[JOSS Review] Reproducibility and functionality

[mbarzegary]

Dear authors,

Generally speaking, the software runs as described in the documentation, and the demos/tutorials can be set up by following the instruction. However, there are minor fixes that can improve the quality of the submission in this regard:

• It can be nice to number the tutorial files so that the users can find out the order in which they need to follow the tutorials. In the online documentation, it’s not a problem because the order is known from the ToC.
• More elaboration is needed in the GPR example (time series example) to demonstrate the effect of applying GPR on the detection process. In the current state of the provided example, it's difficult to see the effect by just running the code.
• It's worth mentioning that the last tutorial (visualization) needs the output of previous tutorials to run. In the notebook file, it is only mentioned that the user should provide a set of files without saying anything about how to get them.
• Gif animations will not be displayed in the visualization notebook file. Is there any prerequisites needed for it? I checked this on both Windows and Linux, resulting in the same empty placeholder.
• A general question: why are the x and y data in a reversed order in all plt.plot calls that we have in tutorials? I expect it to be plt.plot(x, y), but it is always the other way around. Is it not necessary to elaborate on the reason?

P.S. This issue is related to https://github.com/openjournals/joss-reviews/issues/5322

[saeedmhz]

Thank you for your thorough examination of our software and tutorials, as well as your helpful suggestions for improving their quality. We have made the following changes in response to your comments:

1. To make the order of tutorials clearer, we have numbered the tutorial files as follows: t1-basics.ipynb, t2-timeseries.ipynb, t3-analysis.ipynb, and t4-visualization.ipynb.

2. We have expanded the explanation for the use of Gaussian Process Regression (GPR) in the timeseries tutorial (t2-timeseries.ipynb). We discussed the primary purposes of GPR, which are noise reduction and filling missing information, and demonstrated these benefits through additional visualizations in the tutorial.

3. In the t4-visualization.ipynb notebook, we explicitly mentioned which files should be run before executing this tutorial to ensure users have the necessary output files.

4. We have resolved the issue with GIF animations not being displayed in the visualization notebook. They should now display correctly.

5. Regarding the reversed order of x and y data in plt.plot calls, this is due to the use of the skimage.measure.find_contours function, which returns contours with coordinates in (row, column) order, corresponding to (y, x) in Cartesian coordinates. As a result, we use y for the first dimension and x for the second dimension throughout the code (e.g., plt.plot(y, x)). To clarify this for users, we added a warning in the sg.py file under the SarcGraph._detect_contours function.

We appreciate your attention to detail and believe that these changes will enhance the user experience and the overall quality of our software and tutorials. We hope our revisions address your concerns satisfactorily.

Please let us know if you have any further comments or suggestions.