Disable output filename actions

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Greengenes2 changelog
 
+## Version 2024.01
+
+* Removed methods of bulk characterization which are resource, not user, oriented
+
 ## Version 2022.12
 
 * Added a method for collapsing by multifurcation in [#5](https://github.com/biocore/q2-greengenes2/pull/5)

q2_gg2/plugin_setup.py

@@ -131,82 +131,6 @@
 )
 
 
-plugin.methods.register_function(
-    function=q2_gg2.bulk_sequence_v4_asv_assessment,
-    inputs={'phylogeny': Phylogeny[Rooted],
-            'taxa': FeatureData[Taxonomy],
-            'full_length_v4': FeatureData[Sequence],
-            'sequences': FeatureData[Sequence]},
-    parameters={'group': Int,
-                'version': Str,
-                'output_filename': Str},
-    outputs=[('characterization', ASVAssessment)],
-    input_descriptions={
-        'phylogeny': 'The ID annotated phylogeny',
-        'taxa': 'The taxa indexed by ID',
-        'full_length_v4': 'The extracted V4 sequences from the backbone',
-        'sequences': 'The full set of GG2 sequences'},
-    parameter_descriptions={
-        'group': 'The hash group to process',
-        'version': 'The database version to use',
-        'output_filename': 'The file to write assessments too'
-        },
-    output_descriptions={
-        'characterization': "This output is undefined"},
-    name='Bulk ASV assessment',
-    description=("Check what full length records the ASV associates with "
-                 "and members within its placement multifurcation"),
-    citations=[]
-)
-
-
-plugin.methods.register_function(
-    function=q2_gg2.bulk_clade_v4_asv_assessment,
-    inputs={'phylogeny': Phylogeny[Rooted],
-            'taxa': FeatureData[Taxonomy],
-            'full_length_v4': FeatureData[Sequence],
-            'sequences': FeatureData[Sequence]},
-    parameters={'group': Int,
-                'version': Str,
-                'output_filename': Str},
-    outputs=[('characterization', CladeAssessment)],
-    input_descriptions={
-        'phylogeny': 'The ID annotated phylogeny',
-        'taxa': 'The taxa indexed by ID',
-        'full_length_v4': 'The extracted V4 sequences from the backbone',
-        'sequences': 'The full set of GG2 sequences'},
-    parameter_descriptions={
-        'group': 'The hash group to process',
-        'version': 'The database version to use',
-        'output_filename': 'The file to write assessments too'
-        },
-    output_descriptions={'characterization': 'This output is undefined'},
-    name='Bulk Clade ASV level assessment',
-    description=("Test whether the clade is uniquely represented by ASVs "
-                 "and other summary information about the clade"),
-    citations=[]
-)
-
-
-plugin.methods.register_function(
-    function=q2_gg2.clade_lookup,
-    inputs={'taxonomy_as_tree': Phylogeny[Rooted]},
-    parameters={'version': Str,
-                'output_filename': Str},
-    outputs=[('characterization', CladeAssessment)],
-    input_descriptions={
-        'taxonomy_as_tree': 'The taxonomy represented as a newick string'},
-    parameter_descriptions={
-        'version': 'The database version to use',
-        'output_filename': 'The file to write the lookup too'
-        },
-    output_descriptions={'characterization': 'This output is undefined'},
-    description=("Construct a taxonomy lookup suitable for a sqlite database"),
-    citations=[],
-    name='Construct a clade lookup'
-)
-
-
 plugin.methods.register_function(
     function=q2_gg2.taxonomy_from_table,
     inputs={'reference_taxonomy': Phylogeny[Rooted],