NEWS.md

In parabar: Progress Bar for Parallel Tasks

parabar 1.1.1

Added

• Add tests for progress tracking context when executed tasks throw an error. In relation to #44.

Changed

• Update action versions in GitHub workflows.

Fixed

• Fix hanging progress bar on errors in the ProgressTrackingContext.R class. Closes #44.
• Remove duplicated lines in UserApiConsumer class. Closes #41.
• Fix indentation in UML design diagram. Closes #45.
• Add missing apply operation to README documentation.

parabar 1.1.0

Added

• Update implementations of Service$apply operation for Backend classes to validate the provided margin argument before running the parallel operation.
• Add helper Helper$check_array_margins to validate the margins provided to the Service$apply operation.
• Add exception Exception$array_margins_not_compatible for using improper margins in the Service$apply operation.
• Add exception Exception$primitive_as_task_not_allowed for trying to decorate primitive functions with progress tracking in the ProgressTrackingContext class.
• Add helper Helper$is_of_class to check if an object is of a given class.
• Add optional arguments to the get_output operation of SyncBackend for consistency.
• Add more tests to improve coverage.
• Add implementation for Service$lapply and Service$apply operations for all classes that implement the Service interface.
• Add par_lapply and par_apply functions to the user API. These functions can be used to run tasks in parallel akin to parallel::parLapply and parallel::parApply, respectively.
• Add UserApiConsumer R6 class that provides an opinionated wrapper around the developer API of the parabar package. All parallel operations (e.g., par_sapply and par_lapply) follow more or less the same pattern. The UserApiConsumer encapsulates this pattern and makes it easier to extend parabar with new parallel functions (e.g., par_apply) while avoiding code duplication. The UserApiConsumer class can also be used as a standalone class for parallel operations, however, its primary purpose is to be used by the parallel task execution functions in the user API.

Changed

• Force early evaluation for the x argument of task execution functions in ProgressTrackingContext class.
• Update the log file for progress tracking to include parabar in file name.
• Disable warnings for file.create in ProgressTrackingContext class. This warning is superfluous since the code handles creation failures.
• Refactor test helpers to avoid code duplication.
• Update par_sapply to use the UserApiConsumer class.
• Update the developer API R6 classes to implement the lapply parallel operation.

Fixed

• Ensure task execution errors are propagated to the main session in AsyncBackend. Closes #35.
• Fixed the rendering of CC BY 4.0 license icons in README.md for the package website.
• Update .decorate method of ProgressTrackingContext to be more flexible. More specifically, the method will now throw when primitive functions are provided for decoration. The method can now handle both inline functions (i.e., function(x) x) and functions that have a body defined in terms of compound expressions (i.e., function(x) { x }). Closes #32.
• Fix the export operation in the SyncBackend and Context classes to fallback to the parent environment if the argument environment is not provided.

parabar 1.0.3

Fixed

• Fixed moved URL in package NEWS.md per CRAN request.

parabar 1.0.2

Fixed

• Fixed URLs in package documentation per CRAN request.

parabar 1.0.1

Fixed

• Update logo version from v0.x.x to v1.x.x.

parabar 1.0.0

Added

• Add CC BY 4.0 license for package documentation, vignettes, and website content.
• Add code coverage GitHub workflow via codecov and badge in README.
• Add tests for end-user API and developer API.
• Add vignette comparison.Rmd to compare parabar to the pbapply package, and provide rough benchmarks. The comparison.Rmd vignette is locally build from the comparison.Rmd.orig file (i.e., see this resource for more information).
• Add active biding Options$progress_log_path to handle generation of temporary files for tracking the execution progress of tasks ran in parallel. Using a custom path (e.g., for debugging) is also possible by setting this active binding to a desired path.

Changed

• Refactor Specification for testing purposes.
• Replace \dontrun{} statements in examples with try() calls.
• Update example for Options class to feature the progress_log_path active binding.
• Update progress logging injection approach in .decorate method of ProgressTrackingContext to use bquote instead of substitute.
• Breaking. Rename class ProgressDecorator to ProgressTrackingContext to be more consistent with the idea of backends that run in contexts.
• Add ... optional arguments to signature of get_output method in Service interface.
• Update private method .make_log of ProgressDecorator to use the progress_log_path option.
• Update UML diagram to include missing classes and changed methods. Also updated the corresponding diagram figure in the package documentation.

Fixed

• Update Specification to prevent incompatible cluster types (e.g., FORK) on Windows platforms. For such cases, a warning is issues and the cluster type defaults to PSOCK.
• Ensure make_logo can be ran on all platforms.

parabar 0.10.2

Changed

• Update README to add CRAN installation instructions and new badges.

Fixed

• Corrected expression for all files and folders in `.Rbuildignore.

parabar 0.10.1

Changed

• Initially removed \dontrun{} from make_logo function examples as per CRAN request in commit 87678fe. However, this results in the examples failing the R-CMD-check workflow. Reverted the change in commit a9d11ac.
• Update version for constant LOGO from v1.x.x to v0.x.x.

Fixed

• Add missing environment in examples for SyncBackend class.

parabar 0.10.0

Added

• Add new exported wrappers to the pkgdown reference section.
• Add several exported wrappers to the user API:
• clear: to clean a provided backend instance.
• export: to export variables from a given environment to the .GlobalEnv of the backend instance.
• peek: to list the variables names available on the backend instance.
• evaluate: to evaluate arbitrary expressions on the backend instance.
• Add type checks for the exported functions (i.e., the user API).
• Add helper method for checking and validating the type of an object. The Helper$check_object_type method checks if the type of an object matches an expected type. If that is not the case, the helper throws an error (i.e., Exception$type_not_assignable).

Changed

• Add .scss styles to override the table column width for the exported wrappers table in the pkgdown website.
• Update README and package documentation to mention new exported wrappers.
• Update order of topics for website reference section generated via pkgdown.
• Update roxygen2 @examples for exported wrappers. The code for the examples is located in the documentation for the start_backend function. All other exported wrappers (i.e., clear, export, peek, evaluate, and par_sapply) inherit the @examples section from start_backend.
• Update references in @seealso documentation sections.
• Change backend argument of par_sapply to backend = NULL. This implies, that par_sapply without a backend behaves identically to base::sapply.

Fixed

• Update export method to use the .GlobalEnv as fallback when exporting variables.

parabar 0.9.4

Added

• Add custom styles to extra.scss to improve documentation website.
• Add S3 print method for the LOGO object.

Changed

• Improve documentation for exported objects.
• Merge documentations of get_option, set_option, and set_default_options.
• Improved README. More specifically, added description for Service interface methods and enabled documentation linking (i.e., via ?) for pkgdown website.

Fixed

• Add missing export for Options class.
• Ensure the examples in ProgressBar use wait = TRUE when fetching the output.
• Fix bug in the evaluate backend operation. The expression passed to evaluate was not correctly passed down the function chain to parallel::clusterCall. See this question on StackOverflow for clarifications. Closes #9.

parabar 0.9.3

Changed

• Change type of private field .bar_config in ProgressDecorator class to list. This way, the configure_bar() method of ProgressBar class becomes an optional step.

Fixed

• Implement file locking when logging progress from child processes to avoid race conditions. The implementation is based on the filelock package. Closes #8.
• Fix typo in DESCRIPTION.

parabar 0.9.2

Fixed

• Update man-roxygen/parabar.R \html{...} to fix HTML validation errors. Closes #6.
• Fix package description in DESCRIPTION file to comply with CRAN requirements.

parabar 0.9.1

Fixed

• Update broken links in README file.
• Disable examples for par_sapply exported function due to exceeding the CRAN time limit for running examples.

parabar 0.9.0

Added

• Add package website via pkgdown and GitHub pages.
• Add GitHub workflow to automatically check the package on several platforms and R versions.
• Export all R6 classes as developer API and regenerate the namespace.
• Add preliminary package documentation to README file.
• Add exported wrapper par_sapply to run tasks in parallel and display a progress bar if appropriate.
• Add exported wrapper stop_backend to stop a backend instance.
• Add exported wrapper start_backend to create a backend instance based on the specified specification.
• Add exported wrapper configure_bar for configuring the type and behavior of the progress bar.
• Add exported wrapper set_option for Helper$set_option. This function is available to end-users and can be used to set the value of a specific option.
• Add helper method for setting package options. The static method Helper$set_option is a wrapper around base::getOption that sets the value of a specific option if it exists, or throws an error otherwise.
• Add package object documentation and relevant information in DESCRIPTION file.
• Add parabar logo startup message for interactive R sessions.
• Add function to generate package logo based on the ASCII template in inst/assets/logo/parabar-logo.txt.
• Add exported wrapper get_option for Helper$get_option. This function is available to end-users and can be used to get the value of a specific option or its default value.
• Add helper method for getting package options or their defaults. The static method Helper$get_option is a wrapper around base::getOption that returns the value of a specific option if it exists, or the default value set by the Options class otherwise.
• Add Options R6 class and set_default_options function to manage package options for parabar. The documented fields of the Options class represent the options that can be configured by the user. The set_default_options function can be used to set the default package options and is automatically run at package load time. In a nutshell, set_default_options stores an instance of Options in the base::.Options list under the key parabar.
• Implement initial software design. For a helicopter view, the design consists of backend and context objects. A backend represents a set of operations that can be deployed on a cluster produced by parallel::makeCluster. The backend, therefore, interacts with the cluster via specific operations defined by the Service interface. The context represents the specific conditions in which the backend operations are invoked. A regular context object simply forwards the call to the corresponding backend method. However, a more complex context can augment the operation before invoking the backend operation. One example of a complex context is the ProgressDecorator class. This class extends the regular Context class and decorates the backend sapply operation to provide progress tracking and display a progress bar.
• Add context classes to consume and decorate backend APIs. Since the context classes implement the Service interface, the client can interact with context objects as if they represents instances of Backend type. This release introduces the following contexts:
• Context: represents a regular context that wraps backend objects. In other words, all Service methods calls implemented by this context are forwarded to the corresponding methods implemented by the backend object.
• ProgressDecorator: represents a progress tracking context. This context decorates the sapply method available on the backend instance to log the progress after each task execution and display a progress bar.
• ContextFactory: represents a blueprint for obtaining specific context instances.
• Add classes to work with synchronous and asynchronous backends:
• Service: represents an interface that all concrete backends must implement. It contains the methods (i.e., operations) that can be requested from a given backend instance. These methods form the main API of parabar.
• Backend: represents an abstract class that implements the Service interface. It contains fields and methods relevant to all concrete backend implementations that extend the class.
• SyncBackend: represents a concrete implementation for a synchronous backend. When executing a task in parallel via the sapply method, the caller process (i.e., usually the interactive R session) is blocked until the task finishes executing.
• AsyncBackend: represents a concrete implementation for an asynchronous backend. After lunching a task in parallel via the sapply method, the method returns immediately leaving the caller process (e.g., the interactive R session) free. The computation of the task is offloaded to a permanent background R session. One can read the state of the task using the public field (i.e., active binding) task_state. Furthermore, the results can be fetched from the background session using the get_output method, which can either block the main process to wait for the results, or attempt to fetch them immediately and throw an error if not successful.
• Specification: represents an auxiliary class that encapsulates the logic for determining the type of cluster to create (i.e., via parallel::makeCluster), and the number of nodes (i.e., R processes) for the cluster.
• TaskState: represents an auxiliary class that encapsulates the logic for determining the state of a task.
• BackendFactory: represents a blueprint for obtaining concrete backend implementations.
• Add Helper, Warning, and Exception R6 classes. These classes contain static member methods that provide useful utilities, handle warning messages, and throw informative errors, respectively.
• Add UML diagram for package classes. The classes provided by parabar can be split in three categories, namely (1) backend classes responsible for managing clusters, (2) context classes that decorate backend objects with additional functionality (e.g., progress tracking), and (3) progress bar classes providing a common interface for creating and interacting with various progress bars.

parabar 0.1.0

Added

• Add Bar abstraction for working with progress bars in R. Currently, two types of of progress bars are supported (i.e., BasicBar and ModernBar). BasicBar uses as engine the utils::txtProgressBar, and ModernBar relies on the R6 class obtained from progress::progress_bar. Specific concrete instances of these bar types can be requested from the BarFactory.

parabar documentation built on May 29, 2024, 8:42 a.m.