THzTools submission

[jsdodge]

Submitting Author: (@jsdodge)
All current maintainers: (@jsdodge)
Package Name: THzTools
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: TBD
Version accepted: 0.5.5
Date accepted (month/day/year): 11/22/2024

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Description

• Include a brief paragraph describing what your package does:

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.

Scope

• Please indicate which category or categories.
  Check out our package scope page to learn more about our
  scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization¹
  • Workflow automation
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  • Scientific software wrappers
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• Geospatial
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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
below.

• Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
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• Fit The package meets criteria for fit and overlap.
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  • API documentation (documentation for your code's functions, classes, methods and attributes): this includes clearly written docstrings with variables defined using a standard docstring format.
• Core GitHub repository Files
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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!

[jsdodge]

Hi @cmarmo, I have just updated the submission with the latest release, v0.5.2.

Could you please update me on the editor search?

[cmarmo]

Thank you @jsdodge for the follow-up

Could you please update me on the editor search?

I'm sorry to say that I am still looking... I guess the end of summer plus the beginning of the academic year are not making things easier.... thanks for your patience!

[lwasser]

@cmarmo thank you so much for leading the pre-checks for this package!! @jsdodge we just have had a rotation for our EiC (we do this every 3 months). To help us get caught up, I was able to find an editor from our team to take on this package! @banesullivan !! The next step here is to find reviewers. Do you have any reviewers in mind that we could reach out to? This area if quite specific and we'd like to have atleast one person with domain expertise, involved in the review. many thanks for your patience!

[jsdodge]

Thanks @lwasser ! And hello @banesullivan . We look forward to working with you on the review.

Would it be possible for us to contact potential reviewers privately before suggesting them to you? I'm hesitant to list people publicly here without consulting them first.

[lwasser]

@jsdodge of course. I think reaching out to them privately is ideal. Normally we allow one suggestion from the author(s) and then we will try to find a second. The second reviewer can be more generally focused on packaging/usability. Finding reviewers has taken some time lately.

[jsdodge]

Hi @lwasser and @banesullivan , Romain Peretti (ORCID) has kindly agreed to help with the review. He leads the @THzbiophotonics group at CNRS in Lille, France. Please let me know if you need further help with the review.

[lwasser]

@jsdodge this is great. I'll leave a few notes and then will let @banesullivan step in. We may have a second reviewer. In the meantime, does Romain have a GitHub handle so we can add them to this issue? The review will happen fully in this issue with links to any issues or pr's opened of course!

[jsdodge]

Thank you, @lwasser , I'm glad that you may have found a second reviewer. I believe that Romain's GitHub handle is @THzbiophotonics, but I'll check.

[jsdodge]

Hello, please use the GitHub handle @Romain-Peretti for Romain. Thanks!

[banesullivan]

Hi @jsdodge, apologies for my delay, been on vacation for a bit. I will double check everything above and then I'll update on next steps this weekend! Thanks for your patience!

[banesullivan]

Hi @jsdodge, this has come together fantastically! It looks like both @frank1010111 and @Romain-Peretti have checked everything off and are recommending approval (such a quick turn around is a first for me 🎉 ). @frank1010111 and @Romain-Peretti, thank you for your time and effort on these thoughtful reviews!

Aside: apologies for my delay!! Life happened and before I knew it 2 weeks went by. So sorry about that!

A few quick questions before I post the review acceptance and update the metadata in the original post at the top of this thread:

1. The only item left unchecked was in @Romain-Peretti's review (follows). I'm curious if this is something you wish/hope to address or not? With hyper specific scientific tooling like this, my impression is that the available tooling is limited so I understand if there isn't much to compare it to.

   If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.

2. Is version 0.5.4 the version you'd like to be associated with release or are there any developments from this review that have not yet been released?
3. Similarly, do you have a Zendo version and DOI for this as well?

Otherwise, I'm ready to accept THzTools and I'll start double checking everything for the JOSS automatic submission you've opted for.

Excellent work @jsdodge!!

[jsdodge]

Thank you, @banesullivan !

In response to your first question, we included the following list of related projects in the README.

• https://github.com/dotTHzTAG/CaTSper
• https://github.com/THzbiophotonics/Fit-TDS
• https://github.com/YaleTHz/nelly
• https://github.com/puls-lab/phoeniks

All of these projects except Phoeniks have publications associated with them, which we cite in the JOSS paper in the same order as they appear above:

To support this mode of analysis, the THzTools package provides functionality and documentation that are unavailable in existing THz-TDS analysis software (Lee et al., 2023; Peretti et al., 2019; Tayveh et al., 2021).

In response to your other questions,
2. I just bumped the version to 0.5.5, so please use that.
3. The Zenodo DOI is 10.5281/zenodo.13955913.

[banesullivan]

Excellent! Thank you for clarifying the related projects for me and thank you for issue the 0.5.5 release. i'll update the top level post with these details

[banesullivan]

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🎉 With that, THzTools has been approved by pyOpenSci! Thank you @jsdodge for submitting THzTools and many thanks to @frank1010111 and @Romain-Peretti for reviewing this package! 😸

Author Wrap Up Tasks

There are a few things left to do to wrap up this submission, @jsdodge:

• Activate Zenodo, but specificly make sure to watch the repo if you haven't already done so.
• Tag and create a release to create a Zenodo version and DOI.
• Add the badge for pyOpenSci peer-review to the README.md of THzTools. The badge should be [![pyOpenSci Peer-Reviewed](https://pyopensci.org/badges/peer-reviewed.svg)](https://github.com/pyOpenSci/software-review/issues/209).
• Please fill out the post-review survey. All maintainers and reviewers should fill this out.

You're opting to submit this package to JOSS. Here are the next steps:

• @banesullivan: Once the JOSS issue is opened for the package, we strongly suggest that you subscribe to issue updates. This will allow you to continue to update the issue labels on this review as it goes through the JOSS process.
• Login to the JOSS website and fill out the JOSS submission form using your Zenodo DOI. When you fill out the form, be sure to mention and link to the approved pyOpenSci review. JOSS will tag your package for expedited review if it is already pyOpenSci approved.
• Wait for a JOSS editor to approve the presubmission (which includes a scope check).
• Once the package is approved by JOSS, you will be given instructions by JOSS about updating the citation information in your README file.
• When the JOSS review is complete, add a comment to your review in the pyOpenSci software-review repo here that it has been approved by JOSS. An editor will then add the JOSS-approved label to this issue.

🎉 Congratulations! You are now published with both JOSS and pyOpenSci! 🎉

Editor Final Checks

These are for me, @banesullivan:

Please complete the final steps to wrap up this review. Editor, please do the following:

• Make sure that the maintainers filled out the post-review survey
• Invite the maintainers to submit a blog post highlighting their package. Feel free to use / adapt language found in this comment to help guide the author.
• Change the status tag of the issue to 6/pyOS-approved6 🚀🚀🚀.
• Invite the package maintainer(s) and both reviewers to slack if they wish to join.
• If the author submits to JOSS, please continue to update the labels for JOSS on this issue until the author is accepted (do not remove the 6/pyOS-approved label). Once accepted add the label 9/joss-approved to the issue. Skip this check if the package is not submitted to JOSS.
• If the package is JOSS-accepted please add the JOSS doi to the YAML at the top of the issue.

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If you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and documentation in the peer-review-guide.

[banesullivan]

@jsdodge, @Romain-Peretti, @frank1010111: would you each please fill out the post-review survey

[banesullivan]

@jsdodge, I like to invite you to write a blog post (totally optional) on THzTools for us to promote your work! if you are interested - here are a few examples of other blog posts:

• pandera
• movingpandas

and here is a markdown example that you could use as a guide when creating your post.

iIt can even be a tutorial like post that highlights what your package does. Then we can share it with people to get the word out about THzTools.

If you are too busy for this no worries. But if you have time - we'd love to spread the word about your package!

[jsdodge]

Thanks, @banesullivan, and everyone who helped with the review! I'll respond to your requests ASAP.

[jsdodge]

Thanks again, @banesullivan ! Please see my responses below.

• Activate Zenodo, but specificly make sure to watch the repo if you haven't already done so.

I assume you mean here that I have turned on GitHub integration for the repository? If so, then yes, that is on.

• Tag and create a release to create a Zenodo version and DOI.
• Add the badge for pyOpenSci peer-review to the README.md of THzTools. The badge should be [![pyOpenSci Peer-Reviewed](https://pyopensci.org/badges/peer-reviewed.svg)](https://github.com/pyOpenSci/software-review/issues/209).
• Please fill out the post-review survey. All maintainers and reviewers should fill this out.

You're opting to submit this package to JOSS. Here are the next steps:

• @banesullivan: Once the JOSS issue is opened for the package, we strongly suggest that you subscribe to issue updates. This will allow you to continue to update the issue labels on this review as it goes through the JOSS process.
• Login to the JOSS website and fill out the JOSS submission form using your Zenodo DOI. When you fill out the form, be sure to mention and link to the approved pyOpenSci review. JOSS will tag your package for expedited review if it is already pyOpenSci approved.

I didn't see a field for the Zenodo DOI, so I just included it in the comments. I tried entering it as the repository URL but it threw an error and insisted on a GitHub URL.

• Wait for a JOSS editor to approve the presubmission (which includes a scope check).
• Once the package is approved by JOSS, you will be given instructions by JOSS about updating the citation information in your README file.
• When the JOSS review is complete, add a comment to your review in the pyOpenSci software-review repo here that it has been approved by JOSS. An editor will then add the JOSS-approved label to this issue.

[jsdodge]

Hi @banesullivan , when would be the deadline for providing pyOpenSci with a blog post?

[banesullivan]

No deadline! We're flexible and it's totally up to you if you'd like to do it

[banesullivan]

Thought I'd drop a note that we will keep this issue open until THzTools finishes the review process with JOSS but THzTools is accepted by PyOpenSci at this point and the review has concluded 🎉

[banesullivan]

JOSS Pre-Review under way: openjournals/joss-reviews#7521

[jsdodge]

Thanks! As this is wrapping up, I can confirm that we'll provide a blog post soon.

[banesullivan]

JOSS review has been accepted 🎉 openjournals/joss-reviews#7542