diff --git a/.conda/build.sh b/.conda/build.sh index c942c713eb1..c0ec39927a1 100644 --- a/.conda/build.sh +++ b/.conda/build.sh @@ -1,6 +1,15 @@ -# Install RMG +# conda build script +# +# conda executes this script during the build process to make the rmg +# binary make install -# lazy "install" of everything in our 'external' folder. -# most of which should probably be elsewhere -cp -R ${SRC_DIR}/external ${SP_DIR} +# The below code does not work because the Julia programming langauge is a very interesting technical demo that is completely unfit for actual +# deployment in any real world projects. +# +# RMG will be shipped as a pure python package, and then RMS installed by the user. +# +# export PYTHON=$PREFIX/bin/python +# export PYTHONPATH=$SRC_DIR:$PYTHONPATH +# python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" +# julia -e 'using Pkg; Pkg.add(PackageSpec(name="Functors",version="0.4.3")); Pkg.pin("Functors"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator' diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml index 6a0cca7f0c7..4fe9a38c7bc 100644 --- a/.conda/conda_build_config.yaml +++ b/.conda/conda_build_config.yaml @@ -3,6 +3,3 @@ python: numpy: - 1.15 -# Specifically for Travis build. Should change if building locally. -CONDA_BUILD_SYSROOT: - - /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk # [osx] diff --git a/.conda/meta.yaml b/.conda/meta.yaml index 9e74a621fc1..7afdd611e9e 100644 --- a/.conda/meta.yaml +++ b/.conda/meta.yaml @@ -13,64 +13,165 @@ requirements: build: - {{ compiler('c') }} host: + - cairo + - cairocffi + - ffmpeg + - xlrd + - xlwt + - h5py + - graphviz + - markupsafe + - psutil + - ncurses + - suitesparse + + # external software tools for chemistry + - coolprop + - cantera=2.6 + - mopac + - cclib >=1.6.3,!=1.8.0 + - openbabel >=3 + + # Python tools + - python >=3.7 + - coverage - cython >=0.25.2 + - scikit-learn + - scipy + - numpy >=1.10.0 + - pydot + - jinja2 + - jupyter + - pymongo + - pyparsing + - pyyaml + - networkx + - matplotlib >=1.5 + - mpmath + - pandas + + # packages we maintain + - rmgdatabase + - gprof2dot - lpsolve55 - - numpy - - openbabel >=3 - - pydas >=1.0.2 - - pydqed >=1.0.1 + - muq2 + - numdifftools + - pydas >=1.0.3 + - pydqed >=1.0.3 - pyrdl - - python - quantities - - rdkit >=2018 - - scipy - - setuptools + - symmetry + - chemprop==0.0.1 + - rdkit >=2020.03.3.0 + + - liblapack =*=*mkl run: - cairo - cairocffi - - cantera >=2.3.0 - - cclib >=1.6.3 - - chemprop + - ffmpeg + - xlrd + - xlwt + - h5py + - graphviz + - markupsafe + - psutil + - ncurses + - suitesparse + + # external software tools for chemistry - coolprop + - cantera=2.6 + - mopac + - cclib >=1.6.3,!=1.8.0 + - openbabel >=3 + + # Python tools + - python >=3.7 - coverage - cython >=0.25.2 - - ffmpeg - - gprof2dot - - graphviz - - h5py + - scikit-learn + - scipy + - numpy >=1.10.0 + - pydot - jinja2 - jupyter - - lpsolve55 - - markupsafe + - pymongo + - pyparsing + - pyyaml + - networkx - matplotlib >=1.5 - - mopac - mpmath + - pandas + + # packages we maintain + - rmgdatabase + - gprof2dot + - lpsolve55 - muq2 - - networkx - - nose - numdifftools - - {{ pin_compatible('numpy') }} - - openbabel >=3 - - pandas + - pydas >=1.0.3 + - pydqed >=1.0.3 + - pyrdl + - quantities + - symmetry + - chemprop==0.0.1 + - rdkit >=2020.03.3.0 + + - liblapack =*=*mkl +test: + requires: + - cairo + - cairocffi + - ffmpeg + - xlrd + - xlwt + - h5py + - graphviz + - markupsafe - psutil - - pydas >=1.0.2 + - ncurses + - suitesparse + + # external software tools for chemistry + - coolprop + - cantera=2.6 + - mopac + - cclib >=1.6.3,!=1.8.0 + - openbabel >=3 + + # Python tools + - python >=3.7 + - coverage + - cython >=0.25.2 + - scikit-learn + - scipy + - numpy >=1.10.0 - pydot - - pydqed >=1.0.1 + - jinja2 + - jupyter - pymongo - pyparsing - - pyrdl - - python - pyyaml - - pyzmq + - networkx + - matplotlib >=1.5 + - mpmath + - pandas + + # packages we maintain + - rmgdatabase + - gprof2dot + - lpsolve55 + - muq2 + - numdifftools + - pydas >=1.0.3 + - pydqed >=1.0.3 + - pyrdl - quantities - - rdkit >=2018 - - rmgdatabase >=3.2.0 - - scikit-learn - - scipy - symmetry - - xlrd - - xlwt -test: + - chemprop==0.0.1 + - rdkit >=2020.03.3.0 + + - liblapack =*=*mkl source_files: - 'examples/rmg/superminimal' - 'examples/arkane/networks/n-butanol' @@ -78,8 +179,8 @@ test: - rmgpy - arkane commands: - - python-jl rmg.py examples/rmg/superminimal/input.py - - python arkane.py examples/arkane/networks/n-butanol + - rmg.py examples/rmg/superminimal/input.py + - arkane.py examples/arkane/networks/n-butanol about: home: https://github.com/ReactionMechanismGenerator/RMG-Py diff --git a/environment.yml b/environment.yml index 5155a74b099..5080ac20630 100644 --- a/environment.yml +++ b/environment.yml @@ -45,10 +45,6 @@ dependencies: - conda-forge::cclib >=1.6.3,!=1.8.0 - conda-forge::openbabel >= 3 -# general-purpose external software tools - - conda-forge::julia>=1.8.5,!=1.9.0 - - conda-forge::pyjulia >=0.6 - # Python tools - python >=3.7 - coverage @@ -75,21 +71,20 @@ dependencies: - matplotlib >=1.5 - mpmath - pandas + - conda-forge::numdifftools # packages we maintain - rmg::gprof2dot - rmg::lpsolve55 - rmg::muq2 - - rmg::numdifftools - rmg::pydas >=1.0.3 - rmg::pydqed >=1.0.3 - rmg::pyrdl - - rmg::pyrms - rmg::quantities - rmg::symmetry # packages we would like to stop maintaining (and why) - - rmg::diffeqpy + #- 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: @@ -103,8 +98,7 @@ dependencies: # We should use the official channel, not sure how difficult this # change will be. -# conda mutex metapackage - - nomkl + - liblapack =*=*mkl # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) diff --git a/rmg.py b/rmg.py index 26c27c00a4d..0b27098b816 100644 --- a/rmg.py +++ b/rmg.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python-jl +#!/usr/bin/env python ############################################################################### # # diff --git a/setup.py b/setup.py index 604a856eb19..17fdab4a888 100644 --- a/setup.py +++ b/setup.py @@ -215,7 +215,6 @@ 'scripts/standardizeModelSpeciesNames.py', 'scripts/thermoEstimator.py', 'scripts/isotopes.py', - 'testing/databaseTest.py', ] modules = [] diff --git a/utilities.py b/utilities.py index c8e74258186..f84963a6324 100644 --- a/utilities.py +++ b/utilities.py @@ -310,7 +310,7 @@ def update_headers(): start of each file, be sure to double-check the results to make sure important lines aren't accidentally overwritten. """ - shebang = """#!/usr/bin/env python-jl + shebang = """#!/usr/bin/env python """