[med-svn] [Git][med-team/python-bx][upstream] New upstream version 0.15.0

[Michael R. Crusoe (@crusoe)]

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


Commits:
4f665dd0 by Michael R. Crusoe at 2026-08-27T17:21:33+02:00
New upstream version 0.15.0
- - - - -


107 changed files:

- + .flake8
- + .github/dependabot.yml
- .github/workflows/deploy.yaml
- .github/workflows/test.yaml
- + .github/workflows/zizmor.yaml
- LICENSE
- 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/-/commit/4f665dd0e8a06452f15a348cbe3c9e45faa1f9f9

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