pybbi - v0.4.1

Maintenance

• NumPy 2.0 support and backwards compatibility:
  • NumPy 2.x is now required at build time, so that binaries work on NumPy 1.xx and 2.x.
  • Dropped wheels for py38, added py313.

Full Changelog: https://github.com/nvictus/pybbi/compare/v0.4.0...v0.4.1

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Published by nvictus over 1 year ago

pybbi - v0.4.0

New features

• Exact (non-interpolated) summary calculation on binned ranges using fetch(chrom, start, end, ..., exact=True) (https://github.com/nvictus/pybbi/pull/33)
• Zoom record queries via fetch_summaries() (https://github.com/nvictus/pybbi/pull/33)

Full Changelog: https://github.com/nvictus/pybbi/compare/v0.3.6...v0.4.0

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Published by nvictus about 2 years ago

pybbi - v0.3.6

This release is only to mint an initial Zenodo DOI.

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Published by nvictus over 2 years ago

pybbi - v0.3.5

Changes: * Replace OrderedDict in favor of regular dict for f.info: https://github.com/nvictus/pybbi/pull/28

Docs: * Clarify behavior of f.stackup when bins= is provided: https://github.com/nvictus/pybbi/pull/28

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Published by nvictus about 3 years ago

pybbi - v0.3.4

This version restores the full build process (UCSC library and Cython extension module) when installing from source through pip.

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Published by nvictus about 3 years ago

pybbi - v0.3.3

Version bump to release binary wheels for Python 3.11

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Published by nvictus about 3 years ago

pybbi - v0.3.2

Maintenance/bug fix

Removed internal usage of six (was dropped as requirement in previous release).

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Published by nvictus over 4 years ago

pybbi - v0.3.1

Maintenance

• Removed hard-coded library path in setup.py assuming x86-64 architecture to support build on other architectures like Apple Silicon aarch64. By @pkerpedjiev (#18)

Full Changelog: https://github.com/nvictus/pybbi/compare/v0.3.0...v0.3.1

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Published by nvictus over 4 years ago

pybbi - v0.3.0

New features

• Refactored bbi functions into a cdef class BBIFile obtained with bbi.open() (#13). The function API is preserved.
• BBIFile adds support to read and parse a bigBed's AutoSql schema definition
• AutoSql scalar types are mapped to numpy/pandas dtypes
• AutoSql listed/array types or other exotic types are treated as regular strings

API changes

• fetch_intervals takes an additional iterator parameter. If True, it will return an interval iterator (of tuples) with the same behavior as in v0.2. If False, returns a dataframe with columns correctly parsed using the AutoSql schema. The class method returns a dataframe by default, and the function returns the iterator by default to preserve existing behavior.
• Python 2.7 support has been dropped.

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Published by nvictus almost 6 years ago

pybbi - v0.2.3

• Add summary statistic sum #12

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Published by nvictus almost 6 years ago

pybbi - v0.2.2

Bug fixes * Fixed open file leaks when Python exceptions are raised.

API changes * stackup now allows passing unequal interval lengths when the bins parameter is specified.

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Published by nvictus over 6 years ago

pybbi - v0.2.1

Backported fixes to make s3 signed urls, and 307/308 redirects work * My original PR: ucscGenomeBrowser/kent#23 * Their changes: ucscGenomeBrowser/kent@7807b5c

Distributing manylinux and osx wheels

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Published by nvictus over 6 years ago

pybbi -

Added support for all built-in summary statistics: mean, min, max, coverage and standard deviation. These can be specified using the summary parameter of fetch() and stackup().

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Published by nvictus over 7 years ago

pybbi - v0.1.2

Create complete source distribution and upload to PyPI

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Published by nvictus over 7 years ago

pybbi - v0.1.1

First official release.

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Published by nvictus about 8 years ago