genome-sampler

A long-overdue release of genome-sampler which brings it up to date with the most recent release version of QIIME 2 (2024.10). The documentation has also been transitioned to Jupyter Book 2.

Enjoy!

What’s Changed¶

• NEW: Begin adding label_seqs by @Oddant1 in #49
• IMP: Fill missing metadata values with given placeholder by @Oddant1 in #52
• IMP: Use Evans Fancy Open by @Oddant1 in #54
• ENH: adds vcf-based alignment masking by @gregcaporaso in #56
• BUG: fix pseudo-vcf parsing by @ebolyen in #58
• BUG: fix newline handling by @ebolyen in #59
• ENH/DEP: add temporary action pending framework fix by @gregcaporaso in #60
• BUG: fix MSA index using minting from seq ids by @ebolyen in #62
• MAINT: mark label_unaligned_seqs as deprecated by @thermokarst in #61
• CI: Library updates by @thermokarst in #74
• decrease frequency of stochastic test failures by @gregcaporaso in #82
• CI: build env file by @thermokarst in #77
• MAINT: replaces VCFLikeMaskFormat with VCFMaskFormat by @gregcaporaso in #65
• IMP: generalize label-seqs by @gregcaporaso in #72
• DOC: update install instructions for conda envs by @thermokarst in #83
• Benchmarks by @ebolyen in #84
• IMP: use config and cores in snakemake by @ebolyen in #85
• CI/BUG: incorrect package names by @thermokarst in #86
• MAINT: add snakemake to env file by @ebolyen in #87
• DOC: tutorial updates by @gregcaporaso in #69
• VER: 2020.11.0.dev0 by @thermokarst in #91
• CI: set master CI alp target to “staging” by @thermokarst in #90
• address memory issue with large GISAID files by @gregcaporaso in #94
• ci: new set-env api by @thermokarst in #95
• ci: handle conda virtual packages by @thermokarst in #96
• ci/maint: use latest qiime2 staging env by @thermokarst in #97
• MAINT: updates setup files & CI by @lizgehret in #101
• update base branch name by @gregcaporaso in #104
• prep config for read the docs by @gregcaporaso in #106
• add formal usage examples to docs by @gregcaporaso in #107
• update project administrative information by @gregcaporaso in #109
• Update snakemake tutorial by @gregcaporaso in #110
• update for q2doc change by @gregcaporaso in #111

New Contributors¶

• @Oddant1 made their first contribution in #49
• @lizgehret made their first contribution in #101

Full Changelog: #2020.6.1...2025.02.0

This release is timed with the publication of our initial paper on genome-sampler in F1000 Research.

2020.6.0