v1.1.0

[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 improves output, automatic choice of most parameters and adds support for Python 3.10.

Update it using pip:

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

Overreact is licensed under the MIT license.

ℹ️ By the way, our manuscript has been featured in the latest issue of the Journal of Computational Chemistry! 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

Highlights

It just works®:
overreact is easier than ever. We fine-tuned the choice of many parameters, so that your simulations run smoothly right from the start. It is now smart enough to guess for how long to simulate (bde5bec, 3c842a7), which solver to use (928b48d), how fast should an equilibrium be (3a516bd, 1d2cbc8, 645578c), how to handle edge cases when correcting for quantum tunneling (0e5ad84), which species actually make sense to plot when generating a kinetic profile (2de3dbd), how large show the first time step be in a simulation (8eafc35, a4cd60d, ae55264), and more.

Adjust energies per species:
You can now use the extra_energy_term flag to adjust the energy of a single species (777155c).

User-interface and output:
The output has been enhanced and is clearer than ever (13fd9ae, 4f2c0d4, dec2297), which now shows the progress of the calculation as it is being performed (2d4d894). Error messages and warnings have been improved as well (92c7cb0).

Documentation and resources:
We greatly improved consistency between the documentation, API and command-line help (f0bc3b9, d828d37, 0ae4727, 1a2d030, c6daa55). In fact, we now have two sets of documentations: the user guide, focused on the use of the command-line application, and the Python API documentation (b1c7456, 4ecacfc, ea298d0, 8ca1c7f, b6c8886, da22151, 8eb5f06, 0212376). We now have an improved README.md file (79ba5f2, df90408, c2b62ed, 0be2ad8, 64da6b9, #149), as well as a great CONTRIBUTING.md thanks to @Leticia-maria (fcccbd1, f1ce7c0, #133). Thanks, Letícia!

Code quality and API:
The user-facing API is now almost completely type-hinted (37cca8d, 819773c). There might be some rough edges yet, so feel free to open an issue if you see something. Lots of housekeeping has been taken place as well, mostly to keep the code base modern, performant, and easy to use (f47206b, ea27d5b, 2f6a176, fb99f6c, 7622789, f60a705). We now target Python versions 3.8-3.10 (bc67e7d, c089244), and use Ruff and Black to keep the code base as tidy as possible (cddc09d, a0f1be3, 14dde86).

Pull requests

Here are the list of relevant pull requests since last version.

• Update CONTRIBUTING.md by @Leticia-maria in Update CONTRIBUTING.md #133
• Add table to organize badges by @Leticia-maria in Add table to organize badges #149
• Bump actions/checkout from 2 to 3 by @dependabot in Bump actions/checkout from 2 to 3 #182
• Bump bandit from 1.7.3 to 1.7.4 by @dependabot in Bump bandit from 1.7.3 to 1.7.4 #184
• Bump codecov/codecov-action from 2 to 3 by @dependabot in Bump codecov/codecov-action from 2 to 3 #213
• Bump github/codeql-action from 1 to 2 by @dependabot in Bump github/codeql-action from 1 to 2 #227
• Bump thermo from 0.2.20 to 0.2.21 by @dependabot in Bump thermo from 0.2.20 to 0.2.21 #240
• Bump pillow from 9.1.0 to 9.1.1 by @dependabot in Bump pillow from 9.1.0 to 9.1.1 #251
• Bump notebook from 6.4.11 to 6.4.12 by @dependabot in Bump notebook from 6.4.11 to 6.4.12 #257
• Bump abatilo/actions-poetry from 2.1.4 to 2.1.6 by @dependabot in Bump abatilo/actions-poetry from 2.1.4 to 2.1.6 #282
• Bump nbconvert from 6.5.0 to 6.5.1 by @dependabot in Bump nbconvert from 6.5.0 to 6.5.1 #283
• Bump mistune from 0.8.4 to 2.0.3 by @dependabot in Bump mistune from 0.8.4 to 2.0.3 #290
• Bump cclib from 1.7.1 to 1.7.2 by @dependabot in Bump cclib from 1.7.1 to 1.7.2 #288
• Bump flake8 from 4.0.1 to 5.0.4 by @dependabot in Bump flake8 from 4.0.1 to 5.0.4 #292
• Bump pytest from 7.1.2 to 7.1.3 by @dependabot in Bump pytest from 7.1.2 to 7.1.3 #297
• Bump actions/setup-python from 4.2.0 to 4.3.0 by @dependabot in Bump actions/setup-python from 4.2.0 to 4.3.0 #306
• Bump pytest-cov from 3.0.0 to 4.0.0 by @dependabot in Bump pytest-cov from 3.0.0 to 4.0.0 #314
• Bump matplotlib from 3.6.1 to 3.6.2 by @dependabot in Bump matplotlib from 3.6.1 to 3.6.2 #319
• Bump mypy from 0.990 to 0.991 by @dependabot in Bump mypy from 0.990 to 0.991 #328
• Bump pdoc from 12.2.2 to 12.3.0 by @dependabot in Bump pdoc from 12.2.2 to 12.3.0 #329
• Bump debugpy from 1.6.3 to 1.6.4 by @dependabot in Bump debugpy from 1.6.3 to 1.6.4 #336
• Bump flynt from 0.76 to 0.77 by @dependabot in Bump flynt from 0.76 to 0.77 #335
• Bump types-setuptools from 65.6.0.1 to 65.6.0.2 by @dependabot in Bump types-setuptools from 65.6.0.1 to 65.6.0.2 #340
• Bump pyupgrade from 3.3.0 to 3.3.1 by @dependabot in Bump pyupgrade from 3.3.0 to 3.3.1 #341
• Bump black from 22.10.0 to 22.12.0 by @dependabot in Bump black from 22.10.0 to 22.12.0 #342
• Bump jax from 0.3.25 to 0.4.1 by @dependabot in Bump jax from 0.3.25 to 0.4.1 #346
• Bump jaxlib from 0.3.25 to 0.4.1 by @dependabot in Bump jaxlib from 0.3.25 to 0.4.1 #345
• Bump isort from 5.11.3 to 5.11.4 by @dependabot in Bump isort from 5.11.3 to 5.11.4 #348
• Bump seaborn from 0.12.1 to 0.12.2 by @dependabot in Bump seaborn from 0.12.1 to 0.12.2 #350
• Bump rich from 12.6.0 to 13.0.0 by @dependabot in Bump rich from 12.6.0 to 13.0.0 #349
• Bump scipy from 1.9.3 to 1.10.0 by @dependabot in Bump scipy from 1.9.3 to 1.10.0 #351
• Bump ipython from 8.7.0 to 8.8.0 by @dependabot in Bump ipython from 8.7.0 to 8.8.0 #352

New Contributors

• @Leticia-maria made their first contribution in Update CONTRIBUTING.md #133

Full Changelog: v1.0.2...v1.1.0

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This discussion was created from the release v1.1.0.