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[PRE REVIEW]: PolaronMobility.jl: Implementation of the Feynman variational polaron model #444

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whedon opened this Issue Oct 29, 2017 · 36 comments

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whedon commented Oct 29, 2017

Submitting author: @jarvist (Jarvist Moore Frost)
Repository: https://github.com/jarvist/PolaronMobility.jl
Version: ArXiv-v4
Editor: @lheagy
Reviewer: @yxqd

Author instructions

Thanks for submitting your paper to JOSS @jarvist. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@jarvist if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

@whedon whedon added the pre-review label Oct 29, 2017

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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

@whedon commands
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whedon commented Oct 29, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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

@whedon commands
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jarvist commented Oct 29, 2017

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Here are some things you can ask me to do:

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whedon commented Oct 29, 2017

Here are some things you can ask me to do:

# List all of Whedon's capabilities
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# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
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# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
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# Set the software archive DOI at the top of the issue e.g.
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# Open the review issue
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🚧 Important 🚧

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

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From your list of available reviewers:
@jochym and @khinsen both have more than sufficient electronic structure background to understand where these codes are coming from, but do not list any Julia experience. The codes aren't that complex, or use that specific language features (metaprogramming etc.), but it might be nice to have some expertise & feedback from scientific Julia users, in how to (re)structure the package.

@bjmorgan also has the scientific background -- but I know him & we're both employees at the University of Bath!

Of the reviewers who indicate Julia familiarity, perhaps @lheagy is the closest in scientific overlap.

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jarvist commented Oct 29, 2017

From your list of available reviewers:
@jochym and @khinsen both have more than sufficient electronic structure background to understand where these codes are coming from, but do not list any Julia experience. The codes aren't that complex, or use that specific language features (metaprogramming etc.), but it might be nice to have some expertise & feedback from scientific Julia users, in how to (re)structure the package.

@bjmorgan also has the scientific background -- but I know him & we're both employees at the University of Bath!

Of the reviewers who indicate Julia familiarity, perhaps @lheagy is the closest in scientific overlap.

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arfon Dec 9, 2017

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@lheagy - would you be willing to edit this submission for JOSS?

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arfon commented Dec 9, 2017

@lheagy - would you be willing to edit this submission for JOSS?

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lheagy Dec 11, 2017

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@arfon, @jarvist: this is outside of my background, but I am happy to help.

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lheagy commented Dec 11, 2017

@arfon, @jarvist: this is outside of my background, but I am happy to help.

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arfon Dec 11, 2017

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@lheagy - many thanks. Perhaps we could try and find two reviewers here?

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arfon commented Dec 11, 2017

@lheagy - many thanks. Perhaps we could try and find two reviewers here?

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@whedon assign @lheagy as editor

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arfon commented Dec 11, 2017

@whedon assign @lheagy as editor

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OK, the editor is @lheagy

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whedon commented Dec 11, 2017

OK, the editor is @lheagy

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@jarvist: I have looked through the paper and briefly through your software. I have a couple suggestions before we send it out for review.

Paper

  • the paper is quite technical, do you have a couple examples or applications you could discuss briefly in order to reach a wider audience?
  • you can remove the "Spiel from original website below"
  • citations should be in square brackets (eg.
This package is an implementation in the Julia programming language of solving
the Feynman [@Feynman1955]

Software

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lheagy commented Dec 11, 2017

@jarvist: I have looked through the paper and briefly through your software. I have a couple suggestions before we send it out for review.

Paper

  • the paper is quite technical, do you have a couple examples or applications you could discuss briefly in order to reach a wider audience?
  • you can remove the "Spiel from original website below"
  • citations should be in square brackets (eg.
This package is an implementation in the Julia programming language of solving
the Feynman [@Feynman1955]

Software

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jarvist Dec 12, 2017

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Thanks for the feedback! I'll try and get those edits done today or tomorrow, before it's sent out.

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jarvist commented Dec 12, 2017

Thanks for the feedback! I'll try and get those edits done today or tomorrow, before it's sent out.

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lheagy Dec 19, 2017

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Hi @jarvist: just checking in. Please ping when you are happy with your edits

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lheagy commented Dec 19, 2017

Hi @jarvist: just checking in. Please ping when you are happy with your edits

jarvist added a commit to jarvist/PolaronMobility.jl that referenced this issue Dec 20, 2017

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Thanks for the timely reminder :^)

Had to have a read about before getting CI working.

I hope I've made the text a little bit more approachable.

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jarvist commented Dec 20, 2017

Thanks for the timely reminder :^)

Had to have a read about before getting CI working.

I hope I've made the text a little bit more approachable.

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lheagy Dec 29, 2017

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Thanks @jarvist: I had a look and the paper and it doesn't look like the most recent changes have made it to your master branch (the last update was October). Is it on a branch somewhere? Thanks!

image

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lheagy commented Dec 29, 2017

Thanks @jarvist: I had a look and the paper and it doesn't look like the most recent changes have made it to your master branch (the last update was October). Is it on a branch somewhere? Thanks!

image

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jarvist Jan 5, 2018

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My apologies! I had managed to confuse myself + ended up tidying the README instead of the JOOS paper.
I've applied edits as suggested & tried to write a more lay-person introduction.

jarvist/PolaronMobility.jl@215cc55

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jarvist commented Jan 5, 2018

My apologies! I had managed to confuse myself + ended up tidying the README instead of the JOOS paper.
I've applied edits as suggested & tried to write a more lay-person introduction.

jarvist/PolaronMobility.jl@215cc55

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lheagy Jan 7, 2018

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@whedon generate pdf

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lheagy commented Jan 7, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 7, 2018

Attempting PDF compilation. Reticulating splines etc...
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PDF failed to compile for issue #444 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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    15    0    15    0     0     70      0 --:--:-- --:--:-- --:--:--    70
Error reading bibliography ./paper.bib (line 9, column 25):
unexpected "}"
expecting white space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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whedon commented Jan 7, 2018

PDF failed to compile for issue #444 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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    15    0    15    0     0     70      0 --:--:-- --:--:-- --:--:--    70
Error reading bibliography ./paper.bib (line 9, column 25):
unexpected "}"
expecting white space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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lheagy Jan 7, 2018

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Thanks @jarvist, the text looks good. There is an issue with the bibliography when trying to generate the pdf - do you need the citation on line 9 at the moment? It doesn't look like you reference it, so we could potentially remove it for now?

How are things going with getting the testing up and running?

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lheagy commented Jan 7, 2018

Thanks @jarvist, the text looks good. There is an issue with the bibliography when trying to generate the pdf - do you need the citation on line 9 at the moment? It doesn't look like you reference it, so we could potentially remove it for now?

How are things going with getting the testing up and running?

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Ok, I've removed the blank reference.

Travis CI is setup, but the builds sometimes fail due to reasons outside my control - often that Travis fails to get a fresh copy of Julia!

I'll see if I can restrict the architectures it tries on;
https://travis-ci.org/jarvist/PolaronMobility.jl/jobs/325561158

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jarvist commented Jan 9, 2018

Ok, I've removed the blank reference.

Travis CI is setup, but the builds sometimes fail due to reasons outside my control - often that Travis fails to get a fresh copy of Julia!

I'll see if I can restrict the architectures it tries on;
https://travis-ci.org/jarvist/PolaronMobility.jl/jobs/325561158

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As this submission is outside my domain, I would like to find 2 reviewers.

@tacaswell, @khinsen, @betatim, @jochym - would any of you be willing to review this submission for JOSS? You can read more about the process here http://joss.theoj.org/about#reviewer_guidelines, and feel free to ping with questions!

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lheagy commented Jan 11, 2018

As this submission is outside my domain, I would like to find 2 reviewers.

@tacaswell, @khinsen, @betatim, @jochym - would any of you be willing to review this submission for JOSS? You can read more about the process here http://joss.theoj.org/about#reviewer_guidelines, and feel free to ping with questions!

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👋 Hi @tacaswell, @khinsen, @betatim, @jochym - would any of you be willing to review this submission for JOSS?

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lheagy commented Jan 21, 2018

👋 Hi @tacaswell, @khinsen, @betatim, @jochym - would any of you be willing to review this submission for JOSS?

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@jarvist: just a quick update for you, I have sent out emails to potential reviewers and am waiting to hear back. I will keep you posted.

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lheagy commented Jan 26, 2018

@jarvist: just a quick update for you, I have sent out emails to potential reviewers and am waiting to hear back. I will keep you posted.

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Hi @dean0x7d, @ajgpitch, would you be willing to review this submission on PolaronMobility.jl for JOSS? JOSS is a 'developer friendly' journal. That is, we focus on the software as a scientific contribution. If the submitting authors have followed best practices (have documentation, tests, continuous integration, and a license) then their review should be straight-forward. There are more details on reviewing with JOSS here: http://joss.theoj.org/about#reviewer_guidelines

With your background in solid state physics, I would greatly appreciate your input!

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lheagy commented Jan 29, 2018

Hi @dean0x7d, @ajgpitch, would you be willing to review this submission on PolaronMobility.jl for JOSS? JOSS is a 'developer friendly' journal. That is, we focus on the software as a scientific contribution. If the submitting authors have followed best practices (have documentation, tests, continuous integration, and a license) then their review should be straight-forward. There are more details on reviewing with JOSS here: http://joss.theoj.org/about#reviewer_guidelines

With your background in solid state physics, I would greatly appreciate your input!

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👋 Hi, @yxqd, would you be willing to review this submission?

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lheagy commented Jan 31, 2018

👋 Hi, @yxqd, would you be willing to review this submission?

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@lheagy Yes I can help

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yxqd commented Jan 31, 2018

@lheagy Yes I can help

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Thanks @yxqd, as this is outside of my domain of expertise, I would like to find one more reviewer. I am still waiting to hear back from @tacaswell, @betatim and @dean0x7d to see if they are willing (I sent emails as well)

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lheagy commented Jan 31, 2018

Thanks @yxqd, as this is outside of my domain of expertise, I would like to find one more reviewer. I am still waiting to hear back from @tacaswell, @betatim and @dean0x7d to see if they are willing (I sent emails as well)

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ok, well lets get started on the review with @yxqd as lead and we can see if someone else is willing to help out once things are in motion

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lheagy commented Feb 1, 2018

ok, well lets get started on the review with @yxqd as lead and we can see if someone else is willing to help out once things are in motion

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@whedon commands

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lheagy commented Feb 1, 2018

@whedon commands

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Here are some things you can ask me to do:

# List all of Whedon's capabilities
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# Assign a GitHub user as the reviewer of this submission
@whedon assign @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
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# Compile the paper
@whedon generate pdf

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whedon commented Feb 1, 2018

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

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

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@whedon assign @yxqd as reviewer

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lheagy commented Feb 1, 2018

@whedon assign @yxqd as reviewer

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OK, the reviewer is @yxqd

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whedon commented Feb 1, 2018

OK, the reviewer is @yxqd

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@whedon start review

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lheagy commented Feb 1, 2018

@whedon start review

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You didn't say the magic word! Try this:

@whedon start review magic-word=bananas
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whedon commented Feb 1, 2018

You didn't say the magic word! Try this:

@whedon start review magic-word=bananas
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@whedon start review magic-word=bananas

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lheagy commented Feb 1, 2018

@whedon start review magic-word=bananas

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OK, I've started the review over in #566. Feel free to close this issue now!

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whedon commented Feb 1, 2018

OK, I've started the review over in #566. Feel free to close this issue now!

@lheagy lheagy closed this Feb 1, 2018

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