v1.0.0

Major modernization release focused on Python upgrades, dependency cleanup, and architectural refactoring to improve reliability, portability, and test coverage.

Highlights:

• Python 3.8-3.13 support; refresh packaging with pyproject.toml and updated build tooling.
• Replace bx-python with pyBigWig.
• Unify results/statistics model and simplify handler/factory design.
• Stabilize multiprocessing: use spawn start method.
• Introduce tests.

Breaking changes:

• Drop Python2 and <3.8 support.
• Default multiprocessing start method set to spawn.

Architecture and refactoring:

• Move to factory-centric design; remove redundant strategy layer and clarify service/handler responsibilities.
• Migrate from os.path to pathlib; add comprehensive type hints and mypy checks.
• Remove obsolete Python 2 compatibility.

CI/CD and distribution:

• Adopt cibuildwheel and stabilize matrix builds; optimize resource usage.
• Improve BitArray build/link flags for macOS/ARM64 and Linux.

v0.3.2

v0.3.2 (2019-11-04)

Fixed bugs:

• Fix FWHM calculation failure

v0.3.1

v0.3.1 (2019-11-01)

Implemented enhancements:

• Support VSN calculation
• Save number of (mappable) reads as a file for replotting
• Improve minimum coefficient obtaining method

Fixed bugs:

• Avoid arctanh divergence

v0.3.0

v0.3.0 (2019-07-03)

• Drop python3.4 support
  Implemented enhancements:
• Use Fisher's r-to-z transformation to averaging coefficients
• Add chromosome selecting options

v0.2.6

v0.2.6 (2019-01-09)

Implemented enhancements:

• Add --mask-size option to avoid calling the phantom peak a library length.
  Warnings messages were also implemented.

Fixed bugs:

• Fix read counter for unmapped reads.
• Fix bigwig reader.
• Fix mappability stats loader.

v0.2.5

v0.2.5 (2019-01-05)

Implemented enhancements:

• Include pre-built C sources and support both pre-built source installation and
  native Cython compile (cython is no longer mandatory dependency).
• Check compatible python versions. (3.4 and 3.7 additionally)
• Scipy is no longer required.

Fixed bugs:

• Omit functools.partialmethod to keep python2 compatibility.
• Fix minor argparse issues and a error message.

v0.2.4

v0.2.4 (2018-05-09)

Fixed bugs:

• Reduce smooth window default size to 15 (Longer lengths are suitable for
  samples with long fragments (such as broad sources) but it's not robust.)
• Use read lengths calculated from CIGAR alignments instead of sequence lengths
• Fix build issue

v0.2.3

v0.2.3 (2018-05-04)

Implemented enhancements:

• Add pymasc-plot command
• Optimize the default window size for moving average filter for mappability
  sensitive cross-correlation (change from 15 to 100)
• Add annotations to figures about expected library length

Fixed bugs:

• Fix bugs relate to mappability sensitive cross-correlation calculation
  Now bitarray and successive implementations return exactly same results

Merge pull request #4 from ronin-gw/v0.2.2

v0.2.2 (2017-12-26)

Implemented enhancements:

• Warn reference lenth discordancy between alignment and mappability file

Fixed bugs:

• Add forgetted initial rotate for mappability array
• BitArray length shortage if mappability tracks include positions which are out
  of range of alignment file reference length

v0.2.1

v0.2.1 (2017-12-23)

Fixed bugs:

• BitArray length shortage for reverse strand reads
• BitArray implementation fails for chromosomes which have no mapped reads