refactor: scripts/VISS_Sample_Data.R

[IshikaKhandelwal]

This pull request includes several significant updates to the project, primarily focusing on importing new dependencies, adding new functions for climate data analysis, and updating the documentation. Below is a summary of the most important changes:

Dependency Updates:

• Added new dependencies in the DESCRIPTION file: dplyr, purrr, sf, tibble, terra, exactextractr, future, and furrr.
• Updated the NAMESPACE file to import functions from the new dependencies.

Documentation Updates:

• Added documentation for the new functions: exposure, exposure_times, extract_climate_data, get_niche_limits, and prepare_range. [1] [2] [3] [4] [5]

Miscellaneous:

• Added global variables declaration to R/globals.R to avoid R CMD check warnings.- Modularized key functions (prepare_range, extract_climate_data, get_niche_limits, exposure, exposure_times) and moved them to the /R folder for better code reuse and maintainability.

• Created a comprehensive driver script scripts/VISS_Sample_Data.R to orchestrate the workflow, including range preparation, climate data extraction, thermal niche limit computation, exposure calculation, and exposure times analysis.

Addressing: #22

[carlosgjs]

this looks really good, mostly need to address the warnings and I have the question about exporting the core functions.

[carlosgjs]

shouldn't we be also exporting the main package functions here? E.g. exposure, exposure_times, etc?

[carlosgjs]

Can you look into all these warnings?

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 123 lines in your changes missing coverage. Please review.

Project coverage is 0.80%. Comparing base (a8e3866) to head (6f97b21).

Files with missing lines	Patch %	Lines
R/exposure_times.R	0.00%	42 Missing ⚠️
R/get_niche_limits.R	0.00%	34 Missing ⚠️
R/prepare_range.R	0.00%	22 Missing ⚠️
R/exposure.R	0.00%	15 Missing ⚠️
R/extract_climate_data.R	0.00%	10 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (a8e3866) and HEAD (6f97b21). Click for more details.

HEAD has 4 uploads less than BASE

Flag	BASE (a8e3866)	HEAD (6f97b21)
	5	1

Additional details and impacted files

@@             Coverage Diff             @@
##              main     #24       +/-   ##
===========================================
- Coverage   100.00%   0.80%   -99.20%     
===========================================
  Files            1       6        +5     
  Lines            1     124      +123     
===========================================
  Hits             1       1               
- Misses           0     123      +123     

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[IshikaKhandelwal]

I am currently facing an issue where no linting warnings appear when I test the package locally using lintr::lint_package() and after applying fixes like usethis::use_import_from(), adding proper imports in @importFrom directives, and ensuring the namespace is updated.

However, when I push the changes to GitHub, the CI workflow still reports linting warnings, particularly related to missing global function definitions (e.g., %>%, tibble, pull). Despite matching the local linter configuration to the one used in GitHub Actions, I am unable to reproduce these warnings locally, making it challenging to debug effectively.

Any insights on what might be causing this discrepancy or suggestions on how to proceed would be greatly appreciated!

Thanks!

[IshikaKhandelwal]

Added an issue for tracking the warnings issue here: #38

[carlosgjs]

The warnings will be addressed in #38