environment.yml

# 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 dependency list more explicit (@JacksonBurns).
# - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
#   moved diffeqpy to pip and (temporarily) removed chemprop
# - April 17, 2024 Limit versions of cclib at advice of maintainers.
# - August 4, 2024 Restricted pyrms to <2
name: rmg_env
channels:
  - 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
  # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639#issuecomment-2050292972
  - conda-forge::cclib >=1.6.3,<1.9
  - conda-forge::openbabel >= 3
  - conda-forge::rdkit >=2022.09.1

# general-purpose external software tools
  - conda-forge::julia=1.9.1
  - conda-forge::pyjulia >=0.6

# Python tools
  - python >=3.7
  - coverage
  - cython >=0.25.2
  - scikit-learn
  - scipy <1.11
  - numpy >=1.10.0
  - pydot
  - jinja2
  - jupyter
  - pymongo
  - pyparsing
  - pyyaml
  - networkx
  - pytest
  - pytest-cov
  # we use a the pytest-check plugin, which is on Conda and PyPI, but the
  # version compatible with Python 3.7 is only on PyPI
  # switch to the conda version after upgrading to 3.11
  # - conda-forge::pytest-check
  - pip
  - pip:
    - pytest-check
  - matplotlib >=1.5
  - mpmath
  - pandas
  - conda-forge::gprof2dot
  - conda-forge::numdifftools
  - conda-forge::quantities
  - conda-forge::muq
  - conda-forge::lpsolve55
  - conda-forge::ringdecomposerlib-python

# packages we maintain
  - rmg::pydas >=1.0.3
  - rmg::pydqed >=1.0.3
  - rmg::pyrms <2
  - 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
  # Note that _some other_ dep. in this list requires diffeqpy in its recipe
  # which will cause it to be downloaded from the rmg conda channel

# configure packages to use OpenBLAS instead of Intel MKL
  - blas=*=openblas

# 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.