pyEQL 1.3.2__tar.gz → 1.4.0__tar.gz

pyeql-1.4.0/.github/workflows/docs.yml

@@ -0,0 +1,33 @@
+name: docs
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - CHANGELOG.md
+      - AUTHORS.md
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        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-1.4.0/.github/workflows/lint.yml

@@ -0,0 +1,22 @@
+name: lint
+
+on:
+  workflow_call:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Run pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit run

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

@@ -0,0 +1,93 @@
+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
+    # https://docs.pypi.org/trusted-publishers/using-a-publisher/
+    environment: publish
+    permissions:
+      id-token: write
+    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: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

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

@@ -0,0 +1,46 @@
+name: testing-pinned
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - CHANGELOG.md
+      - AUTHORS.md
+      - docs/**
+
+jobs:
+  lint:
+    uses: ./.github/workflows/lint.yml
+
+  test:
+    needs: [lint]
+    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-1.4.0/.github/workflows/testing.yaml

@@ -0,0 +1,56 @@
+name: testing
+
+on:
+  pull_request:
+    branches:
+      - main
+      - pourbaix
+    paths-ignore:
+      - CHANGELOG.md
+      - AUTHORS.md
+      - docs/**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  lint:
+    uses: ./.github/workflows/lint.yml
+
+  test:
+    needs: [lint]
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12","3.13"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        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: |
+          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

{pyeql-1.3.2 → pyeql-1.4.0}/.gitignore

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

{pyeql-1.3.2 → pyeql-1.4.0}/.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-1.3.2 → pyeql-1.4.0}/AUTHORS.md

@@ -5,6 +5,7 @@ developed and maintained by the Kingsbury Lab at Princeton University.
 
 Other contributors, listed alphabetically, are:
 
+- Vineet Basal (@vineetbansal)
 - Arpit Bhardwaj (@abhardwaj73)
 - Nikhil Dhruv (@NikhilDhruv)
 - Dhruv Duseja (@DhruvDuseja)

{pyeql-1.3.2 → pyeql-1.4.0}/CHANGELOG.md

@@ -5,6 +5,47 @@ 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).
 
+## [1.4.0] - 2026-02-17
+
+### Added
+
+- `Phreeqc2026EOS`: 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, #333, # @vineetbansal)
+- `Solution.from_preset`: Added presets for 22 representative industrial wastewater compositions, explained in detail in
+  our recent preprint "Composition and Critical Mineral Content of Major Industrial Wastewaters: Implications for
+  Treatment and Resource Recovery Technologies," available at [https://doi.org/10.21203/rs.3.rs-8743330/v2]
+
+### 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, #339, @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)
+- `Solution.get_property`: Changed the `lru_cache` size to greatly enhance performance when creating `Solution` that
+  contain a large number of solutes (@vineetbansal, @SuixiongTay)
+- Docs: `sphinx-material` theme migrated to `sphinx-immaterial` (#272, @ugognw, @rkingsbury)
+- Docs: resolved all the `spinx` build warnings and errors (#338, @vineetbansal)
+- Docs: Added documentation of `phreeqc2026` engine and new `equilibrate` features (#344, #349, @SuixiongTay, @YitongPan1)
+- CI: Various changes to optimize our continuous integration testing workflows. Notably, changes to the docs (only) no
+  longer trigger unit tests of the code (only of the docs), and now test against a specific set of pinned dependencies
+  from `requirements.txt`. (#285, #314, #320, #327, #328, #330, #340, @vineetbansal, @rkingsbury)
+
+### Fixed
+
+- `NativeEOS` `equilibrate`: Fixed a bug in which instantiating a solution with pure elements (e.g., `{'Na': '0.5 mol/L'}`)
+  and then calling `equilibrate` could cause that element to be "double counted." In other words, speciation calculations
+  would add `Na[+1]` to the solution but retain `Na` as well. This now works correctly. In addition, elements or species
+  that are missing from PHREEQC's database (e.g. Rh) are handled more robustly. (#282, #352, #355, @vineetbansal, @rkingsbury)
+- `from_file`: Instantiating a `Solution` from a .yaml file now gives slightly more accurate results. Previously, there were
+  slight discrepancies in the volume of the loaded solution, compared to loading from .json or `dict`. (#347, @rkingsbury)
+- `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)
+- `FormulaDict`: ensured that quantities are always represented by `python` floats and not `np.float64` (#342, @rkingsbury)
+
 ## [1.3.2] - 2025-09-15
 
 ### Fixed
@@ -71,7 +112,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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: `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`

pyeql-1.4.0/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-1.3.2/src/pyEQL.egg-info → pyeql-1.4.0}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.4
 Name: pyEQL
-Version: 1.3.2
+Version: 1.4.0
 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-1.4.0/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_engine_phreeqc2026.py"

pyeql-1.4.0/docs/authors.md

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

pyeql-1.4.0/docs/changelog.md

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

{pyeql-1.3.2 → pyeql-1.4.0}/docs/class_solution.md

@@ -9,8 +9,7 @@ This page contains detailed information on each of the methods, attributes, and
 ```{eval-rst}
 .. autoclass:: pyEQL.Solution
    :members:
-   :inherited-members:
+   :exclude-members: save
    :private-members: _get_property, _get_diffusion_coefficient, _get_molar_conductivity, _get_mobility
-   :special-members: __init__
    :member-order: bysource
 ```

{pyeql-1.3.2 → pyeql-1.4.0}/docs/conf.py

@@ -47,6 +47,7 @@ templates_path = ["_templates"]
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
+    "sphinx_immaterial",
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
@@ -166,7 +167,7 @@ todo_emit_warnings = True
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "sphinx_material"
+html_theme = "sphinx_immaterial"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -174,16 +175,12 @@ html_theme = "sphinx_material"
 html_theme_options = {
     # "sidebar_width": "300px",
     # "page_width": "1200px",
-    "base_url": "https://pyeql.readthedocs.io/en/latest/",
+    "site_url": "https://pyeql.readthedocs.io/en/latest/",
     "repo_url": "https://github.com/KingsburyLab/pyEQL/",
     "repo_name": "pyEQL",
     # 'logo_icon': 'e798',
-    "html_minify": True,
-    "css_minify": True,
-    "nav_title": "pyEQL: a python interface for water chemistry",
-    "color_primary": "blue",
-    "color_accent": "light-blue",
-    "globaltoc_depth": 2,
+    "toc_title": "pyEQL: a python interface for water chemistry",
+    "palette": { "primary": "blue", "accent": "light-blue" },
     "globaltoc_collapse": True,
 }
 html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]}
@@ -315,7 +312,8 @@ 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-1.3.2 → pyeql-1.4.0}/docs/contributing.md

@@ -128,7 +128,7 @@ Please abide by the following guidelines when contributing code to `pyEQL`:
 
 ## Documentation
 
-Improvements to the documentation are most welcome! Our documentation system uses `sphinx` with the [Materials for Sphinx](https://bashtage.github.io/sphinx-material/) theme. To edit the documentation locally, run `tox -e autodocs` from the repository root directory. This will serve the documents to `http://localhost:8000/` so you can view them in your web browser. When you make changes to the files in the `docs/` directory, the documentation will automatically rebuild and update in your browser (you might have to refresh the page to see changes).
+Improvements to the documentation are most welcome! Our documentation system uses `sphinx` with the [Sphinx-Immaterial](https://jbms.github.io/sphinx-immaterial/) theme. To edit the documentation locally, run `tox -e autodocs` from the repository root directory. This will serve the documents to `http://localhost:8000/` so you can view them in your web browser. When you make changes to the files in the `docs/` directory, the documentation will automatically rebuild and update in your browser (you might have to refresh the page to see changes).
 
 ## Changelog
 

{pyeql-1.3.2 → pyeql-1.4.0}/docs/engines.md

@@ -73,14 +73,25 @@ there may be subtle thermodynamic inconsistencies between the activities and the
 concentrations returned by `equilibrate()`.
 ```
 
+## The `'phreeqc2026'` engine
+
+The `phreeqc2026` engine uses [`pyEQL.phreeqc`](https://github.com/KingsburyLab/pyEQL/tree/d323606e022825737c1663ee620dfa6180d2bebb/src/pyEQL/phreeqc)
+for speciation, activity, and volume calculations. The PHREEQC engine
+uses the `phreeqc.dat (v3.8)` PHREEQC database by default, although it is possible to instantiate
+the engine with other databases such as `llnl.dat`, `pitzer.dat`, `vitens.dat`, `wateq4f_PWN.dat`, and `geothermal.dat`. See
+`pyEQL.engine.Phreeqc2026EOS.equilibrate()` in the [module reference](internal.md#speciation-functions)
+for more details.
+Older version provided in `pyEQL.equilibrium.equilibrate_phreeqc` has been removed and absorbed in `NativeEOS`, `Phreeqc2026EOS`, and `PhreeqcEOS`.
+
 ## The `'phreeqc'` engine
 
 The `phreeqc` engine uses [`phreeqpython`](https://github.com/Vitens/phreeqpython)
 for speciation, activity, and volume calculations. The PHREEQC engine
-uses the `phreeqc.dat` PHREEQC database by default, although it is possible to instantiate
-the engine with other databases such as `llnl.dat`, `pitzer.dat`, etc. See
-`pyEQL.equilibrium.eqiulibrate_phreeqc` in the [module reference](internal.md#speciation-functions)
+uses the `phreeqc.dat (v3.7)` PHREEQC database by default, although it is possible to instantiate
+the engine with other databases such as `llnl.dat`, `pitzer.dat`, `vitens.dat`, `wateq4f_PWN.dat`, and `geothermal.dat`. See
+`pyEQL.engine.PhreeqcEOS.equilibrate()` in the [module reference](internal.md#speciation-functions)
 for more details.
+Older version provided in `pyEQL.equilibrium.equilibrate_phreeqc` has been removed and absorbed in `NativeEOS`, `Phreeqc2026EOS`, and `PhreeqcEOS`.
 
 ### Activity and osmotic coefficients
 

{pyeql-1.3.2 → pyeql-1.4.0}/docs/examples/pyeql_tutorial_activity.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "### Different modeling engines\n",
     "\n",
-    "When creating a `Solution`, you can use the `engine` keyword argument to specify which [Electrolyte Modeling Engine](https://pyeql.readthedocs.io/en/latest/engines.html#engines--page-root) you want to use.\n",
+    "When creating a `Solution`, you can use the `engine` keyword argument to specify which [Electrolyte Modeling Engine](https://pyeql.readthedocs.io/en/latest/engines.html) you want to use.\n",
     "\n",
     "- [`ideal`](https://pyeql.readthedocs.io/en/latest/engines.html#the-ideal-engine): Ideal solution model\n",
     "- [`phreeqc`](https://pyeql.readthedocs.io/en/latest/engines.html#the-phreeqc-engine): Uses `phreeqpython` with `phreeqc.dat`\n",