Prepare for version 5.2.0

CHANGELOG.md

@@ -1,64 +1,66 @@
 # Changelog
+
 All notable changes to the PipeVal tool.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
----
+## [5.2.0] - 2024-12-13
 
-## [Unreleased]
 ### Changed
+
 - Update `pysam` version to `0.22.1`
----
 
 ## [5.1.0] - 2024-07-08
+
 ### Added
+
 - Add validation flowchart
 - Add support for unmapped BAM
 - Add additional MIME type for GZIP compressed files
 - Add support for checksum files formatted with any whitespace separator
 
----
-
 ## [5.0.0] - 2024-02-16
+
 ### Added
-- Validation skip functionality for checksums
 
----
+- Validation skip functionality for checksums
 
 ## [5.0.0-rc.3] - 2023-12-07
+
 ### Added
-- Integrity test for compressed files
 
----
+- Integrity test for compressed files
 
 ## [5.0.0-rc.2] - 2023-12-06
+
 ### Added
-- FASTQ validator
 
----
+- FASTQ validator
 
 ## [5.0.0-rc.1] - 2023-11-22
+
 ### Changed
-- Restructured CLI to have common main command `pipeval`
 
----
+- Restructured CLI to have common main command `pipeval`
 
 ## [4.0.0] - 2023-11-22
+
 ### Added
-- Parallelize validation
 
----
+- Parallelize validation
 
 ## [4.0.0-rc.2] - 2023-04-24
+
 ### Changed
-- Resolve potential symlinks before validation
 
----
+- Resolve potential symlinks before validation
 
 ## [4.0.0-rc.1] - 2023-04-11
+
 ### Added
+
 - Add check for empty BAM files (valid header but no reads).
 - Add auto-build workflow to push image to `uclahs-cds` registry
 - Add repo source label to Dockerfile
@@ -70,6 +72,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Compression validation and detection through `python-magic`
 
 ### Changed
+
 - Make `-t` optional, default to `file-input`
 - Explicitly set Python version to `3.10`
 - Split validation and checksum generation into different CLI commands
@@ -78,38 +81,50 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Update README input tables and command examples
 - Re-structure README with details of current tool
 
-### Fixed
-
 ### Removed
+
 - Remove deprecated parameter options from README
 - Remove inaccessible design doc link from README
 - Remove directory checking
 - Remove user-specified file type option
 
----
-
 ## [3.0.0] - 2022-08-03
-### Updated
-- Updated bl-base to 1.1.0
-- Installed tools using `mamba`
 
 ### Added
+
 - Add `bldocker` user and group to Dockerfile
 - Add support for mutliple input files
 
 ### Changed
+
+- Updated bl-base to 1.1.0
+- Installed tools using `mamba`
 - Convert module to Python CLI package; now runs directly from commandline with `validate`.
-- Single source package version from \_\_init__.py
+- Single source package version from \_\_init\_\_.py
 - Use `pysam` instead of `samtools` in bam file validation.
 
 ### Fixed
-- Add handling for valid file types whose validation is not yet implemented.
 
----
+- Add handling for valid file types whose validation is not yet implemented.
 
 ## [2.1.6] - 2021-10-18
+
 ### Changed
--  File type detection update to properly detect file type when filename contains multiple .
+
+- File type detection update to properly detect file type when filename contains multiple .
 
 ### Fixed
+
 - Fixed bug with detecting fasta files
+
+[2.1.6]: https://github.com/uclahs-cds/package-PipeVal/releases/tag/v2.1.6
+[3.0.0]: https://github.com/uclahs-cds/package-PipeVal/compare/v2.1.6...v3.0.0
+[4.0.0]: https://github.com/uclahs-cds/package-PipeVal/compare/v4.0.0-rc.2...v4.0.0
+[4.0.0-rc.1]: https://github.com/uclahs-cds/package-PipeVal/compare/v3.0.0...v4.0.0-rc.1
+[4.0.0-rc.2]: https://github.com/uclahs-cds/package-PipeVal/compare/v4.0.0-rc.1...v4.0.0-rc.2
+[5.0.0]: https://github.com/uclahs-cds/package-PipeVal/compare/v5.0.0-rc.3...v5.0.0
+[5.0.0-rc.1]: https://github.com/uclahs-cds/package-PipeVal/compare/v4.0.0...v5.0.0-rc.1
+[5.0.0-rc.2]: https://github.com/uclahs-cds/package-PipeVal/compare/v5.0.0-rc.1...v5.0.0-rc.2
+[5.0.0-rc.3]: https://github.com/uclahs-cds/package-PipeVal/compare/v5.0.0-rc.2...v5.0.0-rc.3
+[5.1.0]: https://github.com/uclahs-cds/package-PipeVal/compare/v5.0.0...v5.1.0
+[5.2.0]: https://github.com/uclahs-cds/package-PipeVal/compare/v5.1.0...v5.2.0