[JOSS Review] Suggestions on `paper.md` etc.

yuzie007 commented 2 weeks ago

(This is a part of my review for JOSS https://github.com/openjournals/joss-reviews/issues/7365. cc: @srmnitc)

As a follow-up to #33, I suggest the following for paper.md.

[x] Software paper – Summary: PyPi -> PyPI (The last "I" should be a capital letter.)
[x] Throughout the manuscript, in the present citation style (not in the superscript style but in the bracket style) citations should come before punctuations, not like ,[@plunkett_plunketts_2017] but like [@plunkett_plunketts_2017],.
[x] Software paper – A statement of need: Citations for the "PC-SAFT" theory / methodology may be appreciated.
[x] Section 2.1: Citations for MolSSI Cokkiecutter may be appreciated.
[x] Section 2.3: While in the manuscript the currently available version is written as 0.2.0, in CHANGELOG.md, this is now 0.3.0. This inconsistency should be solved.
[x] Section 3 & References: The authors can provide DOI for MAPSCI (10.5281/zenodo.4271975 or 10.5281/zenodo.4271975) together with its publication year.
[x] References: The hyperlink for the software PC-SAFT (Baird, Z. (2021)) is outdated. The authors can refer to the latest PyPI page (https://pypi.org/project/pcsaft/) or the GitHub page (https://github.com/zmeri/PC-SAFT).
[x] Section 2.3: As written here, "Second derivative properties are a priority in the next release", probably meaning that this is not yet available. As far as I learned from the paper of Papaioannou et al. in (2014), this feature is what users would wish. If this is not yet implemented, this information may be better to be given somewhere in the actual code document in docs as well.

jaclark5 commented 1 week ago

@yuzie007 thank you for the feedback. I addressed your concerns in PR #38. The lack of date and doi for MAPSCI seems to have been an error with bibtex formatting. I need to let the JOSS bot compile the paper to see if it is fixed.

jaclark5 commented 1 week ago

@yuzie007 The paper and docs have compiled and it seems like your comments have been addressed and rendered correctly.: https://github.com/Santiso-Group/despasito/actions/runs/11829116940/artifacts/2185390672 Note the additional sentence in the third paragraph of the documentation: https://despasito--38.org.readthedocs.build/en/38/

yuzie007 commented 6 days ago

Thank you so much @jaclark5 for the update. The changes look very good to me.

Santiso-Group / despasito

[JOSS Review] Suggestions on `paper.md` etc. #34