pyEQL 1.2.0__tar.gz → 1.3.0__tar.gz

{pyeql-1.2.0 → pyeql-1.3.0}/.github/workflows/post-process.yml

@@ -37,6 +37,7 @@ jobs:
           - { 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
@@ -56,8 +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-1.2.0 → 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@v1.10.1
+        uses: pypa/gh-action-pypi-publish@v1.12.4

{pyeql-1.2.0 → pyeql-1.3.0}/.github/workflows/testing.yaml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - main
+      - pourbaix
     paths-ignore:
       - CHANGELOG.md
 
@@ -36,17 +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: ["3.10", "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"
+          - os: ubuntu-latest
+            python-version: "3.12"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -60,8 +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
@@ -73,10 +74,12 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          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-1.2.0 → 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: v0.6.7
+    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: 24.8.0
+    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]
+      - id: check-yaml
+      - id: check-json
       - id: pretty-format-json
-        indent: 4
         exclude_types: [jupyter]
-      - id: check-yaml
-      - id: check-toml
+        args: [--autofix, --indent=4]

{pyeql-1.2.0 → 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-1.2.0 → 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-1.2.0 → pyeql-1.3.0}/CHANGELOG.md

@@ -5,6 +5,74 @@ 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

{pyeql-1.2.0/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: 1.2.0
+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
@@ -18,15 +18,14 @@ Classifier: Topic :: Scientific/Engineering
 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>=2024.9.10
+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"
@@ -44,6 +43,7 @@ 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
 
 [![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-1.2.0 → 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-1.2.0 → pyeql-1.3.0}/docs/changelog.md

@@ -5,6 +5,74 @@ 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

{pyeql-1.2.0 → 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
 ```

{pyeql-1.2.0 → pyeql-1.3.0}/docs/conf.py

@@ -8,8 +8,8 @@
 # serve to show the default.
 
 import os
-import sys
 import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
@@ -28,32 +28,14 @@ sys.path.insert(0, os.path.join(__location__, "../src"))
 # setup.py install" in the RTD Advanced Settings.
 # Additionally it helps us to avoid running apidoc manually
 
-try:  # for Sphinx >= 1.7
-    from sphinx.ext import apidoc
-except ImportError:
-    from sphinx import apidoc
-
 output_dir = os.path.join(__location__, "api")
 module_dir = os.path.join(__location__, "../src/pyEQL")
+
 try:
     shutil.rmtree(output_dir)
 except FileNotFoundError:
     pass
 
-try:
-    import sphinx
-
-    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
-
-    args = cmd_line.split(" ")
-    if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
-        # This is a rudimentary parse_version to avoid external dependencies
-        args = args[1:]
-
-    apidoc.main(args)
-except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
-
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -76,6 +58,7 @@ extensions = [
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "nbsphinx",
+    "IPython.sphinxext.ipython_console_highlighting",
 ]
 
 # Enable markdown
@@ -94,6 +77,8 @@ myst_enable_extensions = [
     "substitution",
     "tasklist",
 ]
+# Required to cross-reference header anchors in markdown files
+myst_heading_anchors = 3
 
 # always execute notebooks when compiling docs
 # nbsphinx_execute = 'always'
@@ -166,6 +151,13 @@ pygments_style = "sphinx"
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
 
+# A list of modules from which warnings will be suppressed
+suppress_warnings = [
+    # This ignores a warning resulting from some extensions storing function, class, or module objects in html_context
+    # see https://github.com/sphinx-doc/sphinx/issues/12300 for details
+    "config.cache"
+]
+
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
@@ -182,21 +174,19 @@ html_theme = "sphinx_material"
 html_theme_options = {
     # "sidebar_width": "300px",
     # "page_width": "1200px",
-    'base_url': 'https://pyeql.readthedocs.io/en/latest/',
-    'repo_url': 'https://github.com/KingsburyLab/pyEQL/',
-    'repo_name': 'pyEQL',
+    "base_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,
-    'globaltoc_collapse': True,
-}
-html_sidebars = {
-    "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
+    "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,
+    "globaltoc_collapse": True,
 }
+html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
@@ -280,9 +270,7 @@ latex_elements = {
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
-    ("index", "user_guide.tex", "pyEQL Documentation", "Ryan Kingsbury", "manual")
-]
+latex_documents = [("index", "user_guide.tex", "pyEQL Documentation", "Ryan Kingsbury", "manual")]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
@@ -309,7 +297,7 @@ python_version = ".".join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
     "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "python": ("https://docs.python.org/" + python_version, None),
-    "matplotlib": ("https://matplotlib.org", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
@@ -318,4 +306,16 @@ intersphinx_mapping = {
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
 
+# -- Linkcheck options -------------------------------------------------------
+linkcheck_allowed_redirects = {
+    r"http://dx\.doi\.org/10\.1016/S0927-5193\(04\)80033-0": r"https://linkinghub\.elsevier\.com/retrieve/pii/S0927519304800330",
+    r"https://doi\.org/10\.1016/j\.desal\.2013\.03\.015": r"https://linkinghub\.elsevier\.com/retrieve/pii/S0011916413001409",
+    r"https://dx\.doi\.org/10\.1016/j\.cemconres\.2017\.08\.030": r"https://linkinghub\.elsevier\.com/retrieve/pii/S0008884617301965",
+    r"https://doi\.org/10\.1016/j\.earscirev\.2021\.103888": r"https://linkinghub.elsevier\.com/retrieve/pii/S0012825221003895",
+    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+/"]
+linkcheck_rate_limit_timeout = 500
+
 print(f"loading configurations for {project} {version} ...", file=sys.stderr)

{pyeql-1.2.0 → pyeql-1.3.0}/docs/contributing.md

@@ -39,22 +39,22 @@ submit your proposal.
 ```
 
 When working on documentation changes in your local machine, you can
-compile them using [tox] :
+compile them using [tox](https://tox.wiki):
 
-```
+```shell
 tox -e docs
 ```
 
-and use Python's built-in web server for a preview in your web browser
+then use Python's built-in web server for a preview in your web browser
 (`http://localhost:8000`):
 
-```
+```shell
 python3 -m http.server --directory 'docs/_build/html'
 ```
 
 ## Contributing Code
 
-To contribute bug fixes, documentation enhancements, or new code, please fork pyEQL and send us a pull request. It's not as hard as it sounds! Beginning with version 0.6.0, we follow the [GitHub flow](https://docs.github.com/en/get-started/quickstart/github-flow) workflow model.
+To contribute bug fixes, documentation enhancements, or new code, please fork pyEQL and send us a pull request. It's not as hard as it sounds! Beginning with version 0.6.0, we follow the [GitHub flow](https://docs.github.com/en/get-started/using-github/github-flow) workflow model.
 
 The [Scientific Python Guide](https://learn.scientific-python.org/development/guides/) is also an excellent technical reference for new and longtime developers.
 
@@ -65,7 +65,7 @@ a report in the [issue tracker](https://github.com/KingsburyLab/pyEQL/issues) to
 
 ### Hacking pyEQL, step by step
 
-1. [Fork the pyEQL repository](https://help.github.com/articles/fork-a-repo/) on Github
+1. [Fork the pyEQL repository](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) on Github
 
 2. Clone your repository to a directory of your choice:
 
@@ -112,13 +112,13 @@ a report in the [issue tracker](https://github.com/KingsburyLab/pyEQL/issues) to
 
 Please abide by the following guidelines when contributing code to `pyEQL`:
 
-- All changes you make to quacc should be accompanied by unit tests and should not break existing tests. To run the full test suite, run `pytest tests/` from the repository directory.
+- All changes you make to `pyEQL` should be accompanied by unit tests and should not break existing tests. To run the full test suite, run `pytest tests/` from the repository directory.
 
-- Code coverage should be maintained or increase. Each PR will report code coverage after the tests pass, but you can check locally using [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/), by running `pytest --cov tests/`
+- Code coverage should be maintained or increase. Each PR will report code coverage after the tests pass, but you can check locally using [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/), by running `pytest --cov tests/`. To produce a detailed HTML report with line and branch coverage statistics, run `pytest --cov-branch --cov=src/pyEQL --cov-report=html -n auto tests`.
 
 - All code should include type hints and have internally consistent documentation for the inputs and outputs.
 
-- Use Google style docstrings
+- Use [Google style docstrings](https://google.github.io/styleguide/pyguide.html)
 
 - Lint your code with [`ruff`](https://github.com/astral-sh/ruff) by running `ruff check --fix src/` from the repo directory. Alternatively, you can install the `pre-commit` hooks by running `pre-commit install` from the repository directory. This will prevent committing new changes until all linting errors are fixed.
 
@@ -128,8 +128,8 @@ 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 [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).
 
 ## Changelog
 
-We keep a `CHANGELOG.md` file in the base directory of the repository. Before submitting your PR, be sure to update the `CHANGELOG.md` file under the "Unreleased" section with a brief description of your changes. Our `CHANGELOG.md` file lossely follows the [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format, beginning with `v0.6.0`.
+We keep a `CHANGELOG.md` file in the base directory of the repository. Before submitting your PR, be sure to update the `CHANGELOG.md` file under the "Unreleased" section with a brief description of your changes. Our `CHANGELOG.md` file loosely follows the [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format, beginning with `v0.6.0`.

{pyeql-1.2.0 → pyeql-1.3.0}/docs/database.md

@@ -14,7 +14,7 @@ its calculations. The database includes:
 - Dielectric constant model parameters for 18 ions
 - Partial molar volumes for 24 ions
 
-`pyEQL` can automatically infer basic chemical informatics such as molecular weight and charge by passing a solute's formula to `pymatgen.core.ion.Ion` (See [chemical formulas](#chemistry)). For other physicochemical properties, it relies on data compiled into the included database. A list of the data and species covered is available [below](#species-included)
+`pyEQL` can automatically infer basic chemical informatics such as molecular weight and charge by passing a solute's formula to `pymatgen.core.ion.Ion` (See [chemical formulas](chemistry.md)). For other physicochemical properties, it relies on data compiled into the included database. A list of the data and species covered is available [below](#species-included)
 
 ## Format