From 6ab6d0fe99b8737c485083a268bd92b08f710411 Mon Sep 17 00:00:00 2001
From: Svetlana Kutuzova <galkina.s.a@gmail.com>
Date: Thu, 26 Oct 2023 14:32:03 +0200
Subject: [PATCH] feat: CLI TaxVAMB

---
 .github/workflows/cli_vamb.yml | 18 +++++++++++++++++-
 vamb/__main__.py               |  2 +-
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cli_vamb.yml b/.github/workflows/cli_vamb.yml
index ff4853ee..52643274 100644
--- a/.github/workflows/cli_vamb.yml
+++ b/.github/workflows/cli_vamb.yml
@@ -37,6 +37,22 @@ jobs:
         pip install -e .
     - name: Run VAMB
       run: |
-        vamb --outdir outdir_vamb --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz -l 32 -e 10 -q 2 -o C --minfasta 200000 -t 10
+        vamb bin basic --outdir outdir_vamb --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz -l 32 -e 10 -q 2 -o C --minfasta 200000 -t 10
         ls -la outdir_vamb
         cat outdir_vamb/log.txt
+    - name: Run TaxVAMB
+      run: |
+        vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -t 10 -o C --minfasta 200000
+        ls -la outdir_vamb
+        cat outdir_vamb/log.txt
+        vamb bin taxvamb --outdir outdir_taxvamb_no_predict --no_predictor --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz --taxonomy taxonomy_mock.tsv e 10 -q -t 10 -o C --minfasta 200000
+        ls -la outdir_vamb_no_predict
+        cat outdir_vamb_no_predict/log.txt
+        vamb bin taxvamb --outdir outdir_taxvamb_preds --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz --taxonomy_predictions outdir_taxvamb/results_taxonomy_predictor.csv e 10 -q -t 10 -o C --minfasta 200000
+        ls -la outdir_vamb_preds
+        cat outdir_vamb_preds/log.txt
+    - name: Run Taxometer
+      run: |
+        vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --rpkm abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10
+        ls -la outdir_taxometer
+        cat outdir_taxometer/log.txt
diff --git a/vamb/__main__.py b/vamb/__main__.py
index 3a581952..3365045d 100755
--- a/vamb/__main__.py
+++ b/vamb/__main__.py
@@ -1934,7 +1934,7 @@ def add_predictor_arguments(subparser):
         metavar="",
         type=int,
         nargs="*",
-        default=[25, 75],
+        default=[],
         help="double batch size at epochs for the taxonomy predictor [25 75]",
     )
     pred_trainos.add_argument(