Merge pull request #51 from mvdh7/develop

Merge for v0.5.3

.github/workflows/docs.yml

@@ -0,0 +1,17 @@
+name: docs 
+on:
+  push:
+    branches:
+      - develop 
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material 
+      - run: mkdocs gh-deploy --force

.github/workflows/python-package.yml

@@ -8,25 +8,19 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        pip install pytest pandas openpyxl
+        pip install .
     - name: Test with pytest
       run: |
         pytest

.misc/coverage.txt

@@ -2,40 +2,56 @@ Name                                         Stmts   Miss  Cover
 ----------------------------------------------------------------
 pytzer/__init__.py                              15      0   100%
 pytzer/constants.py                             14      0   100%
-pytzer/convert.py                               30      6    80%
+pytzer/convert.py                               30     19    37%
 pytzer/debyehueckel.py                          69      9    87%
-pytzer/dissociation.py                         152     70    54%
+pytzer/dissociation.py                         175     54    69%
 pytzer/equilibrate/__init__.py                  41     15    63%
-pytzer/equilibrate/components.py               352    140    60%
+pytzer/equilibrate/components.py               364     86    76%
 pytzer/equilibrate/stoichiometric.py           118      1    99%
-pytzer/equilibrate/thermodynamic.py             83     17    80%
-pytzer/io.py                                    37      5    86%
+pytzer/equilibrate/thermodynamic.py             83     10    88%
+pytzer/get.py                                   37      5    86%
+pytzer/libraries/Clegg22.py                     88      0   100%
+pytzer/libraries/Clegg23.py                    158      0   100%
 pytzer/libraries/Clegg94.py                     11      0   100%
 pytzer/libraries/Greenberg89.py                 25      0   100%
 pytzer/libraries/Harvie84.py                   259      0   100%
-pytzer/libraries/MarChemSpec.py                111      0   100%
+pytzer/libraries/HeMorse93.py                  274      0   100%
+pytzer/libraries/Humphreys22.py                 77      0   100%
 pytzer/libraries/MarChemSpec25.py              107      0   100%
+pytzer/libraries/MarChemSpec.py                111      0   100%
 pytzer/libraries/Millero98.py                  255      0   100%
 pytzer/libraries/Moller88.py                    17      0   100%
-pytzer/libraries/ParameterLibrary.py           247     13    95%
+pytzer/libraries/MyMarChemSpecCO2.py            43      0   100%
+pytzer/libraries/ParameterLibrary.py           333     96    71%
 pytzer/libraries/Seawater.py                   257      0   100%
-pytzer/libraries/Waters13.py                    95      0   100%
+pytzer/libraries/Waters13.py                    98      0   100%
+pytzer/libraries/Waters13_Clegg22.py           110      0   100%
+pytzer/libraries/Waters13_Humphreys22.py        99      0   100%
 pytzer/libraries/Waters13_MarChemSpec25.py      95      0   100%
-pytzer/libraries/__init__.py                    21      0   100%
+pytzer/libraries/__init__.py                    35      0   100%
+pytzer/matrix.py                                48     36    25%
 pytzer/meta.py                                  12      1    92%
-pytzer/model.py                                111      2    98%
-pytzer/parameters.py                          6323   5012    21%
-pytzer/prepare.py                              113     98    13%
+pytzer/model.py                                117      6    95%
+pytzer/parameters/__init__.py                 6382   4403    31%
+pytzer/parameters/heMorse1993.py               165     70    58%
+pytzer/parameters/holmesMesmer1992.py           33     26    21%
+pytzer/parameters/pabalanPitzer1987.py          57     33    42%
+pytzer/parameters/spencer1990.py                33     26    21%
+pytzer/prepare.py                              113     94    17%
 pytzer/properties.py                             5      0   100%
 pytzer/teos10.py                                41     10    76%
 pytzer/unsymmetrical.py                         46      1    98%
 tests/__init__.py                                0      0   100%
-tests/test_CRP94.py                             11      0   100%
-tests/test_M88.py                               16      0   100%
-tests/test_convert.py                           25      0   100%
+tests/test_CRP94.py                             34      0   100%
+tests/test_CWTD23_params.py                    238      2    99%
+tests/test_CWTD23_solver.py                     51      1    98%
+tests/test_HWT22_params.py                     125      9    93%
+tests/test_HWT22_solver.py                     104      0   100%
+tests/test_M88.py                               14      0   100%
 tests/test_jax_settings.py                       4      0   100%
 tests/test_model.py                             41      0   100%
+tests/test_pKs.py                               13      0   100%
 tests/test_stoichiometric.py                   130      0   100%
 tests/test_unsymmetrical.py                     33      0   100%
 ----------------------------------------------------------------
-TOTAL                                         9322   5400    42%
+TOTAL                                        11237   5013    55%

README.md

@@ -1,14 +1,13 @@
 # Pytzer
 
 ![Tests](https://github.com/mvdh7/pytzer/workflows/Tests/badge.svg)
-[![Coverage](https://github.com/mvdh7/pytzer/blob/master/.misc/coverage.svg)](https://github.com/mvdh7/pytzer/blob/master/.misc/coverage.txt)
+[![Coverage](https://github.com/mvdh7/pytzer/blob/main/.misc/coverage.svg)](https://github.com/mvdh7/pytzer/blob/main/.misc/coverage.txt)
 [![pypi badge](https://img.shields.io/pypi/v/pytzer.svg?style=popout)](https://pypi.org/project/pytzer/)
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.2637914-informational)](https://doi.org/10.5281/zenodo.2637914)
-[![Docs](https://readthedocs.org/projects/pytzer/badge/?version=latest&style=flat)](https://pytzer.readthedocs.io/en/latest/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-Pytzer is a Python implementation of the Pitzer model for chemical activities in aqueous solutions [[P91](https://pytzer.readthedocs.io/en/jax/refs/#p)] plus solvers to determine the equilibrium state of the system.
+Pytzer is a Python implementation of the Pitzer model for chemical activities in aqueous solutions [[P91](https://mvdh.xyz/pytzer/refs/#p)] plus solvers to determine the equilibrium state of the system.
 
 **Pytzer is in beta!  Use at your own peril.**
 
@@ -35,25 +34,17 @@ Once installed, you will need to set the environment variable `JAX_ENABLE_X64=Tr
 
     conda env config vars set JAX_ENABLE_X64=True
 
-### For development
-
-Use the [environment.yml](https://github.com/mvdh7/pytzer/blob/master/environment.yml) file to create a new environment with Conda:
-
-    conda env create -f environment.yml
-
-Then, fork and/or clone this repo to somewhere that your Python can see it.
-
 ## Documentation
 
-A work in progress at [pytzer.readthedocs.io](https://pytzer.readthedocs.io/en/latest/).
+A work in progress at [mvdh.xyz/pytzer](https://mvdh.xyz/pytzer).
 
 ## Citation
 
-Pytzer is maintained by [Dr Matthew P. Humphreys](https://humphreys.science) at the [NIOZ Royal Netherlands Institute for Sea Research](https://www.nioz.nl/en) (Texel, the Netherlands).
+Pytzer is maintained by [Dr Matthew P. Humphreys](https://seaco2.group) at the [NIOZ Royal Netherlands Institute for Sea Research](https://www.nioz.nl/en) (Texel, the Netherlands).
 
 For now, the appropriate citation is:
 
-> Humphreys, Matthew P. and Schiller, Abigail J. (2021). Pytzer: the Pitzer model for chemical activities and equilibria in aqueous solutions in Python (beta).  *Zenodo.*  [doi:10.5281/zenodo.2637914](https://doi.org/10.5281/zenodo.2637914).
+> Humphreys, Matthew P. and Schiller, Abigail J. (2023). Pytzer: the Pitzer model for chemical activities and equilibria in aqueous solutions in Python (beta).  *Zenodo.*  [doi:10.5281/zenodo.2637914](https://doi.org/10.5281/zenodo.2637914).
 
 Please report which version of Pytzer you are using.  You can find this in Python with:
 

docs/equilibrate.md

@@ -4,7 +4,9 @@ There are two 'layers' of solver in Pytzer: stoichiometric and thermodynamic.
 
 The stoichiometric solver determines the molality of each solute given a set of total molalities and fixed stoichiometric equilibrium constants.  It uses a Newton-Raphson iterative method that is fully compatible with JAX.
 
-The thermodynamic solver wraps the stoichiometric solver and adjusts the stoichiometric equilibrium constants to agree with thermodynamic constraints.  Because it uses [`scipy.optimize.root`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.root.html), it cannot be differentiated or compiled with JAX.
+The thermodynamic solver wraps the stoichiometric solver and adjusts the stoichiometric equilibrium constants to agree with thermodynamic constraints.  Because it uses [`scipy.optimize.root`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.root.html), it cannot be yet[^1] differentiated or compiled with JAX.
+
+[^1]: We are planning to merge the two solvers together, making the entire program grad-able and jit-able by JAX, in a future release.
 
 You can solve equilibria using the following functions.  Lower-level approaches with more fine control are possible, but not yet documented.
 

docs/index.md

@@ -1,18 +1,17 @@
 # Pytzer
 
-![Tests](https://github.com/mvdh7/pytzer/workflows/Tests/badge.svg)
-[![Coverage](img/coverage.svg)](https://github.com/mvdh7/pytzer/blob/master/.misc/coverage.txt)
+<!-- ![Tests](https://github.com/mvdh7/pytzer/workflows/Tests/badge.svg)
+[![Coverage](img/coverage.svg)](https://github.com/mvdh7/pytzer/blob/main/.misc/coverage.txt)
 [![pypi badge](https://img.shields.io/pypi/v/pytzer.svg?style=popout)](https://pypi.org/project/pytzer/)
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.2637914-informational)](https://doi.org/10.5281/zenodo.2637914)
-[![Docs](https://readthedocs.org/projects/pytzer/badge/?version=latest&style=flat)](https://pytzer.readthedocs.io/en/latest/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -->
 
-Pytzer is a Python implementation of the Pitzer model for chemical activities in aqueous solutions [[P91](refs/#p)] plus solvers to determine the equilibrium state of the system.
+Pytzer is a Python implementation of the Pitzer model for chemical activities in aqueous solutions ([P91](refs/#p)) plus an equilibrium solver.
 
 ## Installation
 
-Consult the [README.md on GitHub](https://github.com/mvdh7/pytzer/tree/master#pytzer) for up-to-date installation instructions.
+Consult the [README.md on GitHub](https://github.com/mvdh7/pytzer/tree/main#pytzer) for up-to-date installation instructions.
 
 ## Development status
 
@@ -22,7 +21,7 @@ Pytzer is in beta.  Tests of the accuracy of its parameters and equations are un
 
 A manuscript describing Pytzer is in preparation.  In the meantime, please cite:
 
-> Humphreys, Matthew P. and Schiller, Abigail J. (2021).  Pytzer: the Pitzer model for chemical activities and equilibria in aqueous solutions in Python (beta).  *Zenodo.* [doi:10.5281/zenodo.2637914](https://doi.org/10.5281/zenodo.2637914).
+> Humphreys, Matthew P. and Schiller, Abigail J. (2023).  Pytzer: the Pitzer model for chemical activities and equilibria in aqueous solutions in Python (beta).  *Zenodo.* [doi:10.5281/zenodo.2637914](https://doi.org/10.5281/zenodo.2637914).
 
 Please report the version you are using.  You can find this in Python with:
 
@@ -33,7 +32,7 @@ pz.hello()
 
 ## Acknowledgements
 
-Pytzer is maintained by [Dr Matthew P. Humphreys](https://humphreys.science) at the NIOZ Royal Netherlands Institute for Sea Research (Texel, the Netherlands).  Its initial development at the University of East Anglia was funded indirectly by the Natural Environment Research Council (NERC, UK).
+Pytzer is maintained by [Dr Matthew P. Humphreys](https://seaco2.group) at the NIOZ Royal Netherlands Institute for Sea Research (Texel, the Netherlands).  Its initial development at the University of East Anglia was funded indirectly by the Natural Environment Research Council (NERC, UK).
 
 Pytzer contains many functions and coefficients representing the effects of different solute interactions on solution properties that have been empirically determined from painstaking experiments and data compilations by hundreds of researchers over the course at least a century.  We have done our best to list the small selection of this enormous body of work brought together here in the [references](refs).
 

docs/params.md

@@ -14,9 +14,11 @@ from pytzer.libraries import Seawater
 
 The options are:
 
+  * `Clegg22`: [CHW22](../refs/#c)
   * `Clegg94`: [CRP94](../refs/#c)
   * `Greenberg89`: [GM89](../refs/#m)
   * `Harvie84`: [HMW84](../refs/#h)
+  * `Humphreys22`: [HWT22](../refs/#h)
   * `MarChemSpec`
   * `MarChemSpec25`
   * `Millero98`: [MP98](../refs/#m), a.k.a. MIAMI