[REVIEW]: mpnum: A matrix product representation library for Python

whedon commented 6 years ago

Submitting author: @dseuss (Daniel Suess) Repository: https://github.com/dseuss/mpnum Version: v1.0.0 Editor: @labarba Reviewer: @SylvainCorlay Archive: 10.5281/zenodo.1115574

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General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@dseuss) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @SylvainCorlay it looks like you're currently assigned as the reviewer for this paper :tada:.

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labarba commented 6 years ago

Hi @SylvainCorlay — ping! Gentle reminder here about the review for JOSS. You can start on it, and report any issues you encounter right here (or post issues on the repo of the submitted software). Cheers!

dsuess commented 6 years ago

After the submission, we noted a compatibility bug in the setup.py that prevents v1.0.0 to be installed with Python2. Could we bump the refereed version to v1.0.1.

labarba commented 6 years ago

I don't see a problem with that, @dseuss—thanks for the update.

SylvainCorlay commented 6 years ago

After the submission, we noted a compatibility bug in the setup.py that prevents v1.0.0 to be installed with Python2. Could we bump the refereed version to v1.0.1.

Same here.

dsuess commented 6 years ago

Same here.

Does that mean 1.0.1 doesn't work for you either?

SylvainCorlay commented 6 years ago

Does that mean 1.0.1 doesn't work for you either?

Absolutely! Pardon my brevity.

SylvainCorlay commented 6 years ago

Note: I checked the box regarding the matched version. I don't know if it matters that the generated issue specifies 1.0.0

SylvainCorlay commented 6 years ago

As I am going through the checklist:

[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

I found that there is a DOI for the reference Enabling High-Dimensional Hierarchical Uncertainty Quantification by ANOVA and Tensor-Train Decomposition.

[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support.

Very minor: on this point, a "contributing" section in the readme could be added (simply linking to the relevant section of the documentation).

[ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

For some reason, I had to install hdf5 to be able to run the tests. The test_requires specify h5py, which probably requires some installation of hdf5. It seems that the test requirements won't use wheels.

dsuess commented 6 years ago

@SylvainCorlay Thanks for the feedback.

I found that there is a DOI for the reference Enabling High-Dimensional Hierarchical Uncertainty Quantification by ANOVA and Tensor-Train Decomposition.

Added DOI and updated arXiv references for another paper in a3aaaf5

Very minor: on this point, a "contributing" section in the readme could be added (simply linking to the relevant section of the documentation).

Done.

For some reason, I had to install hdf5 to be able to run the tests. The test_requires specify h5py, which probably requires some installation of hdf5. It seems that the test requirements won't use wheels.

Right, I recalled that we had to manually install test dependencies on travis for that reason. I have added a note to the README as well as to the documentation. (The latter should appear once readthedocs renders the new version)

SylvainCorlay commented 6 years ago

I could install, run the tests, and the example notebook. The whole process was straightforward. The need for the package is properly justified and prior work appropriately cited. Documentation includes both high-level narrative documentation introducing the package and an API reference generated from the doc strings (although a few items are left as todo).

1) Quick note about the example notebook: I find it extremely useful and detailed. A link to the notebook is provided in the documentation, but the rendered notebook itself could probably be included as-is in the documentation. A good tool to achieve this is to use the nbsphinx sphinx extension.

Quick note: it is a requirement for most linux distributions (e.g. Debian) for the doc package to be self-contained, so using nbsphinx for including the notebook in sphinx would help with that.

Minor suggestion: the notebook could include some visuals from the narrative documentation about the graphical notation, and how it translate with a simple code example, before diving into more advanced examples.

3) About the narrative documentation: the matrix product state representation of a state comes without context. The rest of the paragraph is more self-explanatory but I think that this is domain-specific, and is probably not necessary for introducing MPS and MPO.

labarba commented 6 years ago

@SylvainCorlay : I see that all boxes are checked. Can you confirm that you recommend acceptance now?

dsuess commented 6 years ago

Thanks a lot @SylvainCorlay for the helpful comments. We already implemented remark 1 on the master branch in the repo. We will address the other remarks shortly after fixing some slight mistakes in some images.

@labarba I would move the v1.0.1 tag to a different commit in the repo once we incorporate all the fixes. Since all the fixes are in the documentation, this does not affect the version on PyPi. Would that be okay with you?

SylvainCorlay commented 6 years ago

@SylvainCorlay : I see that all boxes are checked. Can you confirm that you recommend acceptance now?

Yes, this is excellent. I recommend the paper for acceptance. I will also definitely watch this repository, and future development!

labarba commented 6 years ago

Yay! @dseuss —We'll now need you to deposit the final release on an archival host like figshare or Zenodo, and report here the DOI. Then @arfon will press the buttons to publish!

dsuess commented 6 years ago

I have uploaded the final version v1.0.2 with the DOI 10.5281/zenodo.1115574. We have updated the refereed version according to the suggestions of the referee:

Added some images to the notebook
Embedded the notebook on readthedocs
Added remarks on how to contribute
Moved all development dependencies into the requirements.txt

We also migrated all the figures from Inkscape to LaTeX/TikZ and fixed some notation errors.

labarba commented 6 years ago

@whedon set 10.5281/zenodo.1115574 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1115574 is the archive.

labarba commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00465/joss.00465/10.21105.joss.00465.pdf

labarba commented 6 years ago

@arfon On to you to push the accept button!

dsuess commented 6 years ago

Could we wait for another hour? I just noticed that the bibliography in the PDF is everything but consistent. I'll try to fix this now.

dsuess commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00465/joss.00465/10.21105.joss.00465.pdf

dsuess commented 6 years ago

OK, now I am happy with it as well. Just cleaned up the names in the references, removed unnecessary fields from the bib file, and fixed citations of the Oseledets paper, which gave ??? in the old version.

Thanks a lot to @labarba and @SylvainCorlay

milan-hl commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00465/joss.00465/10.21105.joss.00465.pdf

milan-hl commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00465/joss.00465/10.21105.joss.00465.pdf

milan-hl commented 6 years ago

I slightly adapted the spelling of one of the references. I'm looking forward to the paper being published. Thanks everyone!

arfon commented 6 years ago

@SylvainCorlay - many thanks for your review here and to @labarba for editing this submission ✨

@dseuss - your submission is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00465 ⚡️ 🚀 💥

whedon commented 6 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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