v1.2.0

[schneiderfelipe]

⚛️📈 overreact is a library and a command-line tool for building and analyzing homogeneous microkinetic models from first-principles calculations.

This is a feature release of overreact that, among other minor changes, improves integrator stability and parameter choices for the integrators overall. In particular, overreact now makes similar choices to scipy.integrate.solve_ivp, which should lead to fewer surprises. A big part of this was kindly contributed by @bmounssefjr.

⚠️ It was found out that the currently calculated analytical Jacobian leads to problems, which is most relevant when implicit integrators are employed. This affects LSODA, Radau and BDF. As such, the usage of analytical Jacobians has been disabled for this version until we find a fix for the bug. Even though it is a breaking chance per se, it is mild, as most of the change happened in places where user had previously no access. We hope to fix this issue soon. Previous and published results were not affected.

Update it using pip:

$ pip install -U 'overreact[cli,fast]'

Overreact is licensed under the MIT license.

If you use overreact in your research, please cite:

Schneider, F. S. S.; Caramori, G. F. Overreact, an in Silico Lab: Automative Quantum Chemical Microkinetic Simulations for Complex Chemical Reactions. Journal of Computational Chemistry 2022, 44 (3), 209–217. doi:10.1002/jcc.26861.

Here's the reference in BibTeX format:

@article{overreact_paper2022,
  title         = {Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions},
  author        = {Schneider, Felipe S. S. and Caramori, Giovanni F.},
  year          = {2022},
  month         = {Apr},
  journal       = {Journal of Computational Chemistry},
  publisher     = {Wiley},
  volume        = {44},
  number        = {3},
  pages         = {209–217},
  doi           = {10.1002/jcc.26861},
  issn          = {1096-987x},
  url           = {http://dx.doi.org/10.1002/jcc.26861},
}

What's Changed

• Add basic issue templates by @schneiderfelipe in Add some basic issue templates #378
• Enforce ruff rules by @schneiderfelipe in Enforce ruff stuff everywhere #392
• Improve integrator stability by @schneiderfelipe in Improve integrator stability #416
• Bump scipy to 1.10.1 by @dependabot in Bump scipy from 1.10.0 to 1.10.1 #371
• Bump markdown-it-py to 2.2.0 by @dependabot in Bump markdown-it-py from 2.1.0 to 2.2.0 #372
• Bump matplotlib to 3.7.1 by @dependabot in Bump matplotlib from 3.7.0 to 3.7.1 #385
• Bump flynt to 0.78 by @dependabot in Bump flynt from 0.77 to 0.78 #397
• Bump jaxlib to 0.4.7 by @dependabot in Bump jaxlib from 0.4.6 to 0.4.7 #402
• Bump black to 23.3.0 by @dependabot in Bump black from 23.1.0 to 23.3.0 #403
• Bump jax to 0.4.8 by @dependabot in Bump jax from 0.4.7 to 0.4.8 #405
• Bump ipython to 8.12.0 by @dependabot in Bump ipython from 8.11.0 to 8.12.0 #404
• Bump debugpy to 1.6.7 by @dependabot in Bump debugpy from 1.6.6 to 1.6.7 #410
• Bump mypy to 1.2.0 by @dependabot in Bump mypy from 1.1.1 to 1.2.0 #411
• Bump rich to 13.3.4 by @dependabot in Bump rich from 13.3.3 to 13.3.4 #413
• chore(deps-dev): bump pytest to 7.3.1 by @dependabot in chore(deps-dev): bump pytest from 7.3.0 to 7.3.1 #414
• chore(deps): bump thermo to 0.2.24 by @dependabot in chore(deps): bump thermo from 0.2.23 to 0.2.24 #420
• chore(deps-dev): bump pdoc to 13.1.1 by @dependabot in chore(deps-dev): bump pdoc from 13.1.0 to 13.1.1 #419
• chore(deps-dev): bump types-setuptools to 67.7.0.0 by @dependabot in chore(deps-dev): bump types-setuptools from 67.6.0.8 to 67.7.0.0 #418
• chore(deps-dev): bump ruff to 0.0.263 by @dependabot in chore(deps-dev): bump ruff from 0.0.262 to 0.0.263 #421

Full Changelog: v1.1.0...v1.2.0

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This discussion was created from the release v1.2.0.