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Project class to manage a project folder

PMProject.Rd

This object can be used to manage a project folder. Use it to create analyses, freeze input files, etc.

Public fields

path

Full path to the project's folder

Methods

Public methods

Method new()

Create a PMProject object in an existing project's folder

Usage

PMProject$new(path)

Arguments

path

Path to the project

Method print()

Print method for PMProject

Usage

PMProject$print()

Method validate()

Validate the project folder. Makes sure all expected files and folder exist and are valid. Also validates that all input files referenced in inputs.local.yaml exist.

Usage

PMProject$validate()

Method parse_inputs()

Parse project.yaml and inputs.local.yaml into PMData objects. Reads the inputs definition file and the local paths file and combines them to create a list of PMData objects.

Usage

PMProject$parse_inputs()

Returns

A list of PMData objects, one for each input defined in project.yaml that has a corresponding path in inputs.local.yaml

Examples

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)

# After configuring project.yaml and inputs.local.yaml:
# data_list <- pm$parse_inputs()

Method list_analyses()

Get all analysis names from the project. Returns the names of all valid analysis folders in the analyses directory.

Usage

PMProject$list_analyses()

Returns

Character vector of analysis names

Examples

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
invisible(pm$create_analysis("data_preparation"))
invisible(pm$create_analysis("modeling"))
pm$list_analyses()

Method get_analysis()

Get an analysis object by name. Returns a PMAnalysis object for the specified analysis name.

Usage

PMProject$get_analysis(name)

Arguments

name

Character. Name of the analysis (folder name within analyses/).

Returns

PMAnalysis object for the specified analysis

Examples

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
invisible(pm$create_analysis("data_preparation"))
analysis <- pm$get_analysis("data_preparation")
analysis

Method get_artifact()

Get an artifact (output file) from an analysis by ID. Searches for files with the given ID (filename without extension) in analysis output directories.

Usage

PMProject$get_artifact(id, analysis_name = NULL)

Arguments

id

Character. The artifact ID (filename without extension).

analysis_name

Character. Optional name of the analysis to search in. If not provided, searches all analyses and fails if not exactly one match is found.

Returns

A PMData object with the artifact's ID and path.

Examples

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
analysis <- pm$create_analysis("data_preparation")

# Create a test output file
output <- analysis$get_output_path("results.csv", type = "table")
output$write(data.frame(x = 1:5))

# Get artifact from specific analysis
artifact <- pm$get_artifact("results", analysis_name = "data_preparation")

# Get artifact without specifying analysis (if unique across all analyses)
artifact <- pm$get_artifact("results")

Method create_analysis()

Create a new analysis from template. Creates a new analysis folder with template structure including README.md, directories (code/, outputs/, intermediate/, logs/), and .gitignore file.

Usage

PMProject$create_analysis(name)

Arguments

name

Character. Name of the analysis (will be the folder name).

Returns

PMAnalysis object representing the newly created analysis

Examples

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
analysis <- pm$create_analysis("data_preparation")
analysis

Method clone()

The objects of this class are cloneable with this method.

Usage

PMProject$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Create a valid project to load
folder <- withr::local_tempdir()
invisible(pm_create_project(folder))

# Load the project
pm <- PMProject$new(folder)
pm
#> PMProject:
#>   Path: /private/var/folders/0t/mvk3x4hx0pl31l5lcl11krcc0000gn/T/RtmpewLzrE/file102673885303a
#>   Analyses: 0


## ------------------------------------------------
## Method `PMProject$parse_inputs`
## ------------------------------------------------

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)

# After configuring project.yaml and inputs.local.yaml:
# data_list <- pm$parse_inputs()

## ------------------------------------------------
## Method `PMProject$list_analyses`
## ------------------------------------------------

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
invisible(pm$create_analysis("data_preparation"))
invisible(pm$create_analysis("modeling"))
pm$list_analyses()
#> [1] "data_preparation" "modeling"        

## ------------------------------------------------
## Method `PMProject$get_analysis`
## ------------------------------------------------

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
invisible(pm$create_analysis("data_preparation"))
analysis <- pm$get_analysis("data_preparation")
analysis
#> PMAnalysis:
#>   Name: data_preparation
#>   Path: /private/var/folders/0t/mvk3x4hx0pl31l5lcl11krcc0000gn/T/RtmpewLzrE/file102674977d813/analyses/data_preparation
#>   Project: /private/var/folders/0t/mvk3x4hx0pl31l5lcl11krcc0000gn/T/RtmpewLzrE/file102674977d813

## ------------------------------------------------
## Method `PMProject$get_artifact`
## ------------------------------------------------

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
analysis <- pm$create_analysis("data_preparation")

# Create a test output file
output <- analysis$get_output_path("results.csv", type = "table")
output$write(data.frame(x = 1:5))

# Get artifact from specific analysis
artifact <- pm$get_artifact("results", analysis_name = "data_preparation")

# Get artifact without specifying analysis (if unique across all analyses)
artifact <- pm$get_artifact("results")

## ------------------------------------------------
## Method `PMProject$create_analysis`
## ------------------------------------------------

folder <- withr::local_tempdir()
pm <- pm_create_project(folder)
analysis <- pm$create_analysis("data_preparation")
analysis
#> PMAnalysis:
#>   Name: data_preparation
#>   Path: /private/var/folders/0t/mvk3x4hx0pl31l5lcl11krcc0000gn/T/RtmpewLzrE/file102672a52a917/analyses/data_preparation
#>   Project: /private/var/folders/0t/mvk3x4hx0pl31l5lcl11krcc0000gn/T/RtmpewLzrE/file102672a52a917