Fix/testable slurm

[Alon-Alexander]

PR Type

Bug fix, Tests, Enhancement

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Description

• Fix SLURM tests to pass under R CMD check by using full Rscript path

• Improve mock SLURM job runner to return "PENDING" status correctly

• Expand test coverage across SLURM, analysis, project, parse_inputs, and file writing modules

• Bump version to 0.1.12 and update documentation

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Diagram Walkthrough

flowchart LR
  A["SLURM Mock Runner"] -->|"Use full Rscript path"| B["R CMD Check Compatible"]
  C["Mock squeue"] -->|"Return PENDING status"| D["Correct Job Status Detection"]
  E["Test Suite"] -->|"Add 60+ new tests"| F["Improved Coverage"]
  G["Version 0.1.12"] -->|"Update docs"| H["Documentation Updated"]

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File Walkthrough

	Relevant files
Bug fix, tests	1 files test_slurm.R Fix SLURM mock runner and expand test coverage                      +178/-14
Tests	4 files test_parse_inputs.R Add comprehensive input validation and error handling tests +122/-0  test_file_reading.R Add tests for RData object_names parameter                              +25/-0    test_analysis.R Add test for standalone analysis project access error        +20/-0    test_project_creation.R Add test for .gitignore copy failure handling                        +22/-0
Configuration changes	1 files DESCRIPTION Bump version from 0.1.11 to 0.1.12                                              +1/-1
Documentation	25 files NEWS.md Add changelog entry for version 0.1.12                                      +11/-0    index.md Add detailed release notes for 0.1.12                                        +20/-0    index.html Update HTML changelog with 0.1.12 release notes                    +13/-1    authors.md Update version reference to 0.1.12                                              +2/-2      authors.html Update HTML citation with version 0.1.12                                  +3/-3      getting-started.html Update version and regenerate example output                          +13/-13  getting-started.md Update example output paths in markdown                                    +11/-11  file-formats.html Update version and environment object references                  +3/-3      file-formats.md Update environment object reference in examples                    +1/-1      input-definitions.html Update version and build date                                                        +2/-2      slurm-integration.html Update version and build date                                                        +2/-2      PMAnalysis.html Update version and example output paths                                    +6/-6      PMAnalysis.md Update example output paths in markdown                                    +5/-5      PMProject.html Update version and example output paths                                    +6/-6      PMProject.md Update example output paths in markdown                                    +5/-5      PMSlurmRun.html Update version number                                                                        +1/-1      pm_infer_analysis.html Update version and example output paths                                    +7/-7      pm_infer_analysis.md Update example output paths in markdown                                    +6/-6      pm_project.html Update version and example output paths                                    +2/-2      pm_project.md Update example output paths in markdown                                    +1/-1      pm_create_project.html Update version and example output paths                                    +2/-2      pm_create_project.md Update example output paths in markdown                                    +1/-1      pm_write_file.html Update version number                                                                        +1/-1      pm_read_file.html Update version number                                                                        +1/-1      pkgdown.yml Update build timestamp                                                                      +1/-1
Additional files	22 files 404.html +1/-1      LICENSE.html +1/-1      index.html +1/-1      index.html +1/-1      PMData.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      search.json +1/-1

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

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	DRY out Rscript path resolution Extract the duplicated logic for finding the Rscript path into a helper function to reduce code duplication and improve maintainability. tests/testthat/test_slurm.R [231-237] -# R CMD check requires a full path to Rscript; never use bare "Rscript" -rscript_path <- base::file.path(base::R.home(), "bin", "Rscript") -if (!base::file.exists(rscript_path)) { - alt <- .real_sys_which("Rscript") - if (alt != "" && grepl("[/\\\\]", alt)) { - rscript_path <- alt +# at top of file +get_rscript_path <- function() { + path <- file.path(R.home(), "bin", "Rscript") + if (!file.exists(path)) { + alt <- .real_sys_which("Rscript") + if (nzchar(alt) && grepl("[/\\\\]", alt)) path <- alt } + path } +# later in mock_run_slurm_job +rscript_path <- get_rscript_path() [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies duplicated code for resolving the Rscript path and proposes a good refactoring to a helper function, which improves maintainability.	Medium
More

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

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
see 5 files with indirect coverage changes

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