Ecosyste.ms: Issues

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GitHub / molpopgen/fwdpy11 issues and pull requests

#1315 - More macos wheel pain

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

#1314 - Bump pypa/cibuildwheel from 2.17.0 to 2.18.1

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

#1313 - bump pybind11 to 2.12.0

Pull Request - State: closed - Opened by molpopgen about 1 month ago

#1312 - Merge main into dev

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

#1311 - Update docker action to only login for releases

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

#1310 - Bump actions/download-artifact from 4.1.4 to 4.1.7

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 3 comments
Labels: dependencies, github_actions

#1309 - deprecate asblack method

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

#1308 - Moving towards removing "requirements" files.

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

#1307 - Update manual

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

#1306 - disable building C++ for tests in tests_with_cpp/ by default

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

#1305 - remove print statements from tests/

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

#1304 - deprecate redundant demography functions

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

#1303 - Disable compiling by default the C++ files only used by Python tests

Issue - State: closed - Opened by molpopgen 2 months ago - 1 comment
Labels: build system

#1302 - Docs to update

Issue - State: closed - Opened by molpopgen 2 months ago - 1 comment
Labels: documentation

#1301 - remove deprecations

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

#1300 - Deprecate redundant ways to initialize demography

Issue - State: closed - Opened by molpopgen 2 months ago - 3 comments

#1299 - Fix #1217

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

#1298 - Add Python access to demes.Graph from ForwardDemesGraph

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

#1296 - valgrind cpp test suite

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

#1295 - Update Cargo.lock using cargo update

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

#1294 - update demes-forward-capi to 0.5.0

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

#1293 - Access to internal demes.Graph

Issue - State: closed - Opened by molpopgen 3 months ago - 1 comment
Labels: demographic models, demes integration

#1292 - Deprecate TreeIterator

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

#1291 - remove setup.py

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

#1290 - Only push docker images for releases

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

#1289 - Changelog for 0.22.1

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

#1288 - remove options from setup.py

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

#1287 - doc updates

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

#1286 - try ciwheelbuild on macos-latest

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

#1285 - Tracking issue: doc updates

Issue - State: closed - Opened by molpopgen 3 months ago - 1 comment
Labels: documentation

#1284 - Move to scikit build for build backend

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

#1283 - macos wheels

Issue - State: closed - Opened by molpopgen 3 months ago - 2 comments

#1282 - Update workflow action versions

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

#1281 - Add cibuildwheel configuration

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

#1280 - format code using latest version of black

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

#1279 - Bump actions/download-artifact from 3.0.2 to 4.1.4

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, github_actions

#1278 - Bump baptiste0928/cargo-install from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies, github_actions

#1277 - Bump actions/download-artifact from 3.0.2 to 4.1.3

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies, github_actions

#1276 - Bump styfle/cancel-workflow-action from 0.12.0 to 0.12.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, github_actions

#1275 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, github_actions

#1274 - Bump actions/download-artifact from 3.0.2 to 4.1.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, github_actions

#1273 - Mutation counting in Python API

Issue - State: open - Opened by molpopgen 5 months ago

#1272 - Clear table collection indexes early each generation.

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1271 - Deprecate TableCollection.fs

Issue - State: closed - Opened by molpopgen 5 months ago - 1 comment

#1270 - Remove use of oldest-supported-numpy when building wheels.

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1269 - add pyarrow to requirements/docs.txt.

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1268 - Add hard assert on TreeSequence time units

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1267 - update change log

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1266 - add citation info

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1265 - Deprecate some options for exporting to tskit.

Pull Request - State: closed - Opened by molpopgen 5 months ago

#1264 - bump upload/download artifact workflow action versions.

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

#1263 - Bump actions/setup-python from 4 to 5

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

#1262 - Bump actions/download-artifact from 3.0.2 to 4.1.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies, github_actions

#1261 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies, github_actions

#1260 - bump unsafe-libyaml

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

#1259 - Bump unsafe-libyaml from 0.2.7 to 0.2.10 in /rust/fp11rust

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, rust

#1258 - Test for warning needed?

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

#1256 - Deprecate dict as valid type for model_params when exporting to tskit

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

#1255 - Fix export to tskit when demographic models end in the past.

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

#1254 - Clear CI caches

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

#1253 - Demes graphs with end times > 0

Issue - State: closed - Opened by molpopgen 7 months ago
Labels: tskit

#1252 - Fix typo in docs.

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

#1251 - Add time conversion functions to ForwardDemesGraph

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

#1250 - Need "how to cite" info

Issue - State: closed - Opened by molpopgen 7 months ago
Labels: documentation

#1249 - Add tests of demes event timings.

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

#1248 - Update msprime.simulate to msprime.sim_ancestry

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

#1247 - update change log

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

#1246 - Add CI step to check Python code formatting

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

#1245 - format all files with black

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

#1244 - streamline requirements files

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

#1243 - remove dependency on intervaltree

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

#1242 - Set time_units to generations when exporting to tskit.

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

#1241 - start updating recapitation vignette

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

#1240 - Add example of adaptation to different optima.

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

#1239 - Deprecate StrictAdditiveMultivariateEffects.

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

#1238 - add Python 3.12 to all Github work flows

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

#1237 - update change log

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1236 - Refactor PyDiploidGeneticValue as a Python class

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1235 - Warn when prune_selected = True can be a problem

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1234 - Merge dev into main

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1233 - Add stderr_output: error to doc/config.yml

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1232 - warnings for `prune_selected`

Issue - State: closed - Opened by molpopgen 8 months ago
Labels: UI

#1231 - Deprecated behavior being used in manual

Issue - State: closed - Opened by molpopgen 8 months ago - 1 comment
Labels: documentation

#1230 - Need a simpler example of different optima in different demes.

Issue - State: closed - Opened by molpopgen 8 months ago
Labels: documentation

#1229 - Genetic value API

Issue - State: open - Opened by molpopgen 8 months ago - 2 comments
Labels: C++ back end, UI

#1228 - Refine branch choice in add_mutation.

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1227 - merge dev

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1226 - Fix changelog version

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1225 - merge dev

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1224 - update change log

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1223 - Add manual section on invoking python with -Wd or -We

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1222 - Fix link to demes specification.

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1221 - Need a manual section on invoking Python

Issue - State: closed - Opened by molpopgen 8 months ago
Labels: documentation

#1220 - Broken link in manual

Issue - State: closed - Opened by molpopgen 8 months ago
Labels: documentation

#1219 - Deprecate use of None for a demographic model.

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1218 - use tskit.NODE_IS_SAMPLE instead of numerical value

Pull Request - State: closed - Opened by molpopgen 8 months ago

#1217 - Moving optimum models and complex demography

Issue - State: closed - Opened by molpopgen 8 months ago - 8 comments
Labels: UI

#1216 - bump demesdraw in requirements/development.txt

Pull Request - State: closed - Opened by molpopgen 8 months ago