revise conda recipe and github actions to execute it

.conda/build.sh

@@ -1,6 +1,48 @@
-# Install RMG
+set -x
+# as done in the pure-python conda recipe
 make install
+python -c "from rmgpy.molecule import Molecule"
 
-# lazy "install" of everything in our 'external' folder.
-# most of which should probably be elsewhere
-cp -R ${SRC_DIR}/external ${SP_DIR}
+# attempting to run the Julia install
+# from https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2631#issuecomment-1998723914
+#make julia directory
+mkdir -p ${PREFIX}/share/julia/site
+mkdir -p ${PREFIX}/bin
+#set JULIA_DEPOT_PATH in conda env
+export JULIA_DEPOT_PATH="${PREFIX}/share/julia/site"
+ACTIVATE_ENV="${PREFIX}/etc/conda/activate.d/env_vars.sh"
+DEACTIVATE_ENV="${PREFIX}/etc/conda/deactivate.d/env_vars.sh"
+
+if [ -f "$ACTIVATE_ENV" ]; then
+        echo 'python-jl -c "import julia; julia.install()"' >> $ACTIVATE_ENV
+        # echo 'sed -i \'/julia.install/d\' $ACTIVATE_ENV' >> $ACTIVATE_ENV
+else
+        mkdir -p ${PREFIX}/etc/conda/activate.d
+        touch ${PREFIX}/etc/conda/activate.d/env_vars.sh
+        echo '#!/bin/sh' >> $ACTIVATE_ENV
+        echo 'python-jl -c "import julia; julia.install()"' >> $ACTIVATE_ENV
+        # echo 'sed -i \'/julia.install/d\' $ACTIVATE_ENV' >> $ACTIVATE_ENV
+fi
+
+export PYTHON=$PREFIX/bin/python
+export PYTHONPATH=$SRC_DIR:$PYTHONPATH
+echo "testing rmgpy"
+python -c "from rmgpy.molecule import Molecule"
+
+echo "pythonpath"
+echo $PYTHONPATH 
+echo "python"
+echo $PYTHON
+
+
+python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+echo "current python"
+which python
+echo "julia python"
+julia -e "using PyCall; println(PyCall.PYTHONHOME)"
+echo "retest rmgpy"
+python -c "from rmgpy.molecule import Molecule"
+
+julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+
+set +x

.conda/conda_build_config.yaml

@@ -2,7 +2,3 @@ python:
   - 3.7
 numpy:
   - 1.15
-
-# Specifically for Travis build. Should change if building locally.
-CONDA_BUILD_SYSROOT:
-  - /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk # [osx] 

.conda/meta.yaml

@@ -11,78 +11,174 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }} # [unix]
+    - {{ compiler('c') }}
   host:
-    - cython >=0.25.2
-    - lpsolve55
-    - numpy
-    - openbabel >=3
-    - pydas >=1.0.2
-    - pydqed >=1.0.1
-    - pyrdl
-    - python
-    - quantities
-    - rdkit >=2018
-    - scipy
-    - setuptools
+    - conda-forge::libxcrypt  # remove after upgrading Python versions
+    - conda-forge::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::coolprop
+    - cantera::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,!=1.8.0
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.7
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2
+    - conda-forge::scikit-learn
+    - conda-forge::scipy <1.11
+    - conda-forge::numpy >=1.10.0
+    - conda-forge::pydot
+    - conda-forge::jinja2
+    - conda-forge::jupyter
+    - conda-forge::pymongo
+    - conda-forge::pyparsing
+    - conda-forge::pyyaml
+    - conda-forge::networkx
+    - conda-forge::pytest
+    - conda-forge::pytest-cov
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities
+    - rmg::lpsolve55
+    - rmg::muq2
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::pyrdl
+    - rmg::symmetry
+    - rmg::diffeqpy
+    - rmg::pyrms
+    - conda-forge::julia=1.9.1
+    - conda-forge::pyjulia>=0.6
+    - conda-forge::nomkl
   run:
-    - cairo
-    - cairocffi
-    - cantera >=2.3.0
-    - cclib >=1.6.3
-    - coolprop
-    - coverage
-    - cython >=0.25.2
-    - ffmpeg
-    - gprof2dot
-    - graphviz
-    - h5py
-    - jinja2
-    - jupyter
-    - lpsolve55
-    - markupsafe
-    - matplotlib >=1.5
-    - mopac
-    - mpmath
-    - muq2
-    - networkx
-    - nose
-    - numdifftools
-    - {{ pin_compatible('numpy') }}
-    - openbabel >=3
-    - pandas
-    - psutil
-    - pydas >=1.0.2
-    - pydot
-    - pydqed >=1.0.1
-    - pymongo
-    - pyparsing
-    - pyrdl
-    - python
-    - pyyaml
-    - pyzmq
-    - quantities
-    - rdkit >=2018
-    - rmgdatabase >=3.2.0
-    - scikit-learn
-    - scipy
-    - symmetry
-    - xlrd
-    - xlwt
+    - conda-forge::libxcrypt  # remove after upgrading Python versions
+    - jacksonburns::rmgdatabase
+    - conda-forge::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::coolprop
+    - cantera::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,!=1.8.0
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.7
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2
+    - conda-forge::scikit-learn
+    - conda-forge::scipy <1.11
+    - conda-forge::numpy >=1.10.0
+    - conda-forge::pydot
+    - conda-forge::jinja2
+    - conda-forge::jupyter
+    - conda-forge::pymongo
+    - conda-forge::pyparsing
+    - conda-forge::pyyaml
+    - conda-forge::networkx
+    - conda-forge::pytest
+    - conda-forge::pytest-cov
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities
+    - rmg::lpsolve55
+    - rmg::muq2
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::pyrdl
+    - rmg::symmetry
+    - rmg::diffeqpy
+    - rmg::pyrms
+    - conda-forge::julia=1.9.1
+    - conda-forge::pyjulia>=0.6
+    - conda-forge::nomkl
 test:
+  requires:
+    - conda-forge::libxcrypt  # remove after upgrading Python versions
+    - jacksonburns::rmgdatabase
+    - conda-forge::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::coolprop
+    - cantera::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,!=1.8.0
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.7
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2
+    - conda-forge::scikit-learn
+    - conda-forge::scipy <1.11
+    - conda-forge::numpy >=1.10.0
+    - conda-forge::pydot
+    - conda-forge::jinja2
+    - conda-forge::jupyter
+    - conda-forge::pymongo
+    - conda-forge::pyparsing
+    - conda-forge::pyyaml
+    - conda-forge::networkx
+    - conda-forge::pytest
+    - conda-forge::pytest-cov
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities
+    - rmg::lpsolve55
+    - rmg::muq2
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::pyrdl
+    - rmg::symmetry
+    - rmg::diffeqpy
+    - rmg::pyrms
+    - conda-forge::julia=1.9.1
+    - conda-forge::pyjulia>=0.6
+    - conda-forge::nomkl
   source_files:
     - 'examples/rmg/superminimal'
     - 'examples/arkane/networks/n-butanol'
   imports:
     - rmgpy
     - arkane
   commands:
-    - rmg.py examples/rmg/superminimal/input.py # [unix]
-    - Arkane.py examples/arkane/networks/n-butanol/input.py # [unix]
-    - python %SCRIPTS%\rmg.py examples\rmg\superminimal\input.py # [win]
-    - python %SCRIPTS\Arkane.py examples\arkane\networks\n-butanol\input.py # [win]
+    - rmg.py examples/rmg/superminimal/input.py
+    - Arkane.py examples/arkane/networks/n-butanol/input.py
 
 about:
   home: https://github.com/ReactionMechanismGenerator/RMG-Py
   license: MIT
-  summary: "A program for automatically generating kinetic models of chemical reaction mechanisms."
+  summary: "A program for automatically generating kinetic models of chemical reaction mechanisms."

.github/workflows/conda_build.yml

@@ -1,58 +1,47 @@
 name: Conda Build
 
 on:
+  pull_request:
   push:
     branches:
       - stable
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rmg_env
-      - name: Conda info
+          auto-update-conda: false
+          conda-solver: libmamba
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Build Tools
+        run: conda install python anaconda-client conda-build
+      - name: Configure Auto-Upload
+        if: github.ref == 'refs/heads/stable'
         run: |
-          conda info
-          conda list
+          conda config --set anaconda_upload yes
       - name: Build Binary
         env: 
-          CONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          CONDA_TOKEN: "need_to_add_this_secret"  # ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          conda install -y conda-build 
-          conda install -y anaconda-client 
           conda config --add channels rmg
-          conda config --set anaconda_upload yes
-          conda build --token $CONDA_TOKEN --user rmg .conda
-  build-osx:
-    runs-on: macos-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rmg_env
-      - name: Conda info
-        run: |
-          conda info
-          conda list
-      - name: Build Binary
-        env: 
-          CONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          conda config --add channels cantera
+          conda config --add channels conda-forge
+          conda config --add channels jacksonburns
+          conda-build --token $CONDA_TOKEN --user rmg .conda
+      - name: Test Binary Install with RMS
         run: |
-            conda install -y conda-build 
-            conda install -y anaconda-client 
-            conda config --add channels rmg
-            conda config --set anaconda_upload yes
-            xcrun --show-sdk-path
-            conda build --token $CONDA_TOKEN --user rmg .conda
+          conda create --name rmg_test python=3.7*
+          conda activate rmg_test
+          conda install -c local rmg
+          python-jl rmg.py test/regression/RMS_constantVIdealGasReactor_superminimal/input.py

setup.py

@@ -215,7 +215,7 @@
     'scripts/standardizeModelSpeciesNames.py',
     'scripts/thermoEstimator.py',
     'scripts/isotopes.py',
-    'testing/databaseTest.py',
+    'test/database/databaseTest.py',
 ]
 
 modules = []