mluerig
commented
3 years ago @lwasser: done, done and done! Thanks for wrapping this up so quickly. I will submit this to Methods in Ecology and Evolution in the next few days. Any suggestion for how I should bring up this review there? There are options for rOpenSci, but no pyOpenSci - should I just write this in the cover letter?
Feedback: I would not change anything in the review process; there were templates, instructions and at the start the roles were distributed clearly. My only suggestion for improvement is, as you may have guessed, to work with compulsory deadlines, and a stronger role of the editor to make sure they are kept. Otherwise it gets swept away by the flood of other work we all are involved with - at least I would prefer to have a deadline, simply to mark this in my agenda and get my butt going :-).
In any case, I am extremely grateful for the time you spent on reviewing and editing, and I thank everyone involved. pyOpenSci is a great consortium, and I would submit here again!
lwasser
NickleDave
Submitting Author: Moritz Lürig (@mluerig)
JOSS DOI: N/A
Version accepted: 2.0.1
All current maintainers: Moritz Lürig (@mluerig)
Package Name: phenopype One-Line Description of Package: a phenotyping pipeline for Python Repository Link: https://github.com/phenopype/phenopype Version submitted: 1.0.5 Editor: @jbencook
Reviewer 1: @agporto
Reviewer 2: @sdonoughe
Archive:
Date accepted (month/day/year): 05/13/2021
Edit: Bumped from 1.0.4 to 1.0.5 since submission.
Description
Phenopype is a high throughput phenotyping pipeline for Python to support biologists in extracting high dimensional phenotypic data from digital images. The program provides intuitive, high level computer vision functions for image preprocessing, segmentation, and feature extraction. Users can assemble their own function-stacks that can be stored in the human-readable
yaml-format along with raw data and results, facilitating high throughput and full data reproducibility. Phenopype can be run from Python or from a Python Integrated Development Environment (IDE), like Spyder. Phenopype is designed to provide robust image analysis workflows that can be implemented with little or no Python experience.Scope
* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see this section of our guidebook.
Phenopype is designed to extract phenotypic data (https://en.wikipedia.org/wiki/Phenotype) of plants, animals, and other organisms from images and videos. By processing images in Python, through reproducible code and human readable configuration files, phenotyping becomes higher throughput and more reproducible than established GUI programs like "ImageJ".
Phenopype is intended for ecologists and evolutionary biologists that work with phenotypic data. Phenotypic data are an essential component of ecological and evolutionary research (https://www.nature.com/articles/nrg2897).
Only low level computer vision packages like OpenCV or scikit-image are out there that require a lot of configuring and a relatively deep understanding of computer vision and Python in general. Phenopype offers high level functions so that users can focus on the relevant analytic parts of image analysis.
Any other questions or issues we should be aware of?:
[X] does not violate the Terms of Service of any service it interacts with.
[X] has an OSI approved license
[X] contains a README with instructions for installing the development version.
[X] includes documentation with examples for all functions.
[X] contains a vignette with examples of its essential functions and uses.
[X] has a test suite.
[X] has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others.
Publication options
JOSS Checks
- [ ] The package has an **obvious research application** according to JOSS's definition in their [submission requirements](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements). Be aware that completing the pyOpenSci review process **does not** guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS. - [ ] The package is not a "minor utility" as defined by JOSS's [submission requirements](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements): "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria. - [ ] The package contains a `paper.md` matching [JOSS's requirements](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) with a high-level description in the package root or in `inst/`. - [ ] The package is deposited in a long-term repository with the DOI: *Note: Do not submit your package separately to JOSS*Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?
This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.
Code of conduct
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Editor and Review Templates
Editor and review templates can be found here
note: original repo url: https://github.com/mleurig/phenopype