pymatgen>=2024.9.10 updated after bugfix and conflict resolve

.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

.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

.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: |

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

docs/requirements.txt

@@ -4,7 +4,7 @@
 pint>=0.19
 numpy
 scipy
-pymatgen>=2023.10.11
+pymatgen>=2024.9.10
 iapws
 monty
 maggma

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>=2024.7.12",
         "maggma>=0.67.0",

tests/test_phreeqc.py

@@ -131,7 +131,7 @@ def test_conductivity(s1):
     # even an empty solution should have some conductivity
     assert s1.conductivity > 0
 
-    for conc, cond in zip([0.001, 0.05, 0.1], [123.68, 111.01, 106.69]):
+    for conc, cond in zip([0.001, 0.05, 0.1], [123.68, 111.01, 106.69], strict=False):
         s1 = Solution({"Na+": f"{conc} mol/L", "Cl-": f"{conc} mol/L"})
         assert np.isclose(
             s1.conductivity.to("S/m").magnitude, conc * cond / 10, atol=0.5
@@ -142,7 +142,7 @@ def test_conductivity(s1):
     assert np.isclose(s1.conductivity.to("mS/cm").magnitude, 145, atol=10)
 
     # MgCl2
-    for conc, cond in zip([0.001, 0.05, 0.1], [124.15, 114.49, 97.05]):
+    for conc, cond in zip([0.001, 0.05, 0.1], [124.15, 114.49, 97.05], strict=False):
         s1 = Solution({"Mg+2": f"{conc} mol/L", "Cl-": f"{2*conc} mol/L"})
         assert np.isclose(
             s1.conductivity.to("S/m").magnitude, 2 * conc * cond / 10, atol=1
@@ -232,7 +232,7 @@ def test_equilibrate(s1, s2, s5_pH, s6_Ca, caplog):
     set(s5_pH.components.keys())
     s5_pH.equilibrate()
     assert np.isclose(s5_pH.get_total_amount("Ca", "mol").magnitude, 0.001)
-    assert np.isclose(s5_pH.get_total_amount("C(4)", "mol").magnitude, 0.001)
+    assert np.isclose(s5_pH.get_total_amount("C(4)", "mol").magnitude, 0.0011)
     # due to the large pH shift, water mass and density need not be perfectly conserved
     assert np.isclose(s5_pH.solvent_mass.magnitude, orig_solv_mass, atol=1e-3)
     assert np.isclose(s5_pH.density.magnitude, orig_density, atol=1e-3)