JOSS Review -- A list of minor comments

[Farnazmdi]

Congratulations on developing this package, it is very well written and super useful in its relevant field. I just have a few minor comments.

In the manuscript:

• line 44, "from" is repeated.
• line 19 "partioning" is a typo.
• in figure 1a, the word "Transcription fixed delay" has a typo.
• It would be nice to accompany the figure1b with a mathematical equation to clarify if there is a simple closed form expression for it.

In the repository:

• I see that some of the functions have extensive documentation, but it would be clearer if all functions had this, especially specifying the type of the input arguments, such as 'int', 'float', etc. would help with readability of the functions.
• This one is just a suggestion and mostly my curiosity to see how does Numpyro perform versus your implementation of MCMC inference in Cython. Do you have an idea about this?
• It would be nice to add a link or some explanation on how to install jupyter notebook kernels in the installation guide. In case somenone wants to clone your repository I guess it would be necessary to install a kernel.

[ayush9pandey]

Thanks @Farnazmdi for reviewing bioscrape! I will work on fixing these.
Just want to point you to the latest paper PDF https://raw.githubusercontent.com/openjournals/joss-papers/joss.05057/joss.05057/10.21105.joss.05057.pdf
(also available on the review thread). The update after the previous review fixed the typo error so I have marked that task as done.

sorry the other typo is still there.

[ayush9pandey]

• Added instructions about Jupyter notebooks in the Installation page on the Wiki.

[ayush9pandey]

• Added docstrings and types of arguments to all user interface functions. We understand that a detailed documentation of the code is an important software engineering practice. The current status of the documentation is in no way complete or up-to industry standards. So, we will keep improving the documentation of the package.
• For now, I have added a detailed docstring and argument types to all four key functionalities of bioscrape: model construction using Model class constructor, all user-level analysis functions in the analysis module, the inference module's user interface function py_inference, the simulation function py_simulate_model.

All of these changes are on the documentation branch that will be merged soon!

[ayush9pandey]

• Discussion on speeding up inference is on Speeding up Bioscrape Inference #38 .

[ayush9pandey]

• For Figure 1b, since we also have a delay in the model, there is no "nice looking" closed form expression for the model. The delay for each reaction in bioscrape is a probabilistic delay in firing of propensity of that reaction. So, I'm not sure if there is a good closed form expression to write it.

[ayush9pandey]

• Fixed paper typos in the joss-paper branch.

[ayush9pandey]

Hi @Farnazmdi ,

Thanks for reviewing bioscrape. Please let me know if the fixes that I have described are satisfactory and if you have other comments.

[Farnazmdi]

Hi @ayush9pandey Thanks for addressing the comments. I believe these changes resolve all my concerns. Wonderful job!