What's Changed

• GitHub Actions runner ubuntu upgrade 20.04 -> 24.04 by @tomkinsc in #118
• Update docker baseimage viral-baseimage to 0.3.0 by @tomkinsc in #120

Full Changelog: v2.4.2...v2.4.3

What's Changed

• Add splitcode to requirements by @lauraluebbert in #115
• viral-core container Dockerfile: bump viral-baseimage 0.2.3 -> 0.2.4 by @tomkinsc in #117

Full Changelog: v2.4.1...v2.5.0

What's Changed

• update calc_mem.py script used to obtain within-container memory limit for cgroup v2 by @tomkinsc in #114

Full Changelog: v2.4.0...v2.4.1

What's Changed

• add NCBI datasets to conda dependencies by @tomkinsc in #113

Full Changelog: v2.3.6...v2.4.0

What's Changed

• align_and_fix: tolerate whitespace in headers by @dpark01 in #112

Full Changelog: v2.3.5...v2.3.6

What's Changed

• make samtools faidx tolerate spaces in fasta headers by @dpark01 in #111

Full Changelog: v2.3.4...v2.3.5

What's Changed

• handle spaces in fasta headers in Picard indexing by @dpark01 in #110

Full Changelog: v2.3.3...v2.3.4

What's Changed

• in util.version.py::get_project_path(), consider calling modules to report VERSION correctly by @tomkinsc in #109

Full Changelog: v2.3.2...v2.3.3

What's Changed

functionality updates

• In cmd.py argparse common_args(), set default number of threads to all available if --threads is unspecified by @tomkinsc in #104
• index bam before calling samtools idxstats; warn user if input lacks reads by @tomkinsc in #102

dependency updates

• add fgbio to conda dependencies by @tomkinsc in #103
• update viral-baseimage 0.2.2 -> 0.2.3 (with fully-featured qsv) by @tomkinsc in #100

build updates

• update coverage config and testing config inherited by derived docker images by @tomkinsc in #99
• fix docbuild by @dpark01 in #106
• more ReadTheDocs fixes by @dpark01 in #107

Full Changelog: v2.3.1...v2.3.2

• Update docker base image from viral-baseimage 0.2.1 -> 0.2.2 (PR #97)
• Update python version 3.8 -> 3.10, and also associated dependencies necessary for py 3.10 (PR #98)