mn5hk / pyshbundle Goto Github PK

Currently we are planning to publish a software paper at the Journal of Open Source Software (https://joss.theoj.org/). I briefly request the "how to publish"section to be reviewed by the assignee.

Currently, we have made a draft for the paper in a markdown format. A github action (https://github.com/openjournals/joss-papers/actions/workflows/draft-paper.yml) is supposed to convert the markdown into a pdf in the prescribed format for the journal. However, the GH action is giving an error.

I perceive this to be a lower-hanging fruit; that perhaps takes less effort but also has a big impact in getting our draft near completion. I request the assignee to check it out in a new github branch.

Couple possible errors:

• some encoding in the github action file (https://github.com/mn5hk/pyshbundle/blob/main/.github/workflows/draft-pdf.yml ; currently pointed to a different md file named paper_joss.md);
• some error in equations being generated in the markdown file, causing GH action to fail

Also check issue #38

internal imports now seem to be working; recheck requirements text for compatibility issues

Customize a help function in the python script. The function should return the script definition, author contribution, prior contribution attribution, and how to run the script.

More details on how to achieve this: https://stackoverflow.com/questions/21930035/how-to-write-help-description-text-for-python-functions

Please add documentation here: https://github.com/mn5hk/mat2py/wiki

Hi all, request you to create an orcid id https://orcid.org/ and to share your id with me

Add some example input files into the github; change all filepaths to relative paths; maybe have key ipynb file in home directory of the repo

In Github actions (Action tab in the repo), I am getting error in generating pdf for our paper.md file. One of the issues here could be issue with the maths markdown. Request a double check.

Thanks,
Amin

Doublecheck this for every code

Audience; functionalities

Currently, we are loading replacer files as hardcoded paths to our drivespace. This should be rewritten with a relative file path such that the user can load the default values for the replaces when they install the pyshbundle module.

However, this runs into the risk that the replacer file is not updated, or that the user fails to update the replacer text file because of lack of awareness about its need. As such, additionally, the function should prompt the user to use custom replacer file as and when they find it necessary.

GitHub Actions: All Actions will begin running on Node16 instead of Node12

https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/

check float/integer type in notebook

check email on feb 21

https://www.diffen.com/difference/Creative_Commons_License_vs_GPL

Likely resolved by removing chdir

On 2023-2-2, we had an update meeting where we've looked at the current paper draft status. Few updates to be made to the paper draft as agreed:

• Update technical descriptions on the paper draft @mn5hk

• - [x] Validation of the script for a few basins and maybe also a few points or grid areas [@lsmvivek]

• Add some mathematical relationships/appropriate [@Walling9]

• Add some appropriate diagrams of Gaussian filter, spherical harmonics; make diagrams ourselves if possible [@Walling9 , @lsmvivek ]

• Improvise on the current flowchart; make alternative workflow diagrams [@mn5hk , @lsmvivek ]

• Improve our citations of relevant literature [@mn5hk ]

• Write an abstract

• Elaborate GDDC [ @mn5hk ]

• Review few existing tools for GRACE processing [@mn5hk]

• Does GIA need to be removed for the latest version of GRACE SH data?

• Feng (2018) has estimated GRACE measurement error by obtaining RMS over oceans at the same latitude as the study region. How reliable is the method? Also check: Chen JL, Wilson CR, Tapley BD, Yang ZL, Niu GY (2009b) 2005
  drought event in the Amazon River basin as measured by GRACE and estimated by climate models. J Geophys Res 114:B05404. https://doi.org/10.1029/2008jb006056

• Wahr et al. (2006) used the second method to determine the uncertainties in the GRACE SH coefficients as
  the standard deviation of the residuals of coefficients when seasonal cycles were removed. This method may also overestimate the GRACE measurement error because we assume that all non-seasonal variability of Stokes coefficients results from the measurement error.

Few more tasks left beyond the paper draft:

• Test pip compatibility #30
• Rewrite our notebook based on pip usage #32
• Rewrite our documentation based on pip usage #31
• Make our code binder compatible #29
• Cleanup our code #26
• Add proper citations and credits

Clean up comments, proper licensing, etc

The validation section of the file paper_with_equation.md has a minor formatting error, primarily due to the missing closing tag. It is a simple fix. May I fix this issue?

• Add a requirements file
• Add Julian to requirements

Feng (2018) has estimated GRACE measurement error by obtaining RMS over oceans at the same latitude as the study region. How reliable is the method? Also check: Chen JL, Wilson CR, Tapley BD, Yang ZL, Niu GY (2009b) 2005
drought event in the Amazon River basin as measured by GRACE and estimated by climate models. J Geophys Res 114:B05404. https://doi.org/10.1029/2008jb006056

Is the method reliable? if the method is reliable, should the method be included in the package in a future version?

Wahr et al. (2006) used the second method to determine the uncertainties in the GRACE SH coefficients as
the standard deviation of the residuals of coefficients when seasonal cycles were removed. This method may also overestimate the GRACE measurement error because we assume that all non-seasonal variability of Stokes coefficients results from the measurement error.

Is the method reliable? If the method is reliable, should it be added to future version of the package?

In the master file, it appears that numpy version update has made the code incompatible. Request an update to the code.