ReactionMechanismGenerator · JacksonBurns · Jul 10, 2025 · Jul 8, 2025 · Jul 8, 2025 · Jul 9, 2025
diff --git a/.conda/build.sh b/.conda/build.sh
diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -1,84 +1,185 @@
-# For conda build
+# meta.yaml
+#
+# welcome to meta.yaml, poor soul that you are. this file specifies the 'recipe' for compiling
+# RMG-Py into binaries which can then be uploaded for access via the conda package manager
+# to use this file, you can follow the procedure shown in .github/workflows/conda_build.yml
+#
 package:
   name: rmg
-  version: 3.2.0
+  version: 3.3.0
 
 source:
   path: ../
 
 build:
-  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
+  number: 0
+  script: |
+    python utilities.py check-pydas  # write the rmgpy/solver/settings.pxi file
+    python setup.py install --single-version-externally-managed --record=record.txt
 
 requirements:
   build:
-    - {{ compiler('c') }} # [unix]
+    - {{ compiler('c') }}
   host:
-    - cython >=0.25.2
-    - numpy
-    - openbabel >=3
-    - pydas >=1.0.2
-    - pydqed >=1.0.1
-    - pyrdl
-    - python
-    - quantities
-    - rdkit >=2018
-    - scipy
-    - setuptools
+    - conda-forge::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg >=7
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz >=12
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::graphviz 
+    - conda-forge::pyopenssl >20
+    - conda-forge::coolprop
+    - conda-forge::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,<1.9
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.9
+    - conda-forge::setuptools <80
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2,<3.1
+    - conda-forge::scikit-learn
+    - conda-forge::scipy >=1.9
+    - conda-forge::numpy >=1.10.0,<2
+    - 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::pytest-check
+    - conda-forge::pyutilib
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities !=0.16.0,!=0.16.1
+    - conda-forge::ringdecomposerlib-python
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::symmetry
+    - rmg::rmgdatabase =3.3.0
+    - blas=*=openblas
   run:
-    - cairo
-    - cairocffi
-    - cantera >=2.3.0
-    - cclib >=1.6.3
-    - coolprop
-    - coverage
-    - cython >=0.25.2
-    - ffmpeg
-    - gprof2dot
-    - graphviz
-    - h5py
-    - jinja2
-    - jupyter
-    - 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::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg >=7
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz >=12
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::graphviz 
+    - conda-forge::pyopenssl >20
+    - conda-forge::coolprop
+    - conda-forge::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,<1.9
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.9
+    - conda-forge::setuptools <80
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2,<3.1
+    - conda-forge::scikit-learn
+    - conda-forge::scipy >=1.9
+    - conda-forge::numpy >=1.10.0,<2
+    - 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::pytest-check
+    - conda-forge::pyutilib
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities !=0.16.0,!=0.16.1
+    - conda-forge::ringdecomposerlib-python
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::symmetry
+    - rmg::rmgdatabase =3.3.0
+    - blas=*=openblas
 test:
+  requires:
+    - conda-forge::cairo
+    - conda-forge::cairocffi
+    - conda-forge::ffmpeg >=7
+    - conda-forge::xlrd
+    - conda-forge::xlwt
+    - conda-forge::h5py
+    - conda-forge::graphviz >=12
+    - conda-forge::markupsafe
+    - conda-forge::psutil
+    - conda-forge::ncurses
+    - conda-forge::suitesparse
+    - conda-forge::graphviz 
+    - conda-forge::pyopenssl >20
+    - conda-forge::coolprop
+    - conda-forge::cantera =2.6
+    - conda-forge::mopac
+    - conda-forge::cclib >=1.6.3,<1.9
+    - conda-forge::openbabel >=3
+    - conda-forge::rdkit >=2022.09.1
+    - conda-forge::python >=3.9
+    - conda-forge::setuptools <80
+    - conda-forge::coverage
+    - conda-forge::cython >=0.25.2,<3.1
+    - conda-forge::scikit-learn
+    - conda-forge::scipy >=1.9
+    - conda-forge::numpy >=1.10.0,<2
+    - 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::pytest-check
+    - conda-forge::pyutilib
+    - conda-forge::matplotlib >=1.5
+    - conda-forge::mpmath
+    - conda-forge::pandas
+    - conda-forge::gprof2dot
+    - conda-forge::numdifftools
+    - conda-forge::quantities !=0.16.0,!=0.16.1
+    - conda-forge::ringdecomposerlib-python
+    - rmg::pydas >=1.0.3
+    - rmg::pydqed >=1.0.3
+    - rmg::symmetry
+    - rmg::rmgdatabase =3.3.0
+    - blas=*=openblas
   source_files:
     - 'examples/rmg/superminimal'
-    - 'examples/arkane/networks/n-butanol'
+    - 'examples/arkane/networks/n-butanol_msc'
   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_msc/input.py
 
 about:
   home: https://github.com/ReactionMechanismGenerator/RMG-Py

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
@@ -1,58 +1,66 @@
 name: Conda Build
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
+  pull_request:
+  workflow_dispatch:
   push:
     branches:
       - stable
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-latest]
+        numpy-version: ["1.26"]
+        python-version: ["3.9"]
+    runs-on: ${{ matrix.os }}
+    name: Build ${{ matrix.os }} Python ${{ matrix.python-version }} Numpy ${{ matrix.numpy-version }}
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rmg_env
-      - name: Conda info
+          miniforge-variant: Miniforge3
+          miniforge-version: latest
+          auto-update-conda: true
+          show-channel-urls: true
+          conda-remove-defaults: "true"
+          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: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          conda install -y conda-build 
-          conda install -y anaconda-client 
+          # set a default value to the conda_token if needed (like from forks)
+          : "${CONDA_TOKEN:=${{ secrets.ANACONDA_TOKEN }}}"
+          : "${CONDA_TOKEN:=default_value}"
+          echo "CONDA_TOKEN=$CONDA_TOKEN" >> $GITHUB_ENV
           conda config --add channels rmg
-          conda config --set anaconda_upload yes
-          conda build --token $CONDA_TOKEN --user rmg .conda
-  build-osx:
-    runs-on: macos-latest
-    defaults:
-      run:
-        shell: bash -l {0}
+          conda config --add channels conda-forge
+          CONDA_NPY=${{ matrix.numpy-version }} CONDA_PY=${{ matrix.python-version }} conda build --token $CONDA_TOKEN --user rmg .
+
+  result:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    name: Final Results
+    needs: [build]
     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 }}
-        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
+      - run: exit 1
+        # see https://github.com/orgs/community/discussions/26822?sort=new#discussioncomment-8285141
+        if: ${{ contains(needs.*.result, 'failure') || contains(needs.*.result, 'cancelled') || contains(needs.*.result, 'skipped') }}