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

#935 - Numpy 2.0 supporting release

Issue - State: open - Opened by jeromekelleher 11 days ago

#934 - Grep for "sgkit" in names and replace

Issue - State: open - Opened by jeromekelleher 11 days ago

#933 - Investigate AFS bias due to polytomies

Issue - State: open - Opened by hyanwong 20 days ago - 3 comments

#931 - Set node metadata schema

Pull Request - State: open - Opened by hyanwong 24 days ago - 2 comments

#930 - Allow the same scheme name, if description matches

Pull Request - State: closed - Opened by hyanwong 25 days ago - 7 comments

#929 - Overwriting md schema

Issue - State: closed - Opened by hyanwong 25 days ago

#928 - Always read alleles as strings (not bytes)

Pull Request - State: open - Opened by hyanwong 25 days ago - 5 comments
Labels: AUTOMERGE-REQUESTED

#927 - Check all alleles at a site are unique before inference

Issue - State: open - Opened by hyanwong 25 days ago - 6 comments
Labels: bug

#926 - Add dependency on tsdate

Issue - State: open - Opened by jeromekelleher 28 days ago - 3 comments
Labels: enhancement

#925 - How to save an SgkitSampleData instance, e.g. for running the CLI

Issue - State: open - Opened by hyanwong about 1 month ago - 4 comments

#924 - Class method to create simple SgkitSampleData files for demos

Issue - State: open - Opened by hyanwong about 1 month ago - 1 comment

#922 - Rename SgkitSampleData object?

Issue - State: open - Opened by hyanwong about 1 month ago

#921 - Batch job ancestor matching.

Issue - State: open - Opened by benjeffery about 1 month ago - 3 comments

#920 - Reinstate 3.11, 3.12 testing after sgkit fix.

Issue - State: open - Opened by benjeffery about 2 months ago - 1 comment

#919 - Pin to zarr < 3

Issue - State: open - Opened by jeromekelleher about 2 months ago

#918 - Fix CI

Pull Request - State: closed - Opened by benjeffery about 2 months ago - 4 comments

#917 - Batch ancestor matching

Pull Request - State: open - Opened by benjeffery about 2 months ago - 5 comments

#916 - Identifying PC nodes / edges added during match_samples

Issue - State: open - Opened by hyanwong about 2 months ago - 3 comments

#915 - SgkitSampleData.from_tree_sequence bugs out

Issue - State: open - Opened by hyanwong 2 months ago

#914 - Fix OSX tests

Pull Request - State: closed - Opened by benjeffery 2 months ago - 1 comment

#913 - Low density regions and splitting

Issue - State: open - Opened by benjeffery 3 months ago - 2 comments
Labels: enhancement

#912 - Simplify dev reqs and make compatible with tsdate

Pull Request - State: closed - Opened by benjeffery 3 months ago - 1 comment

#911 - Improve ancestor building by using more information

Issue - State: open - Opened by hyanwong 3 months ago

#910 - Tests: allow file closing to pass if name undefined

Pull Request - State: closed - Opened by hyanwong 3 months ago - 1 comment

#909 - Compiling on Apple ARM - mostly works

Issue - State: closed - Opened by hyanwong 3 months ago

#908 - Tweak ma-match progressbar total

Pull Request - State: closed - Opened by hyanwong 4 months ago - 1 comment

#907 - Tests don't work unless you install the package

Issue - State: closed - Opened by hyanwong 4 months ago - 2 comments

#906 - Make tqdm work nicely in notebooks

Pull Request - State: closed - Opened by hyanwong 4 months ago - 14 comments

#905 - Makefile doesn't override CC if it already exists

Pull Request - State: closed - Opened by hyanwong 4 months ago - 1 comment

#904 - Compilation overrides CC

Issue - State: closed - Opened by hyanwong 4 months ago - 1 comment

#903 - Investigate why sample nodes attach to deep roots / ultimate ancestor

Issue - State: open - Opened by hyanwong 5 months ago - 20 comments

#902 - Update cli.py

Pull Request - State: closed - Opened by hyanwong 5 months ago - 1 comment

#901 - Add `mask` option to `insert_missing_sites`

Issue - State: closed - Opened by benjeffery 5 months ago - 1 comment
Labels: enhancement

#900 - Mask names

Pull Request - State: closed - Opened by benjeffery 5 months ago - 3 comments

#899 - Flip polarity

Pull Request - State: closed - Opened by benjeffery 5 months ago - 2 comments

#897 - Flip polarity of masks

Issue - State: closed - Opened by benjeffery 5 months ago - 1 comment

#896 - Add sample mask

Pull Request - State: closed - Opened by benjeffery 5 months ago - 14 comments

#895 - Sample masking from sgkit dataset

Issue - State: open - Opened by benjeffery 5 months ago - 1 comment

#892 - SgkitSampleData format missing data bug

Issue - State: open - Opened by hyanwong 5 months ago - 2 comments
Labels: bug

#891 - Replace node_span in eval_util

Issue - State: open - Opened by hyanwong 5 months ago

#890 - Add seed to simulate_genotype_call_dataset in tests

Issue - State: open - Opened by hyanwong 5 months ago

#889 - Check duplicate positions

Pull Request - State: closed - Opened by hyanwong 5 months ago - 12 comments

#888 - SgkitSampleData allows duplicate positions

Issue - State: closed - Opened by hyanwong 5 months ago

#887 - Better formatted error message for ancestral alleles

Pull Request - State: closed - Opened by hyanwong 5 months ago - 1 comment

#886 - Ancestor.inference_sites_set never used

Issue - State: open - Opened by hyanwong 5 months ago - 1 comment

#885 - Allow empty ancestral alleles

Pull Request - State: closed - Opened by hyanwong 5 months ago - 3 comments

#884 - "Empty alleles must be at the end" error for 1000G VCFs

Issue - State: open - Opened by hyanwong 5 months ago - 1 comment

#883 - SGkit equivalent for tutorial read_vcf

Issue - State: open - Opened by hyanwong 5 months ago - 5 comments

#881 - Set sample node times

Issue - State: open - Opened by hyanwong 6 months ago

#880 - Batching during match ancestors wastes worker CPU.

Issue - State: closed - Opened by benjeffery 6 months ago - 3 comments
Labels: enhancement

#879 - Limit linesweep to 1M ancestors

Pull Request - State: closed - Opened by benjeffery 6 months ago - 2 comments

#878 - Don't double count progress

Pull Request - State: closed - Opened by benjeffery 7 months ago - 1 comment

#877 - Robustness of tsinfer & tsdate to selection

Issue - State: open - Opened by hyanwong 7 months ago - 23 comments

#876 - Parallel matching via batch jobs

Pull Request - State: closed - Opened by benjeffery 8 months ago - 4 comments

#874 - Sample matching progress bar incorrect

Issue - State: open - Opened by benjeffery 8 months ago - 1 comment

#873 - Fix OSX CI failures

Pull Request - State: closed - Opened by benjeffery 8 months ago - 6 comments

#872 - Return sgkit sample_id in individual metadata

Pull Request - State: closed - Opened by benjeffery 8 months ago - 5 comments

#871 - Record sgkit sample_ids in individual metadata

Issue - State: closed - Opened by benjeffery 8 months ago

#870 - No sites used for inference

Issue - State: open - Opened by bgyuris 8 months ago - 4 comments

#868 - polytomies

Issue - State: closed - Opened by frezaei98 8 months ago - 1 comment

#867 - KC Distance of an inferred tree sequence

Issue - State: closed - Opened by frezaei98 9 months ago - 5 comments

#865 - Update docs build

Pull Request - State: open - Opened by benjeffery 9 months ago

#864 - Update README.md

Pull Request - State: closed - Opened by hyanwong 9 months ago - 5 comments

#862 - Document `map_additional_sites`` argument

Issue - State: open - Opened by jeromekelleher 10 months ago

#861 - Make mapping additional sites optional

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment

#859 - Fix windows disk space

Pull Request - State: closed - Opened by benjeffery 10 months ago - 2 comments

#857 - Parallelise mapping additional sites

Issue - State: open - Opened by benjeffery 10 months ago

#856 - Switch to sphinx-book-theme

Pull Request - State: closed - Opened by benjeffery 10 months ago - 5 comments

#854 - Update deps and fix evaluation.py for new pandas

Pull Request - State: closed - Opened by benjeffery 11 months ago - 2 comments

#853 - Dask sample matching

Pull Request - State: closed - Opened by benjeffery 11 months ago - 3 comments

#852 - Update docs deps

Pull Request - State: closed - Opened by benjeffery 11 months ago

#851 - Removing entirely unary nodes

Issue - State: open - Opened by hyanwong 12 months ago - 3 comments

#850 - Cut up root node (not just ultimate ancestor)

Issue - State: open - Opened by hyanwong 12 months ago - 5 comments

#849 - Rework sgkit ancestral allele

Pull Request - State: closed - Opened by benjeffery 12 months ago - 6 comments

#848 - Ancestral alleles from VCF

Issue - State: open - Opened by hyanwong 12 months ago - 1 comment

#847 - Hard error on missing sgkit ancestral state

Issue - State: closed - Opened by benjeffery 12 months ago - 1 comment

#846 - Ancestral allele handling

Issue - State: open - Opened by benjeffery 12 months ago - 1 comment

#845 - Add more tests to ancestral_allele fetching

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

#844 - Update installation.rst

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

#842 - Save mismatch ratio in provenance

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 9 comments

#841 - Tutorial on creating Sample File from VCF giving error

Issue - State: closed - Opened by Tatianabellagio about 1 year ago - 6 comments

#840 - Add "Inferring large datasets" documentation

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

#839 - Add `AncestorData` diagnostic plots function.

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

#838 - Split large ancestor groups up for both caching and dask scheduling.

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

#837 - Fetch ancestors within dask worker

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

#836 - Improve ancestor fetching

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

#835 - Add resume for sample matching

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

#834 - Document resume option

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

#833 - Fix circleCI meson error

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

#832 - Circle CI failure

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

#831 - Docs: clarify alleles list with missing data

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 8 comments

#830 - Refactor low-level code

Pull Request - State: open - Opened by jeromekelleher about 1 year ago - 2 comments