diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index d272feda782..6ffb1b662f2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -112,8 +112,6 @@ jobs: uses: actions/checkout@v3 # 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: @@ -124,6 +122,12 @@ jobs: activate-environment: rmg_env use-mamba: true + # installs the extra RMS conda dependencies + - name: Add RMS dependencies + run: | + conda install -c conda-forge julia>=1.9.1 pyjulia>=0.6 + conda install -c rmg pyrms diffeqpy + # list the environment for debugging purposes - name: mamba info run: | diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index aff19b7b837..b0c11df41e5 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -36,6 +36,12 @@ jobs: activate-environment: rmg_env use-mamba: true + # installs the extra RMS conda dependencies + - name: Add RMS dependencies + run: | + conda install -c conda-forge julia>=1.9.1 pyjulia>=0.6 + conda install -c rmg pyrms diffeqpy + - name: Install sphinx run: mamba install -y sphinx diff --git a/Dockerfile b/Dockerfile index a263199c896..7ff65484d39 100644 --- a/Dockerfile +++ b/Dockerfile @@ -45,6 +45,8 @@ RUN git clone --single-branch --branch main --depth 1 https://github.com/Reactio WORKDIR /rmg/RMG-Py # build the conda environment RUN conda env create --file environment.yml && \ + conda install -c conda-forge julia>=1.9.1 pyjulia>=0.6 && \ + conda install -c rmg pyrms diffeqpy && \ conda clean --all --yes # This runs all subsequent commands inside the rmg_env conda environment diff --git a/environment.yml b/environment.yml index 4596f580ee0..e93c9ef684e 100644 --- a/environment.yml +++ b/environment.yml @@ -14,6 +14,7 @@ # Changelog: # - May 15, 2023 Added this changelog, added inline documentation, # made dependency list more explicit (@JacksonBurns). +# - Mar 11, 2024 Removed Julia dependencies, now considered optional # name: rmg_env channels: @@ -45,10 +46,6 @@ dependencies: - conda-forge::cclib >=1.6.3,!=1.8.0 - conda-forge::openbabel >= 3 -# general-purpose external software tools - - conda-forge::julia=1.9.1 - - conda-forge::pyjulia >=0.6 - # Python tools - python >=3.7 - coverage @@ -85,16 +82,9 @@ dependencies: - rmg::pydas >=1.0.3 - rmg::pydqed >=1.0.3 - rmg::pyrdl - - rmg::pyrms - rmg::symmetry # packages we would like to stop maintaining (and why) - - rmg::diffeqpy - # we should use the official verison https://github.com/SciML/diffeqpy), - # 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. @@ -106,6 +96,19 @@ dependencies: # conda mutex metapackage - nomkl +# optional dependencies for using ReactionMechanismSimulator +# remove the leading '#' to install the required dependencies + # - conda-forge::julia=1.9.1 + # - conda-forge::pyjulia >=0.6 + # - rmg::pyrms + # - rmg::diffeqpy + +# Note about diffeqpy: +# we should use the official verison https://github.com/SciML/diffeqpy), +# 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 + # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) # in the environment. Normally we would add this to the environment file with