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Modify Installation Instructions After RMG Upgrade to Python 3.9 #272

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Modify Installation Instructions After RMG Upgrade to Python 3.9 #272

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@ssun30 ssun30 commented Jul 11, 2025

This will change installation instructions after RMG switched to pyjuliacall and RMS switched to PythonCall for inter-operability between the two.

rwest and others added 30 commits July 29, 2024 09:52
@rwest
Update how to cite in README.md
c4d5435 
The paper is published. It's open access so I figured no need to keep the preprint link.
@ssun30
Fixed processfluxes for interfaces
8dbb07e
@ssun30
Merge pull request ReactionMechanismGenerator#266 from ReactionMechan…
673e5da 
…ismGenerator/fix_processfluxes

Fixed processfluxes for interfaces
@mjohnson541 @ssun30
include electronchange in reaction reconstruction in phase
61ca710
@mjohnson541 @ssun30
add Marcus kinetics type and allow dGrxn dependence of kinetics
f1c175b
@mjohnson541 @ssun30
handle dGrxn and d dependence of reactions in interfaces and phase ca…
61fa7f6 
…lculations
@mjohnson541 @ssun30
adapt Domains to dGrxn and d dependence of forward rate coefficient c…
9709465 
…alculations
@mjohnson541 @ssun30
add a Marcus reaction to the ORR.rms mechanism for testing
8c308fd
@mjohnson541 @ssun30
fix variable naminng
f230853
@ssun30
Added reference potential to Arrheniusq
ae59b8c
@ssun30
Fixed interfaces not setting phi correctly
ff0ef51
@ssun30
Parser uses RMG if RDKit fails to get structure
b2ba84f
@ssun30
Now runs CI upon pushing marcus_development
db6d862
@mjohnson541 @ssun30
fix getKc call in ReactiveInternalInterface
5885823
@mjohnson541 @ssun30
add phi and d to newer domains
2e0e612
@mjohnson541 @ssun30
phase electron change fixes
2586194
@mjohnson541 @ssun30
missing domain tweaks for phi/d
f81e093
@mjohnson541 @ssun30
fix FragmentBasedReactiveFilmGrowthInterfaceConstantT interface
bd94192
@ssun30
Added default values for wr/wp for Marcus Kinetics
c22423a 
Removed an invalid field in a Marcus type reaction
in ORR.rms
@ssun30
Fixed array input format in ORR.rms
3f0396f
@ssun30
Changed variable naming in TestReactors
2cea301 
`cat` is a default Julia function for concatenating
arrays. As a precaution these are renamed to
`catalyst` to avoid conflicts
@mjohnson541 @ssun30
Fixed typos
6dd0fe6
@ssun30
loosen solver tolerances for some tests
c15ad5a
@hwpang @JacksonBurns
ignore automatically generated files
59823ca
@hwpang @JacksonBurns
Add channels
3ece71b
@hwpang @JacksonBurns
Remove yml file as it's not used anymore, using CondaPkg to manage env
625498d
@hwpang @JacksonBurns
Switch to CondaPkg, PythonCall, PythonPlot
1673e59
@hwpang @JacksonBurns
Remove unused dependency
a53dca0
@hwpang @JacksonBurns
Update version
060a85f
@hwpang @JacksonBurns
bump to 1.10
8fdf345
hwpang and others added 25 commits February 25, 2025 16:58
@hwpang @JacksonBurns
Switch plotting to pythonplot
c59c6e4
@hwpang @JacksonBurns
Use PythonCall syntax in module
b1264fc
@hwpang @JacksonBurns
Don't set jacobian prototype if jacobian is not sparse
e53ade9
@hwpang @JacksonBurns
Switch to pythoncall syntax in test
8b70c2b
@hwpang @JacksonBurns
Import necessary packages
3842a93
@hwpang @JacksonBurns
Use SciMLSensitivity
8e007a0
@hwpang @JacksonBurns
Change rtol
cc98ddb
@hwpang @JacksonBurns
Add propane mech test file
7686bad
@hwpang @JacksonBurns
Use >= 3.9
1aa21d2
@hwpang @JacksonBurns
keys(CondaPkg.current_packages()) doesn't actually show the packages …
2fb2129 
…that are only available locally
@hwpang @JacksonBurns
Should be molecule
e25fa1d
@JacksonBurns
skip unused line
65959be 
this causes an error when the conda backend is set to Null (i.e. julia is disallowed from installing conda packages), see: ReactionMechanismGenerator/RMG-Py#2749 (comment)
@JacksonBurns
avoid reducing over empty edge species rates, which is an error
93845bf
@JacksonBurns
port sucessful CI changes from rmg to rms
56fbe5e
@JacksonBurns
update cache version
5e0c059
@JacksonBurns
port ci updates to docs action
04cd72b
@JacksonBurns
Update CI.yml
55f9766
@JacksonBurns
Update documentation.yml
b98949a
@JacksonBurns
let rms figure out conda on its own
5f4ee4a
@JacksonBurns
let rms figure out conda on its own
dc4ef01
@JacksonBurns
remove defaults channel
e839c05
@JacksonBurns
add instantiate
7d3904b
@JacksonBurns
consolidate steps to avoid repeat installs
cf83540
@JacksonBurns
Merge pull request ReactionMechanismGenerator#268 from hwpang/fix_ins…
43018b1 
…tallation

Attempting to Fix the `juliacall` Overhaul on RMG
@ssun30
Modified Installation.md to reflect changes to
b827813 
RMS-RMG linking
@ssun30 ssun30 requested review from mjohnson541 and rwest July 11, 2025 01:39
rwest
rwest reviewed Jul 11, 2025
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Might someone install pyjuliacall in the wrong environment because it says install it then activate?

I haven't tested these, but it reads ok. Who has tried it so far, and on what platforms?

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@ssun30 @rwest @mjohnson541 @hwpang @JacksonBurns