Merge branch 'main' into rms_yaml_write

.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

@@ -58,13 +58,8 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout RMG-Py - Resuable Workflow
-        if: github.repository == 'ReactionMechanismGenerator/RMG-database'
-        uses: actions/checkout@v3
-
-      - name: Clone RMG-Py - RMG-Py
-        if: github.repository != 'ReactionMechanismGenerator/RMG-database'
-        uses: actions/checkout@v3
+      - name: Checkout RMG-Py
+        uses: actions/checkout@v4
 
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
@@ -114,7 +109,7 @@ 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
@@ -135,7 +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

@@ -5,17 +5,27 @@ on:
     branches:
       - main
   pull_request:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron: "0 8 * * 1"
 
 jobs:
   build-documentation:
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
+      - name: Sign into GitHub Actions Bot
+        run: |
+          git config --global user.name "github-actions"
+          git config --global user.email "github-actions@github.com"
+
+      - name: Clone RMG-Py
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -25,52 +35,62 @@ jobs:
           python-version: 3.7
           activate-environment: rmg_env
           use-mamba: true
+
       - name: Install sphinx
         run: mamba install -y sphinx
+
       - name: Mamba info
         run: |
           mamba info
           mamba list
-      - name: Install and link Julia dependencies 
-        run: |
-          julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
-          julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
-          python -c "import julia; julia.install()"
-      - name: Install and compile RMG
+
+      - name: Clone RMG-database
         run: |
           cd ..
           git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
-          cd RMG-Py
-          sed -i '/embedsignature/s/# //g' setup.py
-          make
-      - name: Make documentation - for testing
-        if: ${{  github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }}
+
+      - name: Set Environment Variables
         run: |
-          cd documentation
-          sphinx-build -b html -d build/doctrees/ source/ build/html -w errors.log -W --keep-going
-      - name: Report documentation errors
-        if: ${{ failure() }}
+          RUNNER_CWD=$(pwd)
+          echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
+          echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
+
+      - name: make RMG
         run: |
-          cat documentation/errors.log
-      - name: Make documentation - to publish
-        if: ${{  github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
-        env:
-            GH_TOKEN: ${{ secrets.RMG_DEV_TOKEN }}
+          make clean
+          make
+
+      - name: Install and link Julia dependencies
+        timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          make -C documentation continous_integration_setup clean html
+          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+
+      - name: Checkout gh-pages Branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+          fetch-depth: 0
+          path: documentation/build/html
+          clean: false
+
+      - name: Build Documentation
+        run: |
+          cd documentation
+          make html
+          cd build/html
+          touch .nojekyll
+          git add -A --force .
+          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: Publish documentation
+
+      - name: Publish Updated Documentation
         if: ${{  github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
-        env:
-            GH_TOKEN: ${{ secrets.RMG_DEV_TOKEN }}
-            COMMITMESSAGE: "Automatic documentation rebuild"
-            GIT_AUTHOR_NAME: "RMG Bot"
-            GIT_AUTHOR_EMAIL: "rmg_dev@mit.edu"
-            GIT_COMMITTER_NAME: "RMG Bot"
-            GIT_COMMITTER_EMAIL: "rmg_dev@mit.edu"
         run: |
-          make -C documentation publish
+          cd documentation/build/html
+          git push origin gh-pages

Dockerfile

@@ -13,7 +13,7 @@ RUN ln -snf /bin/bash /bin/sh
 #  - libxrender1 required by RDKit
 RUN apt-get update && \
     apt-get install -y \
-    make \ 
+    make \
     gcc \
     wget \
     git \
@@ -42,8 +42,8 @@ WORKDIR /rmg
 RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
     git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git
 
-# build the conda environment
 WORKDIR /rmg/RMG-Py
+# build the conda environment
 RUN conda env create --file environment.yml && \
     conda clean --all --yes
 
@@ -61,9 +61,11 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 
 # 1. Build RMG
 # 2. Install and link Julia dependencies for RMS
+# setting this env variable fixes an issue with Julia precompilation on Windows
+ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
 RUN make && \
     julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
-    python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" 
+    python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
 RUN python-jl rmg.py examples/rmg/minimal/input.py

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