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Major update of reaction-network #169

Merged
merged 188 commits into from
Oct 24, 2022
Merged

Major update of reaction-network #169

merged 188 commits into from
Oct 24, 2022

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mattmcdermott
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@mattmcdermott mattmcdermott commented Oct 24, 2022

This is a major update to the reaction-network package including much of my work over the last several months. Here is a short PARTIAL summary of some of the changes:

  • Implemented support for jobflow (including running network analysis as a jobflow-based Flow)
  • Minor refactor of ReactionNetwork class
  • Optimization of parallelized reaction enumeration and pathway solving with Ray
  • Removed support for fireworks (this has been moved into the jobflow-based code)
  • Addition of many much-needed tests (addresses Missing tests for much of the firetasks, fireworks, network, and pathways modules #67)
  • Organization/cleanup of repo files (e.g., move to pyproject.toml)

I expect to release a new major version once again sometime next month with additional features; note that this PR is to attempt to incorporate many of the speedups/refactoring that I have done over the past few months.

@mattmcdermott mattmcdermott added the release:major Major release label Oct 24, 2022
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codecov-commenter commented Oct 24, 2022

Codecov Report

Base: 41.90% // Head: 78.25% // Increases project coverage by +36.35% 🎉

Coverage data is based on head (0e3bf31) compared to base (b0b6536).
Patch coverage: 71.24% of modified lines in pull request are covered.

Additional details and impacted files
@@             Coverage Diff             @@
##             main     #169       +/-   ##
===========================================
+ Coverage   41.90%   78.25%   +36.35%     
===========================================
  Files          57       46       -11     
  Lines        3076     3137       +61     
  Branches      583      578        -5     
===========================================
+ Hits         1289     2455     +1166     
+ Misses       1743      551     -1192     
- Partials       44      131       +87     
Impacted Files Coverage Δ
src/rxn_network/core/pathway.py 72.72% <0.00%> (ø)
src/rxn_network/network/gt.py 80.26% <ø> (+80.26%) ⬆️
src/rxn_network/network/visualize.py 18.91% <ø> (+18.91%) ⬆️
src/rxn_network/thermo/chempot_diagram.py 71.42% <41.66%> (+5.12%) ⬆️
src/rxn_network/costs/calculators.py 85.00% <44.44%> (-9.12%) ⬇️
src/rxn_network/reactions/plotting.py 54.73% <52.27%> (+54.73%) ⬆️
src/rxn_network/reactions/reaction_set.py 59.71% <54.19%> (-8.58%) ⬇️
src/rxn_network/reactions/open.py 78.20% <55.17%> (-14.11%) ⬇️
src/rxn_network/enumerators/minimize.py 55.73% <55.55%> (-39.09%) ⬇️
src/rxn_network/entries/entry_set.py 71.15% <56.14%> (+3.96%) ⬆️
... and 63 more

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3 participants