[REVIEW]: primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@dr-joe-wirth@csoneson<!--end-editor-- Reviewers: @flashton2003, @mbhall88 Archive: 10.5281/zenodo.13759569

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/684c8541ebcea328d87fc0927ab17bbe/status.svg)](https://joss.theoj.org/papers/684c8541ebcea328d87fc0927ab17bbe)

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) by leaving comments 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 instructions & questions

@flashton2003 & @mbhall88, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mbhall88

📝 Checklist for @flashton2003

editorialbot commented 5 months ago

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editorialbot commented 5 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gks596 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (730.3 files/s, 151517.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            872           1404           2234
Markdown                         4             57              0            264
YAML                             4              9             12             95
TeX                              1              0              0             12
Dockerfile                       1              6              7              7
-------------------------------------------------------------------------------
SUM:                            24            944           1423           2612
-------------------------------------------------------------------------------

Commit count by author:

   292  dr-joe-wirth
     9  Lee Katz - Aspen
     5  Joe Wirth
     3  Lee Katz
     2  Joe Wirth (Joseph S. Wirth)
     1  Jessica Chen

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 531

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

csoneson commented 5 months ago

👋🏼 @dr-joe-wirth, @flashton2003, @mbhall88 - this is the review thread for the submission. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

mbhall88 commented 5 months ago

Review checklist for @mbhall88

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/dr-joe-wirth/primerForge/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@dr-joe-wirth) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

flashton2003 commented 4 months ago

Review checklist for @flashton2003

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/dr-joe-wirth/primerForge/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@dr-joe-wirth) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

csoneson commented 4 months ago

👋🏻 Just wanted to check in to see how the reviews are going here. Let me know if you have any questions. Thanks!

dr-joe-wirth commented 4 months ago

👋🏻 Just wanted to check in to see how the reviews are going here. Let me know if you have any questions. Thanks!

it's coming along. i am currently working to resolve an issue raised by one of the reviewers

csoneson commented 3 months ago

👋🏻 Just checking in again - @dr-joe-wirth, were you able to address the previous issue? @flashton2003 - could you let us know when you might have a first round of comments for the authors (I see that you generated the checklist but didn't start ticking off the points)?

Thanks everyone 🙂

dr-joe-wirth commented 3 months ago

yes i recently created a new release that addressed the space complexity and time complexity problems. the pip installation and the manual installation and the docker image all work, but i am trying to resolve an issue with the conda installer that is arising because of an incompatible recipe for khmer.

i still need to:

formally compare primerforge to swga
add a contributing template
add an example usage

flashton2003 commented 3 months ago

I've gone through the review checklist, there are some open items that need to be addressed. How do we proceed from here?

csoneson commented 3 months ago

Thanks @flashton2003! You can either write your comments in a post in this issue, or open separate issues in the software repository (in that case, please mention this issue thread in those issues so that a link is created).

dr-joe-wirth commented 3 months ago

Hello @csoneson @mbhall88 @flashton2003

I believe I have addressed all the reviewer feedback that I have received. Here is a list (in no particular order) of some of the things that have been done since the review started.

A comparison of primerForge to swga2 has been added to the manuscript.
An example has been provided in the README.
A CONTRIBUTING document has been added and is referenced in the README
All available installation options should work and are documented in the README.
The compatible versions of python are clearly stated in the README
The pip installation has been designed to fail and raise an informative error message if an incompatible version of python is being used
The high memory usage and runtimes have been mitigated; the libraries used to do this are cited in the manuscript.
A validation step using in silico PCR has been added; the software used to do this is cited in the manuscript.
Instructions for running unit tests have been added to the README
issue templates have been added for both bug reports and feature requests

If there are any additional issues that I need to address, please let me know and/or create issues on the repo.

mbhall88 commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mbhall88 commented 3 months ago

Great work @dr-joe-wirth. All boxes ticked for me now! Thank you for the thorough treatment of the comments.

One tiny thing, columns 1 and 3 in table 2 in the manuscript seem to be overlapping.

mbhall88 commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

Hello @mbhall88, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

dr-joe-wirth commented 3 months ago

Great work @dr-joe-wirth. All boxes ticked for me now! Thank you for the thorough treatment of the comments.

Thanks for the insightful comments!

One tiny thing, columns 1 and 3 in table 2 in the manuscript seem to be overlapping.

There is something going on with the pdf generator that joss uses. We are looking into ways to fix it.

csoneson commented 3 months ago

Thanks @mbhall88! @flashton2003 - please let us know if the process to provide your comments is clear, or if you have further questions!

dr-joe-wirth commented 3 months ago

@csoneson is there a type-setting process or some other opportunity to manually format the tables? Some of the columns in the table have been poorly formatted by the inara tool that is used to automatically create a pdf.

csoneson commented 2 months ago

Hi @dr-joe-wirth - I think you can manually control the relative widths of the columns in the table by changing the number of dashes in the line below the header line in the table, i.e., the

|:-----------:|:-----:|:-------------:|:------:|

part. You can add some more dashes to the columns that you want to give more space, and remove some from the columns that need less.

dr-joe-wirth commented 2 months ago

oh thanks so much @csoneson! i believe i have made the tables a lot more legible.

csoneson commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mbhall88 commented 2 months ago

That looks much better.

dr-joe-wirth commented 2 months ago

Repeated the benchmarking using version 1.3.5. Updated the manuscript to reflect this change.

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

csoneson commented 2 months ago

👋🏻 Checking in after the holidays - @flashton2003, could you let us know how your review is progressing? Thanks!

csoneson commented 2 months ago

Ping @flashton2003

👋🏻 Checking in after the holidays - @flashton2003, could you let us know how your review is progressing? Thanks!

dr-joe-wirth commented 2 months ago

@editorialbot generate pdf

Fixed a typo in Table 2. 61 minutes to 81 minutes for primerForge on the E. coli dataset.

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

flashton2003 commented 2 months ago

Sorry, I've just returned from holiday. All fine by me.

csoneson commented 2 months ago

Thanks @flashton2003 - could you clarify

All fine by me.

There are some unticked boxes in your checklist above, and you had some concerns that required attention some time ago (https://github.com/openjournals/joss-reviews/issues/6850#issuecomment-2245409672). Could you elaborate a bit more on whether there are issues that need the authors' attention? Thanks!

flashton2003 commented 2 months ago

Sorry, all checked now.

csoneson commented 2 months ago

Ok, thanks @flashton2003.

@dr-joe-wirth - as both reviewers have confirmed that all boxes are ticked, I will also take a look at the submission, and will get back to you shortly with the next steps.

dr-joe-wirth commented 2 months ago

@csoneson thanks for the update! looking forward to your comments.

dr-joe-wirth commented 2 months ago

@csoneson it occurred to me that I have updated the version since the paper. The manuscript discusses v1.3.5 but primerForge is currently at v1.3.6.

If you need to evaluate v1.3.5, then here are some instructions to help you out:

installing v1.3.5

since it isn't the latest version here are the installation instructions for v1.3.5

`pip` installation

pip install primerforge==1.3.5
conda install ispcr

manual installation

git clone --branch v1.3.5 https://github.com/dr-joe-wirth/primerForge.git
conda env create -f ./primerForge/environment.yml
conda activate primerforge

`docker` image

docker pull jwirth/primerforge:v1.3.5

csoneson commented 2 months ago

@editorialbot check repository

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (711.6 files/s, 162954.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15           1016           1611           2532
Markdown                         5            105              0            471
YAML                             4              9             12            111
TeX                              1              3              0             45
Dockerfile                       1              9             10             20
-------------------------------------------------------------------------------
SUM:                            26           1142           1633           3179
-------------------------------------------------------------------------------

Commit count by author:

   427  dr-joe-wirth
    12  Joe Wirth (Joseph S. Wirth)
     9  Lee Katz - Aspen
     5  Joe Wirth
     4  Lee Katz
     1  Jessica Chen

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1210

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

csoneson commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.12688/f1000research.6924.1 is OK
- 10.1093/nar/gks596 is OK
- 10.1093/bib/bbs038 is OK
- 10.1371/journal.pcbi.1010137 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

csoneson commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

csoneson commented 2 months ago

@dr-joe-wirth I have gone through the submission, and overall it looks great. A couple of suggestions for the paper:

Could you please spell out 'USA' in the author affiliations?
I'm wondering if it would be worth to add another sentence in the very beginning, explaining the terms 'ingroup' and 'outgroup' in the Summary section, since this is aimed at a very broad audience.
I stumbled on the sentence on lines 40-41. Should 'in' be removed?

You can then generate a new proof with @editorialbot generate pdf.

I will make another post below with the additional next steps.

openjournals / joss-reviews