Joss-reviews: [REVIEW]: dustmaps: A Python interface for maps of interstellar dust

[whedon]

Submitting author: @gregreen (Gregory Green)
Repository: https://github.com/gregreen/dustmaps
Version: v1.0
Editor: @arfon
Reviewer: @jegpeek
Archive: 10.5281/zenodo.1299368

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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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@jegpeek, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Review checklist for @jegpeek

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Repository: Is the source code for this software available at the repository url?
• [x] Version: Does the release version given match the GitHub release (v1.0)?
• [x] Authorship: Has the submitting author (@gregreen) 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]

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

:star: Important :star:

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 😿

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arfon]

@jegpeek - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Any questions/concerns please let me know.

[gregreen]

@arfon Is there an equivalent to \citet{} in mardown? Some of the citations should not be in parentheses.

[arfon]

@gregreen - does this document cover it? http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html

[gregreen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[gregreen]

@arfon Yes, that covered it. Thanks!

[arfon]

👋@jegpeek - friendly reminder to take a look at this review when you get a chance.

[gregreen]

@jegpeek Any progress on the review?

[jegpeek]

Yep — been traveling with crappy wifi so hard to kick all the tires. Will do!

[jegpeek]

I know this is classic referee garbage but... what do you think of adding Peek & Graves 2010?

[gregreen]

I would be happy to do so. I can't access http://peekandgraves2010.com/ though. Is there a newer link to the data? Better yet, is the data stored in some semi-permanent archive (like the Harvard Dataverse)? I write a fetch() function for each dust map, so having a stable URL is best.

[jegpeek]

Thanks for the nudge! https://doi.org/10.7910/DVN/VBSI4A

[gregreen]

I've added an issue, which I'll work on, but don't let that get in the way of looking over the code as it already is!

[gregreen]

@jegpeek Have you had time to test the functionality of the package, or to look at the documentation?

[jegpeek]

@gregreen making progress! Right now I am having this issue: I was following along in the directions here:

import dustmaps.planck
dustmaps.planck.fetch()

and then got

Downloading http://pla.esac.esa.int/pla/aio/product-action?MAP.MAP_ID=HFI_CompMap_ThermalDustModel_2048_R1.20.fits ...
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-10-3c6fb0816ca2> in <module>()
      1 import dustmaps.planck
----> 2 dustmaps.planck.fetch()

/Users/jegpeek/anaconda3/lib/python3.5/site-packages/dustmaps/planck.py in fetch()
    130         'planck',
    131         'HFI_CompMap_ThermalDustModel_2048_R1.20.fits')
--> 132     fetch_utils.download_and_verify(url, md5, fname=fname)
    133 
    134 

/Users/jegpeek/anaconda3/lib/python3.5/site-packages/dustmaps/fetch_utils.py in download_and_verify(url, md5sum, fname, chunk_size, clobber, verbose)
    234 
    235             with open(fname, 'wb') as f:
--> 236                 content_length = int(r.headers['content-length'])
    237                 bar = FileTransferProgressBar(content_length)
    238 

/Users/jegpeek/anaconda3/lib/python3.5/site-packages/requests/structures.py in __getitem__(self, key)
     52 
     53     def __getitem__(self, key):
---> 54         return self._store[key.lower()][1]
     55 
     56     def __delitem__(self, key):

KeyError: 'content-length'

any ideas?

[gregreen]

@jegpeek It looks like the website isn't returning "content-length" in the headers. I'll fix the case where "content-length" is missing.

[jegpeek]

also

[gregreen]

@jegpeek Can you verify that latest commit in the develop branch (gregreen/dustmaps@4c48e989c893a76f8107bf28d3e2620fd704b6ae) fixes the "content-length" issue?

[jegpeek]

Yup, works!

[jegpeek]

@gregreen (sorry, just found the ebv comments) are there automated tests?

[gregreen]

@jegpeek There are tests here. You can go to the dustmaps/ directory in the repository and run

nosetests -v

Be careful though - some of the tests use a lot of memory! If you want to reduce the memory usage of the Bayestar map test, you can change this line to max_samples = 1.

[whedon]

Here are some things you can ask me to do:

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# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
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🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[jegpeek]

OK @arfon I checked off all the things. Awesome piece of work @gregreen. Sorry it took so long.

[gregreen]

@jegpeek No problem. Thanks for looking through my code/docs/paper!

[arfon]

OK @arfon I checked off all the things. Awesome piece of work @gregreen. Sorry it took so long.

🤘

@gregreen - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[gregreen]

@arfon The DOI is now: 10.5281/zenodo.1299368.

[arfon]

@whedon set 10.5281/zenodo.1299368 as archive

[whedon]

OK. 10.5281/zenodo.1299368 is the archive.

[arfon]

@jegpeek - many thanks for your review here ✨

@gregreen - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00695 :zap: :rocket: :boom:

[whedon]

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

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