[PRE REVIEW]: Hydrogen-Transport-Materials: An Open-Source Database for Hydrogen Transport Properties

[editorialbot]

Submitting author: @RemDelaporteMathurin (Remi Delaporte-Mathurin)
Repository: https://github.com/RemDelaporteMathurin/h-transport-materials
Branch with paper.md (empty if default branch): joss
Version: v0.16.1
Editor: Pending
Reviewers: Pending
Managing EiC: Chris Vernon

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[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Hydrogen-storage materials for mobile applications
- No DOI given, and none found for title: Hydrogen embrittlement of steels
- No DOI given, and none found for title: Tritium Transport Phenomena in Molten-Salt Reactor...

❌ MISSING DOIs

- 10.1007/s40195-020-01039-7 may be a valid DOI for title: Review of hydrogen embrittlement in metals: hydrog...
- 10.13182/nt16-101 may be a valid DOI for title: Tritium control and capture in salt-cooled fission...
- 10.1088/1741-4326/abbf35 may be a valid DOI for title: Physics and technology considerations for the deut...

❌ INVALID DOIs

- https://doi.org/10.1016/j.ijhydene.2016.11.195 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1791.5 files/s, 147801.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          87           1404            430           6991
TeX                              2            166              4           2651
CSV                             49              0              0            471
reStructuredText                14            458            577            329
YAML                             6             40             15            251
Markdown                         2             32              0             91
SVG                              4              0              4             79
CSS                              1              9              1             36
DOS Batch                        1              8              1             26
TOML                             1              1              0             10
make                             1              4              7              9
JSON                             3              0              0              3
-------------------------------------------------------------------------------
SUM:                           171           2122           1039          10947
-------------------------------------------------------------------------------

Commit count by author:

   685	RemDelaporteMathurin
    51	J Dark
    47	Rémi Delaporte-Mathurin
    42	natethegreatINL
    29	NATE GEHMLICH
    12	Thomas Fuerst
    10	James laptop
     9	James Dark
     6	jhdark
     3	paulbrrn
     2	Paul
     1	Christian Hill
     1	FuerstT
     1	Paul Barron

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 664

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[RemDelaporteMathurin]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[crvernon]

@editorialbot invite @RMeli as editor

👋 @RMeli are you available to edit this submission?

[editorialbot]

Invitation to edit this submission sent!

[RMeli]

@editorialbot query scope

Hi @RemDelaporteMathurin, since this submission is a database I'm starting a scope review, so that JOSS editors can decide if this submission is in scope of not.

My personal opinion is that storing interesting data within Python is note the way to go, and a proper database would be preferred:
https://github.com/RemDelaporteMathurin/h-transport-materials/blob/b28e41dd81cee9d5d5337df638d46afc094d7aee/h_transport_materials/property_database/tungsten/tungsten.py#L12-L18

[editorialbot]

Submission flagged for editorial review.

[RemDelaporteMathurin]

Hi @RMeli and thanks for your feedback. I understand your point. However, the reasons why we choose a python interface are:

• The sources don't provide properties in the same way (different units, different quantities, no density provided, etc.) and require some post processing to be aggregated in a consistent way. We want this post processing to be transparent, which is why we did things in python. A good example is the property right after the one you mentioned: https://github.com/RemDelaporteMathurin/h-transport-materials/blob/b28e41dd81cee9d5d5337df638d46afc094d7aee/h_transport_materials/property_database/tungsten/tungsten.py#L20-L29

  Here the authors give S_0 at "some reference temperature", we need this choice to be transparent.

• h-transport-materials is not only a database, but provides functionality for plotting properties, exporting groups to bibfiles, exporting properties to Latex, unit conversion, properties calculations.... Users can also add their own properties (for example properties they measured in their lab) in order to compare them with others. See the complete examples to see some of these functionalities

[RemDelaporteMathurin]

@RMeli is it possible to follow up on this?

[RMeli]

@RemDelaporteMathurin sorry for the delay. I followed up with my colleagues, and will let you know as soon as we have some consensus on this.

[RMeli]

The sources don't provide properties in the same way (different units, different quantities, no density provided, etc.) and require some post processing to be aggregated in a consistent way. We want this post processing to be transparent, which is why we did things in python.

I understand this, but in my opinion if this is the case there should be a database with the collected properties, and a transparent post processing pipeline which takes such database and generates a clean/post-processed one. Having the data within a Python codebase doesn't really adhere to FAIR principles IMO.

Let's see if we can reach consensus internally and can move forward.

[RemDelaporteMathurin]

Well we do provide a clean database as JSON compiled at each release. See for instance: https://github.com/RemDelaporteMathurin/h-transport-materials/releases/tag/v0.17

That generated automatically this JSON file.

[crvernon]

@editorialbot reject

Thanks for your submission to JOSS @RemDelaporteMathurin. After review with our larger editorial board we must reject your submission on the following grounds that our editors identified as problematic:

• The pairing of the database and code within this project seemed of concern to several since this is not a standard practice and could hinder community participation in helping this package grow. This concern flagged the initial review per our submission guidelines to provide software "packaged appropriately according to common community standards for the programming language being used."
• Some identified that many of lines of code related to the actual functionality of the package were fixed values and repeated boilerplate.

We do wish you all the best in developing your package further and appreciate you taking time to submit to JOSS!

[crvernon]

@editorialbot reject

[crvernon]

@openjournals/dev this issue did not close upon rejection. Could you provide guidance here?

[crvernon]

@editorialbot reject

[editorialbot]

Paper rejected.

[xuanxu]

@crvernon There was an error in the bot server, It should be fixed now.