Migrate Pourbaix workflow to pyEQL v1.6.1

.github/workflows/testing-pinned.yaml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - main
+      - pourbaix_pyEQL_v1.5
     paths-ignore:
       - CHANGELOG.md
       - AUTHORS.md
@@ -41,7 +42,11 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-          pip install -e . --no-deps
+          pip install -e ".[testing]"
+
+      - name: Install pourbaix deps
+        if: matrix.python-version != '3.10'
+        run: pip install -e ".[pourbaix]"
 
       - name: Run tests
         run: |

.github/workflows/testing.yaml

@@ -38,6 +38,15 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e ".[testing]"
+
+      - name: Install pourbaix deps
+        if: matrix.python-version != '3.10'
+        run: pip install -e ".[pourbaix]"
+
+      - name: List installed requirements
+        run: |
+          pip freeze
+
       - name: Run tests
         run: |
           if [[ "${{ matrix.python-version }}" == "3.13" ]]; then

pyproject.toml

@@ -46,8 +46,16 @@ testing = [
   "mypy>1",
   "ruff>0.0.100",
   "tox<4",
+  "openpyxl",
+]
+pourbaix = [
+  "mp-api>=0.45.0",
+]
+docs = [
+  "sphinx>=3.2.1",
+  "sphinx-rtd-theme",
+  "myst-parser[linkify]",
 ]
-docs = ["sphinx>=3.2.1", "sphinx-rtd-theme", "myst-parser[linkify]"]
 full = ["rich"]
 
 [build-system]
@@ -182,5 +190,5 @@ enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
 
 [tool.codespell]
-ignore-words-list = "nd,formate,Te,CaCl,CaF,ore"
+ignore-words-list = "nd,formate,Te,CaCl,CaF,ore, teh,hte,hsi"
 skip = "tests/test_files/*,src/pyEQL/database/*"

requirements.txt

@@ -43,7 +43,7 @@ contourpy==1.3.3
     # via matplotlib
 coverage==7.14.0
     # via pytest-cov
-cryptography==48.0.0
+cryptography==50.0.0
     # via paramiko
 cycler==0.12.1
     # via matplotlib

src/pyEQL/pourbaix/MITCompatibility.yaml

@@ -0,0 +1,66 @@
+Name: MIT
+Advanced:
+  UCorrections:
+    O:                     #Based on burp version as of Feb 28 2011
+      Mn: -1.687
+      Fe: -1.723
+      Co: -1.751
+      Cr: -2.067
+      Mo: -3.531           # refit number.
+      W:  -2.762
+      V:  -1.764
+      Ni: -2.164
+      Nb: -1.259
+      Re: -1.177
+      Cu: -1.156
+      Ag: -0.324
+      Ta: -1.027           #Adjusted correction for Ta. Shyue May 24 2012
+    F:                     #Based on burp version as of Feb 28 2011
+      Mn: -1.687
+      Fe: -1.723
+      Co: -1.751
+      Cr: -2.067
+      Mo: -3.531           # refit number.
+      W:  -2.762
+      V:  -1.764
+      Ni: -2.164
+      Nb: -1.259
+      Re: -1.177
+      Cu: -1.156
+      Ag: -0.324
+      Ta: -1.027           #Adjusted correction for Ta. Shyue May 24 2012
+    S:                     #Based on burp version as of Feb 28 2011
+      Mn: -1.232
+      Fe: -1.113
+
+  #Fit energies for elements.  Note that these must be energies per atom!
+  #Document the fits PROPERLY. Fits by default are done over all alkali, alkali earth, and Al.
+  #The whole set is ("Li", "Na","K","Rb", "Cs", "Mg", "Ca","Sr", "Ba","Al")
+  #Last update: Sep 13 2011 by Shyue Ping Ong
+  CompoundEnergies:
+    #O2:  -4.25915626315
+    N2:  -8.00185429481
+    F2:  -1.42203822397
+    Cl2: -1.26486611357
+    H2:  -3.302
+    SO3: -6.16649882299    #Sulfur corrections as of Jun 18 2014
+    SO2: -6.08728347651
+
+OxideCorrections:
+  oxide:       -0.66975
+  peroxide:    -0.44317    #Corrections fit to Li2O2, Na2O2, K2O2, SrO2
+  superoxide:  -0.13893    #Superoxide Corrections fit to CsO2, NaO2, KO2
+  ozonide:     0.00
+
+# Entropic Correction term for gases.
+# For H2O, energy is corrected such that the experimental formation energy of water of -2.46 eV is reproduced.
+# H2 is corrected such that the experimental formation energy of water is reproduced.
+AqueousCompoundEnergies:
+  O2:  -0.316731
+  N2:  -0.295729
+  F2:  -0.313025
+  Cl2: -0.344373
+  Br:  -0.235039
+  Hg:  -0.234421
+  H2:  -3.6018845
+  H2O: -4.972

src/pyEQL/pourbaix/MPCompatibility.yaml

@@ -0,0 +1,43 @@
+Name: MP
+Advanced:
+  UCorrections:
+    O:
+      Mn: -1.68085015096   #Fit to MnO, Mn3O4 and MnO2 (BURP:-1.687)
+      Fe: -2.733           #Fit to FeO and Fe2O3 (Fe3O4 probably wrong)
+      Co: -1.874           #Fit to cobalt monoxide, Co3O4 (BURP:-1.751)
+      Cr: -2.013           #Fit to Cr2O3 (CrO3 missing) (BURP: -2.067)
+      Mo: -3.531           #Fit to MoO3 and MoO2 (BURP: -2.668)
+      W:  -4.351           #Fit to WO2 and WO3 (BURP: -2.762)
+      V:  -1.682           #Fit to V2O3 and V2O5 (VO2 fit is way off) (BURP: -1.764)
+      Ni: -2.164           #Based on burp version as of Feb 28 2011
+    F:
+      Mn: -1.68085015096   #Fit to MnO, Mn3O4 and MnO2 (BURP:-1.687)
+      Fe: -2.733           #Fit to FeO and Fe2O3 (Fe3O4 probably wrong)
+      Co: -1.874           #Fit to cobalt monoxide, Co3O4 (BURP:-1.751)
+      Cr: -2.013           #Fit to Cr2O3 (CrO3 missing) (BURP: -2.067)
+      Mo: -3.531           #Fit to MoO3 and MoO2 (BURP: -2.668)
+      W:  -4.351           #Fit to WO2 and WO3 (BURP: -2.762)
+      V:  -1.682           #Fit to V2O3 and V2O5 (VO2 fit is way off) (BURP: -1.764)
+      Ni: -2.164           #Based on burp version as of Feb 28 2011
+
+  #Fit energies for elements.  Note that these must be energies per atom!
+  #Document the fits PROPERLY. Fits by default are done over all alkali, alkali earth, and Al.
+  #The whole set is ("Li", "Na","K","Rb", "Cs", "Mg", "Ca","Sr", "Ba","Al")
+  #Last update: Sep 13 2011 by Shyue Ping Ong
+  CompoundEnergies:
+    #O2:  -4.22986844926    #Fit to all except Cs, which is a serious outlier
+    N2:  -7.95247218762    #Fit to Li3N, Mg3N2, Ca3N2, AlN
+    F2:  -1.42055013381    #Fit to all.
+    Cl2: -1.25385097674    #Fit to all except AlCl3, which is not present in the database.
+    H2:  -3.23973666138
+
+
+OxideCorrections:
+  oxide:       -0.70229    #Oxide Corrections fit to Li2O, Na2O, K2O, Rb2O, MgO, CaO, SrO, BaO, Al2O3 on 09/18
+  peroxide:    -0.46622    #Peroxide Corrections fit to Li2O2, Na2O2, K2O2, SrO2 on 09/18
+  superoxide:  -0.14598    #Superoxide Corrections fit to CsO2, NaO2, KO2 on 09/18
+  ozonide:     0.00
+
+
+SulfideCorrections:
+  sulfide:     -0.66346     #Sulfide Correction fit to Li2S, Na2S, K2S, Rb2S, CsS, MgS, CaS, BaS, Al2S3.