Feature: move database to modern .JSON format

.github/workflows/testing.yaml

@@ -38,12 +38,12 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}${{ matrix.dev }}
-      - name: Install pytest
+      - name: Install test requirements
         run: |
-          python -m pip install pytest pytest-cov
+          python -m pip install --upgrade pip
+          pip install -e ".[testing]"
       - name: Run tests
         run: |
-          pip install -e .
           pytest --cov=src/pyEQL --cov-report=xml
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/upgrade_dependencies.yml

@@ -77,6 +77,10 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         # Only open a PR if the branch is not attached to an existing one
+        # note that this auto-created PR will not trigger the testing workflow, which
+        # is an intentional limitation imposed by GitHub. See
+        # https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#triggering-further-workflow-runs
+        # The simplest workaround is to close and immediately re-open the Auto PR
         run: |
           PR=$(gh pr list --head auto-dependency-upgrades --json number -q '.[0].number')
           if [ -z $PR ]; then

docs/database.rst

@@ -101,7 +101,7 @@ expect certain parameter names. The following are the currently-used internal
 names:
 
  - 'diffusion_coefficient' - diffusion coefficient
- - 'pitzer_parameters_activity' - coefficients for the Pitzer model for activity correction
+ - 'model_parameters.activity_pitzer' - coefficients for the Pitzer model for activity correction
  - 'pitzer_parameters_volume'- coefficients for the Pitzer model for partial molar volume
  - 'erying_viscosity_coefficients' - coefficients for an Erying-type viscosity correction model
  - 'partial_molar_volume'- the partial molar volume (used if Pitzer parameters are not available)

pyproject.toml

@@ -86,3 +86,4 @@ no_implicit_optional = false
 [tool.codespell]
 ignore-words-list = "nd"
 skip = 'tests/test_files/*'
+exclude = 'src/pyEQL/database/pyeql_db.json'

setup.cfg

@@ -55,6 +55,7 @@ install_requires =
     pymatgen>=2022.0.17
     iapws
     monty
+    maggma
 
 [options.packages.find]
 where = src

setup.py

@@ -1,10 +1,10 @@
 """
-    Setup file for pyEQL.
-    Use setup.cfg to configure your project.
+Setup file for pyEQL.
+Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.5.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup
 

src/pyEQL/__init__.py

@@ -46,11 +46,5 @@
 # set the default string formatting for pint quantities
 unit.default_format = "P~"
 
-# this must be imported after instantiating the UnitRegistry()
-from pyEQL.database import Paramsdb  # noqa
-
-# initialize the parameters database
-paramsDB = Paramsdb()
-
 from pyEQL.functions import *  # noqa: E402, F403
 from pyEQL.solution import Solution  # noqa: E402