Joss-reviews: [REVIEW]: pdfsearch: Search Tools for PDF Files

[whedon]

Submitting author: @lebebr01 (Brandon LeBeau)
Repository: https://github.com/lebebr01/pdfsearch
Version: v0.2.0
Editor: @karthik
Reviewers: @lmullen, @jeroen
Archive: 10.5281/zenodo.1294067

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/af15cc742fd31abd760026c1bcb4d54c"><img src="http://joss.theoj.org/papers/af15cc742fd31abd760026c1bcb4d54c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/af15cc742fd31abd760026c1bcb4d54c/status.svg)](http://joss.theoj.org/papers/af15cc742fd31abd760026c1bcb4d54c)

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.)

Reviewer instructions & questions

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @lmullen

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] 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?
• [ ] Version: Does the release version given match the GitHub release (v0.2.0)?
• [x] Authorship: Has the submitting author (@lebebr01) 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

• [ ] 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?
• [ ] 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)?

Review checklist for @jeroen

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] 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 (v0.2.0)?
• [x] Authorship: Has the submitting author (@lebebr01) 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. @lmullen 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 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[karthik]

@whedon add @jeroen as reviewer

[whedon]

OK, @jeroen is now a reviewer

[lmullen]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# 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
@whedon start review

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[jeroen]

@lebebr01 what is the reason pdfsearch 0.2.0 is not on CRAN yet?

[lebebr01]

@jeroen was primarily waiting to submit to CRAN until after the review. I'm open to submitting prior to review and then submitting another version after the review if there are changes made.

[jeroen]

@lebebr01 can you ping me here when https://github.com/lebebr01/pdfsearch/issues/10 has been fixed, so I can proceed with testing and reviewing the package (on macos ;))

[lebebr01]

@jeroen Issue should be fixed. All functions now use tokenizers::tokenize_lines instead of the literal \r\n splitting, thanks for catching this.

Also added unit test here to test for literal "n" characters in result text: test here. Open to other suggestions to test this.

[jeroen]

OK thank you for fixing. LGTM!

[arfon]

Hi @lmullen - please complete your review when you get a chance.

[lmullen]

@arfon I have completed my review and I am willing to come back to it once @lebebr01 has had a chance to respond to the issues posted above.

[lebebr01]

First, a belated thank you to @jeroen for your review.

Secondly, thank you to @lmullen for your review. I have made the suggested edits related to the code and vignette issues identified above.

I also have expanded on the significance and usage of the package in research settings in the JOSS paper and README. My thoughts are that this package would be of primary interest to those doing research syntheses or meta-analyses. I also present description of an ongoing research project using the package to explore the evolution of statistical software and quantitative methods used in published social science research that will be presented at JSM this summer. I'd be interested in your thoughts on whether this expanded discussion is compelling.

Changes and a few additional comments can be seen in the issues above. I also tried to link major changes via commits in the issues above.

[karthik]

Thank you @lebebr01!
Once @lmullen signs off on the last remaining items, I'll proceed with next steps.

[lmullen]

Two minor comments on the revisions to the JOSS paper.

"instead of searching the entire text of a document specific portions of the text": comma after document.

"a preprint will be posted here." I'm not sure from the context where "here" is.

Other than that I am fine with the revisions, which I have reviewed.

[lebebr01]

Thank you @lmullen.

I made the suggested edits to the README file (https://github.com/lebebr01/pdfsearch/commit/90cb73dcb12fb9fb030efb846976aad293270ae7), I was not able to find these lines in the JOSS paper.

[lmullen]

👍

[arfon]

@karthik - I think this is good to accept?

[karthik]

@lebebr01 Just returning from vacation. I'm happy to accept (assuming @lmullen is not waiting on anything else for the final checks). Please archive your software on Zenodo and post the DOI here so we can proceed with next steps. 🙏

[lmullen]

Good by me.

On Tue, Jun 19, 2018 at 7:14 PM Karthik Ram [e-mail]
wrote:

@lebebr01 https://github.com/lebebr01 Just returning from vacation. I'm
happy to accept (assuming @lmullen https://github.com/lmullen is not
waiting on anything else for the final checks). Please archive your
software on Zenodo and post the DOI here so we can proceed with next steps.
🙏

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/668#issuecomment-398574615,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AALNeOf2Hk_q-erW07UYRgu8KMSms88bks5t-YW6gaJpZM4TKu_r
.

>

Lincoln Mullen
Assistant Professor, Department of History & Art History
George Mason University

[lebebr01]

@karthik I've archived the latest version to Zenodo and the DOI is 10.5281/zenodo.1294067 (https://doi.org/10.5281/zenodo.1294067).

Thanks again for the reviews @jeroen and @lmullen.

[karthik]

@whedon set 10.5281/zenodo.1294067 as archive

[whedon]

OK. 10.5281/zenodo.1294067 is the archive.

[karthik]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[arfon]

@karthik are we good to accept here?

[karthik]

Yes good to accept. Was waiting on PDF and forgot to ping you.

[arfon]

@lmullen, @jeroen - many thanks for your reviews here and to @karthik for editing this submission ✨

@lebebr01 - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00668 :zap: :rocket: :boom:

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00668/status.svg)](https://doi.org/10.21105/joss.00668)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00668">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00668/status.svg" alt="DOI badge" >
</a>

This is how it will look in your documentation:

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