From 6e49d3ec009086dd72959b66f9c08b62424cc992 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Tue, 3 Dec 2024 11:34:27 +0100
Subject: [PATCH] Update CI data

---
 .github/workflows/cli_vamb.yml | 5 +----
 vamb/__main__.py               | 2 +-
 vamb/taxonomy.py               | 3 +--
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cli_vamb.yml b/.github/workflows/cli_vamb.yml
index 9018429d..d9afcdcd 100644
--- a/.github/workflows/cli_vamb.yml
+++ b/.github/workflows/cli_vamb.yml
@@ -28,7 +28,7 @@ jobs:
         cache-dependency-path: '**/pyproject.toml'
     - name: Download fixtures
       run: |
-        wget https://www.dropbox.com/scl/fi/xzc0tro7oe6tfm3igygpj/ci_data.zip\?rlkey\=xuv6b5eoynfryp4fba1kfp5jm\&st\=rjb1xccw\&dl\=0 -O ci_data.zip
+        wget https://www.dropbox.com/scl/fi/nvct2aq3o2gdafouio8yg/ci_data.zip\?rlkey\=wg14lskwo1t4pusuk1tf12w9g\&st\=wc7hst48\&dl\=0 -O ci_data.zip
         unzip -o ci_data.zip
     - name: Install dependencies
       run: |
@@ -56,9 +56,6 @@ jobs:
         vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10
         ls -la outdir_taxometer
         cat outdir_taxometer/log.txt
-        vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pt 10
-        ls -la outdir_taxometer_pred
-        cat outdir_taxometer/log.txt
     - name: Run k-means reclustering
       run: |
         vamb recluster --outdir outdir_recluster --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --latent_path outdir_taxvamb/vaevae_latent.npz --clusters_path outdir_taxvamb/vaevae_clusters_split.tsv --markers markers_mock.npz --algorithm kmeans --minfasta 200000
diff --git a/vamb/__main__.py b/vamb/__main__.py
index cd2e2302..11d61b15 100755
--- a/vamb/__main__.py
+++ b/vamb/__main__.py
@@ -417,7 +417,7 @@ def get_taxonomy(args: argparse.Namespace) -> Union[RefinedTaxonomy, UnrefinedTa
 class TaxometerOptions:
     @classmethod
     def from_args(cls, args: argparse.Namespace):
-        tax = get_taxonomy(args.taxonomy)
+        tax = get_taxonomy(args)
         if isinstance(tax, RefinedTaxonomy):
             raise ValueError(
                 f'Attempted to run Taxometer to refine taxonomy at "{args.taxonomy}", '
diff --git a/vamb/taxonomy.py b/vamb/taxonomy.py
index 731a699a..7a9e1d63 100644
--- a/vamb/taxonomy.py
+++ b/vamb/taxonomy.py
@@ -202,7 +202,7 @@ def write_as_tsv(self, file: IO[str], comp_metadata: CompositionMetaData):
                 "Refhash of comp_metadata and predicted taxonomy must match"
             )
         assert self.nseqs == comp_metadata.nseqs
-        print("contigs\tpredictions\tlengths\tscores", file=file)
+        print(PREDICTED_TAXONOMY_HEADER, file=file)
         for i in range(self.nseqs):
             tax = self.contig_taxonomies[i]
             ranks_str = ";".join(tax.contig_taxonomy.ranks)
@@ -210,7 +210,6 @@ def write_as_tsv(self, file: IO[str], comp_metadata: CompositionMetaData):
             print(
                 comp_metadata.identifiers[i],
                 ranks_str,
-                comp_metadata.lengths[i],
                 probs_str,
                 file=file,
                 sep="\t",