Ecosyste.ms: Issues

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

GitHub / tskit-dev/tsdate issues and pull requests

#451 - Better error messages if smaller rescaling intervals needed

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

#450 - Zero division error (with a putative solution)

Issue - State: open - Opened by hanbin973 about 1 month ago

#449 - Add `set_metadata` parameter

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

#448 - Change the default number of ep_iterations to 25

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

#447 - Set default ep_iterations to 25 rather than 10

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

#446 - API for singleton phasing

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

#445 - Update actions ubuntu version

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

#443 - Update GitHub Actions to latest major versions

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

#442 - Record resources used in tsdate inference

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

#441 - Allow the numba cache to be used, for development

Pull Request - State: open - Opened by hyanwong 3 months ago - 13 comments

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

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

#439 - Add allow_unary to CHANGELOG

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

#438 - Reduce import time

Issue - State: open - Opened by nspope 3 months ago - 20 comments

#437 - Allow unary nodes

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

#435 - Add note on mutational posteriors for unphased singletons

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

#434 - A fairly large reworking to allow entire method objects to be returned

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

#433 - Allow internal/non-contemporary samples for dating sc2ts, pedigrees

Pull Request - State: open - Opened by nspope 4 months ago - 19 comments

#432 - Fix Actions versions

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

#431 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, github_actions

#430 - Comparison to "Threads"

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

#429 - KLMinimizationFailedError: Quantiles must be sorted

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

#428 - discrepancy function

Pull Request - State: open - Opened by petrelharp 7 months ago - 3 comments

#427 - Set release data

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

#426 - Fix references to "flat" priors in docs

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

#425 - Mention in docs about not making coalescent assumptions

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

#424 - Make sure to cite SINGER in docs for rescaling idea

Pull Request - State: closed - Opened by nspope 7 months ago

#423 - Update changelog for 0.2.1

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

#422 - Use newer numpy recarray calling convention to avoid warnings

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

#421 - Switch to ruff linting

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

#420 - How should I understand the node age gamma distributions?

Issue - State: closed - Opened by YunDeng98 7 months ago - 3 comments

#418 - Pin to latest msprime/tskit, later scipy

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

#417 - Numpy 2 compatibility

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

#416 - Update msprime in docs

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

#415 - AssertionError for big file while no error for small file

Issue - State: closed - Opened by qianfeng2 8 months ago - 2 comments

#414 - Mutation metadata mean and variance for unphased singleton mutations

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

#413 - Reason for bias in young mutations

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

#412 - Phase-agnostic singletons

Pull Request - State: closed - Opened by nspope 8 months ago - 43 comments

#411 - Pin minimum scipy version for required cython imports

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

#410 - Add `return_node_posteriors` argument.

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

#409 - Fill out more rescaling explanation

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

#408 - Vgamma default

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

#407 - Start describing the rescaling step

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

#406 - Add check for unary nodes

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

#405 - Fix changelog

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

#404 - Switch to ruff linting

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

#403 - Numpy 2 pinning

Issue - State: closed - Opened by benjeffery 9 months ago - 12 comments

#401 - More docs tidying

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

#400 - Italicise _tsdate_

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

#399 - Add nice plot of inverse instantaneous coalescent rate to docs

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

#397 - Start tidying docs

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

#396 - Make variational_gamma method the default, and document

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

#395 - How to allow unary nodes in variational_gamma

Issue - State: closed - Opened by hyanwong 9 months ago - 8 comments

#394 - sample_as_parent in variational_gamma

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

#393 - Remove need for tsinfer (and matplotlib?) from requirements.txt

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

#392 - Put constants at top level

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

#391 - Fail vgamma if no mutations

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

#390 - variational_gamma method fails on tree seq with no mutations

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

#389 - Remove "ignore-oldest" option from the CLI

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

#388 - variational_gamma does not seem to return posteriors

Issue - State: closed - Opened by hyanwong 9 months ago - 13 comments

#387 - Add split-disjoint to CLI preprocess

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

#385 - Document (and undocument) standard params & tidy calling conventions

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

#384 - DeprecationWarning for scipy: quadpack

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

#383 - Set a new descriptive schema on mutations if none exists

Pull Request - State: closed - Opened by hyanwong 9 months ago - 3 comments

#382 - Save flags and metadata when splitting disjoint nodes

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

#381 - TODO before v-gamma release

Issue - State: closed - Opened by hyanwong 9 months ago - 12 comments

#380 - Allow compilation of wheels on mac

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

#379 - Add some more evaluation scripts

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

#378 - Set sensible rescaling-intervals default value and save in provenance

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

#376 - Move population_size and priors out of .date() method

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

#375 - Bump tqdm from 4.65.0 to 4.66.3 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#374 - Phasing singletons with expectation propagation

Issue - State: closed - Opened by nspope 10 months ago - 41 comments

#373 - Add `split_disjoint_nodes` to preprocess routine

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

#372 - unpin numba version

Issue - State: closed - Opened by alxsimon 12 months ago - 6 comments

#371 - Piecewise uniform prior for timescale

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

#370 - Branch/site statistic mismatch and inferred tree sequences

Issue - State: closed - Opened by nspope about 1 year ago - 8 comments

#369 - Extend jupyterbook timeout

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

#368 - Cache JIT compiled code

Issue - State: closed - Opened by nspope about 1 year ago - 5 comments

#367 - Add links to github from the docs

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

#366 - Mismatch between site and branch diversity calculations

Issue - State: closed - Opened by hyanwong about 1 year ago - 5 comments

#365 - Make the doc example smaller

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

#364 - Non-contemporary samples

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

#363 - Break tsinfer polytomies using mutational density

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

#362 - Change URL to docs

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

#361 - Document bugfix

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

#360 - Rescale messages at end of each iteration

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

#359 - Investigate effect of polytomies / topological uncertainty on posteriors

Issue - State: open - Opened by hyanwong about 1 year ago - 15 comments

#358 - Update docs for posterior

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

#357 - Remove readthedocs status from readme

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

#356 - Use direct memory access for checks

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

#355 - Speed up pre-algorithm steps

Issue - State: closed - Opened by nspope about 1 year ago - 4 comments

#354 - Tidy CHANGELOG for 0.1.6

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

#353 - Tidy the documentation and default values

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

#352 - Pass epsilon explicitly

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