diff --git a/CHANGES.md b/CHANGES.md index 17c5d9b38..e2f2c3eda 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -9,6 +9,7 @@ * `augur.io.read_metadata`: A new optional `dtype` argument allows custom data types for all columns. Automatic type inference still happens by default, so this is not a breaking change. [#1252][] (@victorlin) * `augur.io.read_vcf` has been removed and usage replaced with TreeTime's function of the same name which has improved validation of the VCF file. [#1366][] (@jameshadfield) +* export v2: Add support to specify metadata columns to export without using them as colorings. This can be done with the `metadata_columns` property in the Auspice config JSON or via the `--metadata-columns` flag in the command line. [#1384][] (@joverlee521) ### Bug Fixes @@ -18,13 +19,14 @@ [#1252]: https://github.com/nextstrain/augur/pull/1252 [#1366]: https://github.com/nextstrain/augur/pull/1366 +[#1384]: https://github.com/nextstrain/augur/pull/1384 [#1400]: https://github.com/nextstrain/augur/pull/1400 ## 24.0.0 (22 January 2024) ### Major Changes -* ancestral, translate: For VCF inputs please ensure you are using TreeTime 0.11.2 or later. A large number of bugfixes and improvements have been added in both Augur and TreeTime. [#1355][] and [TreeTime #263][] (@jameshadfield) +* ancestral, translate: For VCF inputs please ensure you are using TreeTime 0.11.2 or later. A large number of bugfixes and improvements have been added in both Augur and TreeTime. [#1355][] and [TreeTime #263][] (@jameshadfield) * ancestral, translate: GenBank files now require the (GFF mandatory) source feature to be present. [#1351][] (@jameshadfield) * ancestral, translate: For GFF files, we extract the genome/sequence coordinates by inspecting the sequence-region pragma, region type and/or source type. This information is now required. [#1351][] (@jameshadfield) @@ -41,7 +43,7 @@ * If a Gene/CDS in the GFF/GenBank file is unparsed we now print a warning. * ancestral: For VCF alignments, a VCF output file is now only created when requested via `--output-vcf`. [#1344][] (@jameshadfield) * ancestral: Improvements to command line arguments. [#1344][] (@jameshadfield) - * Incompatible arguments are now checked, especially related to VCF vs FASTA inputs. + * Incompatible arguments are now checked, especially related to VCF vs FASTA inputs. * `--vcf-reference` and `--root-sequence` are now mutually exclusive. * translate: Tree nodes are checked against the node-data JSON input to ensure sequences are present. [#1348][] (@jameshadfield) * utils::load_features: This function may now raise `AugurError`. [#1351][] (@jameshadfield)