Simple ruff setup

anvio/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 
 """Lots of under-the-rug, operational garbage in here. Run. Run away."""

anvio/agglomeration.py

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 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import gc
 import os

anvio/argparse.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 """Overloading Python argparse for anvi'o purposes"""
 

anvio/artifacts/samples_txt.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 
 import os

anvio/authors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 """A library to process anvi'o authors file"""
 

anvio/auxiliarydataops.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 """Module to deal with HDF5 files"""
 

anvio/bamops.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 
 """Classes for anything BAM-related"""

anvio/bottleroutes.py

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-# -*- coding: utf-8
 # pylint: disable=line-too-long
 """
     Common routes for bottle web server.

anvio/cazymes.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """This file contains CAZyme related classes."""
 
 import os

anvio/ccollections.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8
 # pylint: disable=line-too-long
 
 """Implements the collections class (the file name has an extra 'c' to avoid

anvio/cli/add_default_collection.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Adds a DEAFULT collection with EVERYTHING in it into a pan or profile database."""
 
 import sys

anvio/cli/analyze_synteny.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """anvi-analyze-synteny ... let's extract some order from this chaos!
 
 What do we say to loci that appear to have no coherent synteny patterns...?

anvio/cli/annotate_fragmented_genes.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Identify and annotate fragmented genes (pseudogenes) in pangenomes"""
 
 import sys

anvio/cli/as_markdown.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/augustus_output_to_external_gene_calls.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/checkm_tree_to_interactive.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 import os
 import re
 import sys

anvio/cli/cluster_contigs.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to run automatic binning algorithms on a merged anvi'o profile"""
 import os
 import sys

anvio/cli/compute_ani.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/compute_ani_for_fasta.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to export run ANI on every contig in a FASTA file."""
 
 import os

anvio/cli/compute_bayesian_pan_core.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/compute_completeness.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/compute_functional_enrichment.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 import sys
 
 from anvio.errors import ConfigError

anvio/cli/compute_functional_enrichment_across_genomes.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program that computes function enrichment across genomees"""
 
 import os

anvio/cli/compute_functional_enrichment_in_pan.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program that computes functional enrichment in a pangenome"""
 
 import os

anvio/cli/compute_gene_cluster_homogeneity.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/compute_genome_similarity.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to export a FASTA files from sequence sources and compute genome similarity matrices."""
 
 import sys

anvio/cli/compute_metabolic_enrichment.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program that computes metabolic enrichment across groups of genomes and metagenomes"""
 
 import sys

anvio/cli/compute_rarefaction_curves.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program that computes rarefaction curves for a given pan-db"""
 
 import sys

anvio/cli/db_info.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/delete_collection.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/delete_functions.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/delete_hmms.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/delete_misc_data.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Remove stuff from misc data tables"""
 
 import sys

anvio/cli/delete_state.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/dereplicate_genomes.py

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 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to remove replicated genomes from a list of internal and external genome databases or fasta files"""
 
 import sys

anvio/cli/display_codon_frequencies.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Get codon or amino acid frequency statistics from genomes, genes, and functions."""
 
 import sys

anvio/cli/display_contigs_stats.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/display_functions.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program to display the distribution of functions across genomes."""
 
 import sys

anvio/cli/display_metabolism.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/display_pan.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Entry point to the interactive interface for pan genomes.
 
 The massage of the data is being taken care of in the interactive module,

anvio/cli/display_structure.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/draw_kegg_pathways.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 DESCRIPTION = "Write KEGG pathway map files incorporating data sourced from anvi'o databases"
 
 import os

anvio/cli/estimate_genome_completeness.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import os
 import sys

anvio/cli/estimate_genome_size.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/estimate_genome_taxonomy.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/estimate_metabolic_independence.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import os
 import sys

anvio/cli/estimate_metabolism.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/estimate_scg_taxonomy.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/estimate_trna_taxonomy.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import os
 import sys

anvio/cli/experimental_organization.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/export_collection.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Gives you back items in a collection.
 
    Output files can directly be used by anvi-import-collection"""

anvio/cli/export_contigs.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to export a FASTA file of contigs (or splits) from a contigs database."""
 
 import sys

anvio/cli/export_functions.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/export_gene_calls.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 import pandas as pd

anvio/cli/export_gene_clusters.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/export_gene_coverage_and_detection.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 from anvio.argparse import ArgumentParser

anvio/cli/export_items_order.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A program to export an items order from an anvi'o database"""
 
 import sys

anvio/cli/export_locus.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """anvi-export-locus, first of its name, splitter of loci, and generator of mini contigs databases
 
   You want to play with it? This is how you could quickly test it:

anvio/cli/export_misc_data.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Export misc data from target tables into TAB-delimited files"""
 
 import sys

anvio/cli/export_splits_and_coverages.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """A script to export a FASTA file and the coverage table from a merged database.
 
 The purpose of this script is to export two critical files for most genome binning

anvio/cli/export_splits_taxonomy.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Takes a contigs database, and export taxonomy information from it."""
 
 import sys

anvio/cli/export_state.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 

anvio/cli/export_structures.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 import anvio

anvio/cli/export_table.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 """Takes a database and a table name as parameters, stores the content as
 a TAB-delimited matrix."""
 

anvio/cli/filter_fasta_by_blast.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import sys
 import pandas as pd

anvio/cli/filter_hmm_hits_table.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 """
 This script removes the hmm_hits table and replaces it with a filtered version. Filtering of hmm_hits

anvio/cli/find_misassemblies.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 
 import sys
 import anvio

anvio/cli/fix_homopolymer_indels.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8
 
 import os
 import sys