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Sign up[REVIEW]: GEM: A Python package for graph embedding methods #876
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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @jsgalan, it looks like you're currently assigned as the reviewer for this paper If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews To fix this do the following two things:
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@palash1992 - in paper.md, you reference [goyal2017graph] which doesn't compile, rather than the correct [@goyal2017graph] -- i.e. the @ is missing and should be added. |
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@whedon generate pdf |
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@danielskatz Thanks for pointing it out. I have modified the manuscript to reflect the change. |
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Hi all, After installing and revising, a few comments mostly Unrelated on the implementation
Even though is a Theano maybe should be added as a warning of the package
I just got the file and place it in the working directory. Should this dataset be placed inside the package itself under gem.datasets.karate? Also, Ifound the following errors:
_ @palash1992 can you give me pointers to circumvent this errors? Best |
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@jsgalan , thanks for the review! I have revised the library to clarify the above errors. 1. I changed the specification to 'karate.edgelist' so that you can load it from the current directory. 2. Original instructions to run node2vec successfully were in gem/c_exe/readme. I have now merged them with readme on the front page. 3. I have removed the theano.printing import line making it compatible with Tensorflow as well. Let me know if you have any more issues. |
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I'm trying to run the test file but without much success yet:
Not sure what it means. Also, I find it rather difficult to understand what the test.py is supposed to do since there's no documentation (or did I miss the link?). Could you provide some documentation for the software as well as some API description (how to call the library) ? Also, in order to run the test file, I had to install keras and tensorflow but it is not clear if those are dependencies of the test file or the actual library. If the latter is true, you will need to update your dependencies. |
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@rougier Thanks for taking the time to review! The readme clarifies some of your questions. On the repository documentation page (readme.md), under dependencies I have specified that the package in general doesn't require keras and tensorflow/theano, but if you need to run SDNE model, you will need them. Also, the purpose of test.py is mentioned in usage section of the readme. I have also now added it to the test.py file. The error on the dataset can be overcome by copying the gem/data/karate.edgelist to the working directory. I have modified the readme and test.py to clarify this. I also changed TEST_50M.edgelist to karate.edgelist in test.py. Let me know if there are still any issues. |
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I still have some issues but I'll move to your issuer tracker. But again, it is not clear what the test is doing and what kind of output is expected. I think you should definitely add a toy example to make it easier for people to rapidly get a sense of what the software is doing. |
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@rougier : I have replied to the issue on Github. I completely agree that a toy example would make it easier to understand the purpose. I will add it soon. Thanks for the suggestion! |
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And also a documentation (even a small one). Sorry to insist on that but it's very difficult to know what this software is all about when you land on the first page. An explanation, a toy example (with the expected output) would really help. |
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@rougier : I will add that by the end of the day. I can add more examples as well. |
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Hi all, I agree with comments made by @rougier regarding the documentation, even though the referenced papers are explanatory of the methods, it is useful to have some documentation of the parameters of the methods. Otherwise, I am satisfied with the review. Best |
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I still got some problems with missing files (filed an issue on the repo). I think you might want to have an example directory where you can put the |
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@rougier I have now created a "tests" folder with the required files following the instructions. This should resolve the issues. |
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Sorry, I'm attending a conference until Friday and I don't have too much time to re-test right now. The latest change are still not working for me (I opened several issues on the repo). It is a bit frustrating since it is always minor bugs and the core of the software seems to be ok. However, I think also there are room for improvements concerning the documentation (usage + API) and the overall structure. Also, there is not release yet but @palash1992 can make oneonce everything is ok. |
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@rougier : Based on my replies, were you able to make it work? I have also added more examples in the readme along with sample executions. Also, I added parameter descriptions for all methods in the readme. Let me know where else can I make improvements. |
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It still does not work for me. But maybe it's my installation. @jsgalan Did you manage to run the two tests? |
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@rougier : while we wait for @jsgalan 's reply, can you tell me what error you are getting? I asked some of my friends to install it on different machines and they were able to do it. So I am not sure exactly what the problem could be. Perhaps it's a specific Mac issue. Any feedback would be helpful in making the package more robust to platforms. |
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Here is what I get from
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This is where I get lost and I think the culprit is the lack of documentation ;) Is node2vec necessary only to run the tests or is it necessary to run the software? If this is only for the test, then it's fine for me. I can run the karate test and probably @jsgalan can run the other one. However, it would be good in the documentation to explain (for example) the karate example (what is the expected output, what does it mean, etc) and to explain that second example requires the SNAP library. In the end, it would be only a matter of changing the README. Also, maybe the While checking the paper, I think you're missing a DOI for Belkin et al. 2002. |
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@whedon generate pdf |
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@rougier: Yes, node2vec is only required for tests. I have now made the changes you specified and also added an additional argument named node2vec to use if you need to run node2vec. I have clarified this in readme. Hope it is fine now. |
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Thanks. The README looks better. I'm still unable to run the Apart from that, I think it is ready for publication (@danielskatz) even though you could improve a little bit the README (for example, by re-using the summary of the Don't forget to make a release on GitHub, I think it is mandatory for publication. |
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@rougier: I have now added a release and modified readme. To solve the _node issue, did you try uninstalling networkx and installing using pip install networkx==1.11? |
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No, I did not try actually. |
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Hi i've cloned the git a few times now. I cloned and compiled SNAP and added node2vec to my system's path. This is what i got after trying the tests:
attached both runs, @palash1992 could you look at the warnings?. Best |
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@rougier after the pip install networkx==1.11 some parts of the tests where smooth. you might want to try. |
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@rougier : Let me know if the issue still persists |
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@palash1992 Just did and it works (with some warnings though) |
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@rougier : Perfect! I also made a release. Let me know if there is anything else needed from my side. |
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@rougier - I see there are still quite a few checkboxes left empty. Please go through them when you have a chance. |
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@danielskatz Just did. The Functionality documentation and Community guidelines could be improved a bit but it does not prevent publication. Thanks @palash1992 for taking all my comments into account. |
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great, thanks @rougier ! @palash1992 - please make an archive of the current state of the repo in Zenodo or similar, and let me know the DOI of the archive, so that can move forward in publishing this submission. |
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@danielskatz : I used Zenodo to create the archive. Here is the DOI: 10.5281/zenodo.1407178 |
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@whedon set 10.5281/zenodo.1407178 as archive |
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OK. 10.5281/zenodo.1407178 is the archive. |
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@whedon generate pdf |
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@jsgalan, @rougier - many thanks for your reviews here and to @danielskatz for editing this submission @palash1992 - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00876 |
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Hi every one. Using TensorFlow backend. I am really confiused. can anyone help ? |
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whedon commentedAug 5, 2018
•
edited
Submitting author: @palash1992 (Palash Goyal)
Repository: https://github.com/palash1992/GEM
Version: v1.0.0
Editor: @danielskatz
Reviewer: @jsgalan, @rougier
Archive: 10.5281/zenodo.1407178
Status
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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) 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.)
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@jsgalan & @rougier, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @danielskatz know.
Review checklist for @jsgalan
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @rougier
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?