Minor changes

[xiaoruiDong]

I was trying to install the ARC based on the instruction from Wiki and encountered errors when running ESS diagnostics:

• Change the isomorphic_species_list to same_species_list to keep up with the latest update of RMG
• Avoid error when running into local address error (double checking, but treat local as SSH) in ESS check
• No ARC.determine_remote exists. I guess that it updates to ARC.determine_ess_settings, so I changed it. I also removed the output of iPython notebook, but it can be kept if you want.

[codecov]

Codecov Report

Merging #133 into master will decrease coverage by 0.01%.
The diff coverage is 16.66%.

@@            Coverage Diff             @@
##           master     #133      +/-   ##
==========================================
- Coverage   41.03%   41.01%   -0.02%     
==========================================
  Files          23       23              
  Lines        5888     5890       +2     
  Branches     1567     1568       +1     
==========================================
  Hits         2416     2416              
- Misses       3082     3084       +2     
  Partials      390      390

Impacted Files	Coverage Δ
arc/main.py	45.19% <0%> (-0.13%)	⬇️
arc/rmgdb.py	73.5% <25%> (ø)	⬆️

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[alongd]

Thanks for the contribution!

I think the iPython output should stay, as an example of what to expect from this tool, unless it doesn't show well. If we do decide to remove it, then it should have its own commit.

I understand that the ESS check is buggy when running on a server. How does the addition of

            if server == 'local':
                continue

treat local as SSH? I think the expected behaviour is that we will be able to determine ESS when running locally as well.

[xiaoruiDong]

@alongd Thanks for quick reply!

1. I agree it can stay. So, I update the ipython notebook with result being displayed (based on my settings)
2. About ESS. Actually, it has two steps regarding servers:
   First, it checks whether 'local' is in the server list, and, if so, it will search which packages are available locally.
   

Second, it will loop through the server list and tell what packages are available remotely.

However, within the loop, 'local' is not excluded and will be treated as SSH server, but as it does not have address and other properties, an error will be raised. My modification is simply avoiding checking 'local' again in the SSH check.

[alongd]

Thanks, I think the code looks good, just some comments regarding the commits:

1. The iPython notebook change should be in its own separate commit, not joint with the local server check
2. Please rename the Update the rmg_function name: same_species_list. commit message as Updated isomorphic species check method name in rmgdb (since rmg_function with an underscore seems like a real function name)
3. Generally, commit messages should be at a maximal length of one line, then further description can follow after a line break, to avoid getting:

 Update the function name in notebook and avoid local server check err…

…or in ESS diagnostics```

[xiaoruiDong]

@alongd Do you think these changes in commits are slightly better? Thanks.

[alongd]

Looking great! Let's wait for the tests and get the fixes in.
Thanks!