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Merge PR #2415: update installation instructions and enable CI on MacOS
This PR: - enables continuous integration testing on MacOS - updates the developer installation instructions (MacOS users no longer advised to use a system-wide Julia install) - updates the conda environment (now using `conda-forge::julia>=1.8.5`)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,118 @@ | ||
| # environment.yml - conda environment specification file for RMG-Py | ||
| # | ||
| # Usage: conda env create --file environment.yml | ||
| # | ||
| # This file contains all of the software packages needed to run RMG-Py. | ||
| # There is a mixture of the following | ||
| # - packlages would could be installed at OS level, but we install here | ||
| # for better version control | ||
| # - python tools | ||
| # - external software tools specific to chemistry | ||
| # - other software we maintain which RMG depends on | ||
| # + some other categories (see below) | ||
| # | ||
| # Changelog: | ||
| # - May 15, 2023 Added this changelog, added inline documentation, | ||
| # made depdency list more explicit (@JacksonBurns). | ||
| # | ||
| name: rmg_env | ||
| channels: | ||
| - defaults | ||
| - rmg | ||
| - conda-forge | ||
| - cantera | ||
| dependencies: | ||
| # System-level dependencies - we could install these at the OS level | ||
| # but by installing them in the conda environment we get better control | ||
| - cairo | ||
| - cairocffi | ||
| - ffmpeg | ||
| - xlrd | ||
| - xlwt | ||
| - h5py | ||
| - graphviz | ||
| - markupsafe | ||
| - psutil | ||
| # conda-forge not default, since default has a version information bug | ||
| # (see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2421) | ||
| - conda-forge::ncurses | ||
| - conda-forge::suitesparse | ||
|
|
||
| # external software tools for chemistry | ||
| - coolprop | ||
| - cantera::cantera=2.6 | ||
| - conda-forge::mopac | ||
| - conda-forge::cclib >=1.6.3 | ||
| - rmg::chemprop | ||
| - coolprop | ||
| - conda-forge::openbabel >= 3 | ||
|
|
||
| # general-purpose external software tools | ||
| - conda-forge::julia>=1.8.5 | ||
|
|
||
| # Python tools | ||
| - python >=3.7 | ||
| - coverage | ||
| - cython >=0.25.2 | ||
| - rmg::diffeqpy | ||
| - ffmpeg | ||
| - rmg::gprof2dot | ||
| - graphviz | ||
| - h5py | ||
| - scikit-learn | ||
| - scipy | ||
| - numpy >=1.10.0 | ||
| - pydot | ||
| - jinja2 | ||
| - jupyter | ||
| - rmg::lpsolve55 | ||
| - markupsafe | ||
| - pymongo | ||
| - pyparsing | ||
| - pyyaml | ||
| - networkx | ||
| - nose | ||
| - matplotlib >=1.5 | ||
| - conda-forge::mopac | ||
| - mpmath | ||
| - pandas | ||
|
|
||
| # packages we maintain | ||
| - rmg::gprof2dot | ||
| - rmg::lpsolve55 | ||
| - rmg::muq2 | ||
| - networkx | ||
| - nomkl | ||
| - nose | ||
| - rmg::numdifftools | ||
| - numpy >=1.10.0 | ||
| - conda-forge::openbabel >= 3 | ||
| - pandas | ||
| - psutil | ||
| - rmg::pydas >=1.0.3 | ||
| - pydot | ||
| - rmg::pydqed >=1.0.3 | ||
| - rmg::pyjulia | ||
| - pymongo | ||
| - pyparsing | ||
| - rmg::pyrdl | ||
| - rmg::pyrms | ||
| - python >=3.7 | ||
| - pyyaml | ||
| - rmg::quantities | ||
| - rmg::rdkit >=2020.03.3.0 | ||
| - scikit-learn | ||
| - scipy | ||
| - rmg::symmetry | ||
| - xlrd | ||
| - xlwt | ||
| - conda-forge::ncurses | ||
|
|
||
| # 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. | ||
|
|
||
| - rmg::rdkit >=2020.03.3.0 | ||
| # We should use the official channel, not sure how difficult this | ||
| # change will be. | ||
|
|
||
| - rmg::pyjulia | ||
| # This is identical to the conda-forge package, except that we run | ||
| # a hard to decipher sed command during the build process: | ||
| # https://github.com/ReactionMechanismGenerator/conda-recipes/blob/rmg-deps/pyjulia/build.sh#LL15C69-L15C69 | ||
| # | ||
| # We should either remove the need to use this command or add this | ||
| # to the installation steps | ||
| # | ||
| # Both pyrms and diffeqpy depend on this package. | ||
|
|
||
| # conda mutex metapackage | ||
| - nomkl | ||
|
|
||
| # 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 | ||
| # - libgfortran-ng >= 10 | ||
| # but this exact package is only maintained for Linux, meaning that if we were to add | ||
| # it here the environment creation would fail on Mac. The way it ends up working behind | ||
| # the scenes is that conda will find a different package for Mac that provides gfortran, | ||
| # but because we cannot specify per-platform requirements in this file we simply leave | ||
| # it out. |