Commit 95529bf4 authored by Steffen Möller's avatar Steffen Möller
Browse files

lintian overrides for .py suffix in /usr/bin 

Those are kept for better compatibility with external
scripts and the additional binaries that there are to come.
parent 1b6398ba

debian/README.Debian

+12 −2
Original line number Diff line number Diff line 
python-bx for Debian

--------------------



The situation is somewhat unfortunate in that both python2 and python3 occupy the same location in /usr/bin. The -tools packages separate those binaries from the modules.

The situation is somewhat unfortunate in that both python2 and python3

occupy the same location in /usr/bin. The -tools packages separate those

binaries from the modules.



The language suffix ".py" was left for the time being for compatibility with the installation of the same on other distributions and wary of reverse dependencies.

The language suffix ".py" was left for the time being for compatibility

with the installation of the same on other distributions and wary of

reverse dependencies.



Man pages are not provided. The executables offer an answer to --help

to explain options but are silent about the overall purpose of the

respective tool. This is why at this point there are no help2man-generated

pages. The lintian warnings are not overridden as a reminder to contribute

the missing self-description to upstream.



-- 

  Steffen Moeller <moeller@debian.org>  Sat, 14 Jan 2017 10:43:03 +0100

debian/changelog

+11 −4
Original line number Diff line number Diff line 
python-bx (0.8.1-1) unstable; urgency=low

python-bx (0.8.1-2) unstable; urgency=low



  * New upstream version.

  * Initial release (Closes: #851242)

  * Lintian-overrides for .py suffix for executables

  * Reformatting of debian/{README.Debian,copyright}



 -- Steffen Moeller <moeller@debian.org>  Tue, 12 Jun 2018 07:43:51 +0200



python-bx (0.8.1-1) UNRELEASED; urgency=low



  * New upstream version.

  * Policy compliance with 4.1.4.



 -- Steffen Moeller <moeller@debian.org>  Mon, 11 Jun 2018 00:33:54 +0200



python-bx (0.7.4-1) unstable; urgency=low

python-bx (0.7.4-1) UNRELEASED; urgency=low



  * Added Michael and Steffen as uploaders

  * Removing generated files from source tree in debian/copyright
@@ -15,7 +22,7 @@ python-bx (0.7.4-1) unstable; urgency=low 


 -- Steffen Moeller <moeller@debian.org>  Fri, 13 Jan 2017 13:25:31 +0100



python-bx (0.7.2+20150623-1) unstable; urgency=low

python-bx (0.7.2+20150623-1) UNRELEASED; urgency=low



  * Initial packaging.

  * debian/watch added by Steffen

debian/copyright

+1 −1
Original line number Diff line number Diff line
@@ -76,7 +76,7 @@ License: AFL-2.1 
 notice for the Original Work:

 .

 Licensed under the Academic Free License version 2.1



 .

 1) Grant of Copyright License. Licensor hereby grants You a

    world-wide, royalty-free, non-exclusive, perpetual, sublicenseable

    license to do the following:

debian/python-bx-tools.lintian-overrides

0 → 100644
+97 −0
Original line number Diff line number Diff line 
# Not fiddling with .py endings because of reverse-dependencies expected from toil

# We shall revisit this decision once all packages for toil are in the distribution

# and we have learned more about how bx is used in the community in 3rd party scripts.

python-bx-tools: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py

python-bx-tools: script-with-language-extension usr/bin/align_print_template.py

python-bx-tools: script-with-language-extension usr/bin/axt_extract_ranges.py

python-bx-tools: script-with-language-extension usr/bin/axt_to_fasta.py

python-bx-tools: script-with-language-extension usr/bin/axt_to_lav.py

python-bx-tools: script-with-language-extension usr/bin/axt_to_maf.py

python-bx-tools: script-with-language-extension usr/bin/bed_bigwig_profile.py

python-bx-tools: script-with-language-extension usr/bin/bed_build_windows.py

python-bx-tools: script-with-language-extension usr/bin/bed_complement.py

python-bx-tools: script-with-language-extension usr/bin/bed_count_by_interval.py

python-bx-tools: script-with-language-extension usr/bin/bed_count_overlapping.py

python-bx-tools: script-with-language-extension usr/bin/bed_coverage.py

python-bx-tools: script-with-language-extension usr/bin/bed_coverage_by_interval.py

python-bx-tools: script-with-language-extension usr/bin/bed_diff_basewise_summary.py

python-bx-tools: script-with-language-extension usr/bin/bed_extend_to.py

python-bx-tools: script-with-language-extension usr/bin/bed_intersect.py

python-bx-tools: script-with-language-extension usr/bin/bed_intersect_basewise.py

python-bx-tools: script-with-language-extension usr/bin/bed_merge_overlapping.py

python-bx-tools: script-with-language-extension usr/bin/bed_rand_intersect.py

python-bx-tools: script-with-language-extension usr/bin/bed_subtract_basewise.py

python-bx-tools: script-with-language-extension usr/bin/bnMapper.py

python-bx-tools: script-with-language-extension usr/bin/div_snp_table_chr.py

python-bx-tools: script-with-language-extension usr/bin/find_in_sorted_file.py

python-bx-tools: script-with-language-extension usr/bin/gene_fourfold_sites.py

python-bx-tools: script-with-language-extension usr/bin/get_scores_in_intervals.py

python-bx-tools: script-with-language-extension usr/bin/int_seqs_to_char_strings.py

python-bx-tools: script-with-language-extension usr/bin/interval_count_intersections.py

python-bx-tools: script-with-language-extension usr/bin/interval_join.py

python-bx-tools: script-with-language-extension usr/bin/lav_to_axt.py

python-bx-tools: script-with-language-extension usr/bin/lav_to_maf.py

python-bx-tools: script-with-language-extension usr/bin/line_select.py

python-bx-tools: script-with-language-extension usr/bin/lzop_build_offset_table.py

python-bx-tools: script-with-language-extension usr/bin/mMK_bitset.py

python-bx-tools: script-with-language-extension usr/bin/maf_build_index.py

python-bx-tools: script-with-language-extension usr/bin/maf_chop.py

python-bx-tools: script-with-language-extension usr/bin/maf_chunk.py

python-bx-tools: script-with-language-extension usr/bin/maf_col_counts.py

python-bx-tools: script-with-language-extension usr/bin/maf_col_counts_all.py

python-bx-tools: script-with-language-extension usr/bin/maf_count.py

python-bx-tools: script-with-language-extension usr/bin/maf_covered_ranges.py

python-bx-tools: script-with-language-extension usr/bin/maf_covered_regions.py

python-bx-tools: script-with-language-extension usr/bin/maf_div_sites.py

python-bx-tools: script-with-language-extension usr/bin/maf_drop_overlapping.py

python-bx-tools: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py

python-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges.py

python-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py

python-bx-tools: script-with-language-extension usr/bin/maf_filter.py

python-bx-tools: script-with-language-extension usr/bin/maf_filter_max_wc.py

python-bx-tools: script-with-language-extension usr/bin/maf_gap_frequency.py

python-bx-tools: script-with-language-extension usr/bin/maf_gc_content.py

python-bx-tools: script-with-language-extension usr/bin/maf_interval_alignibility.py

python-bx-tools: script-with-language-extension usr/bin/maf_limit_to_species.py

python-bx-tools: script-with-language-extension usr/bin/maf_mapping_word_frequency.py

python-bx-tools: script-with-language-extension usr/bin/maf_mask_cpg.py

python-bx-tools: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py

python-bx-tools: script-with-language-extension usr/bin/maf_percent_columns_matching.py

python-bx-tools: script-with-language-extension usr/bin/maf_percent_identity.py

python-bx-tools: script-with-language-extension usr/bin/maf_print_chroms.py

python-bx-tools: script-with-language-extension usr/bin/maf_print_scores.py

python-bx-tools: script-with-language-extension usr/bin/maf_randomize.py

python-bx-tools: script-with-language-extension usr/bin/maf_region_coverage_by_src.py

python-bx-tools: script-with-language-extension usr/bin/maf_select.py

python-bx-tools: script-with-language-extension usr/bin/maf_shuffle_columns.py

python-bx-tools: script-with-language-extension usr/bin/maf_species_in_all_files.py

python-bx-tools: script-with-language-extension usr/bin/maf_split_by_src.py

python-bx-tools: script-with-language-extension usr/bin/maf_thread_for_species.py

python-bx-tools: script-with-language-extension usr/bin/maf_tile.py

python-bx-tools: script-with-language-extension usr/bin/maf_tile_2.py

python-bx-tools: script-with-language-extension usr/bin/maf_tile_2bit.py

python-bx-tools: script-with-language-extension usr/bin/maf_to_axt.py

python-bx-tools: script-with-language-extension usr/bin/maf_to_concat_fasta.py

python-bx-tools: script-with-language-extension usr/bin/maf_to_fasta.py

python-bx-tools: script-with-language-extension usr/bin/maf_to_int_seqs.py

python-bx-tools: script-with-language-extension usr/bin/maf_translate_chars.py

python-bx-tools: script-with-language-extension usr/bin/maf_truncate.py

python-bx-tools: script-with-language-extension usr/bin/maf_word_frequency.py

python-bx-tools: script-with-language-extension usr/bin/mask_quality.py

python-bx-tools: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py

python-bx-tools: script-with-language-extension usr/bin/nib_intervals_to_fasta.py

python-bx-tools: script-with-language-extension usr/bin/nib_length.py

python-bx-tools: script-with-language-extension usr/bin/one_field_per_line.py

python-bx-tools: script-with-language-extension usr/bin/out_to_chain.py

python-bx-tools: script-with-language-extension usr/bin/prefix_lines.py

python-bx-tools: script-with-language-extension usr/bin/pretty_table.py

python-bx-tools: script-with-language-extension usr/bin/qv_to_bqv.py

python-bx-tools: script-with-language-extension usr/bin/random_lines.py

python-bx-tools: script-with-language-extension usr/bin/table_add_column.py

python-bx-tools: script-with-language-extension usr/bin/table_filter.py

python-bx-tools: script-with-language-extension usr/bin/tfloc_summary.py

python-bx-tools: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py

python-bx-tools: script-with-language-extension usr/bin/wiggle_to_array_tree.py

python-bx-tools: script-with-language-extension usr/bin/wiggle_to_binned_array.py

python-bx-tools: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py

python-bx-tools: script-with-language-extension usr/bin/wiggle_to_simple.py

debian/python3-bx-tools.lintian-overrides

0 → 100644
+97 −0
Original line number Diff line number Diff line 
# Not fiddling with .py endings because of reverse-dependencies expected from toil

# We shall revisit this decision once all packages for toil are in the distribution

# and we have learned more about how bx is used in the community in 3rd party scripts.

python3-bx-tools: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py

python3-bx-tools: script-with-language-extension usr/bin/align_print_template.py

python3-bx-tools: script-with-language-extension usr/bin/axt_extract_ranges.py

python3-bx-tools: script-with-language-extension usr/bin/axt_to_fasta.py

python3-bx-tools: script-with-language-extension usr/bin/axt_to_lav.py

python3-bx-tools: script-with-language-extension usr/bin/axt_to_maf.py

python3-bx-tools: script-with-language-extension usr/bin/bed_bigwig_profile.py

python3-bx-tools: script-with-language-extension usr/bin/bed_build_windows.py

python3-bx-tools: script-with-language-extension usr/bin/bed_complement.py

python3-bx-tools: script-with-language-extension usr/bin/bed_count_by_interval.py

python3-bx-tools: script-with-language-extension usr/bin/bed_count_overlapping.py

python3-bx-tools: script-with-language-extension usr/bin/bed_coverage.py

python3-bx-tools: script-with-language-extension usr/bin/bed_coverage_by_interval.py

python3-bx-tools: script-with-language-extension usr/bin/bed_diff_basewise_summary.py

python3-bx-tools: script-with-language-extension usr/bin/bed_extend_to.py

python3-bx-tools: script-with-language-extension usr/bin/bed_intersect.py

python3-bx-tools: script-with-language-extension usr/bin/bed_intersect_basewise.py

python3-bx-tools: script-with-language-extension usr/bin/bed_merge_overlapping.py

python3-bx-tools: script-with-language-extension usr/bin/bed_rand_intersect.py

python3-bx-tools: script-with-language-extension usr/bin/bed_subtract_basewise.py

python3-bx-tools: script-with-language-extension usr/bin/bnMapper.py

python3-bx-tools: script-with-language-extension usr/bin/div_snp_table_chr.py

python3-bx-tools: script-with-language-extension usr/bin/find_in_sorted_file.py

python3-bx-tools: script-with-language-extension usr/bin/gene_fourfold_sites.py

python3-bx-tools: script-with-language-extension usr/bin/get_scores_in_intervals.py

python3-bx-tools: script-with-language-extension usr/bin/int_seqs_to_char_strings.py

python3-bx-tools: script-with-language-extension usr/bin/interval_count_intersections.py

python3-bx-tools: script-with-language-extension usr/bin/interval_join.py

python3-bx-tools: script-with-language-extension usr/bin/lav_to_axt.py

python3-bx-tools: script-with-language-extension usr/bin/lav_to_maf.py

python3-bx-tools: script-with-language-extension usr/bin/line_select.py

python3-bx-tools: script-with-language-extension usr/bin/lzop_build_offset_table.py

python3-bx-tools: script-with-language-extension usr/bin/mMK_bitset.py

python3-bx-tools: script-with-language-extension usr/bin/maf_build_index.py

python3-bx-tools: script-with-language-extension usr/bin/maf_chop.py

python3-bx-tools: script-with-language-extension usr/bin/maf_chunk.py

python3-bx-tools: script-with-language-extension usr/bin/maf_col_counts.py

python3-bx-tools: script-with-language-extension usr/bin/maf_col_counts_all.py

python3-bx-tools: script-with-language-extension usr/bin/maf_count.py

python3-bx-tools: script-with-language-extension usr/bin/maf_covered_ranges.py

python3-bx-tools: script-with-language-extension usr/bin/maf_covered_regions.py

python3-bx-tools: script-with-language-extension usr/bin/maf_div_sites.py

python3-bx-tools: script-with-language-extension usr/bin/maf_drop_overlapping.py

python3-bx-tools: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py

python3-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges.py

python3-bx-tools: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py

python3-bx-tools: script-with-language-extension usr/bin/maf_filter.py

python3-bx-tools: script-with-language-extension usr/bin/maf_filter_max_wc.py

python3-bx-tools: script-with-language-extension usr/bin/maf_gap_frequency.py

python3-bx-tools: script-with-language-extension usr/bin/maf_gc_content.py

python3-bx-tools: script-with-language-extension usr/bin/maf_interval_alignibility.py

python3-bx-tools: script-with-language-extension usr/bin/maf_limit_to_species.py

python3-bx-tools: script-with-language-extension usr/bin/maf_mapping_word_frequency.py

python3-bx-tools: script-with-language-extension usr/bin/maf_mask_cpg.py

python3-bx-tools: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py

python3-bx-tools: script-with-language-extension usr/bin/maf_percent_columns_matching.py

python3-bx-tools: script-with-language-extension usr/bin/maf_percent_identity.py

python3-bx-tools: script-with-language-extension usr/bin/maf_print_chroms.py

python3-bx-tools: script-with-language-extension usr/bin/maf_print_scores.py

python3-bx-tools: script-with-language-extension usr/bin/maf_randomize.py

python3-bx-tools: script-with-language-extension usr/bin/maf_region_coverage_by_src.py

python3-bx-tools: script-with-language-extension usr/bin/maf_select.py

python3-bx-tools: script-with-language-extension usr/bin/maf_shuffle_columns.py

python3-bx-tools: script-with-language-extension usr/bin/maf_species_in_all_files.py

python3-bx-tools: script-with-language-extension usr/bin/maf_split_by_src.py

python3-bx-tools: script-with-language-extension usr/bin/maf_thread_for_species.py

python3-bx-tools: script-with-language-extension usr/bin/maf_tile.py

python3-bx-tools: script-with-language-extension usr/bin/maf_tile_2.py

python3-bx-tools: script-with-language-extension usr/bin/maf_tile_2bit.py

python3-bx-tools: script-with-language-extension usr/bin/maf_to_axt.py

python3-bx-tools: script-with-language-extension usr/bin/maf_to_concat_fasta.py

python3-bx-tools: script-with-language-extension usr/bin/maf_to_fasta.py

python3-bx-tools: script-with-language-extension usr/bin/maf_to_int_seqs.py

python3-bx-tools: script-with-language-extension usr/bin/maf_translate_chars.py

python3-bx-tools: script-with-language-extension usr/bin/maf_truncate.py

python3-bx-tools: script-with-language-extension usr/bin/maf_word_frequency.py

python3-bx-tools: script-with-language-extension usr/bin/mask_quality.py

python3-bx-tools: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py

python3-bx-tools: script-with-language-extension usr/bin/nib_intervals_to_fasta.py

python3-bx-tools: script-with-language-extension usr/bin/nib_length.py

python3-bx-tools: script-with-language-extension usr/bin/one_field_per_line.py

python3-bx-tools: script-with-language-extension usr/bin/out_to_chain.py

python3-bx-tools: script-with-language-extension usr/bin/prefix_lines.py

python3-bx-tools: script-with-language-extension usr/bin/pretty_table.py

python3-bx-tools: script-with-language-extension usr/bin/qv_to_bqv.py

python3-bx-tools: script-with-language-extension usr/bin/random_lines.py

python3-bx-tools: script-with-language-extension usr/bin/table_add_column.py

python3-bx-tools: script-with-language-extension usr/bin/table_filter.py

python3-bx-tools: script-with-language-extension usr/bin/tfloc_summary.py

python3-bx-tools: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py

python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_array_tree.py

python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_binned_array.py

python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py

python3-bx-tools: script-with-language-extension usr/bin/wiggle_to_simple.py