NEWS.md

In epi-sam/SamsElves: Helper functions for the data science at IHME

ChangeLog for SamsElves Package

2025-05-05 v.0.3.19

• feature:
• build_metadata_shell now tries to find the script_path used to call it, or return NA
  • tries with both interactive and submitted scripts
  • submitted scritps require a script_path object in .GlobalEnv (read from the CLI), which is now provided by submit_job by default

2025-03-09 v0.3.18

• feature:
• parse_all_named_cli_args allows unlock/lockBinding for variables that may already be locked at time of parsing

2025-03-09 v0.3.17

• bugfix:
• save_file csv_writer rewrite - default now only quotes necessary strings (those withd delimeters)

2025-02-21 v0.3.16

• feature:

• save_file now has csv_opt argument and new default (readr::write_excel_csv) to preserve diacritics

• bugfix:

• assert_square has option for 0-row data.table, which is used by aggregate_parents_from_children

2025-02-21 v0.3.15

• improved:
• replaced sys.getenv calls with better cross-platform sys.info

2024-10-22 v0.3.14

• improved:
• build_metadata_shell finds number of cores using 'nproc'

2024-10-22 v0.3.13

• bugfix:
• aggregate_from_children_to_parents
  • assert complete cases

2024-10-22 v0.3.12

• added:
• aggregate_from_children_to_parents and tests
  • roll up values from a data set according to a hierarchy

2024-10-22 v0.3.11

• behavior change:
• save_file overwrites by default - this is normal save function behavior
  • forbid_overwrite argument is in sunset period

2024-10-22 v0.3.10

• documentation updates:
• aggregate_parents_from_children and supporting assertions

2024-10-22 v0.3.9

• bugfix:
• aggregate_parents_from_children and supporting assertions

2024-10-22 v0.3.8

• added:
• get_new_output_dv

2024-10-22 v0.3.7

• added:
• aggregate_parents_from_children and supporting assertions

2024-10-22 v0.3.6

• bugfixes:
• submit_job and parse_all_named_cli_args - fine-tuned NULL and NA value handling
• messaging system - more internally consistent implementation

2024-10-22 v0.3.5

• bugfixes:
• apply_comma_string_to_list - failed for NULL items
• parse_all_named_cli_args - new options to assign NA, NaN and NULL types (default TRUE)
• wait_on_slurm_job_ids - improved messaging

2024-09-30 v0.3.4

• added:
• utils_io.R from ihme.covid package
  • make_new_output_dir - create a version-incremented run-date folder based on a 'YYYY_MM_DD.VV' run-date folder structure
  • supported by get_latest_output_date_index and get_new_output_dir
  • get_latest_output_dir - get the latest output directory based on a 'YYYY_MM_DD.VV' run-date folder structure
  • added tests, updated deprecated methods
• documented:
• some previously undocumented helper functions for various methods (not exported)

2024-09-23 v0.3.3

• updated:
• build_metadata_shell
  • now trims sessionInfo for otherPkgs as well as loadedOnly to reduce metadata bloat.
• added:
• increment_file_version
  • adds a _v1/_v2/etc. to the end of a file name to increment the version number
  • retains original file extension

2024-09-19 v0.3.2

• updated:
• read_file
  • now includes option for custom csv reading function since data.table::fread can have quotation-doubling issues
  • also includes ... arg to pass additional user-desired args to the reader function (works for any underlying reader function)

2024-09-18

• deprecated:
• submit_job_array (functionality now handled by submit_job natively)
• updated:
• submit_job
• parse_all_named_cli_args
  • Now accepts atomic vectors for CLI arguments, converts to a comma-separated string, and then converts back to a vector of the correct type when parsed (behavior allowed by default, but can be turned off).
  • option to send email to user when job completes
• build_metadata_shell
  • switched from sacct to squeue for performance
  • now includes a selection of sessionInfo for R version, package versions, etc. for pipeline provenance

2024-09-06

• added:
• utils
• refined:
• submit_job & submit_job_array
  • added console-style log option (combine stderr and stdout)

2023-12-04

• deprecated:
• define_roots
• detach_user_packages
• get_version_from_path

• preflight_checks

• added:

• test suite
• is_x
• make_versioned_dir
• prep_path
• submit_job
• submit_job_array
• utils_io
• wait_on_jobs

2022-04-15

• added
• preflight_checks
• children_of_parents

epi-sam/SamsElves documentation built on June 12, 2025, 7 a.m.