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View Code? Open in Web Editor NEWFlexible bidsificator for multimodal datasets
License: GNU General Public License v2.0
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bidsme's Issues
JOSS Review — Quality of writing
As part of the JOSS review: openjournals/joss-reviews#5575
Suggestions:
- Please consider splitting the source code over more lines, ideally one line per sentence to make things easier to reference.
- Please consider using the term “directories” instead of “folders”. Directories are file system entities, whereas folders are graphical interface features.
Minor issues:
- Python is a proper noun and should be capitalized, at least in formal writing; python is a type of snake.
Major issues:
- “imposing only the core of BIDS -- the folder structure, the file naming style and the global metadata”. The term “global metadata” is unclear so you would need to introduce and explain it. To my knowledge, “global metadata” is not a core concept in BIDS. I would guess you mean simply
dataset_description.json— but then again, you do not show this file, but you show e.g.participants.tsv, a different metadata file, in the figure.
JOSS review - examples
Ahoi hoi @nbeliy & co-authors,
this is in reference to the review I'm currently conducting for JOSS here .
First of all, thank you very much for your dedicated work on this tool and your respective submission to JOSS.
Based on the review process and included checkboxes, I would like to suggest a few things.
Concerning the examples, I would like to suggest streamlining the existing example and maybe splitting it across fewer files to make it easier for interested users to follow and add examples for the other modalities you support. Both points target utilization and adaptation by the community.
I'm very sorry if I missed something obvious, misunderstood something or assumed something wrong. Please let me know if that is the case, as well as if you have any questions. Thanks again for creating this important software tool.
Cheers, Peer
JOSS Review — Test suite
As part of the JOSS Review → openjournals/joss-reviews#5575
This is analogous with the issue raised here #7
I fully appreciate that it can be difficult to formulate exhaustive or even just comprehensive tests for scientific software, but without a test suite it is impossible for me to determine whether the software can do anything at all.
The other reviewer has mentioned github workflows, which are a very useful feature. However if for some reason you don't want to do that, I'd be satisfied with just a few tests I can run locally, covering some of the functionalities mentioned in the article.
`bidsme map` raises no error but `bidsme bidsify` does
While building the bidsmap for a dataset, I ended up with bidsme map raising no error at all but once I run bidsme bidsify, I get FileExistsError.
This means that bidsme map does not capture some existing conflicts. Maybe this should be fixed to make the process of creating the bidsmap less frustrating. It looks to me like one of the sanity checks performed during bidsme map should handle this.
JOSS Review — Installation Proof
As part of the JOSS review: openjournals/joss-reviews#5575
Could you confirm that the following files constitute a successful installation of the package?
decohost ~ # equery f bidsme
* Searching for bidsme ...
* Contents of dev-python/bidsme-1.4.4:
/usr
/usr/bin
/usr/bin/bidsme -> ../lib/python-exec/python-exec2
/usr/bin/bidsme-pdb -> ../lib/python-exec/python-exec2
/usr/lib
/usr/lib/python-exec
/usr/lib/python-exec/python3.11
/usr/lib/python-exec/python3.11/bidsme
/usr/lib/python-exec/python3.11/bidsme-pdb
/usr/lib/python3.11
/usr/lib/python3.11/site-packages
/usr/lib/python3.11/site-packages/bidsme
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info/METADATA
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info/RECORD
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info/WHEEL
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info/entry_points.txt
/usr/lib/python3.11/site-packages/bidsme-1.4.0.post4.dist-info/top_level.txt
/usr/lib/python3.11/site-packages/bidsme/Modules
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/BrainVision.py
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/EDF.py
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/EEG.py
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/_EDF.py
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/_EEG.py
/usr/lib/python3.11/site-packages/bidsme/Modules/EEG/_MNE.py
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JOSS review - community guidelines
Ahoi hoi @nbeliy & co-authors,
this is in reference to the review I'm currently conducting for JOSS here .
First of all, thank you very much for your dedicated work on this tool and your respective submission to JOSS.
Based on the review process and included checkboxes, I would like to suggest a few things.
Could you maybe add information concerning
1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
for interested users?
I'm very sorry if I missed something obvious, misunderstood something or assumed something wrong. Please let me know if that is the case, as well as if you have any questions. Thanks again for creating this important software tool.
Cheers, Peer
The doc is missing some installation instruction
I don't believe bidsme is installable with pip install, right?
So there should be some minimum installation instruction because otherwise the whole thing could be a non starter.
JOSS review - installation & general structure
Ahoi hoi @nbeliy & co-authors,
this is in reference to the review I'm currently conducting for JOSS here .
First of all, thank you very much for your dedicated work on this tool and your respective submission to JOSS.
Based on the review process and included checkboxes, I would like to suggest a few things.
When I tried to install bidsme following the provided installation guide, I ran into an error saying:
ModuleNotFoundError: No module named 'ruamel'
and thus, I could not evaluate the other tutorials and performance. It might also be nice to add your package to pypi.
Furthermore, it might be beneficial to have everything, ie the software, documentation and examples, in the same github repository and split between github and gitlab as this potentially complicates things for interested users (ie finding information, etc.).
Related to that: the README file could be enhanced by adding more information, e.g. regarding the installation, etc. .
I'm very sorry if I missed something obvious, misunderstood something or assumed something wrong. Please let me know if that is the case, as well as if you have any questions. Thanks again for creating this important software tool.
Cheers, Peer
JOSS Review — Versioning scheme
As part of the JOSS review: openjournals/joss-reviews#5575
I would recommend a versioning scheme that is somewhat cleaner. major.minor.patch is best. While I have seen the post and pre suffixes before, they usually reference a date or some more meaningful information that couldn't otherwise be expressed in the major-minor-patch format. post4 sound like it should have been a patch, i.e. 1.4.4.
Not least of all it causes problems for semantic parsing of the version number.
`bidsme map` command should not remove comments from `bidsmap.yaml`
Building the bidsmap.yaml file is a tedious and repetitive task. The template and checked flags are great to have a broad view of what remains to do. Considering the number of fields to fill in, I'd like to be able to add comments to the bidsmap so that I can remember why I made some choices.
For now, adding comments to the bidsmap does not prevent the bidmse map command from running but the comments are removed by the program.
JOSS review - automated tests
Ahoi hoi @nbeliy & co-authors,
this is in reference to the review I'm currently conducting for JOSS here .
First of all, thank you very much for your dedicated work on this tool and your respective submission to JOSS.
Based on the review process and included checkboxes, I would like to suggest a few things.
It would be great if you could add a few automated tests/CI to the repository, e.g. a little github workflow that tests the installation and follows/implements the example you provide.
I'm very sorry if I missed something obvious, misunderstood something or assumed something wrong. Please let me know if that is the case, as well as if you have any questions. Thanks again for creating this important software tool.
Cheers, Peer
JOSS review - documentation
Ahoi hoi @nbeliy & co-authors,
this is in reference to the review I'm currently conducting for JOSS here .
First of all, thank you very much for your dedicated work on this tool and your respective submission to JOSS.
Based on the review process and included checkboxes, I would like to suggest a few things.
IMHO, it would be great if you could add a small documentation (e.g. via ReadTheDocs, as the current state of the repository and split between github/gitlab complicates navigation and finding information a bit. Additionally, this would allow to add API method documentation and integrating the examples.
I'm very sorry if I missed something obvious, misunderstood something or assumed something wrong. Please let me know if that is the case, as well as if you have any questions. Thanks again for creating this important software tool.
Cheers, Peer
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