Feature/subfolders in outputs

[Alon-Alexander]

User description

Solves #19

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PR Type

Enhancement

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Description

• Add subfolder support to PMAnalysis$get_output_path() method

• Enable both unix-style (/) and windows-style () path delimiters

• Update list_outputs() to handle nested folder structures

• Extend get_artifact() to support subfolder paths in both PMAnalysis and PMProject

• Add comprehensive test coverage for nested output directories

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Diagram Walkthrough

flowchart LR
  A["get_output_path<br/>with subfolders"] -->|"normalize path<br/>delimiters"| B["Create nested<br/>directories"]
  B -->|"recursive=TRUE"| C["list_outputs<br/>finds nested files"]
  A -->|"support both / and \"| D["get_artifact<br/>finds files<br/>in subfolders"]
  C -->|"return PMData<br/>objects"| E["Read/Write<br/>nested outputs"]

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File Walkthrough

	Relevant files
Enhancement	3 files analysis.R Add subfolder support to get_output_path and list_outputs +13/-14  data.R Auto-create parent directories on write operations              +5/-2      project.R Normalize subfolder IDs in get_artifact method                      +4/-0
Tests	1 files test_analysis.R Add comprehensive tests for nested folder operations          +76/-0
Configuration changes	2 files DESCRIPTION Bump version from 0.1.10 to 0.1.11                                              +1/-1      pkgdown.yml Update build timestamp and metadata                                            +1/-1
Documentation	7 files NEWS.md Document new subfolder support features                                    +8/-0      index.md Add changelog entry for version 0.1.11                                      +9/-0      getting-started.md Update documentation with new subfolder examples                  +11/-11  PMAnalysis.md Document subfolder support in get_output_path                        +19/-5    PMAnalysis.Rd Update roxygen documentation for subfolder feature              +11/-0    getting-started.html Regenerate HTML documentation with updates                              +13/-13  PMAnalysis.html Regenerate reference documentation HTML                                    +20/-7
Additional files	41 files data_utils.R +0/-1      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      index.html +12/-1    PMData.html +1/-1      PMProject.html +6/-6      PMProject.md +5/-5      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-find_code_folder_name.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_infer_analysis.html +7/-7      pm_infer_analysis.md +6/-6      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

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PR Code Suggestions ✨

• Author self-review: I have reviewed the PR code suggestions, and addressed the relevant ones.

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Previous suggestions

Suggestions up to commit 40bb8e2

Category	Suggestion	Impact
Possible issue	Filter out directories from results In the list_outputs method, filter the results of list.files to exclude directories, ensuring only files are returned as PMData objects. R/analysis.R [243-255] # Get all files in the directory files <- list.files(outputs_dir, full.names = FALSE, recursive = TRUE) +if (length(files) == 0) { + return(list()) +} + +# Filter to only files (not directories) +full_paths <- file.path(outputs_dir, files) +is_file <- !dir.exists(full_paths) +files <- files[is_file] + if (length(files) == 0) { return(list()) } # Create PMData objects using lapply file_ids <- gsub("\\", "/", tools::file_path_sans_ext(files), fixed = TRUE) file_paths <- normalizePath(file.path(outputs_dir, files), mustWork = FALSE) lapply(seq_along(files), function(i) { PMData$new(id = file_ids[i], path = file_paths[i]) }) Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies a bug where directories would be listed as outputs, and provides a valid fix to filter them out.	Medium
	Prevent writing to an existing directory In the write method, add a check to prevent writing if self$path is an existing directory, and stop with an informative error message. R/data.R [103-115] write = function(x, ...) { + # Stop if path is an existing directory + if (dir.exists(self$path)) { + stop("Cannot write to a path that is an existing directory: ", self$path, call. = FALSE) + } + # Create the folder in case it doesn't exist dir.create(dirname(self$path), showWarnings = FALSE, recursive = TRUE) # For RData files, we need to preserve object names from the original call ext <- tolower(tools::file_ext(self$path)) if (ext %in% c("rdata", "rda")) { # ... } else { # Call pm_write_file for other file types pm_write_file(self$path, x, ...) } invisible(self) } Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies an edge case where writing to a path that is an existing directory would fail, and proposes a reasonable guard clause.	Medium

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

❌ Your project status has failed because the head coverage (68.13%) is below the target coverage (80.00%). You can increase the head coverage or adjust the target coverage.

Files with missing lines	Coverage Δ
R/analysis.R	54.51% <100.00%> (-0.44%)	⬇️
R/data.R	84.05% <100.00%> (+0.47%)	⬆️
R/data_utils.R	95.65% <ø> (ø)
R/project.R	94.02% <100.00%> (+0.04%)	⬆️

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Persistent suggestions updated to latest commit e664cf8