Closed jlarsen-usgs closed 1 year ago
Thanks @jlarsen-usgs these are incredibly helpful comments - I'm working on all of these but to just reply about the timeseries_data.csv
issue, it seems to me to be on the repo in this folder (https://github.com/barneydobson/wsi/tree/main/docs/demo/data/processed).
I should have made it more clear, but there is a comment that says when inputting the data_folder
, that a different address should be used when running in Python on your machine (e.g., line 51 in https://github.com/barneydobson/wsi/blob/main/docs/demo/scripts/quickstart_demo.py)
As part of my revisions, I will make this the default data_folder
address since I only need to use the address it is currently set as to create the documentation (you can switch over to the https://github.com/barneydobson/wsi/tree/joss_revisions branch where I have made the change) - but I am letting you know now so that you can continue looking at them on the main branch if you like.
Thanks @barneydobson, I see that the file is in the WSIMOD repository. I'll update my copy of the repo to make sure I have the most recent version and retry later today.
Hi @jlarsen-usgs
Just providing a quick update on these tasks, note that I have not yet been able to meet with co-authors so I haven't focussed on paper edits. Changes are currently on the https://github.com/barneydobson/wsi/tree/joss_revisions branch and summarised below.
Hi @jlarsen-usgs, thank you so much for your review, it has been incredibly helpful for us! Below I go through the open tasks that you have raised and provide links to locations where the suggestions have been implemented, and a bit of text in response if necessary.
In your WSI docs you have a detailed summary and statement of need. Can you adapt a concise version of this text into your Readme.md file. The Welcome WSIMOD section would be a good place to add this information. Addressed at: https://github.com/barneydobson/wsi/blob/main/README.md
Install/requirements
_Addressed in: https://github.com/barneydobson/wsi/blob/main/README.md https://github.com/barneydobson/wsi/blob/main/requirements.txt https://github.com/barneydobson/wsi/blob/main/requirements_demos.txt https://github.com/barneydobson/wsi/blob/main/requirements_documentation.txt https://github.com/barneydobson/wsi/blob/main/setup.py https://barneydobson.github.io/wsi/installation/_
Community guidelines: A code of conduct, contributing guidelines, and either an issue template or a short statement about where to seek support for the software should be added to the reposity. _Addressed in: https://github.com/barneydobson/wsi/blob/main/docs/CODE_OF_CONDUCT.md https://github.com/barneydobson/wsi/blob/main/docs/CONTRIBUTING.md_
Paper updates (literature)
Addressed in: https://github.com/barneydobson/wsi/blob/main/docs/paper/paper.md https://barneydobson.github.io/wsi/paper/paper/ Note that this is a reasonably small amount of text added, we are currently writing up a full research paper with a more complete explanation of theory.
Capabilities/descriptions now added in: https://barneydobson.github.io/wsi/component-library/ As previous, if you find it acceptable, a more detailed theoretical description will be addressed in a research paper
the demo problems are currently set up to generate your documentation tutorials. These could be adapted into either example scripts or interactive jupyter notebooks (in addition to keeping the current docs workflow) where the user does not have to reset the data_folder path variable to access the correct path to your data. Default folder now updated so that they are interactive
the bulk density of soil in your GrowingSurface module seems low to me (1300 kg/m3), The average bulk denity of soil is around 2650 kg/m3. Addressed in: https://github.com/barneydobson/wsi/blob/main/wsimod/nodes/land.py
@barneydobson thank you for addressing my comments. I think this is ready to move ahead
@barneydobson
I am beginning my review on WSIMOD for your JOSS publication and I will be tracking my review comments here and editing this issue as they come up, I should be finished doing my review by the end of this week. Feel free to address them all within this issue, or convert each of the comments to their own issues.
[x] General reviews
pip install .
). It'd be nice to add instructions on how to install directly from github for those users who aren't likely to dig into the source code (pip install https://github.com/barneydobson/wsi/archive/refs/heads/main.zip
)[x] paper reviews:
[x] code reviews:
data_folder
path variable to access the correct path to your data.GrowingSurface
module seems low to me (1300 kg/m3), The average bulk denity of soil is around 2650 kg/m3.openjournals/joss-reviews#4996