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
#1415 - test failures due to simultaneous tests trying to download AWS files
Issue -
State: open - Opened by grahamgower almost 2 years ago
#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
#1405 - Error with generic `StrAga` contig in msprime engine, due to average GC tract length
Issue -
State: open - Opened by nspope almost 2 years ago
- 2 comments
#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
#1387 - `msprime.RateMap.slice` throws error when contig covers portion of genetic map with no data
Issue -
State: open - Opened by nspope almost 2 years ago
- 1 comment
#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