Open editorialbot opened 1 month ago
editorialbot
commented
1 month ago Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commandsFor example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdfReference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.1038/sdata.2016.18 is OK
- 10.1007/978-3-319-17966-7_21 is OK
- 10.32614/CRAN.package.DiagrammeR is OK
- 10.1145/2757001.2757003 is OK
- 10.32614/CRAN.package.rdflib is OK
🟡 SKIP DOIs
- No DOI given, and none found for title: Graphviz Python Package
- No DOI given, and none found for title: RDFLib: Python Library for working with RDF
- No DOI given, and none found for title: PyPI: The Python Package Index
- No DOI given, and none found for title: CRAN: The Comprehensive R Archive Network
❌ MISSING DOIs
- None
❌ INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=7.97 s (444.2 files/s, 183560.1 lines/s)
--------------------------------------------------------------------------------
Language files blank comment code
--------------------------------------------------------------------------------
Python 3271 177729 266453 817403
C 11 4228 17439 104274
CSV 43 0 0 37450
C/C++ Header 28 1277 2142 7605
SVG 13 0 310 5286
CSS 34 631 591 3623
Cython 11 484 435 2223
HTML 4 356 8 1711
JavaScript 7 187 131 1440
Fortran 90 53 116 86 892
R 4 169 298 797
Markdown 9 150 0 404
Fortran 77 21 26 50 382
reStructuredText 4 91 1 294
TeX 6 53 93 253
C++ 1 13 14 143
PowerShell 1 49 90 108
Meson 3 21 9 102
XML 2 0 1 79
YAML 1 0 0 48
Fish Shell 1 13 14 42
INI 3 5 0 34
Rmd 3 487 3528 33
C Shell 1 10 5 12
Bourne Again Shell 1 1 3 10
zsh 1 1 6 7
Lua 1 0 1 2
JSON 1 0 0 1
--------------------------------------------------------------------------------
SUM: 3539 186097 291708 984658
--------------------------------------------------------------------------------Commit count by author:
12 Jonathan Gordon
1 Jonathan-E-GordonPaper file info:
📄 Wordcount for paper.md is 1391
✅ The paper includes a Statement of need section
editorialbot
commented
1 month ago License info:
✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)
editorialbot
commented
1 month ago :point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
emanueledelsozzo
commented
1 month ago 
berquist
commented
1 month ago python -m venv ./venv; source ./venv/bin/activate; python -m pip install -e .python -m pip install pytest-covpython -m pytest --cov=FAIRmaterials fails, see https://github.com/cwru-sdle/FAIRmaterials/issues/2berquist
commented
1 month ago Software report:
This is misleading because a Python virtualenv was added to version control; it will need to be rerun once https://github.com/cwru-sdle/FAIRmaterials/pull/1 is merged.
Jonathan-E-Gordon
commented
1 month ago @berquist I completed the merge. Are they any other actions I need to take for now?
berquist
commented
1 month ago @berquist I completed the merge. Are they any other actions I need to take for now?
Thank you for the poke. There's nothing with the code, so I can continue with my review. I do have some general questions.
For authorship, there are a number of authors on the paper, but according to Git, you are the only person who has contributed to the code. Could you elaborate on this?
In the absence of running editorialbot (maybe there is a command for this) here are new LOC counts:
$ cloc .
54 text files.
35 unique files.
64 files ignored.
github.com/AlDanial/cloc v 2.02 T=0.07 s (522.2 files/s, 162150.9 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
HTML 1 338 5 1607
SVG 2 0 299 1483
R 4 169 298 797
Python 9 212 287 684
Markdown 4 112 0 271
CSV 10 0 0 145
TeX 1 8 0 96
Rmd 3 487 3528 33
Text 1 4 0 5
-------------------------------------------------------------------------------
SUM: 35 1330 4417 5121
-------------------------------------------------------------------------------I also ran it on just the Python implementation, so no tests, and came up with
Python 5 172 276 425I don't necessarily view this as a measure of novelty, particular when there's an obvious need for the software, but in reading the paper, it's missing references to prior work in the area. I've definitely seen tools that take ontologies defined in CSV or Excel workbooks and convert them to RDF. The paper states that the tooling is for materials and data science ontologies, but aside from this initial mention, there are no references to the existing and surprisingly rich history of ontologies in materials science. I've found at least https://link.springer.com/article/10.1557/s43579-024-00616-6 and https://link.springer.com/article/10.1557/s43580-024-00874-5 that claim usage of FAIRmaterials, so they need to be added.
There are some other criteria that may not be met under "substantial scholarly criteria", particularly age of software, though I get the impression it was simply not version controlled until recently. @atrisovic
Jonathan-E-Gordon
commented
1 month ago @berquist Great thank you! I will look into adding the references.
In terms of the "substantial scholarly criteria" and the authorship you are correct we do not work in github. Due to lab policy, we developed the software in a private Bitbucket repository, which has accumulated over 400 commits since 2021. In January 2024, we initiated a redesign of the software, resulting in 110 commits from 9 authors, representing approximately 7 person-months of work. I can send the whole commit history if that is helpful. This software will also be cited in a Scientific Data paper currently under review, titled “Materials Data Science Ontology (MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science”.
danielskatz
commented
3 weeks ago @atrisovic - Can you update me on the status of this review and what the next steps and/or blocking items are?
berquist
commented
2 weeks ago Apologies for letting my review slip.
I don't think JOSS has a policy about making private code public, but since the review should be in the open, I wouldn't request to see git log > git_log.txt unless you were willing to post it publicly as an attachment in this comment thread. At this point I'm still looking for editor guidance.
I've created an issue on the repo about the failing Python tests and a PR for discussing how the READMEs should be handled, since there is no other project documentation or examples.
Although the READMEs do cover an example of using the code from both Python and R, it would be much better to have this fully-worked example present in the repository. I think it's present in the R package but not the Python package.
Jonathan-E-Gordon
commented
2 weeks ago @editorialbot commands
editorialbot
commented
2 weeks ago Hello @Jonathan-E-Gordon, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Run checks and provide information on the repository and the paper file
@editorialbot check repository
# Check the references of the paper for missing DOIs
@editorialbot check references
# Generates the pdf paper
@editorialbot generate pdf
# Generates a LaTeX preprint file
@editorialbot generate preprint
# Get a link to the complete list of reviewers
@editorialbot list reviewers
Submitting author: !--author-handle-->@Alexhb02<!--end-author-handle-- (Alexander Harding Bradley) Repository: https://github.com/cwru-sdle/FAIRmaterials Branch with paper.md (empty if default branch): main Version: 0.4.2.2 Editor: !--editor-->@atrisovic<!--end-editor-- Reviewers: @berquist, @emanueledelsozzo Archive: Pending
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@berquist & @emanueledelsozzo, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @atrisovic know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
📝 Checklist for @emanueledelsozzo
📝 Checklist for @berquist