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

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
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
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
......
......@@ -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:
......
# 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
# 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
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