Joss-reviews: [REVIEW]: opty: Software For Trajectory Optimization and Parameter Estimation Using Direct Collocation

[whedon]

Submitting author: @moorepants (Jason K. Moore)
Repository: https://github.com/csu-hmc/opty
Version: v0.2.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @stavness
Archive: 10.5281/zenodo.1162870

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.)

Reviewer questions

@cybanical, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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 (@moorepants) made major contributions to the software?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: Have any performance claims of the software been confirmed?

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 for JOSS. @cybanical 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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

[Kevin-Mattheus-Moerman]

@moorepants @tvdbogert this is where the review process happens

[Kevin-Mattheus-Moerman]

@chrisdembia our formal system currently handles a single reviewer but would you be able to act as a second reviewer on this?

[Kevin-Mattheus-Moerman]

@chrisdembia has also agreed to review.

[moorepants]

It is worth nothing that Chris is a co-author of mine (at least in the last few years) and we are good friends. I'm not sure of JOSS rules, but in other journals this would likely be a conflict of interest. FYI.

[Kevin-Mattheus-Moerman]

@moorepants thank you for pointing this out. I will arrange another reviewer.

[moorepants]

Just checking in on this. It's been well over a month since I submitted.

[Kevin-Mattheus-Moerman]

:wave: @cybanical how are you getting on? Have you started the review process?

[Kevin-Mattheus-Moerman]

@demotu @siboles @stavness @melund @jslee02 I am looking for an additional reviewer for this submission. Would you be interested in reviewing this for JOSS? The review guidelines are here.

[stavness]

Hi Kevin,

I'd be happy to help -- I like the idea of JOSS. I'm on vacation for the
next 3 weeks though, so I wouldn't be able to get it done until ~mid
August. Let me know if that's ok for your timeline.

Ian

On Sun, Jul 16, 2017 at 7:02 PM, Kevin Mattheus Moerman <
[email protected]> wrote:

@demotu https://github.com/demotu @siboles https://github.com/siboles
@stavness https://github.com/stavness @melund
https://github.com/melund @jslee02 https://github.com/jslee02 I am
looking for an additional reviewer for this submission
https://github.com/csu-hmc/opty. Would you be interested in reviewing
this for JOSS http://joss.theoj.org/? The review guidelines are here
http://joss.theoj.org/about#reviewer_guidelines.

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[Kevin-Mattheus-Moerman]

Hey @stavness. Mid-August is fine. By then we'll hopefully have some comments from the first reviewer also. Enjoy your vacation.

[cybanical]

I've got a design review this week. Then I can take some time to getting the toolchain up and running.

[jslee02]

I'm currently in the middle of moving to a different city so my timeline would be similar to @stavness for settling down at the new place. If it's fine and still needs an additional reviewer, then I'd be happy to participate. Just let me know what you think.

[melund]

Hi @Kevin-Mattheus-Moerman. Sorry for slow reply. I am also on holiday at the moment. I see you got your second reviewer, but I don't mind helping out some other time if it is biomechanics related. Funny, I had just watched Kyles presentation on Scipy when I got this notification. JOSS is a much needed initiative.

[Kevin-Mattheus-Moerman]

@jslee02 @melund Thanks for getting back to me. It looks like most reviewers have vacation etc. so the mid-august time-line is fine. If this submission is of interest to you, and you have time, I would greatly appreciate if you could also help to review this submission. Our formal system handles 1 "official reviewer". But you can review by leaving comments here (i.e. based on the tick-marks at the top of this issue and http://joss.theoj.org/about#reviewer_guidelines).

[demotu]

Hi @Kevin-Mattheus-Moerman https://github.com/kevin-mattheus-moerman

Here is @demotu https://github.com/demotu. I also can review the
submission. This work interests to me so even if there are enough potential
reviewers, I will look at it.

-
Marcos Duarte
http://demotu.org/

On Sun, Jul 16, 2017 at 10:02 PM, Kevin Mattheus Moerman <
[email protected]> wrote:

@demotu https://github.com/demotu @siboles https://github.com/siboles
@stavness https://github.com/stavness @melund
https://github.com/melund @jslee02 https://github.com/jslee02 I am
looking for an additional reviewer for this submission
https://github.com/csu-hmc/opty. Would you be interested in reviewing
this for JOSS http://joss.theoj.org/? The review guidelines are here
http://joss.theoj.org/about#reviewer_guidelines.

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[Kevin-Mattheus-Moerman]

Excellent. Looking forward to seeing your comments.

[cybanical]

@moorepants Is this only working on a 32-bit install? I just did a fresh anaconda py3.6 64bit windows install and got this error:

PackageNotFoundError: Package missing in current win-64 channels:
  - opty

Also, windows anaconda is not aware of ipopt, cyipopt.
But, I realize it looks like i need to install ipopt separately. This requires cygwin or mingw, and a drawn out process.

Perhaps there could be a bit more clarity/handholding on windows based installation?

[moorepants]

@cybanical Thanks, but i do not support Windows at the moment. You can manually install ipopt and then cyipopt and it should work but I do not have the resources to get it working on windows (or providing instructions). I suggest using a linux VM or docker image and using the install instructions in the readme.

[cybanical]

@moorepants In that case it might make sense to explicitly state that windows is not supported, rather than give partial instructions for a windows installation - it'd save some headache.

[Kevin-Mattheus-Moerman]

@moorepants can you more clearly state if Windows is actively supported?
@cybanical will you still be able to review this submission? If needed I can provide you with a Linux environment for testing this software.

[Kevin-Mattheus-Moerman]

@stavness @jslee02 @melund @demotu we are getting close to mid-august :smile: I hope those who had a vacation had a good one. If you are still able, would you be willing to help review this submission? Thanks!

[moorepants]

I'm pretty sure that the software will work fine on Windows but have never tested it myself. The user would need to manually install all of the dependencies as per their Windows specific instructions. IPOPT, NumPy, SciPy, etc are not necessarily trivial to compile on Windows but one likely can find binaries. I'm happy to do bug fixes wrt to Windows but do not plan on developing installation instructions for all of the dependencies in the opty documentation, as this can be found in the respective packages' docs. I'm happy to make this clearer in the README.

[demotu]

I am reviewing this submission; it will be done by the weekend.

@demotu https://github.com/demotu

-
Marcos Duarte
http://demotu.org/

On Sat, Aug 12, 2017 at 11:05 PM, Kevin Mattheus Moerman <
[email protected]> wrote:

@stavness https://github.com/stavness @jslee02
https://github.com/jslee02 @melund https://github.com/melund @demotu
https://github.com/demotu we are getting close to mid-august 😄 I hope
those who had a vacation had a good one. If you are still able, would you
be willing to help review this submission? Thanks!

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[Kevin-Mattheus-Moerman]

Thanks @demotu you can leave review comments here. Alternatively you can open issues on the repository for this submission and refer to the issues here.

[stavness]

I installed the software and ran the examples. Everything went smoothly on
ubuntu. Will read the paper this week.

On Sun, Aug 20, 2017 at 8:17 PM Kevin Mattheus Moerman <
[email protected]> wrote:

Thanks @demotu https://github.com/demotu you can leave review comments
here. Alternatively you can open issues on the repository for this
submission https://github.com/csu-hmc/opty and refer to the issues here.

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[Kevin-Mattheus-Moerman]

@stavness Great, thanks Ian! Let me know if you have any comments on the other aspects, such as documentation (see tickmarks at the top of this issue).

[demotu]

I tested optpy https://github.com/csu-hmc/opty in a Linux machine (Ubuntu
64 bits with a conda installation of Python 3.6).
The examples ran fine, with the exception of the inverted_pendulum.py; I
opened an issue on its repo.
The software and the paper comply with all the JOSS guidelines (
http://joss.theoj.org/about#reviewer_guidelines).
The paper (a summary with a few lines) is in markdown format, not in PDF as
described in the JOSS guidelines, but this is not a problem.
My congratulations to the authors for the development of optpy.

I recommend optpy https://github.com/csu-hmc/opty for publication in JOSS.

regards,

-
Marcos Duarte
http://demotu.org/

On Sun, Aug 20, 2017 at 11:17 PM, Kevin Mattheus Moerman <
[email protected]> wrote:

Thanks @demotu https://github.com/demotu you can leave review comments
here. Alternatively you can open issues on the repository for this
submission https://github.com/csu-hmc/opty and refer to the issues here.

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[stavness]

Sorry is there also a paper, or just the git repo?

On Sun, Aug 20, 2017 at 8:47 PM, Kevin Mattheus Moerman <
[email protected]> wrote:

@stavness https://github.com/stavness Great, thanks Ian! Let me know if
you have any comments on the other aspects, such as documentation (see
tickmarks at the top of this issue).

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[Kevin-Mattheus-Moerman]

@stavness There is a paper.md file which will be rendered into a PDF later on. Since the software documentation/API etc contains most of the technical descriptions the papers in JOSS are very short (see also our paper guidelines).

[stavness]

Thanks for the clarification Kevin. Please find my review below.

The paper is missing a number of required components according to the JOSS
guidelines:

• A summary describing the high-level functionality and purpose of the
  software for a diverse, non-specialist audience
  — current summary is written in highly technical language, I suggest a lay
  introduction followed by a more detailed technical description of the
  software that includes equations to clarify what types of problems are
  applicable for the software
  — [optional] a full theory guide would be very beneficial for introducing
  the basic concepts of direct colocation. Although this type of information
  can be found in textbooks / papers (e.g. the Betts paper cited), but it can
  be very helpful to include it within the software paper, as the software
  authors typically have their own interpretation of the theory, and the
  equations can be better matched to the software implementation. For
  example, both FEBio and Simbody have excellent theory guides, which are
  arguably one of the main contributions of those works.

• A clear statement of need that illustrates the purpose of the software

• Motivation should be expanded, why is this software useful, what targeted
  applications?

• A list of key references including a link to the software archive

• References are not rendered in the paper.md file
• No link to software archive

• Other than Betts2010, the other citations appear to be just for
  dependencies. The paper should include citations to other software for
  direct colocation, and a comparison of feature sets, etc.

• Mentions (if applicable) of any ongoing research projects using the
  software or recent scholarly publications enabled by it

• Needs to be added

Software license:

• acceptable
  -
  Documentation:
• acceptable

API documentation

• acceptable

Tests

• acceptable — uses Travis-CI

Community guidelines

• Missing, should include:
  There should be clear guidelines for third-parties wishing to:
  Contribute to the software
  Report issues or problems with the software
  Seek support
  Examples

Functionality

• Installation and examples worked

On Tue, Aug 29, 2017 at 7:42 AM, Kevin Mattheus Moerman <
[email protected]> wrote:

@stavness https://github.com/stavness There is a paper.md file
https://github.com/csu-hmc/opty/blob/master/paper.md which will be
rendered into a PDF later on. Since the software documentation/API etc
contains most of the technical descriptions the papers in JOSS are very
short (see also our paper guidelines
http://joss.theoj.org/about#author_guidelines).

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[moorepants]

@stavness Thank you for the helpful review. We will work on addressing these items. They all seem reasonable, except for less-than-clear scope of a theory guide. I agree that the Simbody (have only read that one) guide is a top notch contribution, but that kind of guide seems to be an outlier. I've only seen that kind of detail in the most exceptional packages and it would take a large amount of time to create something similar. I'd rather cite textbooks/articles for this information and simply explain our implementation wrt to those. For example, I think the IPOPT software has a minimal explanation of the theory and cites the relevant literature, which I'd be more keen to replicate.

[stavness]

Yes I intended that as an optional suggestion. Definitely not required for
this publication. And the IPOPT approach would be fine too.

Congratulations on a nice piece of software!

On Tue, Aug 29, 2017 at 5:23 PM Jason K. Moore [e-mail]
wrote:

@stavness https://github.com/stavness Thank you for the helpful review.
We will work on addressing these items. They all seem reasonable, except
for less-than-clear scope of a theory guide. I agree that the Simbody (have
only read that one) guide is a top notch contribution, but that kind of
guide seems to be an outlier. I've only seen that kind of detail in the
most exceptional packages and it would take a large amount of time to
create something similar. I'd rather cite textbooks/articles for this
information and simply explain our implementation wrt to those. For
example, I think the IPOPT software has a minimal explanation of the theory
and cites the relevant literature, which I'd be more keen to replicate.

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[Kevin-Mattheus-Moerman]

@whedon assign @stavness as reviewer

[whedon]

OK, the reviewer is @stavness

[Kevin-Mattheus-Moerman]

@stavness I've spoken with @cybanical who was the primary reviewer here. He does not currently have time to continue this review so I kindly ask if you could take over. Essentially you should now be able to formally tick the boxes at the top of this review issue.

[stavness]

ok I've accepted the invitation

On Wed, Aug 30, 2017 at 10:24 AM, Kevin Mattheus Moerman <
[email protected]> wrote:

@stavness https://github.com/stavness I've spoken with @cybanical
https://github.com/cybanical who was the primary reviewer here. He does
not currently have time to continue this review so I kindly ask if you
could take over. Essentially you should now be able to formally tick the
boxes at the top of this review issue.

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[jslee02]

Sorry for the late response. Below is my review based on the template. There is only one missing component according to the JOSS guidelines.

Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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?
  
  
  
  • comment: The license is not being detected by Github. It would be nice to adjust LICENSE.txt so as to be displayed on the repository overview. (see: https://github.com/blog/2252-license-now-displayed-on-repository-overview)
  
  
• [x] Version: Does the release version given match the GitHub release (v0.2.0)?
• [x] Authorship: Has the submitting author (@moorepants) made major contributions to the software?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: Have any performance claims of the software been confirmed?

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?
• [ ] 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
  
  
  
  • comment: Missing. It would be great to have one. There is a useful instruction on the de facto standard way to add a contribution guideline: https://help.github.com/articles/setting-guidelines-for-repository-contributors/.
  
  

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)?
  
  
  
  • comment: Nitpick: According to the author guidelines of JOSS, it seems paper.bib is the recommended name for the file. Is there a reason that joss.bib was used instead?
  
  

Minor comments

• The link at the top of the repository is http://hmc.csuohio.edu that I believe that it refers to the associated lab's website rather than the software's website. At first, I thought this is because the software website is missing but later found the link to it in README.md that is http://opty.readthedocs.io/. It would be great to put the link to the software website at the top of the repository, which is meant to be used so, and move the link to the lab website to somewhere else.
• All the examples worked on macOS Sierra except examples/inverted_pendulum printing:

$ python pendulum.py
Traceback (most recent call last):
  File "pendulum.py", line 48, in <module>
    import simulate
  File "/Users/jeongseoklee/dev/opty/examples/inverted_pendulum/simulate.py", line 10, in <module>
    from pydy.codegen.code import generate_ode_function
ModuleNotFoundError: No module named 'pydy.codegen.code'

[Kevin-Mattheus-Moerman]

@whedon assign @stavness as reviewer

[whedon]

OK, the reviewer is @stavness

[Kevin-Mattheus-Moerman]

@stavness sorry I assigned you again since I did not you see you assigned at the top here.

[Kevin-Mattheus-Moerman]

@moorepants were you able to address @stavness comments?

@stavness Are you able to tick some of the boxes at the top of this issue?

@jslee02 thanks for your review! @moorepants can you address these comments as well?

[moorepants]

I am planning to address the comments. I have been bogged down with hosting a conference and then prepping two new courses. Things should calm down soon. Thanks for the reminder.

[Kevin-Mattheus-Moerman]

@moorepants great. Thanks for the update.

[moorepants]

A couple of questions:

• What is the recommended way to put tables in the paper.md file?
• How do we check that the bibliography renders correctly?

[arfon]

@moorepants - the command we run is here: https://github.com/openjournals/whedon/blob/master/lib/whedon/processor.rb#L173

How do we check that the bibliography renders correctly?

Looks like there's a small issue with your bibliography:

pandoc-citeproc: reference Watcher2006 not found

What is the recommended way to put tables in the paper.md file?

I'm not sure sorry but the current table looks a bit wonky: 10.21105.joss.00300.pdf

Do any of the @openjournals/joss-editors know how to fix this?

[moorepants]

I wasn't sure if there was a spec for making tables in markdown so I made an restructuredtext table and just wrapped it in markdown literal ticks for the time being. I knew it would render as is.

Is there a simple way to run that command on my computer? I'm not familiar with Ruby.

[Kevin-Mattheus-Moerman]

@arfon obviously we could use Markdown, HTML, or LATEX tables. But I'm not sure how the process of creating the PDF handles these. Does normal Markdown table stuff work?

| Tables | Are | Cool |
| ------------- |:-------------:| -----:|
| col 3 is | right-aligned | Nice |
| col 2 is | centered | Fits well |
| zebra stripes | are neat | 3.14159265359 |

[moorepants]

So Github flavored markdown has the table support that you show above: https://help.github.com/articles/organizing-information-with-tables/, but this isn't in all markdown flavors. It isn't clear to me in the ruby code which flavor of markdown is being used. Pandoc can process a number of them apparently.

[arfon]

Is there a simple way to run that command on my computer? I'm not familiar with Ruby.

      `cd #{paper_directory} && pandoc \
      -V repository="#{repository_address}" \
      -V archive_doi="#{archive_doi}" \
      -V paper_url="#{paper_url}" \
      -V formatted_doi="#{formatted_doi}" \
      -V review_issue_url="#{review_issue_url}" \
      -V graphics="true" \
      -V issue="#{paper_issue}" \
      -V volume="#{paper_volume}" \
      -V page="#{review_issue_id}" \
      -V joss_logo_path="#{Dir.pwd}/resources/joss-logo.png" \
      -V year="#{paper_year}" \
      -V formatted_doi="#{formatted_doi}" \
      -V citation_author="#{citation_author}" \
      -V paper_title="#{paper_title}" \
      -S -o #{filename_doi}.pdf -V geometry:margin=1in \
      --latex-engine=xelatex \
      --filter pandoc-citeproc #{File.basename(paper_path)} \
      --template #{latex_template_path}

The command above is just passing a bunch of variables in but it's a normal(ish) pandoc command so if you have pandoc installed locally you should be able to do something like:

pandoc  -S -o paper.pdf --latex-engine=xelatex --filter pandoc-citeproc paper.md --template latex.template 

...where the latex.template is this file. I'm also happy to try compiling the document a few times with you if you want to debug this here. In the future we plan to give @whedon the ability to compile the PDF on demand for you.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/10.21105.joss.00300.pdf

[moorepants]

That's cool! FYI, still working on the review. I have a few more issues to close, just don't have time at the moment. Maybe I can finish over our Thanksgiving break.

[Kevin-Mattheus-Moerman]

@moorepants Cool eh :smile: btw, in your paper one reference shows ???, it is @Watcher2006 should that be @Wachter2006?

[Kevin-Mattheus-Moerman]

@moorepants thanks for the update. Let me know when we can resume review.

[Kevin-Mattheus-Moerman]

@moorepants any updates to present? It would be good to keep going here.

[Kevin-Mattheus-Moerman]

@stavness Are you able to start ticking some of the boxes at the top of this review issue?

[stavness]

I'm waiting for the revised version, and then I'll look at that time.

On Mon, Jan 8, 2018 at 10:33 AM, Kevin Mattheus Moerman <
[email protected]> wrote:

@stavness https://github.com/stavness Are you able to start ticking
some of the boxes at the top of this review issue?

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[moorepants]

I apologize, my revision stalled due to other priorities. This is near the top of my task list, so I except to finalize this month.

[Kevin-Mattheus-Moerman]

@moorepants great. Thanks for the update.

[moorepants]

We have made all of the changes requested by the reviewers. You can see an issue for each reviewer comment here:

https://github.com/csu-hmc/opty/issues?q=is%3Aissue+is%3Aclosed+label%3Ajoss

And pull requests that close all of these issues here:

https://github.com/csu-hmc/opty/pulls?q=is%3Apr+is%3Aclosed+label%3Ajoss

I have not made a new release of opty yet, so testing from the master branch is required. I would prefer to make the release after the review is done so that I can incorporate all of the changes into the release.

The documentation reflects the master branch:

http://opty.readthedocs.io/en/latest/

Thanks for your patience.

cc @tvdbogert

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #300 with the following error: 

   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    12    0    12    0     0     40      0 --:--:-- --:--:-- --:--:--    40
Error reading bibliography ./paper.bib (line 317, column 100):
unexpected "."
expecting white space, "#", "," or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

Editors, I switched to an HTML table in the markdown file since HTML can be put into markdown files but the PDF does not render the table correctly. Any suggestions on getting a table in the paper?

[Kevin-Mattheus-Moerman]

@arfon any suggestions for @moorepants?

[arfon]

Not really sorry. @karthik - your Markdown-fu exceeds that of most - any ideas here?

[Kevin-Mattheus-Moerman]

@moorepants @arfon I tested the local paper build myself. I was able to get it to create markdown based tables without any issues. What was your issue? Do you perhaps have a table syntax error somewhere?

I did notice that your particular table will spill beyond the margins using pandoc (for both HTML and markdown). Here is a link to how to create tables in pandoc markdown. HTML is not listed there and I could not get that to work.

Is it an idea to render a picture of the table in the right layout and to render the image in markdown instead instead? I suppose the references would not show up.... sigh... this is difficult!

[arfon]

I wonder if we could put the table on its own page and hack the LaTeX template to make this happen. Some ideas here: https://stackoverflow.com/questions/25849814/rstudio-rmarkdown-both-portrait-and-landscape-layout-in-a-single-pdf

[karthik]

@arfon I don't have a good solution unfortunately. :(

[moorepants]

Is it possible to use the markdown "grid-tables" extension? I already have the table typed up like that. If not I can try converting the first table option on the pandoc markdown documentation.

[arfon]

Is it possible to use the markdown "grid-tables" extension? I already have the table typed up like that. If not I can try converting the first table option on the pandoc markdown documentation.

Sure thing. Let's give that a go. Are those commits in master?

[moorepants]

No, I will need to reformat the table. Will work on it.

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

I have updated the paper.md file to make use of the footnotes and grid-tables extensions listed here:

https://pandoc.org/MANUAL.html

[moorepants]

It is close now. Is it possible to choose a smaller font for the table? This is possible in LaTeX.

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[Kevin-Mattheus-Moerman]

Sorry I'm not sure how to change the font locally. @arfon @karthik any ideas?

[moorepants]

I just found this: https://pandoc.org/MANUAL.html#extension-raw_tex

It may be easier to just write the document in LaTeX using this extension. I'll give it a try too. I haven't been able to figure out how to manipulate the font size of the table using markdown.

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00300/joss.00300/10.21105.joss.00300.pdf

[moorepants]

The table fits now. It isn't perfect but it is too difficult to try to fine tune it via markdown and limited control of the LaTeX source. We can go with this.

[arfon]

OK thanks @moorepants. @Kevin-Mattheus-Moerman - is this submission good to accept now? The checklist at the top of the review isn't filled but it sounds like we might be done based on other comments in the thread.

[stavness]

Looks great!. I went through the checklist and checked all the boxes.

On Tue, Jan 30, 2018 at 5:35 AM, Arfon Smith [e-mail]
wrote:

OK thanks @moorepants https://github.com/moorepants.
@Kevin-Mattheus-Moerman https://github.com/kevin-mattheus-moerman - is
this submission good to accept now? The checklist at the top of the review
isn't filled but it sounds like we might be done based on other comments in
the thread.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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or mute the thread
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.

[Kevin-Mattheus-Moerman]

Awesome! Thanks for the review @stavness 🚀 🎉
@demotu @jslee02 thank you as well for your comments!

[Kevin-Mattheus-Moerman]

@moorepants can you provide a DOI of the reviewed software (e.g. through Zenodo)? Then @arfon can proceed to formally accept this submission.

[moorepants]

I will package a new release of the software, push to PyPi, conda, and then Zenodo for archival purposes. Note that the version number will go up.

Do we not need to get @jslee02 @cybanical and @demotu's final approval? I addressed comments from all of them in the new version.

[moorepants]

I've pushed version 1.0.0 to Zenodo:

DOI: 10.5281/zenodo.1162870

https://zenodo.org/record/1162870

[arfon]

@whedon set 10.5281/zenodo.1162870 as archive

[whedon]

OK. 10.5281/zenodo.1162870 is the archive.

[arfon]

@stavness @demotu - many thanks for your reviews here and to @Kevin-Mattheus-Moerman for editing this submission ✨

@moorepants - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00300 ⚡️ 🚀 💥

[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 snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00300/status.svg)](https://doi.org/10.21105/joss.00300)

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html

[moorepants]

Thanks everyone. I appreciate the time and effort spent on reviewing this.