Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / tskit-dev/tsinfer issues and pull requests

#829 - Start on factoring out ResultBuffer

Pull Request - State: closed - Opened by jeromekelleher about 1 year ago - 10 comments

#828 - Add linesweep ancestor grouping

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 11 comments

#827 - Resume using LMDB

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 7 comments

#826 - Store resume buffer of match results

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 2 comments

#825 - match_epoch function

Issue - State: open - Opened by jeromekelleher about 1 year ago

#824 - Checkpointing for ancestor and sample matching

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 2 comments

#823 - Disable phase checks

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 2 comments

#822 - Python 3.11 support

Pull Request - State: open - Opened by benjeffery about 1 year ago - 7 comments

#821 - Package tsinfer for pyodide

Issue - State: closed - Opened by benjeffery about 1 year ago - 10 comments

#820 - Fix codecov

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 1 comment

#819 - Need a bugfix release for zarr issue

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 2 comments

#818 - Dask experiments

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 4 comments

#817 - Out-of-core ancestor matching

Issue - State: open - Opened by benjeffery over 1 year ago

#816 - Speed up bit unpacking in `generate_ancestors`

Issue - State: open - Opened by benjeffery over 1 year ago - 1 comment

#815 - Add two-bit encoding for generate ancestors

Issue - State: open - Opened by jeromekelleher over 1 year ago - 4 comments
Labels: enhancement

#814 - Zero recombination rate, reprise

Issue - State: open - Opened by hyanwong over 1 year ago - 1 comment

#813 - Update mergify

Pull Request - State: closed - Opened by benjeffery over 1 year ago

#812 - Pass through options to tqdm

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 4 comments

#811 - Don't load all ancestors when truncating

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 6 comments

#810 - Default SGkit alleles are byte strings, which confuses tsinfer:

Issue - State: open - Opened by hyanwong over 1 year ago - 2 comments

#809 - One-bit encoding for genotypes

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 31 comments

#808 - Alloc genotype memory from mmap

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 11 comments

#807 - WIP - Match samples in parallel

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#806 - Ancestor generation requires entire genotype array to be in-memory.

Issue - State: closed - Opened by benjeffery over 1 year ago - 10 comments

#805 - Fix lint

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#804 - Write only the extent of ancestors to improve generation perf

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#803 - Add tute code to compare orig and inferred variation

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#802 - Fix dep specification

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#800 - `sgkit` ancestral allele

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#799 - Values of recombination and mismatch rate

Issue - State: open - Opened by frezaei98 over 1 year ago - 6 comments

#798 - Tidy eval util

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#796 - Installation currently fails under python 3.11 due to numba dep

Issue - State: open - Opened by hyanwong over 1 year ago - 1 comment

#795 - Fix doc build

Pull Request - State: closed - Opened by benjeffery over 1 year ago

#794 - Filter out empty string alleles

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 9 comments

#793 - Match chunks of samples

Issue - State: open - Opened by jeromekelleher over 1 year ago - 2 comments

#791 - Add mask to sgkit SampleData

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 4 comments

#790 - Circle CI failure

Issue - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#789 - Fix doc build

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#788 - Doc build failure

Issue - State: closed - Opened by benjeffery over 1 year ago
Labels: documentation

#786 - sgkit: Support `call_genotype_mask`?

Issue - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#785 - Correct length of sites metadata

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#784 - Error if sgkit sample data is unphased

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 4 comments

#783 - Change SgkitSampleData to accept a path or store.

Issue - State: open - Opened by benjeffery over 1 year ago - 2 comments

#782 - Testing CI

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#781 - Fix and update pre-commit

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#780 - Fix docs build

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#779 - Decouple SampleData from AncestorData

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 5 comments

#778 - Sgkit compatible ancestors

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 21 comments

#777 - Remove "extend" code (ported to sc2ts)

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 2 comments

#776 - Parsimoniously explain direct reversions

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 3 comments

#775 - Remove pytest-xdist

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 5 comments

#774 - Tutorial tweaks

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 3 comments

#773 - Run tests sequentially

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment

#772 - sgkit: Error/Warning on unphased data when ploidy > 1.

Issue - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#771 - CI: windows tests failing with parallel running

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 3 comments

#770 - Tweak for CPU time change

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 6 comments

#769 - Fix numpy pip

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 4 comments

#768 - Extend greedy mutation coalescing

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 6 comments

#767 - sgkit: Workflow documentation

Issue - State: open - Opened by benjeffery over 1 year ago - 1 comment

#765 - sgkit: Error out on multiple contigs

Issue - State: open - Opened by benjeffery over 1 year ago

#764 - sgkit: Use ancestral_allele_index

Issue - State: closed - Opened by benjeffery over 1 year ago

#763 - sgkit: Use sequence length from dataset

Issue - State: open - Opened by benjeffery over 1 year ago - 1 comment

#762 - Add info logging during "extend" setup

Issue - State: open - Opened by jeromekelleher over 1 year ago

#761 - Release traceback memory if gets > 2GiB

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 4 comments

#758 - Update CHANGELOG.md

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment

#757 - Fix readme MIME for PyPI

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#756 - 0.3.0 pypi upload failed

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 5 comments
Labels: bug

#755 - Update changelog for release

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment

#754 - Add --keep-intermediates CLI option

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 10 comments

#753 - Allow msprime.RateMap or equivalent to be used in pip installs

Issue - State: open - Opened by hyanwong over 1 year ago - 8 comments

#752 - Temporarily disable --recombination-map in cli

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 3 comments

#751 - Windows install fails because of msprime

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 5 comments
Labels: bug

#748 - Minimum viable sgkit dataset

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 28 comments

#739 - Variant method to return actual states

Issue - State: open - Opened by hyanwong over 1 year ago - 4 comments

#729 - Unify SampleData and AncestorsData file formats

Issue - State: open - Opened by jeromekelleher over 1 year ago - 2 comments

#728 - SampleData frontend for sgkit/xarray dataset

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 4 comments

#707 - How to stop people getting confused when inspecting ancestors tree sequences?

Issue - State: open - Opened by hyanwong almost 2 years ago - 1 comment

#701 - Set individuals table metadata schema to permissive_json

Issue - State: open - Opened by hyanwong almost 2 years ago - 2 comments

#699 - Document SampleData attributes

Issue - State: closed - Opened by szhan almost 2 years ago - 2 comments

#696 - Allow sample data and ancestors files to store their time units

Issue - State: open - Opened by hyanwong almost 2 years ago - 8 comments

#688 - Document numpy array accessors in the sample data files?

Issue - State: closed - Opened by hyanwong about 2 years ago - 7 comments

#687 - Remove the ultimate ancestor and split the grand MRCA

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 23 comments

#683 - Raise warning when zero inference sites provided.

Issue - State: closed - Opened by evolgenomics about 2 years ago - 12 comments

#675 - Initial extend

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 4 comments

#652 - Use imputation accuracy to determine the correct mismatch ratios

Issue - State: open - Opened by hyanwong over 2 years ago - 9 comments

#608 - Possible (minor) bug in PC ancestors?

Issue - State: open - Opened by hyanwong over 2 years ago - 3 comments

#604 - Add ability to indicate that an ancestor is a sample

Issue - State: open - Opened by hyanwong over 2 years ago - 3 comments

#577 - Add recombination rate & tsdate link to the "real data" tute

Issue - State: open - Opened by hyanwong almost 3 years ago - 1 comment

#486 - Use dependency levels rather than epochs

Pull Request - State: closed - Opened by hyanwong over 3 years ago - 12 comments

#437 - Fix HMM for > 2 alleles

Issue - State: open - Opened by jeromekelleher over 3 years ago - 3 comments

#434 - Documentation for metadata schemas

Issue - State: open - Opened by jeromekelleher over 3 years ago
Labels: enhancement

#425 - Identifying Error from tsinfer Trees

Issue - State: open - Opened by awohns over 3 years ago - 3 comments

#422 - Output which haplotype fails

Pull Request - State: closed - Opened by hyanwong over 3 years ago - 12 comments

#419 - Output the haplotype being matched when find_path fails

Issue - State: open - Opened by hyanwong over 3 years ago - 2 comments