Merge Staging for release of 2.4.0 #584
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This commit is to fix few bugs: - #540 : The empty files are skip during the sketch step of Mash, they are then catch in the prodigal step and are returned as Unclassified - #549 : `--force` has been modified to deal with #540 - Prodigal wasn't returning the empty files as failed genomes, it was only skipping them. These genomes are now returned in the summary file and flagged as Unclassified.
package ~= x.y.z is the same as (package >= x.y.z, package == x.*). This prevents the wrong numpy version (2.x) from being installed, such as in #467 (which is not yet properly fixed and should NOT have been closed). See: https://peps.python.org/pep-0440/#compatible-release
Merge master to Staging
fix(setup.py): use ~= to constrain major version
Skani branch
In some cases, when running the 3 classify steps independently, a genome may be filtered out in the alignment step. However, it's still present in the ani screening from the classify step and can have a ANI > 95% ( this can happen with partial genomes, where AF can still be high) Tk would try to report it twice in the summary file and would return an error. Instead we report it as classified with ani, but with a warning from the alignment step ( MSA < 10%). skani should reduce the number of such cases as it keep AF low for partial genomes.
fix(fixing of issue #573):
In the generated summary.tsv files, several columns have been renamed for clarity and consistency. The following columns have been affected: - fastani_reference column has been renamed to closest_genome_reference. - fastani_reference_radius column has been renamed to closest_genome_reference_radius. - fastani_taxonomy column has been renamed to closest_genome_taxonomy. - fastani_ani column has been renamed to closest_genome_ani. - fastani_af column has been renamed to closest_genome_af.
Description of --genes flag is more explicit and mentions input as predicted proteins
Rename summary fields
The summary files are still produces even if all genomes fail the prodigal step
feat(fix of #576):
update md5sum, changelog, and announcement.
# Conflicts: # gtdbtk/ani_screen.py # gtdbtk/main.py # gtdbtk/markers.py
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