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

#992 - Warn when using defaults that aren't explict and not metadata

Pull Request - State: open - Opened by benjeffery 26 days ago - 1 comment

#991 - VariantData.from_tree_sequence

Issue - State: open - Opened by hyanwong 27 days ago

#990 - Record more tsinfer parameters in provenance

Pull Request - State: closed - Opened by hyanwong 29 days ago - 2 comments

#989 - Generating a genome-wide tree topology count

Issue - State: closed - Opened by MatteoSebastianelli about 1 month ago - 2 comments

#988 - Supress subnormal warning

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

#987 - Update actions ubuntu version

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

#986 - Update actions ubuntu version

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

#985 - Update GitHub Actions to latest major versions

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

#984 - Update GitHub Actions to latest major versions

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

#983 - Assertion `right_sib[last_root] == NULL_NODE` failed

Issue - State: open - Opened by nspope 2 months ago - 16 comments

#981 - Do not use mismatch in ancestor matching when using `infer()`

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

#979 - ci(mergify): upgrade configuration to current format

Pull Request - State: closed - Opened by mergify[bot] 3 months ago - 1 comment

#978 - Extra tests for recode_ancestral

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

#977 - Bug in multi-allele matching?

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

#976 - Display issue of code blocs in docs

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

#975 - Include timing information in provenance

Issue - State: open - Opened by benjeffery 4 months ago

#974 - Document path_or_zarr

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

#973 - Update changelog for 0.4.0a2

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

#972 - Improve test coverage for batch matching

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

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

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

#970 - VariantData parameter name

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

#969 - Remove some test warnings

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

#967 - Remove mention of sgkit

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

#965 - Encode numpy arrays in sample batch json

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

#964 - Deal with multiple contigs and sequence lengths

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

#963 - Properly treat blank ancestral alleles

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

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

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

#961 - Override VariantData.from_tree_sequence

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

#960 - Check for duplicate alleles

Pull Request - State: closed - Opened by hyanwong 5 months ago - 6 comments

#959 - Experimental hmm

Pull Request - State: open - Opened by jeromekelleher 5 months ago - 7 comments

#958 - Doc typo

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

#956 - Variant data

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

#955 - Docstring for VariantData needs writing

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

#954 - Refactor batch sample matching

Pull Request - State: closed - Opened by benjeffery 6 months ago - 1 comment

#953 - Plot "edge-node time consistency"

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

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

Issue - State: open - Opened by hyanwong 6 months ago - 10 comments

#951 - Change readme doc links to "latest"

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

#950 - Fix wrong schema used for individual metadata

Pull Request - State: closed - Opened by benjeffery 6 months ago - 1 comment

#948 - Typo in formats.VariantData.individuals_metadata?

Issue - State: closed - Opened by percyfal 6 months ago - 2 comments

#947 - Rename sgkit_sample_id

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

#946 - Release prep

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

#945 - Update tutorial for new VariantData format

Pull Request - State: closed - Opened by hyanwong 7 months ago - 5 comments

#944 - VariantData

Pull Request - State: closed - Opened by benjeffery 7 months ago - 15 comments

#943 - Numpy2 changes

Pull Request - State: closed - Opened by hyanwong 7 months ago - 13 comments

#942 - Fix wheel building

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

#941 - Update CHANGELOG.md

Pull Request - State: closed - Opened by hyanwong 7 months ago - 2 comments

#940 - Specify standard python (not python3)

Pull Request - State: closed - Opened by hyanwong 7 months ago - 2 comments

#939 - Coerce NODE_IS_SAMPLE to correct numpy type before negation

Pull Request - State: closed - Opened by hyanwong 7 months ago - 3 comments

#938 - Incorrect dependencies for package

Issue - State: closed - Opened by jeromekelleher 7 months ago - 2 comments
Labels: bug

#937 - New bitflag error

Issue - State: closed - Opened by hyanwong 7 months ago - 9 comments

#936 - Upgrade actions, build with numpy2

Pull Request - State: closed - Opened by benjeffery 7 months ago - 5 comments

#935 - Numpy 2.0 supporting release

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

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

Issue - State: closed - Opened by jeromekelleher 8 months ago - 2 comments

#933 - Investigate AFS bias due to polytomies

Issue - State: open - Opened by hyanwong 8 months ago - 3 comments

#932 - Bring sample batch matching in line with ancestor matching

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

#931 - Set node metadata schema

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

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

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

#929 - Overwriting md schema

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

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

Pull Request - State: closed - Opened by hyanwong 8 months ago - 11 comments

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

Issue - State: closed - Opened by hyanwong 8 months ago - 7 comments
Labels: bug

#926 - Add dependency on tsdate

Issue - State: open - Opened by jeromekelleher 8 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 9 months ago - 4 comments

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

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

#922 - Rename SgkitSampleData object?

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

#921 - Batch job ancestor matching.

Issue - State: closed - Opened by benjeffery 9 months ago - 4 comments

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

Issue - State: open - Opened by benjeffery 9 months ago - 1 comment

#919 - Pin to zarr < 3

Issue - State: open - Opened by jeromekelleher 9 months ago

#918 - Fix CI

Pull Request - State: closed - Opened by benjeffery 9 months ago - 4 comments

#917 - Batch ancestor matching

Pull Request - State: closed - Opened by benjeffery 9 months ago - 8 comments

#916 - Identifying PC nodes / edges added during match_samples

Issue - State: open - Opened by hyanwong 9 months ago - 3 comments

#915 - SgkitSampleData.from_tree_sequence bugs out

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

#914 - Fix OSX tests

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

#913 - Low density regions and splitting

Issue - State: open - Opened by benjeffery 10 months ago - 2 comments
Labels: enhancement

#912 - Simplify dev reqs and make compatible with tsdate

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

#911 - Improve ancestor building by using more information

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

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

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

#909 - Compiling on Apple ARM - mostly works

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

#908 - Tweak ma-match progressbar total

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

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

Issue - State: closed - Opened by hyanwong 12 months ago - 2 comments

#906 - Make tqdm work nicely in notebooks

Pull Request - State: closed - Opened by hyanwong 12 months ago - 14 comments

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

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

#904 - Compilation overrides CC

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

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

Issue - State: open - Opened by hyanwong almost 1 year ago - 20 comments

#902 - Update cli.py

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

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

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

#900 - Mask names

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

#899 - Flip polarity

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

#898 - Allow names of sample and variant maskes to be specified.

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

#897 - Flip polarity of masks

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

#896 - Add sample mask

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 14 comments

#895 - Sample masking from sgkit dataset

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