[med-svn] [Git][med-team/python-bx][master] lintian overrides for .py suffix in /usr/bin

Steffen Möller gitlab at salsa.debian.org
Wed Oct 17 10:22:42 BST 2018 

Steffen Möller pushed to branch master at Debian Med / python-bx


Commits:
95529bf4 by Steffen Moeller at 2018-06-12T05:52:57Z
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.

- - - - -


5 changed files:

- debian/README.Debian
- debian/changelog
- debian/copyright
- + debian/python-bx-tools.lintian-overrides
- + debian/python3-bx-tools.lintian-overrides


Changes:

=====================================
debian/README.Debian
=====================================
@@ -1,9 +1,19 @@
 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 at debian.org>  Sat, 14 Jan 2017 10:43:03 +0100


=====================================
debian/changelog
=====================================
@@ -1,12 +1,19 @@
-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 at 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 at 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 at 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
=====================================
@@ -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
=====================================
@@ -0,0 +1,97 @@
+# 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
=====================================
@@ -0,0 +1,97 @@
+# 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



View it on GitLab: https://salsa.debian.org/med-team/python-bx/commit/95529bf4674b37eda4df0a4c10c7390c8c0a5017

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