pyEQL 1.3.1__tar.gz → 1.4.0rc9__tar.gz

pyeql-1.4.0rc9/.github/workflows/release.yml

@@ -0,0 +1,94 @@
+name: release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  build_sdist:
+    name: Build source
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        ref: ${{ github.event.release.tag_name }}
+
+    - name: Build source
+      run: |
+        python -m pip install pip --upgrade
+        pip install build --upgrade
+        python -m build --sdist --outdir=wheelhouse
+
+    - name: Upload sdist to github
+      uses: actions/upload-artifact@v6
+      with:
+        name: wheels-sdist
+        path: wheelhouse/*.tar.gz
+        if-no-files-found: error
+
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }} for ${{ matrix.cibw_archs }}
+    needs: [build_sdist]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            cibw_archs: "x86_64"
+          - os: ubuntu-24.04-arm
+            cibw_archs: "auto"
+          - os: windows-2022
+            cibw_archs: "auto64"
+          # macos-15-intel for Intel and maos-latest for Apple Silicon
+          - os: macos-15-intel
+            cibw_archs: "x86_64"
+          - os: macos-latest
+            cibw_archs: "arm64"
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        ref: ${{ github.event.release.tag_name }}
+
+    - name: Build wheels
+      uses: pypa/cibuildwheel@v3.3
+      with:
+        config-file: cibuildwheel.toml
+        output-dir: wheelhouse
+      env:
+        CIBW_ENVIRONMENT_MACOS: CMAKE_OSX_ARCHITECTURES=${{ matrix.cibw_archs }}
+
+    - name: Upload artifacts to github
+      uses: actions/upload-artifact@v6
+      with:
+        name: wheels-${{ runner.os }}-${{ matrix.cibw_archs }}
+        path: ./wheelhouse/*.whl
+        if-no-files-found: error
+
+  publish_to_pypi:
+    name: Publish wheels to PyPi
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download packages
+        uses: actions/download-artifact@v7
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Print out packages
+        run: ls -la dist/*
+
+      - name: Upload wheels to pypi
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.pypi_password }}
+        run: |
+          python -m pip install --upgrade pip setuptools wheel packaging twine
+          twine upload dist/*

pyeql-1.4.0rc9/.github/workflows/testing-pinned.yaml

@@ -0,0 +1,40 @@
+name: testing-pinned
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - CHANGELOG.md
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        # We only test on min. and max. supported Python versions here.
+        python-version: ["3.10", "3.13"]
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - macos-14
+          - windows-latest
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+
+      - name: Install requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -e . --no-deps
+
+      - name: Run tests
+        run: |
+          pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope

{pyeql-1.3.1 → pyeql-1.4.0rc9}/.github/workflows/testing.yaml

@@ -10,22 +10,21 @@ on:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   lint:
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 1
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
+
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.11"
-          cache: pip
+          python-version: "3.12"
+
       - name: Run pre-commit
         run: |
           pip install pre-commit
@@ -34,52 +33,59 @@ jobs:
   test:
     needs: lint
     strategy:
-      max-parallel: 6
       matrix:
-        # for most PRs, test the min and max supported python on every platform, test all python on ubuntu
-        python-version: ["3.10", "3.12","3.13"]
-        os:
-          - ubuntu-latest
-          - macos-latest
-          - macos-14
-          - windows-latest
-        include:
-          - os: ubuntu-latest
-            python-version: "3.11"
-          - os: ubuntu-latest
-            python-version: "3.12"
-    runs-on: ${{ matrix.os }}
+        python-version: ["3.10", "3.11", "3.12","3.13"]
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+
       - name: Install test requirements
         run: |
           python -m pip install --upgrade pip
           pip install -e ".[testing]"
+
+      - name: List installed requirements
+        run: |
+          pip freeze
+
       - name: Run tests
         run: |
-          pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope
+          if [[ "${{ matrix.python-version }}" == "3.12" ]]; then
+            pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope
+          else
+            pytest -n auto --dist=loadscope
+          fi
+
       - uses: codecov/codecov-action@v5
+        if: matrix.python-version == '3.12'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
 
   docs:
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           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-1.3.1 → pyeql-1.4.0rc9}/.gitignore

@@ -51,3 +51,6 @@ MANIFEST
 # Per-project virtualenvs
 .venv*/
 .conda*/
+
+# setuptools-scm managed version file
+src/pyEQL/_version.py

{pyeql-1.3.1 → pyeql-1.4.0rc9}/.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: "^docs/conf.py"
+exclude: ^(docs/conf\.py|src/pyEQL/phreeqc/ext|tests/phreeqc/.*\.dat)
 
 default_stages: [pre-commit]
 
@@ -21,17 +21,12 @@ repos:
       # Run the formatter. This WILL run on .ipynb files
       - id: ruff-format
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
-    hooks:
-      - id: black
-
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
-        exclude_types: [html, svg]
+        exclude_types: [html, svg, jupyter]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/pre-commit/pre-commit-hooks

{pyeql-1.3.1 → pyeql-1.4.0rc9}/CHANGELOG.md

@@ -5,6 +5,42 @@ 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).
 
+## [1.4.0rc9] - 2026-02-05
+
+### Added
+
+- `EOS`: Brand new, custom-compiled wrapper that interfaces directly with IPHREEQC modules distributed by USGS. This
+  new PHREEQC interface is accessible via the new `phreeqc2026` electrolyte modeling engine, and will be used
+  by default in the `native` engine in `v1.5.0`. (#306, #318, #318, #319, @vineetbansal)
+
+### Changed
+
+- `Solution.equilibrate`: Added support for solid-liquid and gas-liquid equilibrium via three new kwargs - `atmopshere`,
+  `solids`, and `gases`. See docstring for details and usage.(#292, #294, @vineetbansal, @YitongPan1, @SuixiongTay)
+- `get_components_by_element`: A new keyword argument `nested` was added to methods `get_components_by_element`
+  and `get_el_amt_dict` of the `Solution` class. It defaults to `False` (no change from prior behavior), but
+  can be set to `True` to return a 2-level dictionary, with the element symbol as the key at the top level, and
+  the valence (float, or "unk" for unknown) as the key at the second level. This should make it easier for future
+  code to calculate the total amount of a given element regardless of its valence. (#284, @vineetbansal)
+
+### Fixed
+
+- `NativeEOS` `equilibrate`: We check if the total amount for any element decreases (within a tolerance of 1e-16 moles)
+  after speciation. If so, we add all species containing that element back in (unless they have been added by Phreeqc
+  already). As a result, we replace neutral (aq) molecules, and ions with incorrect charge, with ions with charge
+  determined by phreeqc, without double-counting. Missing elements (e.g. Rh) are handled correctly as well, since species
+  with the missing element are re-introduced in the solution. (#282, @vineetbansal)
+- `standardize_formula`: Fixed incorrect reduction of dimers. For example, `(CO2)2` was being standardized to `CO2`, which
+  could cause incorrect concentrations to be reported. Dimers are no longer reduced. (#309, @vineetbansal)
+
+## [1.3.2] - 2025-09-15
+
+### Fixed
+
+- `Solution.get_viscosity_kinematic()`: A recent change to get_salt_dict (#258) created a problem with `get_viscosity_kinetmatic`
+  in which an empty solution would cause the method to return an error. This has been fixed, and unit tests added for both
+  `get_viscosity_kinematic` and `get_viscosity_dynamic`.
+
 ## [1.3.1] - 2025-08-18
 
 ### Fixed

pyeql-1.4.0rc9/CMakeLists.txt

@@ -0,0 +1,61 @@
+cmake_minimum_required(VERSION 3.15...3.26)
+project(
+  "${SKBUILD_PROJECT_NAME}"
+  LANGUAGES CXX
+  VERSION "${SKBUILD_PROJECT_VERSION}")
+
+option(PYEQL_ENABLE_EXT "Build and install IPhreeqc support" ON)
+
+if(PYEQL_ENABLE_EXT)
+    find_package(
+      Python
+      COMPONENTS Interpreter Development.Module
+      REQUIRED)
+    find_package(pybind11 CONFIG REQUIRED)
+
+    # -------------------------------------------------------
+    # Setup for IPhreeqc
+    # -------------------------------------------------------
+    set(IPHREEQC_BASE ${CMAKE_CURRENT_SOURCE_DIR}/src/pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100)
+    set(IPHREEQC_DIR         ${IPHREEQC_BASE})
+    set(IPHREEQC_INCLUDE_DIRS
+        ${IPHREEQC_BASE}/src
+        ${IPHREEQC_BASE}/src/phreeqcpp/common
+    )
+    include_directories(${IPHREEQC_INCLUDE_DIRS})
+    set(IPHREEQC_BUILD_DIR   ${IPHREEQC_BASE}/build)
+    add_subdirectory(${IPHREEQC_DIR} ${IPHREEQC_BUILD_DIR})
+    set_target_properties(IPhreeqc PROPERTIES POSITION_INDEPENDENT_CODE ON)
+    # -------------------------------------------------------
+
+    # -------------------------------------------------------
+    # Setup for pyEQL._phreeqc
+    # -------------------------------------------------------
+    pybind11_add_module(_phreeqc ${CMAKE_CURRENT_SOURCE_DIR}/src/pyEQL/phreeqc/bindings.cpp)
+    target_compile_definitions(_phreeqc
+                               PRIVATE VERSION_INFO=${PROJECT_VERSION})
+    target_link_libraries(_phreeqc PRIVATE IPhreeqc)
+    install(TARGETS _phreeqc LIBRARY DESTINATION pyEQL COMPONENT python)
+
+    # -------------------------------------------------------
+    # IPhreeqc databases
+    # -------------------------------------------------------
+    # Till we find a way to extract artifacts from IPhreeqc's install folder
+    # through scikit-build-core, we define a COMPONENT that allows us to
+    # copy the database files.
+    set(IPHREEQC_DATABASE_DIR   ${IPHREEQC_BASE}/database)
+    install(DIRECTORY
+           "${IPHREEQC_DATABASE_DIR}"
+           DESTINATION pyEQL/phreeqc COMPONENT iphreeqc_database)
+    # Make it a python module so we can access it using importlib.resources
+    file(GENERATE
+        OUTPUT "__init__.py"
+        CONTENT ""
+    )
+    install(FILES
+            "${CMAKE_CURRENT_BINARY_DIR}/__init__.py"
+            DESTINATION pyEQL/phreeqc/database
+            COMPONENT iphreeqc_database
+    )
+    # -------------------------------------------------------
+endif()

{pyeql-1.3.1/src/pyEQL.egg-info → pyeql-1.4.0rc9}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.4
 Name: pyEQL
-Version: 1.3.1
+Version: 1.4.0rc9
 Summary: A python interface for solution chemistry
-Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
+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
+License-File: AUTHORS.md
+License-File: LICENSE.txt
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -15,10 +14,10 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
+Project-URL: Docs, https://pyeql.readthedocs.io/
+Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
+Project-URL: Package, https://pypi.org/project/pyEQL
 Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-License-File: AUTHORS.md
 Requires-Dist: pint>=0.24.4
 Requires-Dist: numpy>1.26
 Requires-Dist: scipy>=1.12
@@ -43,7 +42,7 @@ 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
+Description-Content-Type: text/markdown
 
 [![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)

pyeql-1.4.0rc9/cibuildwheel.toml

@@ -0,0 +1,10 @@
+[tool.cibuildwheel]
+build = "cp3*"
+skip = ["cp314*", "*-win32", "*-manylinux_i686", "*-musllinux_*"]
+build-verbosity = 1
+test-extras = ["testing"]
+# 01/24/26 - The latest version of scipy, 1.17.0, cannot be built on
+# manylinux without OpenBLAS. Skip it by pre-installing a binary version.
+before-test = "pip install scipy --prefer-binary"
+# For now, we only run the tests that are wrapper specific in cibuildwheel.
+test-command = "python -m pytest {project}/tests/test_pyeql_phreeqc.py"

pyeql-1.4.0rc9/docs/authors.md

@@ -0,0 +1 @@
+../AUTHORS.md

pyeql-1.4.0rc9/docs/changelog.md

@@ -0,0 +1 @@
+../CHANGELOG.md

{pyeql-1.3.1 → pyeql-1.4.0rc9}/docs/conf.py

@@ -315,7 +315,8 @@ linkcheck_allowed_redirects = {
     r"http://pint\.readthedocs\.io": r"https://pint\.readthedocs\.io/.*/stable",
     r"https://tox\.wiki": r"https://tox\.wiki/.*",
 }
-linkcheck_ignore = [r"https://localhost:\d+/"]
+# https://idst.inl.gov/ is reachable, just not from the github runner.
+linkcheck_ignore = [r"https://localhost:\d+/", r"^https://idst\.inl\.gov/$"]
 linkcheck_rate_limit_timeout = 500
 
 print(f"loading configurations for {project} {version} ...", file=sys.stderr)

{pyeql-1.3.1 → pyeql-1.4.0rc9}/docs/examples/pyeql_tutorial_carbonate.ipynb

@@ -62,7 +62,7 @@
     "# Import the pyEQL library and other necessary modules\n",
     "import pyEQL\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -143,9 +143,9 @@
    "outputs": [],
    "source": [
     "initial_conditions = {\n",
-    "    'HCO3-': 1.0e-3,\n",
-    "    'CO3--': 1.0e-4,\n",
-    "    'H+': 1.0e-7 # Note: instead of including H+ here, you could use the pH keyword argument\n",
+    "    \"HCO3-\": 1.0e-3,\n",
+    "    \"CO3--\": 1.0e-4,\n",
+    "    \"H+\": 1.0e-7,  # Note: instead of including H+ here, you could use the pH keyword argument\n",
     "}"
    ]
   },
@@ -225,7 +225,7 @@
    ],
    "source": [
     "# Retrieve equilibrium concentrations using get_amount\n",
-    "{species: solution.get_amount(species, 'mol/L').magnitude for species in solution.components}"
+    "{species: solution.get_amount(species, \"mol/L\").magnitude for species in solution.components}"
    ]
   },
   {
@@ -272,7 +272,7 @@
    "source": [
     "solution.equilibrate()\n",
     "# Retrieve equilibrium concentrations using get_amount\n",
-    "{species: solution.get_amount(species, 'mol/L').magnitude for species in solution.components}"
+    "{species: solution.get_amount(species, \"mol/L\").magnitude for species in solution.components}"
    ]
   },
   {
@@ -322,7 +322,7 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# iterate through several pH values, re-equilibrating the solution each time the pH changes\n",
-    "phs = np.arange(0,13.5, 0.5)\n",
+    "phs = np.arange(0, 13.5, 0.5)\n",
     "# store the species concentrations in these lists\n",
     "h2co3 = []\n",
     "hco3 = []\n",
@@ -333,25 +333,25 @@
     "    # create a solution with 1 mM total carbonate, then equilibrate\n",
     "    s = pyEQL.Solution({\"Na+\": \"1e-3 mol/L\", \"HCO3-\": \"1e-3 mol/L\"}, pH=ph)\n",
     "    s.equilibrate()\n",
-    "    h2co3.append(s.get_amount('H2CO3', 'mM').magnitude)\n",
-    "    hco3.append(s.get_amount('HCO3-', 'mM').magnitude)\n",
-    "    co3.append(s.get_amount('CO3-2', 'mM').magnitude)\n",
-    "    co2.append(s.get_amount('CO2', 'mM').magnitude)\n",
+    "    h2co3.append(s.get_amount(\"H2CO3\", \"mM\").magnitude)\n",
+    "    hco3.append(s.get_amount(\"HCO3-\", \"mM\").magnitude)\n",
+    "    co3.append(s.get_amount(\"CO3-2\", \"mM\").magnitude)\n",
+    "    co2.append(s.get_amount(\"CO2\", \"mM\").magnitude)\n",
     "\n",
     "# Plotting the equilibrium concentrations\n",
-    "plt.figure(figsize=(8,4))\n",
-    "plt.plot(phs, h2co3, color='skyblue', label=r\"H$_2$CO$_3$\")\n",
-    "plt.plot(phs, hco3, color='g', label=r\"HCO$_3^{-1}$\")\n",
-    "plt.plot(phs, co3, color='r', label=r\"CO$_3^{-2}$\")\n",
-    "plt.plot(phs, co2, color='b', label=r\"CO$_2$(aq)\")\n",
+    "plt.figure(figsize=(8, 4))\n",
+    "plt.plot(phs, h2co3, color=\"skyblue\", label=r\"H$_2$CO$_3$\")\n",
+    "plt.plot(phs, hco3, color=\"g\", label=r\"HCO$_3^{-1}$\")\n",
+    "plt.plot(phs, co3, color=\"r\", label=r\"CO$_3^{-2}$\")\n",
+    "plt.plot(phs, co2, color=\"b\", label=r\"CO$_2$(aq)\")\n",
     "\n",
     "# add a horizontal line for the total carbonate concentration\n",
     "plt.axhline(1, ls=\"--\", color=\"k\")\n",
     "# add labels and legend\n",
-    "plt.xlabel('pH')\n",
-    "plt.ylabel('Concentration (mmol/L)')\n",
+    "plt.xlabel(\"pH\")\n",
+    "plt.ylabel(\"Concentration (mmol/L)\")\n",
     "plt.legend()\n",
-    "plt.title('Equilibrium Concentrations of Carbonate System Species')\n",
+    "plt.title(\"Equilibrium Concentrations of Carbonate System Species\")\n",
     "plt.show()"
    ]
   },

{pyeql-1.3.1 → pyeql-1.4.0rc9}/docs/installation.md

@@ -68,7 +68,7 @@ pyEQL also requires the following packages:
 - [pint](https://github.com/hgrecco/pint) - for automated unit conversion
 - [pymatgen](https://github.com/materialsproject/pymatgen/) - used to interpret chemical formulas
 - [iapws](https://github.com/jjgomera/iapws/) - used to calculate the properties of water
-- [monty](https://github.com/materialsvirtuallab/monty) - used for saving and loading `Solution` objects to files
+- [monty](https://github.com/materialyzeai/monty) - used for saving and loading `Solution` objects to files
 - [maggma](https://materialsproject.github.io/maggma/) - used by the internal property database
 - [scipy](https://scipy.org/)
 - [numpy](https://numpy.org/)

{pyeql-1.3.1 → pyeql-1.4.0rc9}/pyproject.toml

@@ -56,9 +56,15 @@ docs = [
 full = ["rich"]
 
 [build-system]
-# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
-requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core", "pybind11", "setuptools_scm[toml]>=5"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+install.components = ["python", "iphreeqc_database"]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+
+[tool.scikit-build.cmake.define]
+PYEQL_ENABLE_EXT = {env="PYEQL_ENABLE_EXT"}
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -66,7 +72,7 @@ exclude = ["tests"]
 
 [tool.setuptools_scm]
 # See configuration details in https://github.com/pypa/setuptools_scm
-version_scheme = "no-guess-dev"
+write_to = "src/pyEQL/_version.py"
 
 [tool.black]
 line-length = 120