[med-svn] [Git][med-team/python-bx][master] 12 commits: New upstream version

Fri Aug 28 07:42:04 BST 2026

Michael R. Crusoe pushed to branch master at Debian Med / python-bx

Commits:
2873d811 by Michael R. Crusoe at 2026-08-27T17:21:32+02:00
New upstream version

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4f665dd0 by Michael R. Crusoe at 2026-08-27T17:21:33+02:00
New upstream version 0.15.0
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42da335d by Michael R. Crusoe at 2026-08-27T17:21:34+02:00
Update upstream source from tag 'upstream/0.15.0'

Update to upstream version '0.15.0'
with Debian dir 2b4508d5458380290f38c2b3bff6c470274a3abd
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1924ea8e by Michael R. Crusoe at 2026-08-27T17:21:35+02:00
Standards-Version: 4.7.4 (routine-update)

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2ac9b292 by Michael R. Crusoe at 2026-08-27T17:21:45+02:00
Changes made by cme

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27862c26 by Michael R. Crusoe at 2026-08-27T16:21:47+01:00
Update watch file format version to 5.

Changes-By: lintian-brush
Fixes: lintian: older-debian-watch-file-standard
See-also: https://lintian.debian.org/tags/older-debian-watch-file-standard.html

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25238866 by Michael R. Crusoe at 2026-08-27T16:21:48+01:00
Use GitHub template in watch file instead of explicit Source/Matching-Pattern.

Changes-By: lintian-brush

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072da2ea by Michael R. Crusoe at 2026-08-27T16:21:56+01:00
Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

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15446363 by Michael R. Crusoe at 2026-08-27T17:21:57+02:00
debputy lint --auto-fix (routine-update)

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0d75e25a by Michael R. Crusoe at 2026-08-27T17:24:52+02:00
Refreshed patches.

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2464cd2b by Michael R. Crusoe at 2026-08-27T16:25:28+01:00
Set upstream metadata fields: Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

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c60efaca by Michael R. Crusoe at 2026-08-27T17:28:08+02:00
routine-update: Ready to upload to unstable

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114 changed files:

- + .flake8
- + .github/dependabot.yml
- .github/workflows/deploy.yaml
- .github/workflows/test.yaml
- + .github/workflows/zizmor.yaml
- LICENSE
- debian/changelog
- debian/control
- debian/patches/fix_BIN_OFFSETS_MAX
- debian/patches/shebang.patch
- debian/patches/spelling
- debian/upstream/metadata
- debian/watch
- doc/source/conf.py
- lib/bx/__init__.py
- lib/bx/align/axt.py
- lib/bx/align/core.py
- lib/bx/align/epo.py
- lib/bx/align/epo_tests.py
- lib/bx/align/lav.py
- lib/bx/align/lav_tests.py
- lib/bx/align/maf.py
- lib/bx/align/maf_tests.py
- lib/bx/align/score.py
- lib/bx/align/sitemask/__init__.py
- lib/bx/align/tools/__init__.py
- lib/bx/arrays/array_tree_tests.py
- lib/bx/bbi/bbi_file.pyx
- lib/bx/binned_array.py
- lib/bx/binned_array_tests.py
- lib/bx/bitset_utils.py
- lib/bx/cookbook/__init__.py
- lib/bx/cookbook/doc_optparse.py
- lib/bx/interval_index_file.py
- lib/bx/interval_index_file_tests.py
- lib/bx/intervals/io.py
- lib/bx/intervals/operations/concat.py
- lib/bx/intervals/operations/join.py
- lib/bx/intervals/operations/quicksect.py
- lib/bx/intervals/random_intervals.py
- lib/bx/misc/seekbzip2_tests.py
- lib/bx/motif/io/transfac.py
- lib/bx/motif/pwm.py
- lib/bx/phylo/newick.py
- lib/bx/pwm/bed_score_aligned_pwm.py
- lib/bx/pwm/bed_score_aligned_string.py
- lib/bx/pwm/maf_select_motifs.py
- lib/bx/pwm/position_weight_matrix.py
- lib/bx/pwm/pwm_score_maf.py
- lib/bx/pwm/pwm_score_motifs.py
- lib/bx/pwm/pwm_score_positions.py
- lib/bx/seq/fasta.py
- lib/bx/seq/nib.py
- lib/bx/seq/qdna.py
- lib/bx/seq/seq.py
- lib/bx/seq/seq_tests.py
- lib/bx/seq/twobit.py
- lib/bx/seq/twobit_tests.py
- lib/bx_extras/fpconst.py
- lib/bx_extras/lrucache.py
- lib/bx_extras/stats.py
- + mypy.ini
- pyproject.toml
- script_tests/line_select_tests.py
- script_tests/maf_select_tests.py
- scripts/axt_to_lav.py
- scripts/axt_to_maf.py
- scripts/bed_build_windows.py
- scripts/bed_complement.py
- scripts/bed_coverage.py
- scripts/bed_diff_basewise_summary.py
- scripts/bed_extend_to.py
- scripts/bed_intersect_basewise.py
- scripts/bed_merge_overlapping.py
- scripts/bed_rand_intersect.py
- scripts/bed_subtract_basewise.py
- scripts/bnMapper.py
- scripts/div_snp_table_chr.py
- scripts/find_in_sorted_file.py
- scripts/gene_fourfold_sites.py
- scripts/lav_to_axt.py
- scripts/lav_to_maf.py
- scripts/mMK_bitset.py
- scripts/maf_chop.py
- scripts/maf_chunk.py
- scripts/maf_col_counts.py
- scripts/maf_col_counts_all.py
- scripts/maf_covered_regions.py
- scripts/maf_div_sites.py
- scripts/maf_extract_ranges_indexed.py
- scripts/maf_filter.py
- scripts/maf_interval_alignibility.py
- scripts/maf_percent_columns_matching.py
- scripts/maf_percent_identity.py
- scripts/maf_randomize.py
- scripts/maf_species_in_all_files.py
- scripts/maf_split_by_src.py
- scripts/maf_tile.py
- scripts/maf_tile_2.py
- scripts/maf_tile_2bit.py
- scripts/maf_to_axt.py
- scripts/maf_to_concat_fasta.py
- scripts/maf_to_fasta.py
- scripts/maf_truncate.py
- scripts/maf_word_frequency.py
- scripts/out_to_chain.py
- scripts/pretty_table.py
- scripts/tfloc_summary.py
- scripts/wiggle_to_array_tree.py
- scripts/wiggle_to_chr_binned_array.py
- scripts/wiggle_to_simple.py
- − setup.cfg
- tox.ini
- + zizmor.yml

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/cab4e23bc9f3a326c11671eb91d431e8b73d176f...c60efaca3edd5faca41a5b8cc7e5505a060abe1c

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/cab4e23bc9f3a326c11671eb91d431e8b73d176f...c60efaca3edd5faca41a5b8cc7e5505a060abe1c
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