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indicate that Julia is optional but recommended, list features
also update the final run example - the point of specifying the `PYTHONPATH` was so that users _don't_ have to give the full path to `rmg.py` - the `python` executable can search it out
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documentation/source/users/rmg/installation/anacondaDeveloper.rst

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@@ -115,7 +115,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
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make
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#. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder.
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*This is important before the next step in which julia dependencies are installed.*
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Also, add your RMG-Py folder to PATH to launch ``rmg.py`` from any folder.
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In general, these commands should be placed in the appropriate shell initialization file.
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Be sure to either close and reopen your terminal to refresh your environment variables (``source ~/.bashrc`` or ``source ~/.zshrc``).
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#. Install and Link Julia dependencies: ::
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#. **Optional (Recommended)**: Install and Link Julia dependencies. Ensure that you have modified your environment variables as described above, and then run the following: ::
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julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
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python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
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Installing these dependencies will allow using ``method='ode'`` when solving the Master Equation with Arkane and using ``ReactionMechanismSimulator.jl``-based reactors in RMG.
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#. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). ::
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python-jl replace/with/path/to/rmg.py input.py
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python-jl rmg.py input.py
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or, if the Julia dependencies are not installed: ::
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python rmg.py input.py
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You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
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