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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| juliaup update | ||
| python -c "from pyrms import rms" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,42 @@ | ||
| #for conda build | ||
| package: | ||
| name: pyrms | ||
| version: {{ environ.get('GIT_DESCRIBE_TAG', '') }} | ||
|
|
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| source: | ||
| path: ../ | ||
|
|
||
| build: | ||
| number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }} | ||
| script_env: | ||
| - JULIAUP_DEPOT_PATH=$PREFIX/share/juliaup | ||
| - JULIA_DEPOT_PATH=$PREFIX/share/julia | ||
| - JULIA_CONDAPKG_ENV=$PREFIX | ||
|
|
||
| requirements: | ||
| host: | ||
| - pyjuliacall | ||
| - rmgmolecule >=0.3 | ||
| - rdkit >=2015.09.2 | ||
| - setuptools | ||
| - juliaup | ||
| - numpy | ||
| run: | ||
| - pydot >=2.0 | ||
| - yaml | ||
| - pyjuliacall | ||
| - rmgmolecule >=0.3 | ||
| - rdkit >=2015.09.2 | ||
| - juliaup | ||
| - jupyter | ||
| - matplotlib | ||
| - nose | ||
| test: | ||
| imports: | ||
| - pyrms | ||
| commands: | ||
| - nosetests pyrms/rmsTest.py # [unix] | ||
| about: | ||
| home: http://github.com/ReactionMechanismGenerator/pyrms | ||
| license: MIT | ||
| summary: "A program for simulating and analyzing kinetic models of chemical reaction mechanisms." |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| name: CI | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| tags: '*' | ||
| pull_request: | ||
| workflow_dispatch: | ||
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|
||
| jobs: | ||
| test: | ||
| runs-on: ${{ matrix.os }} | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
| strategy: | ||
| matrix: | ||
| os: | ||
| - ubuntu-latest | ||
| architecture: [x64] | ||
| python-version: ['3.9'] | ||
| fail-fast: false | ||
| name: Test ${{ matrix.os }} ${{ matrix.architecture }} | ||
| Python ${{ matrix.python-version }} | ||
| steps: | ||
| - uses: actions/checkout@v1 | ||
| - name: Setup python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: ${{ matrix.architecture }} | ||
| - name: Setup Conda Environment | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| activate-environment: rms_env | ||
| environment-file: environment.yml | ||
| miniforge-variant: Mambaforge | ||
| miniforge-version: "latest" | ||
| python-version: ${{ matrix.python-version }} | ||
| use-mamba: true | ||
| - name: Install packages | ||
| run: | | ||
| python -m pip install pytest nbmake | ||
| python -m pip install -e . | ||
| - name: Conda Info | ||
| run: | | ||
| mamba info | ||
| mamba list | ||
| - name: Run test | ||
| run: | | ||
| nosetests pyrms/rmsTest.py | ||
| pytest --nbmake Ipython/pyrms_example.ipynb |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| name: pyrms_env | ||
| channels: | ||
| - defaults | ||
| - mjohnson541 | ||
| - conda-forge | ||
| dependencies: | ||
| - juliaup | ||
| - nose | ||
| - pyjuliacall | ||
| - rmgmolecule >= 0.3 | ||
| - rdkit | ||
| - pydot >= 2.0 | ||
| - matplotlib | ||
| - numpy | ||
| - jupyter |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,45 @@ | ||
| import os | ||
| import subprocess | ||
| import shutil | ||
| from subprocess import run | ||
| # juliacall must be loaded after `_ensure_julia_installed()` is run, | ||
| # so this import is in `load_julia_packages()` | ||
| # from juliacall import Main | ||
|
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||
| def install(): | ||
| def _find_julia(): | ||
| return shutil.which("julia") | ||
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| def _ensure_julia_installed(): | ||
| if not _find_julia(): | ||
| print("No Julia version found. Installing Julia.") | ||
| run("juliaup update") | ||
| if not _find_julia(): | ||
| raise RuntimeError( | ||
| "Julia installed with jill but `julia` binary cannot be found in the path" | ||
| ) | ||
|
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||
| # TODO: upstream this function or an alternative into juliacall | ||
| def load_julia_packages(*names): | ||
| """ | ||
| Install Julia packages required for diffeqpy. | ||
| Load Julia packages and return references to them, automatically installing julia and | ||
| the packages as necessary. | ||
| """ | ||
| import julia | ||
| import diffeqpy | ||
| julia.install() | ||
| diffeqpy.install() | ||
| from julia.api import Julia | ||
| jl = Julia(compiled_modules=False) | ||
| from julia import Pkg | ||
| Pkg.add("ReactionMechanismSimulator") | ||
| from julia import ReactionMechanismSimulator | ||
| # This is terrifying to many people. However, it seems SciML takes pragmatic approach. | ||
| _ensure_julia_installed() | ||
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| script = """import Pkg | ||
| Pkg.activate(\"pyrms\", shared=true) | ||
| try | ||
| import {0} | ||
| catch e | ||
| e isa ArgumentError || throw(e) | ||
| Pkg.add([{1}]) | ||
| import {0} | ||
| end | ||
| {0}""".format(", ".join(names), ", ".join(f'"{name}"' for name in names)) | ||
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| # Unfortunately, `seval` doesn't support multi-line strings | ||
| # https://github.com/JuliaPy/PythonCall.jl/issues/433 | ||
| script = script.replace("\n", ";") | ||
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| # Must be loaded after `_ensure_julia_installed()` | ||
| from juliacall import Main | ||
| return Main.seval(script) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,59 +1,9 @@ | ||
| import os | ||
| import sys | ||
| from IPython.display import Image | ||
| import IPython.display | ||
| from . import load_julia_packages | ||
| rms, _, = load_julia_packages("ReactionMechanismSimulator", "PythonCall") | ||
| from juliacall import Main | ||
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| from julia import Main | ||
| from julia import ReactionMechanismSimulator | ||
| sys.modules[__name__] = rms | ||
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| from julia.ReactionMechanismSimulator import makefluxdiagrams | ||
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| def pygetfluxdiagram(bsol,t,centralspecieslist=[],superimpose=False, | ||
| maximumnodecount=50, maximumedgecount=50, concentrationtol=1e-6, speciesratetolerance=1e-6, | ||
| maximumnodepenwidth=10.0,maximumedgepenwidth=10.0,radius=1,centralreactioncount=-1,outputdirectory="fluxdiagrams", | ||
| colorscheme="viridis"): | ||
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| fd = makefluxdiagrams(bsol,[t], centralspecieslist=centralspecieslist,superimpose=superimpose, | ||
| maximumnodecount=maximumnodecount, maximumedgecount=maximumedgecount, concentrationtol=concentrationtol, | ||
| speciesratetolerance=speciesratetolerance,maximumnodepenwidth=maximumnodepenwidth, | ||
| maximumedgepenwidth=maximumedgepenwidth,radius=radius,centralreactioncount=centralreactioncount, | ||
| outputdirectory=outputdirectory,colorscheme=colorscheme) | ||
|
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| IPython.display.display(IPython.display.Image(os.path.join(fd.outputdirectory,"flux_diagram_1.png"))) | ||
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| ReactionMechanismSimulator.getfluxdiagram = pygetfluxdiagram | ||
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| # These functions force the returned object to be a jlwrap object, | ||
| # to avoid the solution object gets converted into list of lists | ||
| _threadedsensitivities_inds = Main.pyfunctionret(ReactionMechanismSimulator.threadedsensitivities, Main.Any, Main.PyAny, Main.PyAny) | ||
| _threadedsensitivities = Main.pyfunctionret(ReactionMechanismSimulator.threadedsensitivities, Main.Any, Main.PyAny) | ||
| # Allow us the get the solution object in the julia wrapped object without | ||
| # it being converted into list of lists | ||
| get = Main.pyfunctionret(Main.get, Main.Any, Main.PyAny, Main.PyAny, Main.PyAny) | ||
| def pythreadedsensitivities(react, inds=None, | ||
| odesolver=Main.nothing, senssolver=Main.nothing, | ||
| odekwargs={"abstol": 1e-20, "reltol": 1e-6}, | ||
| senskwargs={"abstol": 1e-6, "reltol": 1e-3}): | ||
| if inds is not None: | ||
| # the sol_dict returned here is a jlwrap object and is not easy to access the contents | ||
| sol_dict = _threadedsensitivities_inds(react, inds, | ||
| odesolver=odesolver, senssolver=senssolver, | ||
| odekwargs=odekwargs, senskwargs=senskwargs) | ||
| # pysol_dict is the python dictionary, but the solution object got turned into list of lists | ||
| pysol_dict = Main.PyObject(sol_dict) | ||
| # this remakes the dictionary with the values as julia wrapped object ODEsolution, | ||
| # but at the same time allows the user to access it normally like a dictionary | ||
| return {key: get(sol_dict, key, Main.Any) for key in pysol_dict.keys()} | ||
| else: | ||
| sol = _threadedsensitivities(react, | ||
| odesolver=odesolver, senssolver=senssolver, | ||
| odekwargs=odekwargs, senskwargs=senskwargs) | ||
| return sol | ||
|
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| ReactionMechanismSimulator.threadedsensitivities = pythreadedsensitivities | ||
|
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| for item in dir(ReactionMechanismSimulator): | ||
| try: | ||
| locals()[item] = getattr(ReactionMechanismSimulator,item) | ||
| except AttributeError: | ||
| pass |
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