Ecosyste.ms: Issues

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

GitHub / popsim-consortium/stdpopsim issues and pull requests

#1477 - Inconsistent factors of 2 in human gamma DFE models?

Issue - State: closed - Opened by RyanGutenkunst over 1 year ago - 4 comments

#1476 - Bump pytest-xdist from 3.2.0 to 3.3.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1475 - Bump sphinx from 4.3.2 to 7.0.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1474 - Bump demesdraw from 0.3.1 to 0.4.0 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1473 - Bump demes from 0.2.2 to 0.2.3 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1472 - Bump sphinx from 4.3.2 to 7.0.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1471 - Wrong human population size?

Issue - State: closed - Opened by regevs over 1 year ago - 9 comments

#1470 - add lognormal (or at least not gamma) DFE for humans

Issue - State: closed - Opened by petrelharp over 1 year ago - 8 comments

#1469 - add beneficial-containing DFE

Issue - State: open - Opened by petrelharp over 1 year ago - 2 comments

#1468 - Bump sphinx from 4.3.2 to 6.2.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1467 - Add per-chromosome ploidy checks to test stubs in maintenance scripts

Issue - State: open - Opened by nspope over 1 year ago - 1 comment

#1466 - QC for rice demographic model

Pull Request - State: closed - Opened by minesrebollo over 1 year ago - 4 comments

#1465 - Bump docs/precommit ubuntu version to 20.04

Pull Request - State: closed - Opened by nspope over 1 year ago - 1 comment

#1464 - Bump codecov to 2.1.13

Pull Request - State: closed - Opened by nspope over 1 year ago - 8 comments

#1463 - Bump pytest from 7.2.1 to 7.3.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: dependencies

#1462 - Add rice

Pull Request - State: closed - Opened by ornobalam over 1 year ago - 3 comments

#1461 - QC for Oryza Sativa

Pull Request - State: closed - Opened by minesrebollo over 1 year ago - 11 comments

#1460 - Bump pytest from 7.2.1 to 7.3.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1459 - QC for BottleneckMigration_3C07 (OrySat)

Issue - State: closed - Opened by nspope over 1 year ago - 18 comments
Labels: Model QC

#1458 - QC for Oryza sativa

Issue - State: closed - Opened by nspope over 1 year ago - 22 comments
Labels: Species QC

#1457 - Add MusMus to catalog/changelog

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

#1456 - Vignette on sampling parameter values

Issue - State: open - Opened by RyanGutenkunst over 1 year ago - 3 comments
Labels: enhancement

#1455 - Bump pytest-xdist from 3.2.0 to 3.2.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1454 - QC implemented for MusMus

Pull Request - State: closed - Opened by igronau over 1 year ago - 6 comments

#1453 - Add rice

Pull Request - State: closed - Opened by ornobalam over 1 year ago - 14 comments

#1452 - Mus mus cox map

Pull Request - State: closed - Opened by peterdfields over 1 year ago - 15 comments

#1451 - CLI returning haploid samples, API diploid

Issue - State: open - Opened by andrewkern over 1 year ago - 6 comments
Labels: bug

#1450 - adding slack channel to docs

Pull Request - State: closed - Opened by chriscrsmith over 1 year ago - 6 comments

#1449 - add ploidy line in species catalog description

Issue - State: closed - Opened by lauterbur over 1 year ago - 1 comment
Labels: docs

#1448 - Bump pytest from 7.2.1 to 7.2.2 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1447 - Bump sphinx-rtd-theme from 1.1.1 to 1.2.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1446 - Bump biopython from 1.80 to 1.81 in /requirements/CI

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1444 - Bump scipy from 1.9.3 to 1.10.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1443 - Bump humanize from 4.4.0 to 4.6.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1442 - add info about type of data used to demographic model descriptions

Issue - State: open - Opened by petrelharp over 1 year ago
Labels: enhancement

#1441 - Bump pytest-xdist from 3.0.2 to 3.2.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1440 - Modifications made for QC review of Mus mus addition, #1439

Pull Request - State: closed - Opened by peterdfields over 1 year ago - 7 comments

#1439 - QC for Mus musculus (MusMus)

Issue - State: closed - Opened by nspope over 1 year ago - 24 comments
Labels: Species QC

#1438 - How does one verify population of simulated sample ?

Issue - State: closed - Opened by sidAvad over 1 year ago - 3 comments

#1437 - Add Mus mus

Pull Request - State: closed - Opened by peterdfields over 1 year ago - 8 comments

#1436 - pytest: error: unrecognized arguments: -n

Issue - State: closed - Opened by peterdfields over 1 year ago - 1 comment

#1435 - Unable to verify if simulation is using specified model

Issue - State: open - Opened by sidAvad over 1 year ago - 2 comments

#1434 - update flake8 link, closes #1433

Pull Request - State: closed - Opened by petrelharp over 1 year ago - 1 comment

#1433 - Problem committing due to repo address of flake8

Issue - State: closed - Opened by peterdfields over 1 year ago

#1432 - Bump pytest from 7.2.0 to 7.2.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1431 - Bump sphinx from 4.3.2 to 6.1.3 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1430 - Bump scipy from 1.9.3 to 1.10.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#1429 - Bump sphinx from 4.3.2 to 6.1.2 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1428 - Bump sphinx from 4.3.2 to 6.0.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#1427 - Bump setuptools-scm from 7.0.5 to 7.1.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1426 - ValueError: Simulation engine 'slim' not registered

Issue - State: open - Opened by JaneeshBansal almost 2 years ago - 6 comments

#1425 - Bump pytest-xdist from 3.0.2 to 3.1.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1424 - Bump flake8 from 5.0.4 to 6.0.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1423 - Bump biopython from 1.79 to 1.80 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1422 - No variants are simulated in zero-recombination region of chr22

Issue - State: open - Opened by nspope almost 2 years ago - 17 comments

#1421 - Bump sphinx-argparse from 0.3.1 to 0.4.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1420 - Bump scipy from 1.7.3 to 1.9.3 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1419 - Only load QC models when running tests

Pull Request - State: open - Opened by grahamgower almost 2 years ago - 5 comments

#1418 - load QC models only when the tests are run

Issue - State: open - Opened by grahamgower almost 2 years ago - 1 comment

#1417 - Bump sphinx-rtd-theme from 1.0.0 to 1.1.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1416 - Don't use scipy and pandas for OutOfAfricaExtendedNeandertalAdmixture…

Pull Request - State: closed - Opened by grahamgower almost 2 years ago - 9 comments

#1414 - AWS downloads can be slow from outside USA

Issue - State: open - Opened by grahamgower almost 2 years ago

#1413 - unnecessary zarr dependency?

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

#1412 - Missing dependency on scipy

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

#1411 - Add preprint DOI to docs for 0.2.0

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

#1410 - Bump pytest-xdist from 2.4.0 to 3.0.2 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1409 - Bump pytest from 7.1.3 to 7.2.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#1408 - Bump pandas from 1.3.4 to 1.5.1 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1407 - Rescale haploid population size in SLiM engine

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

#1406 - SLiM and msprime engines handle population sizes differently for haploid species

Issue - State: closed - Opened by nspope almost 2 years ago - 1 comment
Labels: bug

#1404 - When using `left`/`right`, output coordinate system is relative to start of contig

Issue - State: closed - Opened by nspope almost 2 years ago - 6 comments

#1403 - Various issues in the docs to be resolved by the "selection release"

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

#1402 - Bump sphinx from 4.3.2 to 5.3.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1401 - Remove comment in setup.cfg causing build issues

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

#1400 - Update macOS GitHub Actions runner

Issue - State: closed - Opened by nspope almost 2 years ago - 1 comment

#1399 - Adding genetic map for honeybee

Pull Request - State: open - Opened by janaobsteter almost 2 years ago - 35 comments

#1397 - Clean version of new section on adding new species

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

#1396 - Adding a genetic map for Apis mellifera

Issue - State: open - Opened by janaobsteter almost 2 years ago - 6 comments
Labels: enhancement

#1395 - Bump zarr from 2.11.3 to 2.13.3 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1394 - Add 'adding species' preprint to `docs/introduction.rst` for 0.2.0

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

#1389 - major edits in section for adding species (incl. moving it up)

Pull Request - State: closed - Opened by igronau almost 2 years ago - 7 comments

#1383 - Bump sphinx from 4.3.2 to 5.2.3 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1382 - Bump sphinx-argparse from 0.3.1 to 0.3.2 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#1374 - Add ploidy to `Adding new species` in developer docs

Issue - State: closed - Opened by nspope about 2 years ago - 4 comments

#1373 - Move contents of `stdpopsim/ext` into `stdpopsim`

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

#1371 - Handle haploids correctly in SLiM engine

Issue - State: open - Opened by nspope about 2 years ago - 1 comment

#1367 - add more gene conversion rates

Issue - State: open - Opened by petrelharp about 2 years ago - 3 comments

#1366 - QC machinery for GC?

Issue - State: open - Opened by petrelharp about 2 years ago - 1 comment

#1365 - Recombination rate placeholder used for AnoCar

Issue - State: open - Opened by nspope about 2 years ago

#1364 - Update mergify to match test environment

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

#1363 - Bump pandas from 1.3.4 to 1.5.0 in /requirements/CI

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 2 comments
Labels: dependencies

#1350 - Update demographic model BonoboGhost_4K19

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

#1349 - deprecate `--length-multiplier` CLI option

Issue - State: open - Opened by grahamgower about 2 years ago - 3 comments

#1347 - Mention species inclusion criteria in development docs

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

#1344 - QC for AraThal DFE

Issue - State: open - Opened by chriscrsmith about 2 years ago - 9 comments
Labels: Model QC

#1343 - require SLiM version 4.0++

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

#1342 - enable SLiM on Windows

Pull Request - State: open - Opened by petrelharp about 2 years ago - 17 comments