Add different options for code folder

[Alon-Alexander]

User description

Implements the request by @ cristian

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PR Type

Enhancement

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Description

• Support multiple code folder naming options: "code", "src", "scripts"

• Add .find_code_folder_name() helper to detect actual folder name

• Update PMProject$create_analysis() to accept code_folder_name parameter

• Enhance pm_infer_analysis() to work with any valid code folder name

• Update documentation and examples to reflect new flexibility

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Diagram Walkthrough

flowchart LR
  A["User creates analysis"] -->|code_folder_name param| B["PMProject$create_analysis()"]
  B -->|rename folder if needed| C["Analysis with custom code folder"]
  D["pm_infer_analysis()"] -->|detect folder name| E[".find_code_folder_name()"]
  E -->|validate against options| F["Return analysis object"]
  G["Constants"] -->|ANALYSIS_CODE_DIR_OPTIONS| B
  G -->|ANALYSIS_CODE_DIR_OPTIONS| E

Loading

File Walkthrough

	Relevant files
Enhancement	3 files constants.R Add code folder naming options constant                                    +1/-0      project.R Add code_folder_name parameter to create_analysis                +14/-1    analysis.R Implement code folder detection and flexible naming            +28/-3
Tests	1 files test_analysis.R Add tests for different code folder names                                +50/-0
Configuration changes	1 files DESCRIPTION Bump version to 0.1.10                                                                      +1/-1
Documentation	16 files NEWS.md Document new code folder naming feature                                    +7/-0      index.md Update changelog with new features                                              +8/-0      index.html Regenerate changelog HTML documentation                                    +9/-1      PMProject.Rd Update PMProject documentation with new parameter                +7/-1      dot-find_code_folder_name.Rd Add documentation for helper function                                        +16/-0    pm_infer_analysis.Rd Update pm_infer_analysis documentation                                      +1/-1      PMProject.html Regenerate PMProject reference documentation                          +15/-7    PMProject.md Update PMProject markdown reference                                            +14/-6    dot-find_code_folder_name.html Generate new helper function reference page                            +82/-0    dot-find_code_folder_name.md Generate new helper function markdown reference                    +16/-0    pm_infer_analysis.html Regenerate pm_infer_analysis reference page                            +10/-10  pm_infer_analysis.md Update pm_infer_analysis markdown reference                            +7/-7      getting-started.html Update getting started guide with new feature                        +17/-14  getting-started.md Update getting started markdown with examples                        +15/-12  getting-started.Rmd Update vignette with code folder naming examples                  +4/-1      README.md Add template project README with package reference              +8/-0
Additional files	39 files 404.html +1/-1      LICENSE.html +1/-1      file-formats.html +3/-3      file-formats.md +1/-1      index.html +1/-1      input-definitions.html +2/-2      slurm-integration.html +2/-2      authors.html +3/-3      authors.md +2/-2      index.html +1/-1      pkgdown.yml +1/-1      PMAnalysis.html +6/-5      PMAnalysis.md +7/-4      PMData.html +1/-1      PMSlurmRun.html +1/-1      dot-cancel_slurm_job.html +1/-1      dot-check_missing_entries.html +1/-1      dot-check_missing_files.html +1/-1      dot-check_slurm_job_done.html +1/-1      dot-check_slurm_job_success.html +1/-1      dot-extract_input_ids.html +1/-1      dot-format_validation_error.html +1/-1      dot-get_slurm_job_error.html +1/-1      dot-submit_slurm_job_with_env.html +1/-1      dot-validate_input_fields.html +1/-1      dot-validate_input_files.html +1/-1      dot-validate_inputs_schema.html +1/-1      dot-validate_local_inputs_schema.html +1/-1      index.html +1/-1      is_slurm_available.html +1/-1      pm_create_project.html +2/-2      pm_create_project.md +1/-1      pm_project.html +2/-2      pm_project.md +1/-1      pm_read_file.html +1/-1      pm_write_file.html +1/-1      search.json +1/-1      sitemap.xml +1/-0      test_slurm.R +0/-2

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[qodo-free-for-open-source-projects]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Use correct default for code_folder_name Fix the create_analysis function by setting a single default value for code_folder_name and explicitly providing the choices to match.arg to ensure correct argument matching. R/project.R [352-353] -create_analysis = function(name, code_folder_name = constants$ANALYSIS_CODE_DIR_OPTIONS) { - code_folder_name <- match.arg(code_folder_name) +create_analysis = function(name, code_folder_name = constants$ANALYSIS_CODE_DIR_OPTIONS[1]) { + code_folder_name <- match.arg(code_folder_name, constants$ANALYSIS_CODE_DIR_OPTIONS) Apply / Chat Suggestion importance[1-10]: 8 __ Why: The suggestion fixes a bug in the use of match.arg which would behave unexpectedly when the code_folder_name argument is not provided, making the function more robust and correct.	Medium
	Handle ambiguous code folder detection Modify .find_code_folder_name to detect if multiple valid code folders exist (e.g., code and src) and throw an error to prevent ambiguous behavior, instead of just returning the first one found. R/analysis.R [663-671] .find_code_folder_name <- function(analysis_path) { + existing_options <- c() for (option in constants$ANALYSIS_CODE_DIR_OPTIONS) { - if (dir.exists(file.path(analysis_path, option))){ - return(option) + if (dir.exists(file.path(analysis_path, option))) { + existing_options <- c(existing_options, option) } } - stop(paste("Failed to find code folder with valid name for analysis at", analysis_path)) + if (length(existing_options) == 1) { + return(existing_options) + } + + if (length(existing_options) == 0) { + stop(paste("Failed to find code folder with valid name for analysis at", analysis_path)) + } + + stop( + paste( + "Found multiple valid code folders for analysis at", + analysis_path, + ":", + paste(existing_options, collapse = ", ") + ) + ) } Apply / Chat Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies an edge case where multiple valid code folders could exist, leading to ambiguity, and proposes a more robust check to ensure exactly one is present.	Medium
	Validate code folder rename success Add a check for the return value of file.rename() and throw an error if the operation fails to rename the code folder. R/project.R [386-391] if (code_folder_name != "code") { - file.rename( + success <- file.rename( from = file.path(analysis_path, "code"), to = file.path(analysis_path, code_folder_name) ) + if (!success) { + stop(sprintf("Failed to rename code folder to '%s'", code_folder_name)) + } } Apply / Chat Suggestion importance[1-10]: 7 __ Why: This suggestion improves error handling by verifying the success of the file.rename operation, preventing silent failures and making the function more robust.	Medium
General	Include valid options in error Improve the error message in .find_code_folder_name to include the list of valid folder names when no valid folder is found. R/analysis.R [670] -stop(paste("Failed to find code folder with valid name for analysis at", analysis_path)) +stop(sprintf( + "Failed to find code folder in '%s'; expected one of: %s", + analysis_path, + paste(constants$ANALYSIS_CODE_DIR_OPTIONS, collapse = ", ") +)) Apply / Chat Suggestion importance[1-10]: 5 __ Why: This suggestion improves the user experience by providing a more informative error message that lists the valid options for the code folder name.	Low
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• Author self-review: I have reviewed the PR code suggestions, and addressed the relevant ones.

[codecov]

Codecov Report

❌ Patch coverage is 94.11765% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/analysis.R	88.88%	1 Missing ⚠️

Files with missing lines	Coverage Δ
R/constants.R	100.00% <ø> (ø)
R/project.R	93.97% <100.00%> (-0.59%)	⬇️
R/analysis.R	54.94% <88.88%> (+0.53%)	⬆️

... and 2 files with indirect coverage changes

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