FIX: remove genomad functionality

q2_viromics/citations.bib

@@ -16,12 +16,3 @@ @article{CheckV
   year={2021},
   publisher={Nature Publishing Group US New York}
 }
-
-@article{geNomad,
-  title={Identification of mobile genetic elements with geNomad},
-  author={Camargo, Antonio Pedro and Roux, Simon and Schulz, Frederik and Babinski, Michal and Xu, Yan and Hu, Bin and Chain, Patrick SG and Nayfach, Stephen and Kyrpides, Nikos C},
-  journal={Nature Biotechnology},
-  pages={1--10},
-  year={2023},
-  publisher={Nature Publishing Group US New York}
-}

q2_viromics/plugin_setup.py

@@ -15,14 +15,11 @@
 
 from q2_viromics.checkv_analysis import checkv_analysis
 from q2_viromics.checkv_fetch_db import checkv_fetch_db
-from q2_viromics.genomad_analysis import genomad_analysis
-from q2_viromics.genomad_fetch_db import genomad_fetch_db
 from q2_viromics.types._format import (
     CheckVDBDirFmt,
-    GenomadDBDirFmt,
     ViromicsMetadataDirFmt,
 )
-from q2_viromics.types._type import CheckVDB, GenomadDB, ViromicsMetadata
+from q2_viromics.types._type import CheckVDB, ViromicsMetadata
 
 citations = Citations.load("citations.bib", package="q2_viromics")
 
@@ -40,45 +37,22 @@
 
 plugin.register_formats(
     CheckVDBDirFmt,
-    GenomadDBDirFmt,
     ViromicsMetadataDirFmt,
 )
 
-plugin.register_semantic_types(CheckVDB, GenomadDB, ViromicsMetadata)
+plugin.register_semantic_types(CheckVDB, ViromicsMetadata)
 
 plugin.register_artifact_class(
     CheckVDB,
     directory_format=CheckVDBDirFmt,
     description=("CheckV database."),
 )
 
-plugin.register_artifact_class(
-    GenomadDB,
-    directory_format=GenomadDBDirFmt,
-    description=("Genomad database."),
-)
-
 plugin.register_semantic_type_to_format(
     SampleData[ViromicsMetadata],
     directory_format=ViromicsMetadataDirFmt,
 )
 
-plugin.methods.register_function(
-    function=genomad_fetch_db,
-    inputs={},
-    parameters={},
-    outputs=[("database", GenomadDB)],
-    parameter_descriptions={},
-    output_descriptions={"database": "geNomad database."},
-    name="Fetch geNomad database",
-    description=(
-        "Fetch the geNomad database that contains the profiles of the markers "
-        "that are used to classify sequences, their taxonomic information and "
-        "their functional annotation."
-    ),
-    citations=[citations["geNomad"]],
-)
-
 plugin.methods.register_function(
     function=checkv_fetch_db,
     inputs={},
@@ -131,52 +105,4 @@
     citations=[citations["CheckV"]],
 )
 
-plugin.methods.register_function(
-    function=genomad_analysis,
-    inputs={
-        "sequences": SampleData[Contigs],
-        "database": GenomadDB,
-    },
-    parameters={
-        "num_threads": Int % Range(1, None),
-        "splits": Int % Range(0, None),
-        "min_score": Float % Range(0, 1),
-        "min_number_genes": Int % Range(0, None),
-        "conservative_taxonomy": Bool,
-    },
-    input_descriptions={
-        "sequences": "Input sequences.",
-        "database": "GeNomad database.",
-    },
-    parameter_descriptions={
-        "num_threads": "Number of threads to use for prodigal-gv and DIAMOND.",
-        "splits": "Split the data for the MMseqs2 search. Higher values will "
-        "reduce memory usage, but will make the search slower. If the "
-        "MMseqs2 search is failing, try to increase the number of splits.",
-        "min_score": "Minimum score to flag a sequence as virus or plasmid.",
-        "min_number_genes": "The minimum number of genes a sequence must encode to "
-        "be considered for classification as a plasmid or virus.",
-        "conservative_taxonomy": "Make the virus taxonomic assignment process more "
-        "conservative. This might reduce the amount of "
-        "genomes assigned to the family level, but will "
-        "decrease the rate of family misassignment.",
-    },
-    outputs=[
-        ("viruses", SampleData[Contigs]),
-        ("proviruses", SampleData[Contigs]),
-        ("plasmid", SampleData[Contigs]),
-        ("virus_summary", SampleData[ViromicsMetadata]),
-    ],
-    output_descriptions={
-        "viruses": "Viral sequences.",
-        "proviruses": "Proviral sequences.",
-        "plasmid": "Plasmid sequences.",
-        "virus_summary": "Virus classification summary.",
-    },
-    name="Identify and classify viral genomes",
-    description="Perform comprehensive viral genome analysis to identify and "
-    "classify viral, proviral, and plasmid sequences.",
-    citations=[citations["geNomad"]],
-)
-
 importlib.import_module("q2_viromics.types._transformer")