Compatibility with latest version of PySB

[acorbat]

I merely swapped <> operator for | in order to recover compatibility with latest version of PySB. I only replaced this occurrences in the code, not replacing them in the comments as I find <> more visually appealing to describe chemical reactions.

[jmuhlich]

@clopezx @johnbachman Looks good to me. How do you guys feel about leaving <> in the comments unchanged?

[clopezx]

Hi Guys, I think the best is to be consistent. I think <> in the comments and | in the code could be confusing to new users that don’t know the history… just my $0.02

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On Mar 30, 2020, at 8:01 AM, Jeremy Muhlich ***@***.***> wrote: @clopezx <https://github.com/clopezx> @johnbachman <https://github.com/johnbachman> Looks good to me. How do you guys feel about leaving <> in the comments unchanged? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADKVBONJ337EWDY2WGL4YTRKCJ35ANCNFSM4LWQNG6Q>.

[acorbat]

I thought the same as you @clopezx, that would make the code consistent and easier to understand for someone with programming background. On the other hand, I thought that someone coming from a chemical or biological background would find <> more suitable.

[clopezx]

hmmm. I see your point. I think if we define early on in the documentation that the | symbol means reversible, that should be enough. I worry that someone looking at the code and conflicting explanations would have issues. You can’t assume users are super smart (from my own user experience!) c

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On Mar 30, 2020, at 10:12 AM, Agustín Andrés Corbat ***@***.***> wrote: I thought the same as you @clopezx <https://github.com/clopezx>, that would make the code consistent and easier to understand for someone with programming background. On the other hand, I thought that someone coming from a chemical or biological background would find <> more suitable. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADKVBNBVNTJ47L2C36V5LDRKCZFRANCNFSM4LWQNG6Q>.

[jmuhlich]

Another potential solution is changing the comments to use a syntax that's definitely not Python so the chance of confusion should be far lower. Maybe something like A + B <-> AB?

[alubbock]

Related: I added Python 3 support to the lolab-vu/earm fork back in 2018 in this commit: LoLab-MSM@9236b55

Happy to PR that if you like. I didn't change the documentation re: the issue above.