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Use a version of RMG's molecule that is built in place, rather than from a separate molecule repo #232

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JacksonBurns
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By changing the CI to use mamba instead of conda, the environment file without molecule separate from RMG can be solved.

Will add more notes later, opening this as a draft for now for off-line discussion.

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codecov bot commented Sep 7, 2023

Codecov Report

Merging #232 (d5259c5) into main (3538dbd) will increase coverage by 0.01%.
Report is 34 commits behind head on main.
The diff coverage is 36.82%.

@@            Coverage Diff             @@
##             main     #232      +/-   ##
==========================================
+ Coverage   49.81%   49.82%   +0.01%     
==========================================
  Files          31       31              
  Lines        7908     8087     +179     
==========================================
+ Hits         3939     4029      +90     
- Misses       3969     4058      +89     
Files Changed Coverage Δ
src/TestEdgeAnalysis.jl 100.00% <ø> (ø)
src/Domain.jl 55.20% <4.91%> (-1.28%) ⬇️
src/EdgeAnalysis.jl 48.80% <66.32%> (+2.85%) ⬆️
src/Interface.jl 91.75% <88.23%> (+0.12%) ⬆️
src/TestReactors.jl 100.00% <100.00%> (ø)

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@JacksonBurns
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Less some error in the documentation, it appears that this patch is working. I'm leaving this as a draft for the time being, since I will bring this up at the big developer meeting instead. This solves the problem of running the CI, but would undo the work on molecule and require RMS to carry around all of RMG again - but let's hash out these points at the developer meeting.

see jacksonburns/rmg-py branch molecule_subpackage
@JacksonBurns JacksonBurns changed the title Switching the CI to use mamba circumvents need for new molecule package Use a version of RMG's molecule that is built in place, rather than from a separate molecule repo Sep 13, 2023
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