.gitignore

@@ -22,3 +22,6 @@ nose*.egg
 
 # .eggs directory
 .eggs
+
+# Virtualenv
+.venv

.travis.yml

 language: python
-sudo: false
+cache: pip
 os:
   - linux
-    ## - osx
 python:
-    - 2.7
-    - 3.3
+  - '2.7'
+  - '3.5'
+
+env:
+  global:
+    - PYTHON=python
+    - TWINE_USERNAME=nsoranzo
+    - secure: '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'
+
+_deploy_common: &deploy_common
+  if: tag IS present
+  install:
+    - $PYTHON -m pip install cibuildwheel twine
+
+matrix:
+  include:
+    - stage: deploy
+      python: '3.5'
+      services:
+        - docker
+      env: CIBW_BEFORE_BUILD="yum install -y zlib-devel && pip install Cython numpy"
+      <<: *deploy_common
+      script:
+        - cibuildwheel --output-dir dist
+        - $PYTHON -m pip install Cython nose numpy python-lzo six
+        - $PYTHON setup.py build_ext --inplace
+        - $PYTHON setup.py sdist
+        - twine check dist/*
+        - twine upload --skip-existing dist/*
+    - stage: deploy
+      os: osx
+      language: generic
+      env:
+        - PYTHON=python3
+        - CIBW_BEFORE_BUILD="pip install Cython numpy"
+      addons: {}
+      <<: *deploy_common
+      script:
+        - cibuildwheel --output-dir dist
+        - twine check dist/*
+        - twine upload --skip-existing dist/*
+
 addons:
   apt:
     packages:
       - liblzo2-dev
-before_install:
-    # Use miniconda for dependencies, pip is too slow -- https://gist.github.com/zonca/9958333
-    - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-    - chmod +x miniconda.sh
-    - ./miniconda.sh -b
-    - export PATH=/home/travis/miniconda2/bin:$PATH
-    - conda update --yes conda
+
 install:
-    - conda create --yes -n testenv python=$TRAVIS_PYTHON_VERSION Cython numpy nose
-    - source activate testenv
-    - pip install python-lzo
-    - python setup.py build_ext --inplace
-    - python setup.py install
+  - $PYTHON -m pip install Cython nose numpy python-lzo six
+  - $PYTHON setup.py build_ext --inplace
+  - $PYTHON setup.py install
+
 script:
   - nosetests

README.md

@@ -7,7 +7,7 @@
 The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
 
   * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
-  * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems)
+  * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
   * Data structures for working with intervals on sequences
     * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
     * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation

debian/README.Debian

 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 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.

debian/changelog

+python-bx (0.8.4-1) unstable; urgency=medium
+
+  * New upstream release. Removed Python2 binary packages; enabled the tests
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 23 Jul 2019 15:10:11 +0200
+
 python-bx (0.8.2-1) unstable; urgency=low
 
   * New upstream version.

debian/control

@@ -8,55 +8,26 @@ Build-Depends:
 	debhelper (>= 9),
 	dh-python,
 	zlib1g-dev,
-# Python2
-	python-setuptools,
-	python-all-dev,
-	python-nose,
-	python-numpy,
-	cython,
-# Python3
 	python3-setuptools,
 	python3-all-dev,
+	python3-lzo,
 	python3-nose,
 	python3-numpy,
+	python3-six,
 	cython3
 Standards-Version: 4.2.1
 Homepage:  https://github.com/bxlab/bx-python
 Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
 Vcs-Browser: https://salsa.debian.org/med-team/python-bx
 
-Package: python-bx
-Architecture: any
-Depends:
-	${shlibs:Depends},
-	${misc:Depends},
-	${python:Depends},
-Description: library to manage genomic data and its aligment
- The bx-python project is a python library and associated set of scripts to
- allow for rapid implementation of genome scale analyses. The library contains
- a variety of useful modules, but the particular strengths are:
-  * Classes for reading and working with genome-scale multiple local
-  alignments (in MAF, AXT, and LAV formats)
-  * Generic data structure for indexing on disk files that contain blocks of
-  data associated with intervals on various sequences (used, for example, to
-  provide random access to individual alignments in huge files; optimized for
-  use over network filesystems)
-  * Data structures for working with intervals on sequences
-  * "Binned bitsets" which act just like chromosome sized bit arrays, but
-  lazily allocate regions and allow large blocks of all set or all unset bits
-  to be stored compactly
-  * "Intersecter" for performing fast intersection tests that preserve both
-  query and target intervals and associated annotation
- .
- This package provides the Python 2 library.
-
 Package: python3-bx
 Architecture: any
-Depends:
+Depends: python3-lzo,
 	 ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends},
-Recommends: python-bx-tools
+Replaces: python3-bx-tools
+Provides: python3-bx-tools
 Description: library to manage genomic data and its alignment
  The bx-python project is a python library and associated set of scripts to
  allow for rapid implementation of genome scale analyses. The library contains
@@ -73,21 +44,3 @@ Description: library to manage genomic data and its alignment
   to be stored compactly
   * "Intersecter" for performing fast intersection tests that preserve both
   query and target intervals and associated annotation
- .
- This package provides the Python 3 library.
-
-Package: python-bx-tools
-Architecture: all
-Conflicts: python3-bx-tools
-Depends: python-bx, ${misc:Depends}, ${python:Depends}
-Description: command line interface to python3-bx
- This package collects all command line tools to access the functionality
- of the python-bx library. All scripts have python2 in their shebang line.
-
-Package: python3-bx-tools
-Architecture: all
-Conflicts: python-bx-tools
-Depends: python3-bx, ${misc:Depends}, ${python3:Depends}
-Description: command line interface to python3-bx
- This package collects all command line tools to access the functionality
- of the python-bx library. All scripts have python3 in their shebang line.

debian/lintian-overrides

+# 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: script-with-language-extension usr/bin/aggregate_scores_in_intervals.py
+python3-bx: script-with-language-extension usr/bin/align_print_template.py
+python3-bx: script-with-language-extension usr/bin/axt_extract_ranges.py
+python3-bx: script-with-language-extension usr/bin/axt_to_fasta.py
+python3-bx: script-with-language-extension usr/bin/axt_to_lav.py
+python3-bx: script-with-language-extension usr/bin/axt_to_maf.py
+python3-bx: script-with-language-extension usr/bin/bed_bigwig_profile.py
+python3-bx: script-with-language-extension usr/bin/bed_build_windows.py
+python3-bx: script-with-language-extension usr/bin/bed_complement.py
+python3-bx: script-with-language-extension usr/bin/bed_count_by_interval.py
+python3-bx: script-with-language-extension usr/bin/bed_count_overlapping.py
+python3-bx: script-with-language-extension usr/bin/bed_coverage.py
+python3-bx: script-with-language-extension usr/bin/bed_coverage_by_interval.py
+python3-bx: script-with-language-extension usr/bin/bed_diff_basewise_summary.py
+python3-bx: script-with-language-extension usr/bin/bed_extend_to.py
+python3-bx: script-with-language-extension usr/bin/bed_intersect.py
+python3-bx: script-with-language-extension usr/bin/bed_intersect_basewise.py
+python3-bx: script-with-language-extension usr/bin/bed_merge_overlapping.py
+python3-bx: script-with-language-extension usr/bin/bed_rand_intersect.py
+python3-bx: script-with-language-extension usr/bin/bed_subtract_basewise.py
+python3-bx: script-with-language-extension usr/bin/bnMapper.py
+python3-bx: script-with-language-extension usr/bin/div_snp_table_chr.py
+python3-bx: script-with-language-extension usr/bin/find_in_sorted_file.py
+python3-bx: script-with-language-extension usr/bin/gene_fourfold_sites.py
+python3-bx: script-with-language-extension usr/bin/get_scores_in_intervals.py
+python3-bx: script-with-language-extension usr/bin/int_seqs_to_char_strings.py
+python3-bx: script-with-language-extension usr/bin/interval_count_intersections.py
+python3-bx: script-with-language-extension usr/bin/interval_join.py
+python3-bx: script-with-language-extension usr/bin/lav_to_axt.py
+python3-bx: script-with-language-extension usr/bin/lav_to_maf.py
+python3-bx: script-with-language-extension usr/bin/line_select.py
+python3-bx: script-with-language-extension usr/bin/lzop_build_offset_table.py
+python3-bx: script-with-language-extension usr/bin/mMK_bitset.py
+python3-bx: script-with-language-extension usr/bin/maf_build_index.py
+python3-bx: script-with-language-extension usr/bin/maf_chop.py
+python3-bx: script-with-language-extension usr/bin/maf_chunk.py
+python3-bx: script-with-language-extension usr/bin/maf_col_counts.py
+python3-bx: script-with-language-extension usr/bin/maf_col_counts_all.py
+python3-bx: script-with-language-extension usr/bin/maf_count.py
+python3-bx: script-with-language-extension usr/bin/maf_covered_ranges.py
+python3-bx: script-with-language-extension usr/bin/maf_covered_regions.py
+python3-bx: script-with-language-extension usr/bin/maf_div_sites.py
+python3-bx: script-with-language-extension usr/bin/maf_drop_overlapping.py
+python3-bx: script-with-language-extension usr/bin/maf_extract_chrom_ranges.py
+python3-bx: script-with-language-extension usr/bin/maf_extract_ranges.py
+python3-bx: script-with-language-extension usr/bin/maf_extract_ranges_indexed.py
+python3-bx: script-with-language-extension usr/bin/maf_filter.py
+python3-bx: script-with-language-extension usr/bin/maf_filter_max_wc.py
+python3-bx: script-with-language-extension usr/bin/maf_gap_frequency.py
+python3-bx: script-with-language-extension usr/bin/maf_gc_content.py
+python3-bx: script-with-language-extension usr/bin/maf_interval_alignibility.py
+python3-bx: script-with-language-extension usr/bin/maf_limit_to_species.py
+python3-bx: script-with-language-extension usr/bin/maf_mapping_word_frequency.py
+python3-bx: script-with-language-extension usr/bin/maf_mask_cpg.py
+python3-bx: script-with-language-extension usr/bin/maf_mean_length_ungapped_piece.py
+python3-bx: script-with-language-extension usr/bin/maf_percent_columns_matching.py
+python3-bx: script-with-language-extension usr/bin/maf_percent_identity.py
+python3-bx: script-with-language-extension usr/bin/maf_print_chroms.py
+python3-bx: script-with-language-extension usr/bin/maf_print_scores.py
+python3-bx: script-with-language-extension usr/bin/maf_randomize.py
+python3-bx: script-with-language-extension usr/bin/maf_region_coverage_by_src.py
+python3-bx: script-with-language-extension usr/bin/maf_select.py
+python3-bx: script-with-language-extension usr/bin/maf_shuffle_columns.py
+python3-bx: script-with-language-extension usr/bin/maf_species_in_all_files.py
+python3-bx: script-with-language-extension usr/bin/maf_split_by_src.py
+python3-bx: script-with-language-extension usr/bin/maf_thread_for_species.py
+python3-bx: script-with-language-extension usr/bin/maf_tile.py
+python3-bx: script-with-language-extension usr/bin/maf_tile_2.py
+python3-bx: script-with-language-extension usr/bin/maf_tile_2bit.py
+python3-bx: script-with-language-extension usr/bin/maf_to_axt.py
+python3-bx: script-with-language-extension usr/bin/maf_to_concat_fasta.py
+python3-bx: script-with-language-extension usr/bin/maf_to_fasta.py
+python3-bx: script-with-language-extension usr/bin/maf_to_int_seqs.py
+python3-bx: script-with-language-extension usr/bin/maf_translate_chars.py
+python3-bx: script-with-language-extension usr/bin/maf_truncate.py
+python3-bx: script-with-language-extension usr/bin/maf_word_frequency.py
+python3-bx: script-with-language-extension usr/bin/mask_quality.py
+python3-bx: script-with-language-extension usr/bin/nib_chrom_intervals_to_fasta.py
+python3-bx: script-with-language-extension usr/bin/nib_intervals_to_fasta.py
+python3-bx: script-with-language-extension usr/bin/nib_length.py
+python3-bx: script-with-language-extension usr/bin/one_field_per_line.py
+python3-bx: script-with-language-extension usr/bin/out_to_chain.py
+python3-bx: script-with-language-extension usr/bin/prefix_lines.py
+python3-bx: script-with-language-extension usr/bin/pretty_table.py
+python3-bx: script-with-language-extension usr/bin/qv_to_bqv.py
+python3-bx: script-with-language-extension usr/bin/random_lines.py
+python3-bx: script-with-language-extension usr/bin/table_add_column.py
+python3-bx: script-with-language-extension usr/bin/table_filter.py
+python3-bx: script-with-language-extension usr/bin/tfloc_summary.py
+python3-bx: script-with-language-extension usr/bin/ucsc_gene_table_to_intervals.py
+python3-bx: script-with-language-extension usr/bin/wiggle_to_array_tree.py
+python3-bx: script-with-language-extension usr/bin/wiggle_to_binned_array.py
+python3-bx: script-with-language-extension usr/bin/wiggle_to_chr_binned_array.py
+python3-bx: script-with-language-extension usr/bin/wiggle_to_simple.py

debian/python-bx-tools.dirs

-usr

debian/python-bx-tools.lintian-overrides

-# 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/python-bx.dirs

-usr/bin

debian/python-bx.install

-#usr/bin

debian/python3-bx-tools.dirs

-usr

debian/python3-bx-tools.lintian-overrides

-# 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

debian/python3-bx.dirs

-usr/bin

debian/python3-bx.install

-#usr/bin

debian/rules

@@ -6,15 +6,11 @@
 export LC_ALL=C.UTF-8
 
 export NOSE_VERBOSE=2
-
-export PYBUILD_DESTDIR_python2=debian/python-bx/
-#export PYBUILD_DESTDIR_python2-dbg=debian/python-foo-dbg/
-export PYBUILD_DESTDIR_python3=debian/python3-bx/
-#export PYBUILD_DESTDIR_python3-dbg=debian/python3-foo-dbg/
-
+export PYBUILD_NAME=bx-python
+export PYBUILD_BEFORE_TEST=cp -r {dir}/test_data {build_dir}/
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_clean:
 	dh_auto_clean
@@ -24,13 +20,9 @@ override_dh_auto_clean:
 # Changes perpetually redone
 	rm -rf lib/bx_python.egg-info
 
-override_dh_install:
-	dh_install --autodest
-	dh_install
-	mkdir -p $(CURDIR)/debian/python-bx-tools/usr
-	mv $(CURDIR)/debian/python-bx/usr/bin $(CURDIR)/debian/python-bx-tools/usr/
-	mkdir -p $(CURDIR)/debian/python3-bx-tools/usr
-	mv $(CURDIR)/debian/python3-bx/usr/bin $(CURDIR)/debian/python3-bx-tools/usr/
+# override_dh_install:
+# 	dh_install --autodest
+# 	dh_install
+# 	mkdir -p $(CURDIR)/debian/python3-bx-tools/usr
+# 	mv $(CURDIR)/debian/python3-bx/usr/bin $(CURDIR)/debian/python3-bx-tools/usr/
 
-override_dh_auto_test:
-	# skipped

doc/source/index.rst

@@ -4,7 +4,7 @@ About bx-python
 The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
 
  * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
- * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems)
+ * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
  * Data structures for working with intervals on sequences
  * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
  * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation 

lib/bx/align/score_tests.py

 """
 Tests for `bx.align.score`.
 """
-import sys
 import unittest
 
 from numpy import array, cumsum, allclose
@@ -24,8 +23,7 @@ aligns = [ ( "CCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAA
            -299),
           ("gggaattgaacaatgagaacacatggacacaggaaggggaacatcacacacc----------ggggcctgttgtggggtggggggaag",
            "ggaactagaacaagggagacacatacaaacaacaacaacaacaacacagcccttcccttcaaagagcttatagtctgatggaggagag",
-             1690 )
-         ]
+           1690)]
 
 mafs = """##maf
 a score=2883.0
@@ -46,9 +44,7 @@ nonsymm_scheme = bx.align.score.build_scoring_scheme ( """  A    C    G    T
 
 aligns_for_nonsymm_scheme = [("AAAACCCCGGGGTTTT",
                               "ACGTACGTACGTACGT",
-                                -580 )
-                            ]
-
+                              -580)]
 
 asymm_scheme = bx.align.score.build_scoring_scheme("""    01   02    A    C    G    T
                                                        01  200 -200  -50  100  -50  100
@@ -57,8 +53,7 @@ asymm_scheme = bx.align.score.build_scoring_scheme ( """    01   02    A    C
 
 aligns_for_asymm_scheme = [("\x01\x01\x01\x01\x01\x01",
                             "ACGT\x01\x02",
-                              100 )
-                          ]
+                            100)]
 
 
 class BasicTests(unittest.TestCase):
@@ -66,12 +61,12 @@ class BasicTests( unittest.TestCase ):
     def test_scoring_text(self):
         ss = bx.align.score.hox70
         for t1, t2, score in aligns:
-            self.assertEquals( bx.align.score.score_texts( ss, t1, t2 ), score )
+            self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)
 
     def test_align(self):
         ss = bx.align.score.hox70
         for block in bx.align.maf.Reader(StringIO(mafs)):
-            self.assertEquals( bx.align.score.score_alignment( ss, block ), float( block.score ) )
+            self.assertEqual(bx.align.score.score_alignment(ss, block), float(block.score))
 
     def test_accumulate(self):
         ss = bx.align.score.hox70
@@ -83,9 +78,9 @@ class BasicTests( unittest.TestCase ):
     def test_nonsymm_scoring(self):
         ss = nonsymm_scheme
         for t1, t2, score in aligns_for_nonsymm_scheme:
-            self.assertEquals( bx.align.score.score_texts( ss, t1, t2 ), score )
+            self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)
 
     def test_asymm_scoring(self):
         ss = asymm_scheme
         for t1, t2, score in aligns_for_asymm_scheme:
-            self.assertEquals( bx.align.score.score_texts( ss, t1, t2 ), score )
+            self.assertEqual(bx.align.score.score_texts(ss, t1, t2), score)

lib/bx/bbi/bpt_file.pyx

@@ -54,7 +54,7 @@ cdef class BPTFile:
             self.reader.read( self.key_size )
             offset = self.reader.read_uint64()
             # Loop until correct subtree is found
-            for i from 0 <= i < child_count:
+            for i from 0 <= i < child_count - 1:
                 node_key = self.reader.read( self.key_size )
                 if node_key > key:
                     break

lib/bx/bitset_tests.py

@@ -5,12 +5,13 @@ Tests for `bx.bitset`.
 import bx.bitset
 import unittest
 
+
 class AbstractTests(object):
 
     def assert_bits(self, bits, list):
         assert bits.size == len(list), "Bitset size and verification list size do not match"
         for i in range(bits.size):
-            self.assertEquals( bits[i], list[i] )
+            self.assertEqual(bits[i], list[i])
 
     def test_overflow_create(self):
         self.assertRaises(ValueError, self.new_bits, 4000000000)
@@ -43,7 +44,8 @@ class AbstractTests( object ):
         # Set some positions
         for b, e in ((11, 14), (20, 75), (90, 99)):
             bits.set_range(b, e-b)
-            for pos in range( b, e ): l[ pos ] = 1
+            for pos in range(b, e):
+                l[pos] = 1
         self.assert_bits(bits, l)
 
     def test_count(self):
@@ -52,11 +54,11 @@ class AbstractTests( object ):
         # Set some positions
         for b, e in ((11, 14), (20, 75), (90, 100)):
             bits.set_range(b, e-b)
-        self.assertEquals( bits.count_range( 0, 0 ), 0 )
-        self.assertEquals( bits.count_range( 0, 20 ), 3 )
-        self.assertEquals( bits.count_range( 25, 25 ), 25 )
-        self.assertEquals( bits.count_range( 80, 20 ), 10 )
-        self.assertEquals( bits.count_range( 0, 100 ), 68 )
+        self.assertEqual(bits.count_range(0, 0), 0)
+        self.assertEqual(bits.count_range(0, 20), 3)
+        self.assertEqual(bits.count_range(25, 25), 25)
+        self.assertEqual(bits.count_range(80, 20), 10)
+        self.assertEqual(bits.count_range(0, 100), 68)
 
     def test_find(self):
         # Create and assert empty
@@ -65,14 +67,14 @@ class AbstractTests( object ):
         for b, e in ((11, 14), (20, 75), (90, 100)):
             bits.set_range(b, e-b)
         # Next set
-        self.assertEquals( bits.next_set( 0 ), 11 )
-        self.assertEquals( bits.next_set( 13 ), 13 )
-        self.assertEquals( bits.next_set( 15 ), 20 )
+        self.assertEqual(bits.next_set(0), 11)
+        self.assertEqual(bits.next_set(13), 13)
+        self.assertEqual(bits.next_set(15), 20)
         # Next clear
-        self.assertEquals( bits.next_clear( 0 ), 0 )
-        self.assertEquals( bits.next_clear( 11 ), 14 )
-        self.assertEquals( bits.next_clear( 20 ), 75 )
-        self.assertEquals( bits.next_clear( 92 ), 100 )
+        self.assertEqual(bits.next_clear(0), 0)
+        self.assertEqual(bits.next_clear(11), 14)
+        self.assertEqual(bits.next_clear(20), 75)
+        self.assertEqual(bits.next_clear(92), 100)
 
     def test_and(self):
         bits1 = self.new_bits(100)
@@ -81,7 +83,8 @@ class AbstractTests( object ):
         bits2.set_range(50, 25)
         bits1.iand(bits2)
         l = [0]*100
-        for i in range( 50, 60 ): l[i] = 1
+        for i in range(50, 60):
+            l[i] = 1
         self.assert_bits(bits1, l)
 
     def test_or(self):
@@ -91,7 +94,8 @@ class AbstractTests( object ):
         bits2.set_range(50, 25)
         bits1.ior(bits2)
         l = [0]*100
-        for i in range( 20, 75 ): l[i] = 1
+        for i in range(20, 75):
+            l[i] = 1
         self.assert_bits(bits1, l)
 
     def test_not(self):
@@ -99,13 +103,16 @@ class AbstractTests( object ):
         bits.set_range(20, 40)
         bits.invert()
         l = [1]*100
-        for i in range( 20, 60 ): l[i] = 0
+        for i in range(20, 60):
+            l[i] = 0
         self.assert_bits(bits, l)
 
+
 class BitSetTests(AbstractTests, unittest.TestCase):
     def new_bits(self, size):
         return bx.bitset.BitSet(size)
 
+
 class BinnedBitSetTests(AbstractTests, unittest.TestCase):
     def new_bits(self, size):
         granularity = size % 11