Usability Improvements

[miketynes]

I was asked to give feedback on #57, but because I hadn't touched this repo in quite some time, I ran into some more general usability issues that I think would be pretty easy to clear up.

Installation

• The conda install failed for me. Tried it before attempting the pip install. Running with conda version is 4.8.3, I got the error:

  
  Collecting package metadata (repodata.json): done  
  Solving environment: failed   
  ResolvePackageNotFound:  

• numpy-base==1.18.1=py38h6575580_1

• tk==8.6.8=ha441bb4_0

• sqlite==3.31.1=h5c1f38d_1

• python==3.8.2=hc70fcce_0

• pandas==1.0.3=py38h6c726b0_0

• rdkit==2020.03.1=py38h415f5aa_1

  
  ​   Have I done something wrong? 

• pip install directions also contain a minor confusion which we should clear up:

  • Step 1 creates conda env escalate
  • Step 2 activates conda env escalate_report
  • I just activated the env from step 1 in and moved on to step 3.
  • I'll leave which of these names to choose up to you

• Authentication

  • Creds:
  • I like the rick roll joke
  • Are there any creds I should have besides creds.json and cliensecrets.json? I never touched expworkup/creds/ and that didnt seem to matter. Its not celar what goes in this folder from the README.
  • is downloading the ChemAxon JChemSuite really part of authentication? I ended up completely breezing past this in the README and I suspect others will do the same. JChemSuite install should probably should be given its own small subsection in the installation part of the README. just briefly what it is, what it does for us, and what happens if the users do/dont install it.

    Test Runs:

Followed instructions from video, but targeted dev folder.

Notes:

• runme.py -h is only so helpful. Particularly, the first two arguments local_directory and -d seem to be important but I couldn't really tell if I was using them right. I think this could be pretty easy to clarify in either the argument help messages or in the README (or both):
  • local_directory I found myself asking: what is this? Should that exist already or will it be created by runme.pyif i specify it as an argument? What goes in there? is it for human consumption or just a folder of intermediates? This will likely intimidate a novice user
  • -d seems to take a pair of arguments, but I can't tell exactly how that affects what gets read in by the code and then what it spits out. A few sentences could probably clarify that.

[miketynes]

Further notes on installing Jchem:

• May want to point users to this page to help them get setup more quickly https://docs.chemaxon.com/display/docs/Installation+Guide. This took me a little while to find and triggered my dependency hell flashbacks. Would be kind to speed that along for future Escalate Report newbies.
• Also may want to warn users to note down where the JChem installer writes the executables. I didnt do this and then lost a lot of time finding them again. Lets help people learn from my mistakes. Be better than me! On Linux they're probably somewhere like ~/opt/chemaxon/jchemsuite/bin so we can note that in the docs as well.

[miketynes]

Final note on Jchem:

May also want to let users know they'll have to 'install' their license (inform jchem where license file lives)

I just guessed how to do this: went into the jchemsuite/bin directory and called the license executable on the two license files. There are also docs on how to do this through a gui here:

https://docs.chemaxon.com/display/docs/Licenses.html

(I havent tried the gui, no idea if/how it works given my particular setup)