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

#1585 - various fixes after msprime api updates

Pull Request - State: open - Opened by silastittes about 1 month ago - 3 comments

#1584 - beware of recapitation and missing data

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

#1581 - Catalog updates

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

#1579 - should post-SLiM simplify have `keep_input_roots=True`?

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

#1578 - test regions outside left, right aren't simulated; closes #1577

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

#1576 - allow users to enable SLiM on Windows if they Really Want To

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

#1575 - Update changelog for 0.2.1a release

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

#1574 - more windows CI

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

#1573 - revisit ExtendedEvents docs

Issue - State: open - Opened by petrelharp 3 months ago

#1572 - debug windows CI

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

#1571 - enable slim on windows

Pull Request - State: open - Opened by petrelharp 3 months ago - 8 comments

#1570 - Remove shifting of coordinates

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

#1569 - Move sweep API and extended events from `stdpopsim.ext` to `stdpopsim`

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

#1568 - macos runners >12 won't support conda

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

#1567 - Fix SLiM time units warning, bump minimum version to 4.0

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

#1566 - numpy v2 and requirements.txt

Issue - State: open - Opened by petrelharp 3 months ago - 1 comment

#1565 - Release 0.2.1 checklist

Issue - State: open - Opened by andrewkern 3 months ago - 3 comments
Labels: enhancement

#1564 - migration rates fixed to be consistent with the code (issue #1562)

Pull Request - State: closed - Opened by jiseonmin 4 months ago - 2 comments

#1563 - SLiM Support in Windows

Issue - State: open - Opened by daikitag 4 months ago - 3 comments
Labels: enhancement

#1562 - Typo in documentation?

Issue - State: closed - Opened by jiseonmin 4 months ago - 3 comments

#1561 - move PhoSin QC where it should go

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

#1560 - added QC for vaquita DFE

Pull Request - State: closed - Opened by ckyriazis 5 months ago - 4 comments

#1558 - Restarting simulations in SLiM engine (community.allScriptBlocks.active property)

Issue - State: closed - Opened by jmurga 5 months ago - 3 comments
Labels: bug

#1557 - document QC procedure for DFEs

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

#1556 - Getting started with DFE for MusMus

Pull Request - State: open - Opened by peterdfields 6 months ago

#1555 - DFE for MusMus

Issue - State: open - Opened by peterdfields 6 months ago - 10 comments
Labels: enhancement

#1554 - orangutan model how to add adaptive introgression?

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

#1553 - updates to hash codes and file names

Pull Request - State: closed - Opened by silastittes 7 months ago - 11 comments

#1552 - change to pip install in dev docs

Issue - State: open - Opened by petrelharp 7 months ago

#1551 - cached files need python version information in filenames

Issue - State: closed - Opened by petrelharp 7 months ago - 15 comments

#1550 - remove custom log message editing (closes #1545)

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

#1549 - time units mismatch warning

Issue - State: closed - Opened by petrelharp 7 months ago - 1 comment

#1548 - QC for DFE model Gamma_R22 for Vaquita (PhoSin)

Issue - State: closed - Opened by igronau 7 months ago - 9 comments
Labels: Model QC

#1547 - Implementation for Vaquita DFE

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

#1546 - Mutation model

Issue - State: open - Opened by daikitag 8 months ago - 1 comment
Labels: enhancement, good first issue

#1545 - error in logging from SLiM engine

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

#1544 - Deprecated pandas operation (`Calling int on a single element Series`)

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

#1541 - Add detail about SLiM install to installation docs

Issue - State: open - Opened by hyanwong 11 months ago - 2 comments
Labels: enhancement

#1540 - add docs for using DFEs in other species

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

#1539 - Mus mus Cox map, try two

Pull Request - State: open - Opened by peterdfields 11 months ago - 3 comments

#1538 - Vaquita QC

Pull Request - State: closed - Opened by ckyriazis 11 months ago - 6 comments

#1537 - new checksums

Pull Request - State: closed - Opened by chriscrsmith 11 months ago - 4 comments

#1536 - updated to ensembl release 110; did some patching

Pull Request - State: open - Opened by andrewkern 11 months ago - 3 comments

#1535 - Add journal & volume / page to citation

Pull Request - State: closed - Opened by hyanwong 11 months ago - 3 comments

#1534 - Fix find-conda step in tests.yml

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

#1533 - Replicate CI failure

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

#1532 - Fix conda failure in CI

Pull Request - State: closed - Opened by nspope 12 months ago - 2 comments

#1531 - Implemented QC for three mouse demographic models

Pull Request - State: closed - Opened by igronau 12 months ago - 2 comments

#1530 - QC for Vaquita2Epoch_1R22 (PhoSin)

Issue - State: closed - Opened by igronau 12 months ago - 1 comment
Labels: Model QC

#1529 - Fix CI

Issue - State: closed - Opened by petrelharp 12 months ago - 5 comments

#1528 - QC for DomesticusEurope_1F22, MusculusKorea_1F22, and CastaneusIndia_1F22 (MusMus)

Issue - State: closed - Opened by igronau 12 months ago - 2 comments
Labels: Model QC

#1526 - Implemented 2-epoch demographic model for Vaquita

Pull Request - State: closed - Opened by igronau 12 months ago - 5 comments

#1525 - QC for Vaquita

Issue - State: closed - Opened by igronau 12 months ago - 1 comment
Labels: Species QC

#1524 - fixup of QC for OrySat (Rice) model BottleneckMigration_3C07

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

#1523 - failing tests

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

#1522 - bug fix on annotation script

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

#1521 - What to do about shifting ensembl build?

Issue - State: open - Opened by petrelharp 12 months ago - 11 comments

#1520 - PhoSin annotations

Pull Request - State: closed - Opened by chriscrsmith 12 months ago - 9 comments

#1518 - test that requirements in `setup.cfg` are sufficient

Issue - State: open - Opened by petrelharp about 1 year ago

#1517 - Adding GorGor species and demography

Pull Request - State: open - Opened by ChristianHuber about 1 year ago - 5 comments

#1515 - Error on import: ModuleNotFoundError: No module named 'scipy

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

#1514 - Vaquita species add

Pull Request - State: closed - Opened by igronau about 1 year ago - 5 comments

#1513 - Bump sphinx from 5.0.2 to 7.2.5 in /requirements/CI

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

#1512 - Bump pytest from 7.3.2 to 7.4.1 in /requirements/CI

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

#1511 - Bump sphinx from 5.0.2 to 7.2.4 in /requirements/CI

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

#1510 - Bump sphinx from 5.0.2 to 7.2.2 in /requirements/CI

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

#1509 - include parameter values in catalogue for DFEs

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

#1508 - add vaquita

Issue - State: closed - Opened by petrelharp about 1 year ago - 10 comments
Labels: enhancement

#1507 - QC for new DFE: "generic" human DFE

Issue - State: open - Opened by chriscrsmith about 1 year ago

#1506 - Bump sphinx from 4.3.2 to 7.1.2 in /requirements/CI

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

#1505 - adding "generic" human DFE

Pull Request - State: closed - Opened by chriscrsmith about 1 year ago - 11 comments

#1504 - add fox?

Issue - State: closed - Opened by petrelharp about 1 year ago - 4 comments
Labels: enhancement

#1503 - Bump flake8 from 5.0.4 to 6.1.0 in /requirements/CI

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

#1502 - Bump sphinx from 4.3.2 to 7.1.1 in /requirements/CI

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

#1501 - Bump sphinx from 4.3.2 to 7.1.0 in /requirements/CI

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

#1500 - Ancient Europe demographic model

Issue - State: closed - Opened by apragsdale about 1 year ago - 2 comments

#1499 - remove python 3.7 from CI?

Issue - State: closed - Opened by petrelharp about 1 year ago - 2 comments

#1498 - h-s relationship (closes #1488)

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

#1497 - Bump pytest from 7.2.1 to 7.4.0 in /requirements/CI

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

#1496 - bug in adding mutations to the recapitated portion of the tree sequence

Issue - State: open - Opened by mufernando over 1 year ago - 4 comments

#1495 - document how to simulate from one species' DFE with another species

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

#1494 - add 'best' DFE from Kyriazis et al

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

#1492 - add uniform DFE (closes #1481)

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

#1491 - Bump pytest from 7.2.1 to 7.3.2 in /requirements/CI

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

#1490 - Use codecov upload token

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

#1489 - Bump version of macOS runner

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

#1488 - add discretized h-s relationship DFE

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

#1487 - Add final changes

Pull Request - State: closed - Opened by ornobalam over 1 year ago - 5 comments

#1486 - Bump pytest-xdist from 3.2.0 to 3.3.1 in /requirements/CI

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

#1485 - add mus mus domesticus demographic model

Pull Request - State: closed - Opened by peterdfields over 1 year ago - 20 comments

#1484 - QC for LogNormalDFE (HomSap)

Issue - State: open - Opened by RyanGutenkunst over 1 year ago
Labels: Model QC

#1483 - teensy tiny typo in the citation of the American admixture demographi…

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

#1482 - Changed parameters for rice

Pull Request - State: closed - Opened by ornobalam over 1 year ago - 5 comments

#1481 - add `uniform` DFE

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

#1480 - Add Human Lognormal DFE

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

#1479 - AraTha DFE QC

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

#1478 - Fix factor of 2 in Gamma_K17 DFE

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