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

#975 - Include timing information in provenance

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

#974 - Document path_or_zarr

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

#973 - Update changelog for 0.4.0a2

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

#972 - Improve test coverage for batch matching

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

#971 - "Ancestral state" or "ancestral allele"?

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

#970 - VariantData parameter name

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

#969 - Remove some test warnings

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

#967 - Remove mention of sgkit

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

#966 - Allow VariantData to take either a vcz path or the zarr store itself

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

#965 - Encode numpy arrays in sample batch json

Pull Request - State: closed - Opened by benjeffery 3 months ago - 2 comments

#964 - Deal with multiple contigs and sequence lengths

Pull Request - State: open - Opened by hyanwong 3 months ago - 2 comments

#963 - Properly treat blank ancestral alleles

Pull Request - State: closed - Opened by hyanwong 3 months ago - 8 comments

#962 - Do not warn about unknown states if ancestral allele is "N"

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

#961 - Override VariantData.from_tree_sequence

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

#960 - Check for duplicate alleles

Pull Request - State: closed - Opened by hyanwong 3 months ago - 6 comments

#959 - Experimental hmm

Pull Request - State: open - Opened by jeromekelleher 3 months ago - 1 comment

#958 - Doc typo

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

#956 - Variant data

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

#955 - Docstring for VariantData needs writing

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

#954 - Refactor batch sample matching

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

#953 - Plot "edge-node time consistency"

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

#952 - Extra sample nodes being created from .vcz file when ploidies are uneven

Issue - State: open - Opened by hyanwong 3 months ago - 10 comments

#951 - Change readme doc links to "latest"

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

#950 - Fix wrong schema used for individual metadata

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

#948 - Typo in formats.VariantData.individuals_metadata?

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

#947 - Rename sgkit_sample_id

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

#946 - Release prep

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

#945 - Update tutorial for new VariantData format

Pull Request - State: closed - Opened by hyanwong 4 months ago - 5 comments

#944 - VariantData

Pull Request - State: closed - Opened by benjeffery 4 months ago - 15 comments

#943 - Numpy2 changes

Pull Request - State: closed - Opened by hyanwong 4 months ago - 13 comments

#942 - Fix wheel building

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

#941 - Update CHANGELOG.md

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

#940 - Specify standard python (not python3)

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

#939 - Coerce NODE_IS_SAMPLE to correct numpy type before negation

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

#938 - Incorrect dependencies for package

Issue - State: closed - Opened by jeromekelleher 5 months ago - 2 comments
Labels: bug

#937 - New bitflag error

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

#936 - Upgrade actions, build with numpy2

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

#935 - Numpy 2.0 supporting release

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

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

Issue - State: closed - Opened by jeromekelleher 5 months ago - 2 comments

#933 - Investigate AFS bias due to polytomies

Issue - State: open - Opened by hyanwong 6 months ago - 3 comments

#931 - Set node metadata schema

Pull Request - State: closed - Opened by hyanwong 6 months ago - 4 comments

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

Pull Request - State: closed - Opened by hyanwong 6 months ago - 7 comments

#929 - Overwriting md schema

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

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

Pull Request - State: closed - Opened by hyanwong 6 months ago - 11 comments

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

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

#926 - Add dependency on tsdate

Issue - State: open - Opened by jeromekelleher 6 months ago - 3 comments
Labels: enhancement

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

Issue - State: open - Opened by hyanwong 6 months ago - 4 comments

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

Issue - State: open - Opened by hyanwong 6 months ago - 2 comments

#922 - Rename SgkitSampleData object?

Issue - State: closed - Opened by hyanwong 6 months ago - 1 comment

#921 - Batch job ancestor matching.

Issue - State: open - Opened by benjeffery 6 months ago - 3 comments

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

Issue - State: open - Opened by benjeffery 7 months ago - 1 comment

#919 - Pin to zarr < 3

Issue - State: open - Opened by jeromekelleher 7 months ago

#918 - Fix CI

Pull Request - State: closed - Opened by benjeffery 7 months ago - 4 comments

#917 - Batch ancestor matching

Pull Request - State: closed - Opened by benjeffery 7 months ago - 8 comments

#916 - Identifying PC nodes / edges added during match_samples

Issue - State: open - Opened by hyanwong 7 months ago - 3 comments

#915 - SgkitSampleData.from_tree_sequence bugs out

Issue - State: closed - Opened by hyanwong 7 months ago

#914 - Fix OSX tests

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

#913 - Low density regions and splitting

Issue - State: open - Opened by benjeffery 8 months ago - 2 comments
Labels: enhancement

#912 - Simplify dev reqs and make compatible with tsdate

Pull Request - State: closed - Opened by benjeffery 8 months ago - 1 comment

#911 - Improve ancestor building by using more information

Issue - State: open - Opened by hyanwong 8 months ago

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

Pull Request - State: closed - Opened by hyanwong 9 months ago - 1 comment

#909 - Compiling on Apple ARM - mostly works

Issue - State: closed - Opened by hyanwong 9 months ago

#908 - Tweak ma-match progressbar total

Pull Request - State: closed - Opened by hyanwong 9 months ago - 1 comment

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

Issue - State: closed - Opened by hyanwong 9 months ago - 2 comments

#906 - Make tqdm work nicely in notebooks

Pull Request - State: closed - Opened by hyanwong 9 months ago - 14 comments

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

Pull Request - State: closed - Opened by hyanwong 9 months ago - 1 comment

#904 - Compilation overrides CC

Issue - State: closed - Opened by hyanwong 9 months ago - 1 comment

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

Issue - State: open - Opened by hyanwong 10 months ago - 20 comments

#902 - Update cli.py

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

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

Issue - State: closed - Opened by benjeffery 10 months ago - 1 comment
Labels: enhancement

#900 - Mask names

Pull Request - State: closed - Opened by benjeffery 10 months ago - 3 comments

#899 - Flip polarity

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

#897 - Flip polarity of masks

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

#896 - Add sample mask

Pull Request - State: closed - Opened by benjeffery 10 months ago - 14 comments

#895 - Sample masking from sgkit dataset

Issue - State: open - Opened by benjeffery 10 months ago - 1 comment

#892 - SgkitSampleData format missing data bug

Issue - State: open - Opened by hyanwong 10 months ago - 2 comments
Labels: bug

#891 - Replace node_span in eval_util

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

#890 - Add seed to simulate_genotype_call_dataset in tests

Issue - State: open - Opened by hyanwong 11 months ago

#889 - Check duplicate positions

Pull Request - State: closed - Opened by hyanwong 11 months ago - 12 comments

#888 - SgkitSampleData allows duplicate positions

Issue - State: closed - Opened by hyanwong 11 months ago

#887 - Better formatted error message for ancestral alleles

Pull Request - State: closed - Opened by hyanwong 11 months ago - 1 comment

#886 - Ancestor.inference_sites_set never used

Issue - State: open - Opened by hyanwong 11 months ago - 1 comment

#885 - Allow empty ancestral alleles

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

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

Issue - State: open - Opened by hyanwong 11 months ago - 1 comment

#883 - SGkit equivalent for tutorial read_vcf

Issue - State: open - Opened by hyanwong 11 months ago - 5 comments

#881 - Set sample node times

Issue - State: open - Opened by hyanwong 11 months ago

#880 - Batching during match ancestors wastes worker CPU.

Issue - State: closed - Opened by benjeffery 11 months ago - 3 comments
Labels: enhancement

#879 - Limit linesweep to 1M ancestors

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

#878 - Don't double count progress

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

#877 - Robustness of tsinfer & tsdate to selection

Issue - State: open - Opened by hyanwong about 1 year ago - 23 comments

#876 - Parallel matching via batch jobs

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