Update required version of rdkit to avoid severe memory leaks

[kspieks]

Motivation or Problem

Significant memory leaks have been observed when using an rmg_env containing rdkit version 2019.03.4.0 as referenced in issue #1850. The issue is documented on the rdkit page rdkit/rdkit#2639

Memory leaks are not observed when using a more recent rdkit version of 2019.09.1.0 (and it looks like they've already released a version 2019.09.2.0)

Description of Changes

Updated the minimum required version number for rdkit in the environment.yml file

Testing

I used this environment.yml file to create an rmg_env. Doing conda list rdkit produced the following output, confirming that the change is implemented correctly

# Name                    Version                   Build  Channel
rdkit                     2019.09.2.0      py37h65625ec_1    rdkit

[codecov]

Codecov Report

Merging #1851 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1851   +/-   ##
=======================================
  Coverage   44.23%   44.23%           
=======================================
  Files          83       83           
  Lines       21539    21539           
  Branches     5645     5645           
=======================================
  Hits         9527     9527           
+ Misses      10956    10942   -14     
- Partials     1056     1070   +14

Impacted Files	Coverage Δ
rmgpy/data/statmech.py	42.2% <0%> (ø)	⬆️
rmgpy/rmg/pdep.py	12.21% <0%> (ø)	⬆️
arkane/kinetics.py	12.14% <0%> (ø)	⬆️
rmgpy/data/kinetics/family.py	49.06% <0%> (ø)	⬆️
rmgpy/statmech/ndTorsions.py	59.78% <0%> (ø)	⬆️
rmgpy/yml.py	15.71% <0%> (ø)	⬆️
arkane/sensitivity.py	10% <0%> (ø)	⬆️
rmgpy/data/kinetics/database.py	50.61% <0%> (ø)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 150aec0...598e2eb. Read the comment docs.

[alongd]

The updated Linux x64 version is v2019.09.2.0

[mliu49]

I think this looks good. Alon, were you suggesting any changes, or confirming that this is ok?

[alongd]

Suggesting to change 2019.09.1.0 into 2019.09.2.0

[mliu49]

Ah, ok. I think this is fine though, since 2019.09.1.0 is the release which fixes the issue, so anything newer is acceptable.

[mliu49]

Of course, unless there are other reasons that 2019.09.1.0 does not work for us, in which case we can increment it to 2019.09.2.0.

[kspieks]

Of course, unless there are other reasons that 2019.09.1.0 does not work for us, in which case we can increment it to 2019.09.2.0.

Both versions have not had memory leaks for me, so I think this PR is good to go