Switch to CLI11 and addition of a cell metadata runmode

[atchox]

well, it is longer "mostly CLI updates"

Changes

• replaced boost::program options with CLI11
• updated some print functions to use ostreams for R portability
• --metadata mode for working with clusters efficiently
• --cell also accepts a container of containers as defined here in the CLI11 docs
• added tests for this
• update actions for this
• removal of the R package

[imallona]

Thanks @atchox ! can you describe the specific tests added for the cluster-aware use mode?

[Copilot]

Pull request overview

This pull request modernizes the yamet command-line interface and improves R portability by replacing boost::program_options with CLI11 and refactoring print functions to use output streams. The PR also removes the R package bindings and adds support for metadata files with cell clustering.

Changes:

• Replaced boost::program_options with CLI11 for command-line argument parsing
• Updated print functions to accept std::ostream& parameters instead of writing directly to std::cout for better R portability
• Added metadata file support with cluster-based aggregation capabilities
• Removed R package bindings (yamet-r directory) and build infrastructure

Reviewed changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
yamet-r/src/bindings.cpp	Deleted - R bindings removed
yamet-r/src/.clang-format	Deleted - R package configuration removed
yamet-r/configure	Deleted - R package build script removed
yamet-r/build.sh	Deleted - R package build script removed
yamet-r/R/yamet.R	Deleted - R wrapper function removed
yamet-r/NAMESPACE	Deleted - R package namespace removed
yamet-r/DESCRIPTION	Deleted - R package metadata removed
yamet-r/.Rbuildignore	Deleted - R package configuration removed
method/src/reference.cpp	Updated print method to accept ostream parameter
method/src/main.cpp	Migrated to CLI11, added metadata/cluster support
method/src/intervals.cpp	Updated print method to accept ostream parameter
method/src/file_map.cpp	Updated print/export methods for ostream and cluster support
method/src/cli_config.cpp	New file implementing CLI11-based argument parsing
method/src/boost.cpp	Deleted - replaced by cli_config.cpp
method/src/align.cpp	Added metadata parsing and FilesMeta support
method/include/lib/file_stream.h	Made detectCompression static
method/include/lib/file_classes.h	Added FileMeta structure and cluster support in aggregation
method/include/lib/chrData.h	Updated print method signatures to accept ostream
method/include/lib/align.h	Updated to use FilesMeta instead of string vectors
method/include/cli/cli_config.h	New header for CLI configuration structure
method/include/cli/boost.h	Deleted - replaced by cli_config.h
method/config/version.h.in	Added PROJECT_DESCRIPTION macro
method/CMakeLists.txt	Updated dependencies from boost::program_options to CLI11
.github/workflows/test.yml	Updated to install CLI11 and use new CLI syntax
.github/workflows/tar.yml	Updated to install CLI11 dependency
.github/workflows/memleaks.yml	Updated to install CLI11 and use new CLI syntax
.github/workflows/debug.yml	Updated to install CLI11 and use new CLI syntax

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[Copilot]

The error_code ec is passed to std::filesystem::exists but is never checked. If the filesystem operation itself fails (e.g., permission denied on parent directory), the error would be stored in ec but the code would still throw based on the return value of exists. Consider checking ec and throwing a more specific error if the filesystem operation failed rather than just treating it as "file doesn't exist".

[atchox]

Thanks @atchox ! can you describe the specific tests added for the cluster-aware use mode?

don't have a test for that currently – will add something now

[atchox]

added a test suite at b9a9beb generated from bruijnmeth