6978980268

Committed 24 Nov 2023 09:23AM UTC coverage: 73.54% (-0.002%) from 73.542%

Build # 6978980268

Build Type

push

github

Committed by

cokelaer

Commit Message

Fix regression due to multiqc

Run Details

3 of 9 new or added lines in 2 files covered. (33.33%)

28 existing lines in 3 files now uncovered.

13371 of 18182 relevant lines covered (73.54%)

2.2 hits per line

Source File
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0.0

/sequana/scripts/main/main.py

#  This file is part of Sequana software
#
#  Copyright (c) 2016-2020 - Sequana Development Team
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
import click
import rich_click as click

from sequana import version

from .biomart import biomart
from .enrichment_kegg import enrichment_kegg
from .enrichment_panther import enrichment_panther
from .enrichment_uniprot import enrichment_uniprot
from .fasta import fasta
from .fastq import fastq
from .feature_count import feature_counts
from .g4hunter import g4hunter
from .gff_to_gtf import gff_to_gtf
from .gff_to_light_gff import gff_to_light_gff
from .gtf_fixer import gtf_fixer
from .ribodesigner import ribodesigner
from .rnadiff import rnadiff
from .rnaseq_compare import rnaseq_compare
from .salmon import salmon_cli
from .samplesheet import samplesheet
from .summary import summary
from .taxonomy import taxonomy
from .utils import CONTEXT_SETTINGS
from .mapping import mapping
from .lane_merging import lane_merging
from .variants_comparison import variants_comparison


click.rich_click.USE_MARKDOWN = True
click.rich_click.SHOW_METAVARS_COLUMN = False
click.rich_click.APPEND_METAVARS_HELP = True
click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
click.rich_click.SHOW_ARGUMENTS = True
click.rich_click.FOOTER_TEXT = "Authors: Thomas Cokelaer, Dimitri Desvillechabrol, Etienne Kornobis -- Documentation: http://sequana.readthedocs.io -- Issues: http://github.com/sequana/sequana"




@click.group(context_settings=CONTEXT_SETTINGS)
@click.version_option(version=version)
def main(**kwargs):
    """This is the main entry point for a set of Sequana applications.

    Pipelines such as sequana_rnaseq, sequana_variant_calling have their own
    application and help.

    In addition, more advanced tools such as sequana_taxonomy or
    sequana_coverage have their own standalone.


    To setup completion, type this command depending on your shell (bash):

        eval "$(_SEQUANA_COMPLETE=bash_source sequana)"
        eval "$(_SEQUANA_COMPLETE=source_zsh sequana)"
        eval (env _SEQUANA_COMPLETE=source_fish sequana)

    """
    pass


main.add_command(biomart)
main.add_command(enrichment_kegg)
main.add_command(enrichment_panther)
main.add_command(enrichment_uniprot)
main.add_command(fastq)
main.add_command(fasta)
main.add_command(feature_counts)
main.add_command(g4hunter)
main.add_command(gff_to_gtf)
main.add_command(gff_to_light_gff)
main.add_command(gtf_fixer)
main.add_command(lane_merging)
main.add_command(mapping)
main.add_command(ribodesigner)
main.add_command(rnadiff)
main.add_command(rnaseq_compare)
main.add_command(salmon_cli, name="salmon")
main.add_command(samplesheet)
main.add_command(summary)
main.add_command(taxonomy)
main.add_command(variants_comparison)

1	# This file is part of Sequana software
2	#
3	# Copyright (c) 2016-2020 - Sequana Development Team
4	#
5	# Distributed under the terms of the 3-clause BSD license.
6	# The full license is in the LICENSE file, distributed with this software.
7	#
8	# website: https://github.com/sequana/sequana
9	# documentation: http://sequana.readthedocs.io
10	#
11	##############################################################################
12	import click	×
13	import rich_click as click	×
14
15	from sequana import version	×
16
17	from .biomart import biomart	×
18	from .enrichment_kegg import enrichment_kegg	×
19	from .enrichment_panther import enrichment_panther	×
20	from .enrichment_uniprot import enrichment_uniprot	×
21	from .fasta import fasta	×
22	from .fastq import fastq	×
23	from .feature_count import feature_counts	×
24	from .g4hunter import g4hunter	×
25	from .gff_to_gtf import gff_to_gtf	×
26	from .gff_to_light_gff import gff_to_light_gff	×
27	from .gtf_fixer import gtf_fixer	×
28	from .ribodesigner import ribodesigner	×
29	from .rnadiff import rnadiff	×
30	from .rnaseq_compare import rnaseq_compare	×
31	from .salmon import salmon_cli	×
32	from .samplesheet import samplesheet	×
33	from .summary import summary	×
34	from .taxonomy import taxonomy	×
35	from .utils import CONTEXT_SETTINGS	×
36	from .mapping import mapping	×
37	from .lane_merging import lane_merging	×
UNCOV 38	from .variants_comparison import variants_comparison	×
39
40
41	click.rich_click.USE_MARKDOWN = True	×
42	click.rich_click.SHOW_METAVARS_COLUMN = False	×
43	click.rich_click.APPEND_METAVARS_HELP = True	×
44	click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"	×
45	click.rich_click.SHOW_ARGUMENTS = True	×
UNCOV 46	click.rich_click.FOOTER_TEXT = "Authors: Thomas Cokelaer, Dimitri Desvillechabrol, Etienne Kornobis -- Documentation: http://sequana.readthedocs.io -- Issues: http://github.com/sequana/sequana"	×
47
48
49
50
51	@click.group(context_settings=CONTEXT_SETTINGS)	×
52	@click.version_option(version=version)	×
UNCOV 53	def main(**kwargs):	×
54	"""This is the main entry point for a set of Sequana applications.
55
56	Pipelines such as sequana_rnaseq, sequana_variant_calling have their own
57	application and help.
58
59	In addition, more advanced tools such as sequana_taxonomy or
60	sequana_coverage have their own standalone.
61
62
63	To setup completion, type this command depending on your shell (bash):
64
65	eval "$(_SEQUANA_COMPLETE=bash_source sequana)"
66	eval "$(_SEQUANA_COMPLETE=source_zsh sequana)"
67	eval (env _SEQUANA_COMPLETE=source_fish sequana)
68
69	"""
UNCOV 70	pass	×
71
72
73	main.add_command(biomart)	×
74	main.add_command(enrichment_kegg)	×
75	main.add_command(enrichment_panther)	×
76	main.add_command(enrichment_uniprot)	×
77	main.add_command(fastq)	×
78	main.add_command(fasta)	×
79	main.add_command(feature_counts)	×
80	main.add_command(g4hunter)	×
81	main.add_command(gff_to_gtf)	×
82	main.add_command(gff_to_light_gff)	×
83	main.add_command(gtf_fixer)	×
84	main.add_command(lane_merging)	×
85	main.add_command(mapping)	×
86	main.add_command(ribodesigner)	×
87	main.add_command(rnadiff)	×
88	main.add_command(rnaseq_compare)	×
89	main.add_command(salmon_cli, name="salmon")	×
90	main.add_command(samplesheet)	×
91	main.add_command(summary)	×
UNCOV 92	main.add_command(taxonomy)	×
UNCOV 93	main.add_command(variants_comparison)	×

cokelaer / sequana / 6978980268

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