THzTools submission

Question

THzTools submission

jsdodge opened this issue a year ago · 64 comments

Answer 1 · 2024-08-13T08:00:27.000Z

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!

Answer 2 · 2024-08-15T03:02:52.000Z

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?

Answer 3 · 2024-08-15T09:51:26.000Z

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?

Answer 4 · 2024-08-15T13:31:58.000Z

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.

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. 🙌

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.

Answer 5 · 2024-08-15T17:36:21.000Z

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.

Answer 6 · 2024-08-15T19:07:16.000Z

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.

Answer 7 · 2024-08-15T23:46:49.000Z

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

Answer 8 · 2024-08-16T08:06:06.000Z

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

Answer 9 · 2024-09-11T19:35:10.000Z

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

Could you please update me on the editor search?

Answer 10 · 2024-09-12T06:33:24.000Z

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!

Answer 11 · 2024-10-07T19:55:57.000Z

@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!

Answer 12 · 2024-10-07T20:37:01.000Z

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.

Answer 13 · 2024-10-07T21:33:39.000Z

@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.

Answer 14 · 2024-10-08T20:49:35.000Z

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.

Answer 15 · 2024-10-08T21:46:28.000Z

@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!

Answer 16 · 2024-10-08T22:16:32.000Z

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.

Answer 17 · 2024-10-09T13:38:17.000Z

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

Answer 18 · 2024-10-09T15:03:23.000Z

ok fantastic.
✅ we have two reviewers now assigned to this issue. @frank1010111 and @Romain-Peretti
I believe we are at this step in the review process and @banesullivan can take the review forward from here!! Bane can you please onboard the reviewers and kick things off?

Thank you all. Please let me know if i can be helpful moving forward!

Answer 19 · 2024-10-10T05:13:57.000Z

👋 Hi @frank1010111 and @Romain-Peretti! Thank you for volunteering to review THzTools for pyOpenSci! I'm excited to kick off this review and I'll try to chime in with a few comments of my own but overall THzTools is looking in great shape -- wonderful work, @jsdodge!

Please fill out our pre-review survey

Before beginning your review, please fill out our pre-review survey. This helps us improve all aspects of our review and better understand our community. No personal data will be shared from this survey - it will only be used in an aggregated format by our Executive Director to improve our processes and programs.

@frank1010111 survey completed.
@Romain-Peretti survey completed.

The following resources will help you complete your review:

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Please get in touch with any questions or concerns!

Your review is due: November ~8th, 2024

I've set the due date ~3 weeks out from now, but we're flexible here so please don't rush yourself if life or other things pop up and require you to delay a bit.

Reviewers: @frank1010111 @Romain-Peretti
Due date: 2024-11-08

Answer 20 · 2024-10-12T16:49:20.000Z

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README.
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
Community guidelines including contribution guidelines in the README or CONTRIBUTING.
Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
Package installation instructions
Any additional setup required to use the package (authentication tokens, etc.)
Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
Link to your documentation website.
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
All functions have documentation and associated examples for use
The package is easy to install

Functionality

For packages also submitting to JOSS

The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

A short summary describing the high-level functionality of the software
Authors: A list of authors with their affiliations
A statement of need clearly stating problems the software is designed to solve and its target audience.
References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 4

Review Comments

Answer 21 · 2024-10-12T20:15:18.000Z

Hi @frank1010111 , thanks for your feedback so far. How would you like to proceed with the code updates? I've already addressed the issues that you posted, but just in my local dev branch. At what point would you recommend that I push these changes to the remote, merge them with the main branch, and create a new release? Should I wait for you to complete your review before doing any or all of these?

Answer 22 · 2024-10-13T00:55:38.000Z

I appreciate it. If you want me to review the dev branch, I'm okay doing that. Whatever works best for you is good for me.

Answer 23 · 2024-10-13T03:18:50.000Z

In that case, I merged the changes into the main branch and created a new release, THzTools v0.5.3 (beta). I also closed the issues that you raised. I see that there are several unchecked items, so I'll wait for further recommendations.

Answer 24 · 2024-10-14T20:39:40.000Z

Hey @jsdodge, I anticipate that a few more changes will be made during this review process, so there is no need to issue a new release for each of these changes during the review (unless you prefer to do so!). As the review finalizes though, we can make sure a release is issued and update the version specifier in the submission.

Moving forward, would you please try to link back to this GitHub issue by pasting the URL link in the descriptions of any Pull Requests or new Issues? This will help us track changes to the software that were a direct result of this review and help us check off items in the reviewers comments. Thanks!

Answer 25 · 2024-10-15T01:08:11.000Z

Thanks for the suggestions, @banesullivan , will do.

Answer 26 · 2024-10-16T01:48:10.000Z

Today, I checked the paper draft created by a github action and found it meets JOSS specifications.

Answer 27 · 2024-10-17T01:39:27.000Z

I've got to say, your documentation is beautifully organized.

Answer 28 · 2024-10-17T01:59:08.000Z

Thank you! It's nice to have that effort recognized.

Answer 29 · 2024-10-18T00:58:04.000Z

A nit for your documentation is that you've got docstrings for the parameters of your dataclasses, but Sphinx expects docstrings for your attributes. For instance, the lines here in NoiseModel are rendered fine, but Sphinx doesn't know to put them with these attributes.

The solution to this oddity is something like this

@dataclass
class Snake:
    """Oh no, it's a snake!"""

    width: float
    """Width of the snake."""
    
    length: float
    """Length of the snake."""

Once again, it's a nit that you don't have to change. Your documentation is perfectly readable as is. Just a fun fact for you if you're as obsessive about these things as me.

Answer 30 · 2024-10-18T06:07:32.000Z

Thanks for that suggestion. Just to clarify, I'm using the numpydoc extension, so are you recommending that I repeat the class Parameters section in a separate Attributes section, as in the ExampleError class listed in the Sphinx Example NumPy Style Python Docstrings?

Answer 31 · 2024-10-19T15:05:30.000Z

I did not know about that example. That's amazing

Answer 32 · 2024-10-19T15:22:06.000Z

I've run and played around with the example notebooks, and I'm overall very pleased with the package and documentation. Very nice work. After that last issue is closed, my review ought to be complete and I can recommend acceptance.

Answer 33 · 2024-10-19T16:11:58.000Z

Sorry I did not begin yet I ll try to do it from next Monday. Romain

On 19/10/2024 17:22, Frank Male wrote: I've run and played around with the example notebooks, and I'm overall very pleased with the package and documentation. Very nice work. After that last issue is closed, my review ought to be complete and I can recommend acceptance. — Reply to this email directly, view it on GitHub <#209 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BL6ZGXYHOADPEILNLRCTZ6TZ4J2LJAVCNFSM6AAAAABL2M3B32VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRTHE3DENJUGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Dr. Romain PERETTI (hab.) Leader of TeraHertz Biophotonics activity TeraHertz Photonics Group @ IEMN - CNRS (UMR 8520) Senior Member and Optics Express Associate editor @ OPTICA Phone: +33 32 019 78 76 ***@***.***

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Answer 34 · 2024-10-19T20:00:55.000Z

Thanks for your help, @frank1010111 ! I've made the changes that you requested and created a new release, THzTools v0.5.4 (beta), in anticipation of your review approval. I appreciate your suggestions and your promptness in completing the review.

Answer 35 · 2024-10-19T20:04:35.000Z

Thanks, @Romain-Peretti , I look forward to your feedback. As noted in the comment above, I have issued a new release in response to several helpful suggestions from @frank1010111 . I've updated the submission to indicate the updated release.

Answer 36 · 2024-10-23T15:21:56.000Z

So I feel very the same way as @frank1010111 it is very impressive and I bet useful for quite a lot of people (at least a great playground for my next students to understand a bit all of that).

I have a question about the way the Hessian are computed. We struggled during month to find a good way to calculate the hessian in one of our project and I am not sure to follow how it is done here. It looks like you are computing the Hessian by yourself or am I wrong ?

Romain

Answer 37 · 2024-10-23T16:51:20.000Z

Thank you for your feedback! I'm glad you think the software will be useful.

To your question, for the noisefit function we use scipy.minimize with the BFGS method to do the optimization, which does not require the Hessian. We tried other methods that did require the Hessian, however, so we have an internal function, _hess_noisefit to compute it that we left in the main code, in case we find a way to use it later to improve the computational speed. We compute the Jacobian explicitly in _jac_noisefit.

For the fit function, we use scipy.least_squares to do the minimization (see here), which also just uses the Jacobian. Internally, we fit for mu in addition to the fit parameters of the frequency response function, so the Jacobian that we compute internally is different from the Jacobian with respect to the fit parameters supplied to fit. We compute that Jacobian here.

Answer 38 · 2024-11-05T09:50:45.000Z

Ok sorry for the silence ... I had a bit to do outside of the office. I finished the review process the only very small comment I would have and that is maybe a misunderstanding from my side is that the author list for JOSS is maybe the one of the Software Package but maybe adding it to the paper.md together with the affiliation would clarify it.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README.
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
Community guidelines including contribution guidelines in the README or CONTRIBUTING.
Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
Package installation instructions
Any additional setup required to use the package (authentication tokens, etc.)
Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
Link to your documentation website.
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
All functions have documentation and associated examples for use
The package is easy to install

Functionality

For packages also submitting to JOSS

The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

A short summary desribing the high-level functionality of the software
Authors: A list of authors with their affiliations
A statement of need clearly stating problems the software is designed to solve and its target audience.
References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 5

Answer 39 · 2024-11-05T16:34:25.000Z

Thanks @Romain-Peretti ! I'd like to clarify your comment: the author list for the paper (linked here) is the same as the authors listed in the pyproject.toml metadata (linked here). Are you recommending that we change that?

Answer 40 · 2024-11-05T16:52:54.000Z

Hum not at all, I simply missed it .. Sorry about that Romain

On 05/11/2024 17:34, J. Steven Dodge wrote: Thanks @Romain-Peretti <https://github.com/Romain-Peretti> ! I'd like to clarify your comment: the author list for the paper (linked here <https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/paper/paper.md?plain=1#L12C1-L38C19>) is the same as the authors listed in the |pyproject.toml| <https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/pyproject.toml#L15C1-L24C1> metadata (linked here <https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/pyproject.toml#L15C1-L24C1>). Are you recommending that we change that? — Reply to this email directly, view it on GitHub <#209 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BL6ZGX2QMJRUH6BQHHYTNCDZ7DXSRAVCNFSM6AAAAABL2M3B32VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJXGY2TEOJZGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Dr. Romain PERETTI (hab.) Leader of TeraHertz Biophotonics activity TeraHertz Photonics Group @ IEMN - CNRS (UMR 8520) Senior Member and Optics Express Associate editor @ OPTICA Phone: +33 32 019 78 76 ***@***.***

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--------------leOlVCjdudh7miLwqXGGC4y0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: 8bit <!DOCTYPE html> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> <body> Hum not at all, I simply missed it .. Sorry about that Romain <div class="moz-cite-prefix">On 05/11/2024 17:34, J. Steven Dodge wrote: </div> <blockquote type="cite" ***@***.***"> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> Thanks <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Romain-Peretti/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Romain-Peretti" ***@***.***</a> ! I'd like to clarify your comment: the author list for the paper (linked <a href="https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/paper/paper.md?plain=1#L12C1-L38C19" moz-do-not-send="true">here</a>) is the same as the authors listed in the <a href="https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/pyproject.toml#L15C1-L24C1" moz-do-not-send="true"><code class="notranslate">pyproject.toml</code></a> metadata (linked <a href="https://github.com/dodge-research-group/thztools/blob/92d074f85dfe093e11225c92770c382259643834/pyproject.toml#L15C1-L24C1" moz-do-not-send="true">here</a>). Are you recommending that we change that? — Reply to this email directly, <a href="#209 (comment)" moz-do-not-send="true">view it on GitHub</a>, or <a href="https://github.com/notifications/unsubscribe-auth/BL6ZGX2QMJRUH6BQHHYTNCDZ7DXSRAVCNFSM6AAAAABL2M3B32VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJXGY2TEOJZGA" moz-do-not-send="true">unsubscribe</a>. You are receiving this because you were mentioned.<img src="https://github.com/notifications/beacon/BL6ZGX4MYK7GY3I733G27DTZ7DXSRA5CNFSM6AAAAABL2M3B32WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTUSPTHP4.gif" alt="" moz-do-not-send="true" width="1" height="1">Message ID: <pyOpenSci/software-submission/issues/209/2457652990@github.com> </blockquote> <div class="moz-signature">-- <pre class="moz-signature">Dr. Romain PERETTI (hab.) Leader of TeraHertz Biophotonics activity TeraHertz Photonics Group @ IEMN - CNRS (UMR 8520) Senior Member and Optics Express Associate editor @ OPTICA Phone: +33 32 019 78 76 <a ***@***.***" ***@***.***</a> </pre> <img src="https://www.cnrs.fr/themes/custom/cnrs/logo.svg" name="Image1" style="padding-right: 55px" width="55" height="55" border="0" align="middle"> <img src="https://opticaorgdev.blob.core.windows.net/media/optica/media/osa.media/osa-logos/trianglebranding/senior_member_shadow.png" name="Image2" width="65" height="65" border="0" align="middle"> </div> </body> </html>

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Answer 41 · 2024-11-05T17:37:09.000Z

No problem, thanks again @Romain-Peretti !

Answer 42 · 2024-11-05T17:39:11.000Z

Hi @banesullivan , now that both reviewers have indicated their approval, what's next?

Answer 43 · 2024-11-09T00:01:53.000Z

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!

Answer 44 · 2024-11-19T07:35:46.000Z

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:

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.
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?
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!!

Answer 45 · 2024-11-20T00:07:20.000Z

Thank you, @banesullivan !

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

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.

Answer 46 · 2024-11-23T01:48:13.000Z

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

Answer 47 · 2024-11-23T01:59:41.000Z

🎉 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.

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.

Answer 48 · 2024-11-23T02:02:45.000Z

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

Answer 49 · 2024-11-23T02:04:42.000Z

@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:

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!

Answer 50 · 2024-11-23T02:58:21.000Z

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

Answer 51 · 2024-11-23T07:40:23.000Z

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.

Answer 52 · 2024-11-24T18:34:08.000Z

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

Answer 53 · 2024-11-24T18:37:50.000Z

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

THzTools submission

Code of Conduct & Commitment to Maintain Package

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Please fill out our survey

Editor and Review Templates

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Please fill out our pre-review survey

Your review is due: November ~8th, 2024

Package Review

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Review Comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

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Author Wrap Up Tasks

Editor Final Checks

Code of Conduct & Commitment to Maintain Package

Description

Scope

Domain Specific

Community Partnerships

Technical checks

Publication Options

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

Please fill out our survey

Editor and Review Templates

Footnotes

Editor in Chief checks

Editor comments

Please fill out our pre-review survey

Your review is due: November ~8th, 2024

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Review Comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Author Wrap Up Tasks

Editor Final Checks