Cleanup unneeded modules

[akotlar]

• Cleanup unneeded modules

Summary by CodeRabbit

• Chores
  • Removed multiple GitHub Actions workflows related to building, testing, and installing Perl applications.
  • Deleted various configuration and documentation files, including installation guides and changelogs.
  • Removed several Perl modules and packages related to genomic data processing and annotations.
  • Eliminated scripts for managing database interactions and file handling.
  • Cleaned up unused or redundant files and directories across the project.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

This pull request involves the deletion of multiple files related to the Bystro Annotator project, including GitHub Actions workflows for building, testing, and installing the application, as well as various Perl scripts and configuration files. The removed files encompassed workflows for Docker builds, code quality checks, package builds, and installation scripts, along with documentation files and Perl modules that handled genomic data processing. The overall change signifies a significant reduction in the project's complexity and functionality.

Changes

File Path	Change Summary
.github/workflows/perl-build-docker.yml	Deleted workflow for building Docker images for the Perl application.
.github/workflows/perl-code-tidy.yml	Deleted workflow for performing code quality checks on Perl files.
.github/workflows/perl-package-build.yml	Deleted workflow for building the Bystro Annotator Perl package.
.github/workflows/perl-test-install-apt.yml	Deleted workflow for automating installation and verification using APT.
.github/workflows/perl-test-install-rpm.yml	Deleted workflow for automating installation and verification using RPM.
BUILD.md	Deleted documentation for configuring the Bystro tool for building databases.
Changes.md	Deleted changelog documenting updates and changes across software versions.
Dockerfile.perl	Deleted Dockerfile defining the environment for Perl development.
FIELDS.md	Deleted documentation for annotation fields used in Bystro.
INSTALL.md	Deleted installation instructions for the Bystro ancestry CLI and Annotator.
Makefile	Removed install-go target and updated dependencies for installation and development.
README.md	Modified for formatting and content organization, with some sections marked as "coming soon."
TUTORIAL.md	Deleted comprehensive tutorial for the Bystro web application.
config/.gitignore	Deleted ignore rule for beanstalk.yml.
config/hg19.yml	Deleted configuration settings for the hg19 genome assembly.
config/hg38.yml	Deleted configuration settings for the hg38 genome assembly.
dev-startup.yml	Deleted configuration for Bystro development environment applications.
go/cmd/dosage/main.go	Deleted command-line application for processing ARROW data files.
go/decompress/decompress.go	Deleted functionality for reading and decompressing data from BGZF and Gzip formats.
go/decompress/decompress_test.go	Deleted unit tests for decompression functionality.
go/go.mod	Deleted module definition and dependency management for Go.
go/test/opensearch/testdata/input.txt	Deleted test data formatted for specific input processing.
install-apt.sh	Deleted installation script for various software components.
install-rpm.sh	Deleted installation script for RPM dependencies.
install/detect-shell-profile.sh	Deleted script for detecting and managing shell profile files.
install/export-bystro-libs.sh	Deleted script for exporting Bystro libraries to the shell profile.
install/install-apt-deps.sh	Deleted script for automating installation of APT dependencies.
install/install-go.sh	Deleted script for automating the installation of the Go programming language.
install/install-htslib.sh	Deleted script for installing libdeflate and HTSlib libraries.
install/install-liftover-linux.sh	Deleted script for installing the liftOver tool.
install/install-lmdb-linux.sh	Deleted script for installing the LMDB library.
install/install-mac-deps.sh	Deleted script for installing Homebrew and MacOS dependencies.
install/install-perl-libs.sh	Deleted script for installing various Perl libraries.
install/install-perlbrew-linux.sh	Deleted script for installing Perl using perlbrew.
install/install-rpm-deps.sh	Deleted script for installing RPM dependencies for MariaDB and development tools.
install/utils.sh	Deleted utility script for appending lines to profile files.
perl/.gitignore	Deleted ignore rules for the Perl project.
perl/.perlcriticrc	Deleted configuration for Perl::Critic static analysis tool.
perl/.perltidyrc	Deleted configuration for Perl Tidy code formatting tool.
perl/.tidyallrc	Deleted configuration for Code::TidyAll coding standards enforcement.
perl/INSTALL.md	Deleted installation and configuration instructions for the Bystro Annotator package.
perl/README.md	Deleted comprehensive documentation for the Bystro High Dimensional Genomic Annotator.
perl/bin/bystro-annotate.pl	Deleted script for annotating input files using the Bystro database.
perl/bin/bystro-build.pl	Deleted script for building binary genome assemblies.
perl/bin/bystro-utils.pl	Deleted script for executing utility functions based on configurations.
perl/bin/read_db_util.pl	Deleted script for reading genomic data based on specified parameters.
perl/cpanfile	Deleted file listing prerequisite Perl modules.
perl/dist.ini	Deleted configuration settings for the Bystro Perl distribution.
perl/issues/subtxn_bug.pl	Deleted script for managing a database using LMDB.
perl/lib/Interface.pm	Deleted package for command-line interaction for data processing.
perl/lib/Seq.pm	Deleted package responsible for annotating SNP files.
perl/lib/Seq/Base.pm	Deleted base class for configuring logging and database settings.
perl/lib/Seq/Build.pm	Deleted package for managing the construction of genome assembly files.
perl/lib/Seq/DBManager.pm	Deleted package for managing database connections using LMDB.
perl/lib/Seq/Definition.pm	Deleted package for managing attributes related to sequence processing.
perl/lib/Seq/Headers.pm	Deleted module for managing header features in sequence data.
perl/lib/Seq/InputFile.pm	Deleted module for validating input files related to SNP data.
perl/lib/Seq/Output.pm	Deleted package for generating output strings from genomic data.
perl/lib/Seq/Output/Delimiters.pm	Deleted package for managing delimiters used in output formatting.
perl/lib/Seq/Output/Fields.pm	Deleted package for managing output fields in genomic data.
perl/lib/Seq/Role/ConfigFromFile.pm	Deleted role for configuring classes using a YAML file.
perl/lib/Seq/Role/IO.pm	Deleted role for handling file operations, particularly for compressed files.
perl/lib/Seq/Role/Message.pm	Deleted role for logging and messaging functionalities.
perl/lib/Seq/Role/Validator.pm	Deleted role for validating input files.
perl/lib/Seq/Statistics.pm	Deleted package for managing statistical data related to genomic sequences.
perl/lib/Seq/Tracks.pm	Deleted base class for managing track classes within genomic data processing.
perl/lib/Seq/Tracks/Base.pm	Deleted base class for track-related functionalities.
perl/lib/Seq/Tracks/Base/MapFieldNames.pm	Deleted package for managing feature name mappings.
perl/lib/Seq/Tracks/Base/MapTrackNames.pm	Deleted package for managing track names and their identifiers.
perl/lib/Seq/Tracks/Base/Types.pm	Deleted package for managing track types and conversions.
perl/lib/Seq/Tracks/Build.pm	Deleted base class for building track objects.
perl/lib/Seq/Tracks/Build/CompletionMeta.pm	Deleted package for tracking completion status of track builds.
perl/lib/Seq/Tracks/Build/LocalFilesPaths.pm	Deleted package for constructing absolute paths for local files.
perl/lib/Seq/Tracks/Cadd.pm	Deleted package for handling CADD data in genomic contexts.
perl/lib/Seq/Tracks/Cadd/Build.pm	Deleted package for integrating CADD data into a main database.
perl/lib/Seq/Tracks/Cadd/Order.pm	Deleted package for managing nucleotide ordering.
perl/lib/Seq/Tracks/Gene.pm	Deleted package for managing gene-related data.
perl/lib/Seq/Tracks/Gene/Build.pm	Deleted package for building gene tracks from reference data.

Possibly related PRs

• reduce perl docker image size #579: The changes in this PR involve modifications to the Dockerfile.perl, which is directly related to the deleted .github/workflows/perl-build-docker.yml file in the main PR, as both pertain to the Docker image for the Perl application.
• created doesn't act in the same way as expected, doesn't work on draft releases #592: This PR modifies the workflow configuration in .github/workflows/perl-build-docker.yml, which is directly related to the main PR that deleted this file, as both involve the workflow for building the Docker image.
• Feature/remove unused go modules #595: The removal of unused Go modules in this PR may not directly relate to the main PR, but it involves changes to the Dockerfile and overall project structure, which could indirectly affect the build process described in the main PR.

Suggested reviewers

• cristinaetrv

🐇 In the meadow, where changes abound,
Files have vanished, no longer found.
Workflows and scripts, all gone with a hop,
Bystro's journey takes a new stop.
With less in the basket, we tidy the way,
For brighter tomorrows, come what may! 🌼

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📥 Commits

Reviewing files that changed from the base of the PR and between 82aa318 and 7fcd607.

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[cristinaetrv]

Lgtm!