Ecosyste.ms: Issues

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

GitHub / tskit-dev/tskit issues and pull requests

#2697 - Freeze docs environment

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

#2696 - Implement Tree.seek_index using C code

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#2695 - implementing Variant.__repr__

Pull Request - State: closed - Opened by chriscrsmith almost 2 years ago - 8 comments

#2694 - Implement Variant.__repr__

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 7 comments
Labels: enhancement, good first issue, Python API

#2693 - Add 311 changelog

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#2692 - Fix wheel building for 3.11

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

#2691 - 0.5.4 Release prep

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

#2690 - Update linting action

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

#2689 - Lint failing, maybe due to removed package archive

Issue - State: closed - Opened by benjeffery almost 2 years ago - 1 comment
Labels: Infrastructure and tools

#2688 - Clear docs CI cache

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#2687 - Doc build failure

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

#2686 - Add codecov token

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

#2685 - Implement edge differences from table collections.

Pull Request - State: closed - Opened by molpopgen almost 2 years ago - 12 comments

#2684 - Improve error messages for legacy and compressed formats

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

#2683 - `nose` tests being removed from pytest

Issue - State: closed - Opened by benjeffery almost 2 years ago - 3 comments
Labels: Infrastructure and tools

#2682 - Detect `tszip`ed files and give a helpful error.

Issue - State: closed - Opened by benjeffery almost 2 years ago - 6 comments
Labels: Python API

#2681 - Shorthand filter_all argument for simplify

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 10 comments

#2680 - Codecov 404ing

Issue - State: closed - Opened by benjeffery almost 2 years ago - 5 comments
Labels: Infrastructure and tools

#2679 - Document RateMap etc

Issue - State: open - Opened by hyanwong almost 2 years ago - 4 comments

#2678 - Port over intervals

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago - 12 comments

#2672 - Release 0.5.4?

Issue - State: closed - Opened by benjeffery almost 2 years ago - 8 comments
Labels: Infrastructure and tools

#2671 - Method or attribute for start and end of tree sequence data

Issue - State: closed - Opened by hyanwong almost 2 years ago - 14 comments

#2669 - Implement is_root

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#2666 - Method to in-place subset a table

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 3 comments
Labels: enhancement, C API

#2665 - Multichrom example

Pull Request - State: open - Opened by jeromekelleher almost 2 years ago - 28 comments

#2663 - Don't update sample flags in simplify

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago - 16 comments

#2662 - Add TSK_SIMPLIFY_NO_UPDATE_SAMPLE_FLAGS

Issue - State: closed - Opened by jeromekelleher almost 2 years ago
Labels: C API

#2661 - Efficient seeking to trees.

Pull Request - State: closed - Opened by molpopgen almost 2 years ago - 41 comments

#2659 - Add tsk_tree_seek_index

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 3 comments
Labels: C API

#2651 - extend edges method

Pull Request - State: closed - Opened by petrelharp almost 2 years ago - 35 comments

#2643 - Add unweighted_rf_distance (symmetric_distance) function and tests

Pull Request - State: closed - Opened by Billyzhang1229 almost 2 years ago - 15 comments

#2637 - Metadata size in tables

Issue - State: open - Opened by hyanwong about 2 years ago - 6 comments
Labels: enhancement, Python API

#2636 - Put intervals.py into tskit

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 19 comments

#2631 - Mutation's "inherited" state

Issue - State: open - Opened by jeromekelleher about 2 years ago - 4 comments
Labels: enhancement, Python API

#2627 - Tree distance between two samples

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

#2625 - Make tqdm(ts.variants()) work better

Issue - State: open - Opened by jeromekelleher about 2 years ago - 6 comments
Labels: enhancement, Python API

#2624 - Support Py3.11

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

#2621 - Use recursive updates for weights in ``CoalescenceTimeDistribution``

Pull Request - State: closed - Opened by nspope about 2 years ago - 9 comments

#2618 - Add Tree.siblings()

Pull Request - State: closed - Opened by szhan about 2 years ago - 32 comments
Labels: enhancement, Python API

#2617 - Add `states()` method to return actual genotype states as characters

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 11 comments

#2616 - Add Tree.siblings(u) method

Issue - State: closed - Opened by jeromekelleher about 2 years ago
Labels: enhancement, good first issue, Python API

#2611 - Tree.tmrca() should allow more than 2 args

Issue - State: closed - Opened by hyanwong about 2 years ago
Labels: enhancement, Python API

#2604 - Document example of using ts.simplify(filter=None).draw_svg() to the viz docs, for large trees

Issue - State: closed - Opened by hyanwong about 2 years ago - 9 comments
Labels: documentation, Visualisation

#2597 - Drop support for python 3.7

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 3 comments

#2538 - 0.5.3 release prep

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

#2531 - Access the left and right of an edge as an interval

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 9 comments

#2515 - Ls missingness

Pull Request - State: closed - Opened by astheeggeggs about 2 years ago - 5 comments

#2460 - Added methods to sort and squash segments in the IbdFinder output.

Pull Request - State: closed - Opened by gtsambos over 2 years ago - 10 comments

#2459 - Provide option to squash IBD output?

Issue - State: closed - Opened by gtsambos over 2 years ago - 20 comments
Labels: enhancement

#2457 - Memory profiling

Issue - State: open - Opened by benjeffery over 2 years ago - 2 comments
Labels: Infrastructure and tools

#2449 - Check VCF output for conformance with VCF 4.3 and update version number

Issue - State: open - Opened by jeromekelleher over 2 years ago
Labels: enhancement, Python API

#2440 - Use MetadataTable to implement metadata functionality

Issue - State: open - Opened by jeromekelleher over 2 years ago
Labels: Python API, refactoring

#2436 - Implement state machine for tsk_variant_t and keep reference to ``tree_sequence`` in restricted_copy.

Issue - State: open - Opened by jeromekelleher over 2 years ago - 2 comments
Labels: C API, Python API

#2406 - Move reference documentation for "Variant" class

Issue - State: open - Opened by hyanwong over 2 years ago
Labels: documentation

#2381 - Keep unary for coalescent nodes in simplify

Pull Request - State: closed - Opened by jeromekelleher over 2 years ago - 23 comments

#2372 - Visual ways of summarising subtrees (clades) when plotting

Issue - State: open - Opened by hyanwong over 2 years ago - 21 comments
Labels: Visualisation

#2368 - Add Wattersons_theta

Pull Request - State: closed - Opened by szhan over 2 years ago - 3 comments
Labels: enhancement, Python API, statistics

#2350 - Adding path function and tests

Pull Request - State: closed - Opened by jeremyguez over 2 years ago - 4 comments

#2262 - Document Pyodide/PyScript usage.

Issue - State: open - Opened by benjeffery over 2 years ago - 4 comments
Labels: documentation

#2248 - Support for python 3.11

Issue - State: closed - Opened by benjeffery over 2 years ago - 9 comments
Labels: Python API, Infrastructure and tools

#2239 - Add metadata criteria to `TreeSequence` row accessors.

Issue - State: open - Opened by benjeffery over 2 years ago - 2 comments
Labels: enhancement, Python API

#2190 - Add selection test p-values

Issue - State: open - Opened by a-ignatieva over 2 years ago - 13 comments

#2187 - High performance newick parsing.

Issue - State: open - Opened by benjeffery over 2 years ago - 12 comments
Labels: enhancement, Python API

#2181 - Variant method to get all alleles as a string

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 9 comments
Labels: Python API

#2147 - Method to clear metadata

Issue - State: closed - Opened by hyanwong over 2 years ago - 8 comments

#2146 - Flesh out metadata doc schema example

Pull Request - State: closed - Opened by hyanwong over 2 years ago - 9 comments

#2136 - IBD segment definition and memory storage issues

Issue - State: closed - Opened by sdtemple over 2 years ago - 5 comments

#2135 - Makes stats cache optional

Pull Request - State: closed - Opened by jeromekelleher over 2 years ago - 3 comments

#2080 - Cache table references

Issue - State: closed - Opened by jeromekelleher almost 3 years ago
Labels: Python API, Performance

#2070 - tree.tmrca errors when given two nodes having no mrca

Issue - State: closed - Opened by petrelharp almost 3 years ago - 4 comments
Labels: enhancement, Python API

#2057 - Initial sketch of read-only tables implementatation

Pull Request - State: closed - Opened by jeromekelleher almost 3 years ago - 6 comments

#1988 - Implement __getitem__ in ReferenceSequence

Issue - State: open - Opened by jeromekelleher almost 3 years ago - 2 comments
Labels: Python API

#1937 - Remove general_stat cacheing

Pull Request - State: closed - Opened by brieuclehmann almost 3 years ago - 19 comments

#1896 - Support missing data in alignments

Issue - State: open - Opened by jeromekelleher about 3 years ago - 6 comments

#1834 - Ibd data structures

Pull Request - State: closed - Opened by jeromekelleher about 3 years ago - 3 comments

#1770 - Highlevel docs for time_units

Issue - State: open - Opened by benjeffery about 3 years ago
Labels: documentation

#1697 - specify samples by population name

Issue - State: open - Opened by petrelharp about 3 years ago - 6 comments
Labels: enhancement, Python API

#1623 - Adding a centre=False option to genetic_relatedness statistic

Pull Request - State: closed - Opened by mmosmond over 3 years ago - 55 comments

#1547 - add more linear algebra tools

Issue - State: open - Opened by petrelharp over 3 years ago - 27 comments
Labels: enhancement, statistics

#1469 - Implement split_edges

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

#1462 - iterating over count_topologies method never stops

Issue - State: open - Opened by hyanwong over 3 years ago - 7 comments
Labels: bug

#1296 - Add dict_of_dicts to tree sequence

Pull Request - State: closed - Opened by hyanwong over 3 years ago - 15 comments

#1246 - "matrix multiplication" statistic

Pull Request - State: closed - Opened by petrelharp over 3 years ago - 26 comments

#1117 - Time join

Pull Request - State: closed - Opened by jelliotthiggins almost 4 years ago - 11 comments

#858 - Clarify which version of Fst we compute

Issue - State: open - Opened by jeromekelleher about 4 years ago - 15 comments
Labels: documentation, statistics

#840 - draw_ methods ignore mutation_time

Issue - State: closed - Opened by hyanwong about 4 years ago - 5 comments
Labels: enhancement, Python API

#809 - Randomly resolve polytomies

Issue - State: closed - Opened by hyanwong about 4 years ago - 10 comments
Labels: enhancement, C API, Python API

#798 - Add Tree.draw_tikz() to output tex/tikz drawing code.

Pull Request - State: closed - Opened by grahamgower about 4 years ago - 21 comments

#684 - Index required for efficient random access for trees

Issue - State: closed - Opened by jeromekelleher over 4 years ago - 15 comments
Labels: enhancement, C API, Python API

#670 - Documentation Example for Counting Population Topologies

Issue - State: closed - Opened by daniel-goldstein over 4 years ago - 5 comments
Labels: documentation

#665 - Windowed Genealogical Nearest Neighbours (GNN)

Issue - State: open - Opened by awohns over 4 years ago - 24 comments
Labels: enhancement, C API, Python API, statistics

#647 - Memory consumption of tree sequence statistics

Issue - State: closed - Opened by molpopgen over 4 years ago - 8 comments
Labels: Performance, statistics

#548 - Implement incremental KC Distance on tree sequences

Pull Request - State: closed - Opened by daniel-goldstein over 4 years ago - 14 comments

#432 - Generalized LD matrix calculator

Pull Request - State: closed - Opened by apragsdale almost 5 years ago - 15 comments

#328 - Replace mean_descendants with a node stat

Pull Request - State: closed - Opened by jeromekelleher about 5 years ago - 20 comments

#287 - Deal with missing data in stats

Issue - State: open - Opened by petrelharp over 5 years ago - 7 comments
Labels: enhancement

#281 - Method to 'prune back' a tree sequence

Issue - State: open - Opened by jeromekelleher over 5 years ago - 18 comments
Labels: enhancement