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CVS log for pkgsrc/biology/py-dnaio/distinfo

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Keyword substitution: kv
Default branch: MAIN


Revision 1.6: download - view: text, markup, annotated - select for diffs
Sat Feb 10 13:07:54 2024 UTC (9 months, 4 weeks ago) by bacon
Branches: MAIN
CVS tags: pkgsrc-2024Q3-base, pkgsrc-2024Q3, pkgsrc-2024Q2-base, pkgsrc-2024Q2, pkgsrc-2024Q1-base, pkgsrc-2024Q1, HEAD
Diff to: previous 1.5: preferred, colored
Changes since revision 1.5: +4 -4 lines
biology/py-dnaio: Update to 1.2.0

Numerous bug fixes and enhancements since 0.9.1
Changes: https://github.com/marcelm/dnaio/tags

Revision 1.5: download - view: text, markup, annotated - select for diffs
Mon Nov 14 10:39:40 2022 UTC (2 years ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2023Q4-base, pkgsrc-2023Q4, pkgsrc-2023Q3-base, pkgsrc-2023Q3, pkgsrc-2023Q2-base, pkgsrc-2023Q2, pkgsrc-2023Q1-base, pkgsrc-2023Q1, pkgsrc-2022Q4-base, pkgsrc-2022Q4
Diff to: previous 1.4: preferred, colored
Changes since revision 1.4: +4 -4 lines
py-dnaio: update to 0.9.1.

v0.9.1 (2022-08-01)
-------------------

* :pr:`85`: macOS wheels are now also built as part of the release procedure.
* :pr:`81`: API documentation improvements and minor code refactors for
  readability.

v0.9.0 (2022-05-17)
-------------------

* :pr:`79`: Added a `records_are_mates` function to be used for checking whether
  three or more records are mates of each other (by checking the ID).
* :pr:`74`, :pr:`68`: Made FASTQ parsing faster by implementing the check for
  ASCII using SSE vector instructions.
* :pr:`72`: Added a `tutorial <https://dnaio.readthedocs.io/en/latest/tutorial.html>`_.

v0.8.0 (2022-03-26)
-------------------

* Preliminary documentation is available at
  <https://dnaio.readthedocs.io/>.
* :pr:`53`: Renamed ``Sequence`` to `SequenceRecord`.
  The previous name is still available as an alias
  so that existing code will continue to work.
* When reading a FASTQ file, there is now a check that ensures that
  all characters are ASCII.
* Function ``record_names_match`` is deprecated, use `SequenceRecord.is_mate` instead.
* Dropped Python 3.6 support as it is end-of-life.

v0.7.1 (2022-01-26)
-------------------

* :pr:`34`: Fix parsing of FASTA files that just contain a comment and no reads

v0.7.0 (2022-01-17)
-------------------

* @rhpvorderman contributed many performance improvements in :pr:`15`,
  :pr:`17`, :pr:`18`, :pr:`20`, :pr:`21`, :pr:`22`, :pr:`23`. Reading
  and writing FASTQ files and reading of paired-end FASTQ files was
  sped up significantly. For example, reading uncompressed FASTQ is
  50% faster (!) than before.
* :pr:`28`: Windows support added


v0.6.0 (2021-09-28)
-------------------

* :pr:`12`: Improve FASTQ writing speed twofold (thanks to @rhpvorderman)


v0.5.2 (2021-09-07)
-------------------

* :issue:`7`: Ignore a trailing "3" in the read id

Revision 1.4: download - view: text, markup, annotated - select for diffs
Tue Oct 26 10:03:43 2021 UTC (3 years, 1 month ago) by nia
Branches: MAIN
CVS tags: pkgsrc-2022Q3-base, pkgsrc-2022Q3, pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1, pkgsrc-2021Q4-base, pkgsrc-2021Q4
Diff to: previous 1.3: preferred, colored
Changes since revision 1.3: +2 -2 lines
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

Revision 1.3: download - view: text, markup, annotated - select for diffs
Thu Oct 7 13:19:42 2021 UTC (3 years, 2 months ago) by nia
Branches: MAIN
Diff to: previous 1.2: preferred, colored
Changes since revision 1.2: +1 -2 lines
biology: Remove SHA1 hashes for distfiles

Revision 1.2: download - view: text, markup, annotated - select for diffs
Fri May 21 11:38:13 2021 UTC (3 years, 6 months ago) by adam
Branches: MAIN
CVS tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2
Diff to: previous 1.1: preferred, colored
Changes since revision 1.1: +5 -5 lines
py-dnaio: updated to 0.5.1

v0.5.1
Add py.typed and distribute .pyi files

Revision 1.1: download - view: text, markup, annotated - select for diffs
Mon Feb 8 01:52:24 2021 UTC (3 years, 10 months ago) by bacon
Branches: MAIN
CVS tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1
biology/py-dnaio: import py38-dnaio-0.5.0

dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files.
It supports paired-end data in separate files, interleaved paired-end in a
single file and compression using gzip, bzip, and xz.

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