Merge branch 'main' of https://github.com/ReactionMechanismGenerator/…

…RMG-Py into cov_dep_therm

.conda/meta.yaml

@@ -30,7 +30,6 @@ requirements:
     - cairocffi
     - cantera >=2.3.0
     - cclib >=1.6.3
-    - chemprop
     - coolprop
     - coverage
     - cython >=0.25.2

.github/workflows/CI.yml

@@ -59,7 +59,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout RMG-Py
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
@@ -109,11 +109,9 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout RMG-Py
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # configures the mamba environment manager and builds the environment
-      - name: Patch Environment File
-        run: sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -132,7 +130,6 @@ jobs:
 
       # Clone RMG-database
       - name: Clone RMG-database
-        if: github.repository != 'ReactionMechanismGenerator/RMG-database'
         run: |
           cd ..
           git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git

.github/workflows/docs.yml

@@ -81,20 +81,14 @@ jobs:
           cd build/html
           touch .nojekyll
           git add -A --force .
-          git commit -m "Automated documentation rebuild"
+          git diff --staged --exit-code --quiet || git commit -m "Automated documentation rebuild"  # only commit if changes were made
 
       - name: Check documentation links
         continue-on-error: true
         run: |
           cd documentation
           sphinx-build -b linkcheck -d build/doctrees/ source/ build/linkcheck | grep -e broken -e redirect | grep -v -e 'redirect  https://doi.org/' -e 'broken    https://doi.org/.* 403 Client Error: Forbidden'
 
-      - name: Test Publish Documentation
-        if: ${{  github.event_name != 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
-        run: |
-          cd documentation/build/html
-          git push --dry-run origin gh-pages
-
       - name: Publish Updated Documentation
         if: ${{  github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
         run: |

arkane/common.py

@@ -191,11 +191,11 @@ def update_species_attributes(self, species=None):
             self.multiplicity = species.molecule[0].multiplicity
             self.formula = species.molecule[0].get_formula()
             try:
-                inchi = to_inchi(species.molecule[0], backend='try-all', aug_level=0)
+                inchi = to_inchi(species.molecule[0], backend='openbabel-first', aug_level=0)
             except ValueError:
                 inchi = ''
             try:
-                inchi_key = to_inchi_key(species.molecule[0], backend='try-all', aug_level=0)
+                inchi_key = to_inchi_key(species.molecule[0], backend='openbabel-first', aug_level=0)
             except ValueError:
                 inchi_key = ''
             self.inchi = inchi

environment.yml

@@ -14,6 +14,8 @@
 # Changelog:
 # - May 15, 2023 Added this changelog, added inline documentation,
 #   made dependency list more explicit (@JacksonBurns).
+# - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
+#   moved diffeqpy to pip and (temporarily) removed chemprop
 #
 name: rmg_env
 channels:
@@ -42,8 +44,9 @@ dependencies:
   - coolprop
   - cantera::cantera=2.6
   - conda-forge::mopac
-  - conda-forge::cclib >=1.6.3,!=1.8.0
+  - conda-forge::cclib >=1.6.3,<1.8.0
   - conda-forge::openbabel >= 3
+  - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
   - conda-forge::julia=1.9.1
@@ -54,7 +57,7 @@ dependencies:
   - coverage
   - cython >=0.25.2
   - scikit-learn
-  - scipy
+  - scipy <1.11
   - numpy >=1.10.0
   - pydot
   - jinja2
@@ -94,14 +97,8 @@ dependencies:
   # rather than ours (which is only made so that we can get it from conda)
   # It is only on pip, so we will need to do something like:
   # https://stackoverflow.com/a/35245610
-
-  - rmg::chemprop
-  # Our build of this is version 0.0.1 (!!) and we are using parts
-  # of the API that are now gone. Need a serious PR to fix this.
-
-  - rmg::rdkit >=2020.03.3.0
-  # We should use the official channel, not sure how difficult this
-  # change will be.
+  # Note that _some other_ dep. in this list requires diffeqpy in its recipe
+  # which will cause it to be downloaded from the rmg conda channel
 
 # conda mutex metapackage
   - nomkl

rmgpy/ml/estimator.py

@@ -32,17 +32,27 @@
 from argparse import Namespace
 from typing import Callable, Union
 
+chemprop = None
 try:
     import chemprop
 except ImportError as e:
-    chemprop = None
     chemprop_exception = e
 import numpy as np
 
 from rmgpy.molecule import Molecule
 from rmgpy.species import Species
 from rmgpy.thermo import ThermoData
 
+ADMONITION = """
+Support for predicting thermochemistry using chemprop has been temporarily removed
+from RMG, pending official chemprop support for Python 3.11 and newer.
+
+To use chemprop and RMG, install a previous version of RMG (3.1.1 or earlier).
+
+See the link below for status of re-integration of chemprop:
+https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2559
+"""
+
 
 class MLEstimator:
     """
@@ -118,7 +128,7 @@ def load_estimator(model_dir: str) -> Callable[[str], np.ndarray]:
     if chemprop is None:
         # Delay chemprop ImportError until we actually try to use it
         # so that RMG can load successfully without chemprop.
-        raise chemprop_exception
+        raise RuntimeError(ADMONITION + "\nOriginal Exception:\n" + str(chemprop_exception))
 
     args = Namespace()  # Simple class to hold attributes