add `create_config()` function for yaml file creation #164

Attalowe · 2025-04-15T14:04:32Z

This PR is the config creation function for the pipeline:

Improved User Experience:
- Adds status messages about file creation
- Better error reporting for file editing issues
- Normalized path display in messages
Code Quality:

Strict YAML-safe type serialization using yaml::write_yaml()
Consistent 2-space indentation throughout the configuration structure
Separated file creation logic from editing operations
Added proper return value handling (invisible(path))

user interaction:
- out but open for ideas if the need to add any.
Enhanced Documentation:
- Using roxygen2 doc to be done later
Validation & Safety:
- Added existence check before file creation
- Standardized NA types for expected values (NA_real_, NA_character_)

…nfig.

… editing

…ssing distribution name placeholder.

…ale placeholder

… and path invisibly for piping

…ot current directory

… style

- Refined test for config file structure to reflect updated template - Added checks for top-level keys: `data`, `disease_name`, `severity` - Updated severity section expectations (e.g., added `epidist`) - Included assertions for NA placeholders at correct levels - Minor comments and formatting improvements for clarity

Attalowe · 2025-05-19T17:50:13Z

@Karim-Mane can you check the new changes .

Karim-Mane · 2025-05-20T15:19:20Z

R/create_config.R

+#' create_config("my_config.yaml")
+#'
+#' @note
+#' - Replace `NA` with appropriate values before using the configuration.


Suggested change

#' - Replace `NA` with appropriate values before using the configuration.

#' - Users need to replaces `NA` with appropriate values before using the configuration.

Karim-Mane · 2025-05-20T15:22:50Z

R/create_config.R

+        total_cases = NA_real_,
+        total_deaths = NA_real_,
+        death_in_confirmed = NA_real_,
+        account_for_delay = TRUE,


This argument is redundant - so could be removed.

Karim-Mane · 2025-05-20T15:26:59Z

R/create_config.R

+  #   "Linux" = system(paste("xdg-open", shQuote(path)), wait = FALSE)
+  # )
+
+   if (Sys.info()["sysname"] == "Darwin") {


use the switch instead of if statement. It has an else option that you can use to specify instruction for other conditions.

Karim-Mane · 2025-05-20T15:30:47Z

R/load_config.R

+#' Load Configuration Parameters
+#'
+#' @param path Path to config file (default: tempdir()/config.yaml)
+#' @return List with loaded data and parameters


Suggested change

#' @return List with loaded data and parameters

#' @returns List with loaded data and parameters

Karim-Mane · 2025-05-20T15:32:21Z

R/load_config.R

+  total_death <- NULL
+
+  # Load data if path provided
+  if (!is.na(config$data)) {


Suggested change

if (!is.na(config$data)) {

if (!is.na(config[["data"]])) {

replace all occurrences of $ with [[""]].

Karim-Mane · 2025-05-20T15:39:30Z

R/load_config.R

+      stop("Data file not found: ", config$data)
+    }
+
+    ext <- tools::file_ext(config$data)


No need to check for file extension. We will use {rio} for data import.

Karim-Mane · 2025-05-20T15:45:22Z

R/load_config.R

+
+  # Validate mutual exclusivity
+  if (!is.null(data) && (!is.null(total_count) || !is.null(total_death))) {
+    stop("Configuration conflict: Provide either data OR counts, not both")


Suggested change

stop("Configuration conflict: Provide either data OR counts, not both")

stop("Configuration conflict: Provide either the data path OR the count of total cases and deaths, not both")

Karim-Mane · 2025-05-20T15:45:49Z

R/load_config.R

+  total_death <- severity$total_deaths %||% NULL
+
+  # Validate mutual exclusivity
+  if (!is.null(data) && (!is.null(total_count) || !is.null(total_death))) {


use {checkmate} for this validation

Karim-Mane · 2025-05-20T15:48:01Z

R/load_config.R

+    stop("Configuration conflict: Provide either data OR counts, not both")
+  }
+
+  if (is.null(data) && (is.null(total_count) || is.null(total_death))) {


Try use {checkmate} here too.

Karim-Mane · 2025-05-20T15:48:30Z

R/load_config.R

+    stop("Must provide either data file or both total_cases/total_deaths")
+  }
+
+  list(


use a return() function

Attalowe added 20 commits April 7, 2025 12:06

added: config, check and report config file

9e3a72c

Add YAML Template for pipeline congig setup

8abb44b

Add epidist config for distribution setting

7ae5d51

add param subsection for distribution in YAML Tem.

ecc999a

add interval time estimate in YAML Tem

949b63c

add: error handing for config file

3cc2658

fix syntax

c17c88f

add: interactive file opening option with open_file flag in create_co…

e879db2

…nfig.

Add config file creation with error handling and optional interactive…

4aa175f

… editing

Redefine config function with default path

ec47526

Set string-type missing value for path

8b57a51

Initialize missing disease name placeh

0807f17

Add: Numeric placeholder for total_cases total_deaths count

25f21ca

Missing probability value placeholder

82fb4ed

Set default boolean(TRUE) for delay correction

7985275

Add: Nested distribution parameters, missing distribution type and mi…

be420d6

…ssing distribution name placeholder.

Add: distribution parameter subtree, Lognormal mean, SD, shape and sc…

c9b07b5

…ale placeholder

Add:Missing time interval placeholder

ee22bd6

ADD: Write template to YAML using type-safe serialization.

8f6cd60

Attempt to open config file in default editor with utils,handle error…

9c9df26

… and path invisibly for piping

Karim-Mane changed the title ~~create_config(), for yaml creation~~ add create_config() function for yaml file creation Apr 15, 2025

Attalowe and others added 9 commits April 23, 2025 15:26

redefine config file path from users directory to temporary directory

2be7447

system command change to reference the file from temp directory and n…

7710a50

…ot current directory

add cross-platform way to open the yaml file

257fd4c

Added: Documentation

6d129c2

updated

7ab7acf

Added: create_config test

4ce2822

update code

c06dce2

Refactor roxygen2 documentation for create_config() for clarity and…

20b9c2e

… style

Attalowe added 4 commits May 19, 2025 16:54

Add:function to read and load values from yaml

d8ae51f

restructure sentence

0212dbe

Add: funtion data_type to call 'get_data_type()'

f732a2b

added to man

461e84e

Karim-Mane requested changes May 20, 2025

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add `create_config()` function for yaml file creation #164

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Attalowe commented Apr 15, 2025 •

edited by Karim-Mane

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	#' - Replace `NA` with appropriate values before using the configuration.
	#' - Users need to replaces `NA` with appropriate values before using the configuration.

	#' @return List with loaded data and parameters
	#' @returns List with loaded data and parameters

	stop("Configuration conflict: Provide either data OR counts, not both")
	stop("Configuration conflict: Provide either the data path OR the count of total cases and deaths, not both")

add create_config() function for yaml file creation #164

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add `create_config()` function for yaml file creation #164

add `create_config()` function for yaml file creation #164

Attalowe commented Apr 15, 2025 •

edited by Karim-Mane

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