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.11_extras.txt b/requirements/windows-latest_py3.11_extras.txt
@@ -52,7 +52,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.12.txt b/requirements/windows-latest_py3.12.txt
@@ -35,7 +35,7 @@ colorama==0.4.6
     # via tqdm
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.12_extras.txt b/requirements/windows-latest_py3.12_extras.txt
@@ -52,7 +52,7 @@ contourpy==1.2.1
     # via matplotlib
 coverage[toml]==7.6.1
     # via pytest-cov
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib

diff --git a/requirements/windows-latest_py3.9.txt b/requirements/windows-latest_py3.9.txt
@@ -35,7 +35,7 @@ colorama==0.4.6
     # via tqdm
 contourpy==1.2.1
     # via matplotlib
-cryptography==43.0.0
+cryptography==43.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib