[PRE REVIEW]: Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services

[editorialbot]

Submitting author: @ljwoods2 (Lawson Woods)
Repository: https://github.com/Becksteinlab/zarrtraj
Branch with paper.md (empty if default branch):
Version: v0.3.0
Editor: @srmnitc
Reviewers: @samwaseda, @mattwthompson
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (755.8 files/s, 124007.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              0             54           4288
Python                          22            538            600           2344
Markdown                        12            158              1            518
YAML                            10             76             31            370
TeX                              1             33              0            285
reStructuredText                 8             99             41            206
Jupyter Notebook                 2              0            262            152
TOML                             1             16              8            102
JSON                             1             18              0             80
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            63            950           1004           8382
-------------------------------------------------------------------------------

Commit count by author:

   213	Lawson Woods
    30	ljwoods2
     7	Oliver Beckstein
     1	Richard Gowers

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1713

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Lawson Woods, perhaps the affiliations index need quoting?.

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/d41586-019-01720-7 is OK
- 10.1016/j.tibs.2019.06.004 is OK
- 10.1038/s41592-020-0884-y is OK
- 10.25080/majora-1b6fd038-005 is OK
- 10.25080/Majora-629e541a-00e is OK
- 10.1093/nar/gkac398 is OK
- 10.7554/eLife.90061 is OK
- 10.1021/acs.jctc.3c00735 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3389/fclim.2021.782909 is OK
- 10.1021/acs.jcim.9b00665 is OK
- 10.18637/jss.v040.i01 is OK
- 10.6084/m9.figshare.8202149.v1 is OK
- 10.5281/ZENODO.3773449 is OK
- 10.17487/RFC8878 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Foldingathome COVID-19 Datasets
- No DOI given, and none found for title: The need to implement FAIR principles in biomolecu...
- No DOI given, and none found for title: Accelerating parallel analysis of scientific simul...

❌ MISSING DOIs

- 10.25080/gerudo-f2bc6f59-00a may be a valid DOI for title: MDAKits: A framework for FAIR-compliant molecular ...
- 10.1002/jcc.21439 may be a valid DOI for title: Fast determination of the optimal rotational matri...

❌ INVALID DOIs

- https://doi.org/10.1016/j.cpc.2014.01.018 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jcc.21787 is INVALID because of 'https://doi.org/' prefix

[Kevin-Mattheus-Moerman]

@ljwoods2 Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• The paper compilation error appears to relate to the fact that you used [1,2] etc instead of the required format "1, 2". Please update the paper and retry compilation here by calling @editorialbot generate pdf. Thanks

[Kevin-Mattheus-Moerman]

@ljwoods2 - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editors most appropriate for your area are all already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[Kevin-Mattheus-Moerman]

@ljwoods2 Can you look at the above points? ☝️

[ljwoods2]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/d41586-019-01720-7 is OK
- 10.1016/j.tibs.2019.06.004 is OK
- 10.1038/s41592-020-0884-y is OK
- 10.1016/j.cpc.2014.01.018 is OK
- 10.25080/majora-1b6fd038-005 is OK
- 10.25080/gerudo-f2bc6f59-00a is OK
- 10.25080/Majora-629e541a-00e is OK
- 10.1002/jcc.21787 is OK
- 10.48550/arXiv.2407.16584 is OK
- 10.1093/nar/gkac398 is OK
- 10.7554/eLife.90061 is OK
- 10.1021/acs.jctc.3c00735 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3389/fclim.2021.782909 is OK
- 10.1021/acs.jcim.9b00665 is OK
- 10.18637/jss.v040.i01 is OK
- 10.6084/m9.figshare.8202149.v1 is OK
- 10.5281/ZENODO.3773449 is OK
- 10.17487/RFC8878 is OK
- 10.1002/jcc.21439 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Foldingathome COVID-19 Datasets
- No DOI given, and none found for title: Accelerating parallel analysis of scientific simul...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None