pyEQL 0.12.2__tar.gz → 0.14.0__tar.gz

pyEQL-0.14.0/.github/workflows/post-process.yml

@@ -0,0 +1,62 @@
+name: Post-merge
+
+# triggered when PRs are merged into main branch
+on:
+  pull_request:
+    branches:
+      - main
+    types:
+      - closed
+
+jobs:
+  lint:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: pip
+      - name: Run pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit run
+
+  test-comprehensive:
+    needs: lint
+    strategy:
+      max-parallel: 6
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+          - macos-14
+        exclude:
+          - os: macos-14
+            python-version: "3.9"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+      - name: Install test requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[testing]"
+      - name: Run tests
+        run: |
+          pytest --cov=src/pyEQL --cov-report=xml
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml

pyEQL-0.14.0/.github/workflows/release.yml

@@ -0,0 +1,60 @@
+name: release
+
+# runs when the Post merge workflow completes successfully
+# tags new release and pushes to PyPi
+# see https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_run
+on:
+  workflow_run:
+    workflows: [Post merge]
+    types: [completed]
+
+  workflow_dispatch:
+
+jobs:
+  # https://github.com/marketplace/actions/tag-release-on-push-action
+  tag-release:
+    name: Tag/Release on merge of labeled PRs
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: rymndhng/release-on-push-action@v0.28.0
+        with:
+          # loonly release when PRs with release:major/minor/patch labels are merged
+          bump_version_scheme: norelease
+          use_github_release_notes: true
+          release_body: "See [CHANGELOG](https://github.com/KingsburyLab/pyEQL/blob/main/CHANGELOG.md) for a detailed explanation of changes."
+
+  # https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
+
+  deploy:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    needs: tag-release
+    environment:
+      name: publish
+      url: https://pypi.org/p/pyEQL
+
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools setuptools_scm wheel tox
+
+      - name: Build packages for distribution
+        run: |
+          tox -e clean,build
+
+      - name: Upload to PyPi
+        uses: pypa/gh-action-pypi-publish@v1.8.12

{pyEQL-0.12.2 → pyEQL-0.14.0}/.github/workflows/testing.yaml

@@ -1,17 +1,12 @@
 name: testing
 
 on:
-  push:
+  pull_request:
     branches:
       - main
     paths-ignore:
-      - 'docs/'
       - CHANGELOG.md
 
-  pull_request:
-    branches:
-      - main
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -40,18 +35,29 @@ jobs:
     strategy:
       max-parallel: 6
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        platform:
-        - ubuntu-latest
-        - macos-latest
-        - windows-latest
-    runs-on: ubuntu-latest
+        # for most PRs, test the min and max supported python on every platform, test all python on ubuntu
+        python-version: ["3.9", "3.12"]
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - macos-14
+          - windows-latest
+        include:
+          - os: ubuntu-latest
+            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
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python }}${{ matrix.dev }}
+          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
       - name: Install test requirements
         run: |
           python -m pip install --upgrade pip

{pyEQL-0.12.2 → pyEQL-0.14.0}/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).
 
+## [0.14.0] - 2024-03-05
+
+### Added
+
+- `NativeEOS` / `PhreeqcEOS`: Added `try`/`catch` so that `pyEQL` can still be used on platforms that PHREEQC does
+  not support, such as Apple Silicon. In such cases, functions like `equilibrate` that depend on PHREEQC will
+  raise errors, but everything else can still be used.
+- CI: Added Apple M1 runner (GitHub: `macos-14`) to the CI tests.
+
+### Fixed
+
+- CI: Addressed several issues in the testing configuration which had resulted in testing
+  fewer operating systems x python version combinations than intended. CI tests now
+  correctly and comprehensively test every supported version of python on every os
+  (macos, windows, ubuntu).
+- `utils.FormulaDict`: implemented `__contains__` so that `get()` works correctly in
+  python 3.12+. See https://github.com/python/cpython/issues/105524
+- Docs: fixed many small problems in documentation causing equations and examples to
+  render incorrectly.
+- `Solution.from_file`: Add missing `@classmethod` decorator; update documentation.
+
+## [0.13.0] - 2024-03-05
+
+### Fixed
+
+- `equilibrium.alpha()`: Fixed incorrect calculation of acid-base distribution coefficient for multiprotic acids.
+
 ## [0.12.2] - 2024-02-25
 
 ### Fixed

{pyEQL-0.12.2/src/pyEQL.egg-info → pyEQL-0.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 0.12.2
+Version: 0.14.0
 Summary: Python tools for solution chemistry
 Home-page: https://github.com/KingsburyLab/pyEQL
 Author: Ryan Kingsbury

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/amounts.md

@@ -30,11 +30,11 @@ unit of mass or volume.
 <Quantity(1.21525e+10, 'nanogram / liter')>
 ```
 
-:::{important}
+```{important}
 The unit `'ppt'` is ambiguous in the water community. To most researchers, it means
 "parts per trillion" or ng/L, while to many engineers and operators it means "parts
 per THOUSAND" or g/L. `pyEQL` interprets `ppt` as **parts per trillion**.
-:::
+```
 
 You can also request dimensionless concentrations as weight percent (`'%'`),
 mole fraction (`'fraction'`) or the total _number_

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/arithmetic.md

@@ -20,10 +20,10 @@ as volume-weighted averages.
 <Quantity(1.99989659, 'liter')>
 ```
 
-:::{note}
+```{note}
 Both `Solution` involved in an addition operation must use the same [electrolyte
 modeling engine](engines.md).
-:::
+```
 
 Subtraction is not implemented and will raise a `NotImplementedError`.
 

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/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).
 
+## [0.14.0] - 2024-03-05
+
+### Added
+
+- `NativeEOS` / `PhreeqcEOS`: Added `try`/`catch` so that `pyEQL` can still be used on platforms that PHREEQC does
+  not support, such as Apple Silicon. In such cases, functions like `equilibrate` that depend on PHREEQC will
+  raise errors, but everything else can still be used.
+- CI: Added Apple M1 runner (GitHub: `macos-14`) to the CI tests.
+
+### Fixed
+
+- CI: Addressed several issues in the testing configuration which had resulted in testing
+  fewer operating systems x python version combinations than intended. CI tests now
+  correctly and comprehensively test every supported version of python on every os
+  (macos, windows, ubuntu).
+- `utils.FormulaDict`: implemented `__contains__` so that `get()` works correctly in
+  python 3.12+. See https://github.com/python/cpython/issues/105524
+- Docs: fixed many small problems in documentation causing equations and examples to
+  render incorrectly.
+- `Solution.from_file`: Add missing `@classmethod` decorator; update documentation.
+
+## [0.13.0] - 2024-03-05
+
+### Fixed
+
+- `equilibrium.alpha()`: Fixed incorrect calculation of acid-base distribution coefficient for multiprotic acids.
+
 ## [0.12.2] - 2024-02-25
 
 ### Fixed

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/chemistry.md

@@ -10,32 +10,33 @@ used in subsequent calculations.
 ## How to Enter Valid Chemical Formulas
 
 Generally speaking, type the chemical formula of your solute the "normal" way
-and `pyEQL` should be able to inerpret it. Internally, `pyEQL` uses a utility function `pyEQL.utils.standardize_formula`
+and `pyEQL` should be able to interpret it. Internally, `pyEQL` uses a utility function `pyEQL.utils.standardize_formula`
 to process all formulas into a standard form. At present, this is done by passing the formula through the
 [`pymatgen.core.ion.Ion`](https://pymatgen.org/pymatgen.core.html#pymatgen.core.ion.Ion) class. Anything that the `Ion`
 class can understand will be processed into a valid formula by `pyEQL`.
 
 Here are some examples:
 
-| Substance | You enter | `pyEQL` understands |
-| :--- | :---: | :---: |
-| Sodium Chloride | "NaCl", "NaCl(aq)", or "ClNa" | "NaCl(aq)" |
-| Sodium Sulfate | "Na(SO4)2" or "NaS2O8" | "Na(SO4)2(aq)" |
-| Sodium Ion | "Na+", "Na+1", "Na1+", or "Na[+]" | "Na[+1]" |
-| Magnesium Ion | "Mg+2", "Mg++", or "Mg[++]" | "Mg[+2]" |
-| Methanol | "CH3OH", "CH4O" | "'CH3OH(aq)'" |
+| Substance       |             You enter             | `pyEQL` understands |
+| :-------------- | :-------------------------------: | :-----------------: |
+| Sodium Chloride |   "NaCl", "NaCl(aq)", or "ClNa"   |     "NaCl(aq)"      |
+| Sodium Sulfate  |      "Na2(SO4)" or "Na2SO4"       |    "Na(SO4)(aq)"    |
+| Sodium Ion      | "Na+", "Na+1", "Na1+", or "Na[+]" |      "Na[+1]"       |
+| Magnesium Ion   |    "Mg+2", "Mg++", or "Mg[++]"    |      "Mg[+2]"       |
+| Methanol        |          "CH3OH", "CH4O"          |    "'CH3OH(aq)'"    |
 
 Specifically, `standardize_formula` uses `Ion.from_formula(<formula>).reduced_formla` (shown in the right hand column
 of the table) to identify solutes. Notice that for charged species, the charges are always placed inside square brackets
 (e.g., `Na[+1]`) and always include the charge number (even for monovalent ions). Uncharged species are always suffixed
 by `(aq)` to disambiguate them from solids.
 
-:::{important}
+```{important}
 **When writing multivalent ion formulas, it is strongly recommended that you put the charge number AFTER the + or -
 sign** (e.g., type "Mg+2" NOT "Mg2+"). The latter formula is ambiguous - it could mean $Mg_2^+$ or $Mg^{+2}$ and it will be processed incorrectly into `Mg[+0.5]`
-:::
+```
 
 (manual-testing)=
+
 ## Manually testing a formula
 
 If you want to make sure `pyEQL` is understanding your formula correctly, you can manually test it as follows:

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/contributing.md

@@ -8,7 +8,9 @@ You can help the project simply by using pyEQL and comparing the output to exper
 If you encounter any bugs, packaging issues, feature requests, comments, or questions, please report them
 using the [issue tracker](https://github.com/KingsburyLab/pyEQL/issues) on [github](https://github.com/KingsburyLab/pyeql).
 
-:::{tip} Please don't forget to include the closed issues in your search. Sometimes a solution was already reported, and the problem is considered solved. :::
+```{tip}
+Please don't forget to include the closed issues in your search. Sometimes a solution was already reported, and the problem is considered solved.
+```
 
 New issue reports should include information about your programming environment (e.g., operating system, Python version) and steps to reproduce the problem. Please try also to simplify the reproduction steps to a very minimal example that still illustrates the problem you are facing. By removing other factors, you help us to identify the root cause of the issue.
 
@@ -17,31 +19,23 @@ New issue reports should include information about your programming environment
 You can help improve `pyEQL` docs by making them more readable and coherent, or
 by adding missing information and correcting mistakes.
 
-`pyEQL` documentation uses [Sphinx] as its main documentation compiler.
+`pyEQL` documentation uses [Sphinx](https://www.sphinx-doc.org/en/master/) as its main documentation compiler.
 This means that the docs are kept in the same repository as the project code, and
 that any documentation update is done in the same way was a code contribution.
 
-```{todo} Don't forget to mention which markup language you are using.
-
-    e.g.,  [reStructuredText] or [CommonMark] with [MyST] extensions.
-```
-
-```{todo} If your project is hosted on GitHub, you can also mention the following tip:
-
-   :::{tip}
-      Please notice that the [GitHub web interface] provides a quick way of
-      propose changes in `pyEQL`'s files. While this mechanism can
-      be tricky for normal code contributions, it works perfectly fine for
-      contributing to the docs, and can be quite handy.
-
-      If you are interested in trying this method out, please navigate to
-      the `docs` folder in the source [repository], find which file you
-      would like to propose changes and click in the little pencil icon at the
-      top, to open [GitHub's code editor]. Once you finish editing the file,
-      please write a message in the form at the bottom of the page describing
-      which changes have you made and what are the motivations behind them and
-      submit your proposal.
-   :::
+```{tip}
+Please notice that the [GitHub web interface] provides a quick way of
+propose changes in `pyEQL`'s files. While this mechanism can
+be tricky for normal code contributions, it works perfectly fine for
+contributing to the docs, and can be quite handy.
+
+If you are interested in trying this method out, please navigate to
+the `docs` folder in the source [repository], find which file you
+would like to propose changes and click in the little pencil icon at the
+top, to open [GitHub's code editor]. Once you finish editing the file,
+please write a message in the form at the bottom of the page describing
+which changes have you made and what are the motivations behind them and
+submit your proposal.
 ```
 
 When working on documentation changes in your local machine, you can
@@ -91,11 +85,15 @@ a report in the [issue tracker](https://github.com/KingsburyLab/pyEQL/issues) to
    ```
    git checkout -b mybranch
    ```
+
    or
+
    ```
    git checkout -b doc-mydoc
    ```
+
    or
+
    ```
    git checkout -b feature-myfeature
    ```
@@ -110,7 +108,6 @@ a report in the [issue tracker](https://github.com/KingsburyLab/pyEQL/issues) to
 
 7. Create a pull request with your changes. See [this tutorial](https://yangsu.github.io/pull-request-tutorial) for instructions.
 
-
 ## Guidelines
 
 Please abide by the following guidelines when contributing code to `pyEQL`:
@@ -133,7 +130,6 @@ Please abide by the following guidelines when contributing code to `pyEQL`:
 
 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`.

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/engines.md

@@ -21,6 +21,16 @@ as needed to particular use cases.
 `pyEQL` currently supports three modeling engines: `ideal`, `native`, and `phreeqc`, which
 are selected via the `engine` kwarg to `Solution.__init__()`. Each engine is briefly described below.
 
+```{warning}
+If you are using a Mac with an Apple M1, M2, etc. chip (i.e., Arm64 architecture), some features of `pyEQL` will be
+unavailable. Specifically, anything which depends on PHREEQC (e.g., the
+`equilibrate` method in the native engine and the entire
+ [`phreeqc` engine](engines.md#the-phreeqc-engine)) will not work. This is because `phreeqpython` is currently
+ not available for this platform. All other functions of `pyEQL` should work as expected.
+
+Feel free to post your experiences or proposed solutions at https://github.com/KingsburyLab/pyEQL/issues/109
+```
+
 ## The `'native'` engine (Default)
 
 The `native` engine is the default choice and was the only option available prior to
@@ -55,14 +65,13 @@ number of species included (see [Lu et al.](https://doi.org/10.1016/j.earscirev.
 See `pyEQL.equilibrium.eqiulibrate_phreeqc` in the [module reference](internal.md#speciation-functions)
 for more details.
 
-
-:::{warning}
+```{warning}
 Speciation support was added to the `native` engine in `v0.8.0` and should be considered
 experimental. Specifically, because the `native` engine uses a non-Pitzer PHREEQC database
 for speciation but uses the Pitzer model (when possible) for activity coefficients. As such,
 there may be subtle thermodynamic inconsistencies between the activities and the equilibrium
 concentrations returned by `equilibrate()`.
-:::
+```
 
 ## The `'phreeqc'` engine
 
@@ -81,11 +90,11 @@ concentration of the solute.
 Due to limitations in the `phreeqpython` interface, the osmotic coefficient is always
 returned as 1 at present.
 
-:::{warning}
+```{warning}
 The `phreeqc` engine currently returns an osmotic coefficient of 1 and solute volume of
 0 for all solutions. There appear to be limitations in the `phreeqpython` interface that
 make it difficult to access these properties.
-:::
+```
 
 ### Solute volumes
 
@@ -94,17 +103,16 @@ the `ideal` engine). More
 research is needed to determine whether this is consistent with intended PHREEQC behavior
 (when using the default database) or not.
 
-:::{warning}
+```{warning}
 The `phreeqc` engine currently returns an osmotic coefficient of 1 and solute volume of
 0 for all solutions. There appear to be limitations in the `phreeqpython` interface that
 make it difficult to access these properties.
-:::
+```
 
 ### Speciation
 
 Speciation calculations are provided by PHREEQC via `phreeqpython`.
 
-
 ## The `'ideal'` engine
 
 The `'ideal'` engine applies ideal solution behavior. Activity and osmotic coefficients

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/index.md

@@ -1,6 +1,6 @@
 ---
-Date: '{{ today }}'
-Release: '{{ release }}'
+Date: "{{ today }}"
+Release: "{{ release }}"
 ---
 
 ![pyeql-logo](../pyeql-logo.png)
@@ -30,11 +30,12 @@ pip install pyEQL
 
 ```python
 >>> from pyEQL import Solution
->>> s1 = pyEQL.Solution({'Na+':'0.5 mol/kg', 'Cl-': '0.5 mol/kg'},
+>>> s1 = Solution({'Na+':'0.5 mol/kg', 'Cl-': '0.5 mol/kg'},
                          pH=8,
                          temperature = '20 degC',
                          volume='8 L')
 ```
+
 ### Get properties
 
 ```python

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/installation.md

@@ -6,10 +6,9 @@
 
 We highly recommend installing python in an isolated environment using [`conda`](https://docs.conda.io/en/latest/) (or its speedier, backward-compatible successor, [mamba](https://mamba.readthedocs.io/en/latest/)). In particular, we recommend the [miniforge](https://github.com/conda-forge/miniforge#miniforge3) or [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) distributions of Python, which are lightweight distributions of conda that automatically activate the `conda-forge` channel for up-to-date scientific packages.
 
-
-:::{note}
+```{note}
 If you are on a Windows machine, we recommend you install the [Windows Subsystem for Linux (WSL)](https://learn.microsoft.com/en-us/windows/wsl/install) and set up your conda environments inside the WSL environment.
-:::
+```
 
 After installing `conda` / `mamba`, follow their instructions to create an environment. The steps should be similar to the following:
 
@@ -28,10 +27,12 @@ pip install pyEQL
 
 This should automatically pull in the required [dependencies](#other-dependencies) as well.
 
-:::{important}
+```{important}
 If you are NOT using a `conda` environment, may have to run 'pip3' rather than 'pip'. This will be the case if Python 2.x and Python 3.x are installed side-by-side on your system.
 You can tell if this is the case by typing the following command:
 
+```
+
 ```
 $ python --version
 Python 2.7.12
@@ -46,7 +47,16 @@ Python 3.9.7
 ```
 
 To get to Python 3.x, you have to type 'python3'. In this case, you would run 'pip3 install'
-:::
+
+```{warning}
+If you are using a Mac with an Apple M1, M2, etc. chip (i.e., Arm64 architecture), some features of `pyEQL` will be
+unavailable. Specifically, anything which depends on PHREEQC (e.g., the
+`equilibrate` method in the native engine and the entire
+ [`phreeqc` engine](engines.md)) will not work. This is because `phreeqpython` is currently
+ not available for this platform. All other functions of `pyEQL` should work as expected.
+
+Feel free to post your experiences or proposed solutions at https://github.com/KingsburyLab/pyEQL/issues/109
+```
 
 ## Other dependencies
 
@@ -62,7 +72,6 @@ pyEQL also requires the following packages:
 
 If you use pip to install pyEQL (recommended), they should be installed automatically.
 
-
 ## Installing the development branch
 
 If you want to use the bleeding edge version before it is released to PyPi instead of the latest stable release, you can substitute the following for the above 'pip install' command:
@@ -85,6 +94,6 @@ Then install by executing:
 pip install -e pyEQL
 ```
 
-:::{note}
+```{note}
 You may have to run 'pip3' rather than 'pip'. See the note in the [pip install](#pip-install) section.
-:::
+```

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/quickstart.md

@@ -15,10 +15,10 @@ Create a Solution object by invoking the Solution class:
 ```{eval-rst}
 .. doctest::
 
-   >>> import pyEQL
-   >>> s1 = pyEQL.Solution()
+   >>> from pyEQL import Solution
+   >>> s1 = Solution()
    >>> s1
-   <pyEQL.pyEQL.Solution at 0x7f9d188309b0>
+   <pyEQL.Solution at 0x7f9d188309b0>
 
 ```
 
@@ -30,7 +30,7 @@ More usefully, you can specify solutes and bulk properties:
 ```{eval-rst}
 .. doctest::
 
-    >>> s2 = pyEQL.Solution({'Na+':'0.5 mol/kg', 'Cl-': '0.5 mol/kg'}, pH=8, temperature = '20 degC', volume='8 L')
+    >>> s2 = Solution({'Na+':'0.5 mol/kg', 'Cl-': '0.5 mol/kg'}, pH=8, temperature = '20 degC', volume='8 L')
 ```
 
 See [Creating a Solution](creating.md) for more details.
@@ -83,7 +83,7 @@ Quantity objects that contain both a magnitude and a unit.
 1.0
 ```
 
-Many `pyEQL` methods require physical quantities to be input as strings, then these methods return pint `Quantity`  objects. A string quantity must contain both a magnitude and a unit (e.g. '0.5 mol/L').
+Many `pyEQL` methods require physical quantities to be input as strings, then these methods return pint `Quantity` objects. A string quantity must contain both a magnitude and a unit (e.g. '0.5 mol/L').
 In general, pint recognizes common abbreviations and SI prefixes. Compound units must follow Python math syntax (e.g. cm\*\*2 not cm2).
 
 See the [Converting Units](units.md) for more details.

{pyEQL-0.12.2 → pyEQL-0.14.0}/docs/serialization.md

@@ -16,33 +16,27 @@ using `from_dict()`.
 
 ## Saving to a `.json` file
 
-`Solution` can be serialized (and later recreated from) a `.json` file using
+`Solution` can be serialized (and later recreated from) a `.json` file using `to_file`, which is based on
 [`monty.serializtaion.dumpfn`](https://pythonhosted.org/monty/monty.html#module-monty.serialization).
 
 ```python
 >>> from pyEQL import Solution
->>> from monty.serialization import dumpfn
 >>> s = Solution({"Na+": "0.5 mol/L", "Cl-": "0.5 mol/L"})
->>> dumpfn(s, 'test.json')
+>>> s.to_file('test.json')
 ```
 
 ## Loading from a `.json` file
 
-Similarly, [monty.serialization.loadfn](https://pythonhosted.org/monty/monty.html#module-monty.serialization) can be used to create a `Solution` from a compatible
+Similarly, `from_file` (based on [monty.serialization.loadfn](https://pythonhosted.org/monty/monty.html#module-monty.serialization)) can be used to create a `Solution` from a compatible
 `.json` file.
 
 ```python
->>> from monty.serialization import loadfn
->>> s = loadfn('test.json')
-print(s)
+>>> from pyEQL import Solution
+>>> s = Solution.from_file('test.json')
+<pyEQL.solution.Solution object at 0x7febf742d8a0>
+>>> print(s)
 Volume: 1.000 l
 Pressure: 1.000 atm
 Temperature: 298.150 K
 Components: ['H2O(aq)', 'H[+1]', 'OH[-1]']
 ```
-
-:::{note}
-In a future release, `to_file()` / `from_file()` methods may be added to `Solution` to
-make the above steps easier. Please post on GitHub if you have strong opinions about
-this!
-:::