THzTools submission

[jsdodge]

Submitting Author: (@jsdodge)
All current maintainers: (@jsdodge)
Package Name: THzTools
One-Line Description of Package: Data analysis software tools for terahertz time-domain spectroscopy (THz-TDS)
Repository Link: https://github.com/dodge-research-group/thztools
Version submitted: 0.5.4
EiC: @cmarmo
Editor:@banesullivan
Reviewer 1: @frank1010111
Reviewer 2: @Romain-Peretti
Archive:
JOSS DOI:
Version accepted: 0.5.5
Date accepted (month/day/year): 11/22/2024

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Description

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THzTools provides tools to simplify and improve procedures for data analysis in terahertz time-domain spectroscopy (THz-TDS). Some of the methods included in the package were described previously in the paper at this link. As the name suggests, terahertz time-domain spectroscopy involves measurements of terahertz-frequency electromagnetic waveforms that are are acquired as a function of time. A variety of methods exist to transform these measurements into functions of frequency, but the standard procedures have several pitfalls. THzTools provides software tools that make it easier for researchers to use the best available methods for analyzing their data.

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  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
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  • Who is the target audience and what are scientific applications of this package?
    The target audience is researchers working with THz-TDS, although the procedures may be useful in other areas that use time-domain measurement systems. The package is designed for characterizing the time-domain noise performance of THz-TDS measurement systems and for analyzing the results from these systems in the frequency domain.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ?
    The Fit-TDS package provides a graphical user interface that simplifies THz-TDS data analysis with standard analysis methods. THzTools focuses on lower-level statistical procedures, and implements algorithms that are not available in Fit-TDS.

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[cmarmo]

Hello @jsdodge ! Thank you for submitting THzTools to pyOpenSci.
Sorry for the delay of my answer!
I'm Chiara and I'm going to take care of your submission for the initial editorial checks.
I will be back to you by the end of the week.
Thanks for your patience!

[jsdodge]

Hi Chiara,

Thanks for the update on the timeline. Do you have any suggestions for ways that we can continue development without disrupting the review? Would it be ok, for example, to continue developing on the dev branch as long as we don't merge these into the main branch?

[cmarmo]

Do you have any suggestions for ways that we can continue development without disrupting the review? Would it be ok, for example, to continue developing on the dev branch as long as we don't merge these into the main branch?

I'm starting the editorial checks right now: I can perform them on the main branch if you prefer, once we agree on a version to be submitted you can tag the last modifications and we can update the description of the issue. Would that be ok for you?

[cmarmo]

Editor in Chief checks

Hi @jsdodge ! Thank you again for submitting your package for pyOpenSci review.
Below are the basic checks that your package needs to pass to begin our review.
If some of these are missing, we will ask you to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements
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• Initial onboarding survey was filled out
  We appreciate each maintainer of the package filling out this survey individually. 🙌
  Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌

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Editor comments

THzTools is in excellent shape, congratulations!
I have some minor comments before starting looking for an editor:

• in the README.md file installation and development instructions are missing: a simple pip install and/or conda install will be enough (this explicits the fact that the package is available from both the channels), and then links to installation and development pages in the documentation.
• the CONTRIBUTING.md file is missing: do you mind adding it with some basic instructions and a link to the contribuuting section in the documentation?
• I noticed that in the issue template for bug reports the explanation says "help us improve SciPy" ... 😁

Do you have any suggestions for ways that we can continue development without disrupting the review? Would it be ok, for example, to continue developing on the dev branch as long as we don't merge these into the main branch?

I'm starting the editorial checks right now: I can perform them on the main branch if you prefer, once we agree on a version to be submitted you can tag the last modifications and we can update the description of the issue. Would that be ok for you?

I realize my answer was a bit out of scope... sorry for that. Indeed, I believe it is a good idea to continue the development in a separate branch during review: however, reviewers might ask for modifications too and everything would in principle end in a new version accepted at the end of the review process. Please just clarify with reviewers in which branch you are addressing their comments, we had some misunderstanding in the past.

[jsdodge]

Hi Chiara,

Thanks! We can add installation instructions to the README.md file and change the issue template right away. This raises a similar question to my earlier one: should we do this in the main branch? Normally we would also bump the version number when making changes in main, but the submission version is listed as v0.5.0.

Regarding the CONTRIBUTING.md file, we have a contributing.rst file in /docs/source/. Could you recommend a way to include this information at the top level in a CONTRIBUTING.md file and in the documentation without duplicating it? A related question is whether we can do the same thing with the CODE_OF_CONDUCT.md file. Currently we just have a GitHub link to CODE_OF_CONDUCT.md in contributing.rst, but it would be better to include it directly in the documentation. We used a link because we didn't know how to use ReST to pull it into the documentation source.

[cmarmo]

Thanks! We can add installation instructions to the README.md file and change the issue template right away. This raises a similar question to my earlier one: should we do this in the main branch? Normally we would also bump the version number when making changes in main, but the submission version is listed as v0.5.0.

Technically the review is not started yet: once done with the changes we can edit the issue description.

Regarding the CONTRIBUTING.md file, we have a contributing.rst file in /docs/source/. Could you recommend a way to include this information at the top level in a CONTRIBUTING.md file and in the documentation without duplicating it?

Some general information would be enough in the CONTRIBUTING.md file: a link to contributing.rst there will complete the instructions. See for example what is done in one of the previously accepted packages.

A related question is whether we can do the same thing with the CODE_OF_CONDUCT.md file. Currently we just have a GitHub link to CODE_OF_CONDUCT.md in contributing.rst, but it would be better to include it directly in the documentation. We used a link because we didn't know how to use ReST to pull it into the documentation source.

Your solution is fine with our standards: if you prefer to have the code of conduct in the documentation then you can use the same approach suggested for the CONTRIBUTING.md file and link the documentation reference inside.

[jsdodge]

I just released THzTools v0.5.1 with the changes that you requested. I've also updated the version number in the submission documentation.

[cmarmo]

Thank you @jsdodge ! Time for me to look for an editor!