Skip to content

issues Search Results · repo:tskit-dev/tszip language:Python

Filter by

43 results
 (75 ms)

43 results

intskit-dev/tszip (press backspace or delete to remove)

tskit-dev/tszip
Zarr v3

I had a quick go at zarr v3 as the tskit CI broke due to tszip. It seems more involved than I expected, so will come back to it. Ideally we wish to support both v2 and v3, but this may not be easy.
  • benjeffery
  • 1
  • Opened 
    on Jan 15
  • #97

tskit-dev/tszip
Tszip can't decompress with struct metadata

In the attached file, there is struct metadata associated with the tree sequence at the top level (a simple array). Tszip can load the .trees file, and compress it to .tsz, but then can t load the .tsz ...
  • hyanwong
  • Opened 
    on Dec 14, 2024
  • #95

tskit-dev/tszip
Consistency, chromosome number

Thanks for developing tszip, and for documenting it! Maybe a little nitpicky, in docs/index.md (welcome page of the documentation), the text speaks of chromosome 22, but the code suggests it might be ...
  • hannesbecher
  • 2
  • Opened 
    on Oct 17, 2024
  • #90

tskit-dev/tszip
Deactivate RTD docs build

I m getting emails from RTD about docs build failures (https://readthedocs.org/projects/tszip/builds/25316066/ ) I think we can just turn off RTD now @benjeffery?
  • jeromekelleher
  • 1
  • Opened 
    on Aug 27, 2024
  • #89

tskit-dev/tszip
Worse compression in recent versions?

I m loading https://zenodo.org/records/5495535/files/hgdp_tgp_sgdp_chr20_p.dated.trees.tsz. When I decompress and then compress it again, with the latests tszip, I get a file which is about 20% larger ...
  • hyanwong
  • 2
  • Opened 
    on Jul 13, 2024
  • #87

tskit-dev/tszip
requires-python should be 3.9

We currently have requires-python = =3.8 in pyproject.toml. Should be 3.9, right?
  • jeromekelleher
  • 3
  • Opened 
    on Jul 11, 2024
  • #86

tskit-dev/tszip
Pin zarr<3

Zarr version 3 is coming soon and will likely break compatibility.
  • benjeffery
  • 1
  • Opened 
    on Jul 3, 2024
  • #81

tskit-dev/tszip
Documentation out of date

The docs on https://tszip.readthedocs.io/en/latest/python-api.html don t refer to 0.2.3, so were probably not updated. Related #67
  • jeromekelleher
  • 2
  • Opened 
    on Jun 3, 2024
  • #80

tskit-dev/tszip
cannot write to stdout

I installed tszip via conda, and -c (and --stdout) are not recognized as arguments I tried: tszip -c test.ts usage: tszip [-h] [-V] [-v] [--variants-only] [-S SUFFIX] [-k] [-f] [-d | -l] files [files ...
  • ShyamieG
  • 5
  • Opened 
    on Jun 19, 2023
  • #71

tskit-dev/tszip
Cannot handle columns > 2GiB

I am experiencing an error when trying to compress certain tree sequence files: ValueError: Codec does not support buffers of 2147483647 bytes It seems that this error is originating from some function ...
bug
  • ShyamieG
  • 8
  • Opened 
    on Apr 5, 2023
  • #69
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Restrict your search to the title by using the in:title qualifier.
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Restrict your search to the title by using the in:title qualifier.
Issue search results · GitHub