Ecosyste.ms: Issues

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GitHub / xin-huang/dadi-cli issues and pull requests

#121 - Update and implement --pdf-file flag

Pull Request - State: open - Opened by tjstruck 9 days ago

#120 - Neg bounds update

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

#119 - Delete tests/example_data/LowPass-files/cov.fs.coverage.pickle

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

#118 - Small LowPass update

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

#117 - Bugfix for unit tests

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

#116 - Integrate dadi LowPass functions and some streamlining code

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

#115 - TypeError was given when using GenerateCache

Issue - State: closed - Opened by jyw-atgithub 4 months ago - 7 comments

#113 - Update manual

Pull Request - State: open - Opened by xin-huang 5 months ago - 1 comment

#112 - Update dadi_cli/GenerateFs.py

Pull Request - State: closed - Opened by xin-huang 5 months ago

#111 - Update GenerateFs for checking the AA INFO field when --polarized is …

Pull Request - State: closed - Opened by xin-huang 5 months ago - 1 comment

#110 - Update docstrings

Pull Request - State: closed - Opened by xin-huang 5 months ago

#109 - Update Plot and Add --interactive option

Pull Request - State: closed - Opened by xin-huang 5 months ago - 1 comment

#108 - priority of --maxtime and --force-convergence

Issue - State: open - Opened by QianXiaobo 5 months ago - 1 comment

#108 - priority of --maxtime and --force-convergence

Issue - State: open - Opened by QianXiaobo 5 months ago - 1 comment

#107 - Update user guide

Issue - State: open - Opened by xin-huang 6 months ago

#106 - Refactor parsers

Pull Request - State: closed - Opened by xin-huang 6 months ago - 1 comment

#105 - Check AA info in the input VCF file if `--polarized` is used

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

#104 - Update docstrings and add type hint

Pull Request - State: closed - Opened by xin-huang 6 months ago - 1 comment

#103 - Update codecov

Pull Request - State: closed - Opened by xin-huang 6 months ago - 1 comment

#102 - Readme update

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

#101 - readthedocs update

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

#101 - readthedocs update

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

#100 - Readme update

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

#100 - Readme update

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

#99 - Remove stale branches

Issue - State: open - Opened by xin-huang 6 months ago

#99 - Remove stale branches

Issue - State: open - Opened by xin-huang 6 months ago

#98 - --check-convergence & --force-convergence

Issue - State: open - Opened by QianXiaobo 7 months ago - 2 comments
Labels: documentation

#97 - Add --interactive flag for Plot subcommand

Pull Request - State: closed - Opened by tjstruck 8 months ago - 2 comments

#96 - Replace `multiprocessing.Queue` with `Manager.Queue`

Issue - State: open - Opened by xin-huang 8 months ago
Labels: enhancement

#95 - add an `--interactive` option to the `Plot` command

Issue - State: open - Opened by xin-huang 8 months ago - 6 comments
Labels: enhancement

#94 - Issue with dadi-cli and the Numerics.py script

Issue - State: open - Opened by kchiou 9 months ago - 1 comment

#93 - Plot3d

Pull Request - State: closed - Opened by tjstruck 10 months ago

#92 - Update version in install file to 0.9.4

Pull Request - State: closed - Opened by tjstruck 10 months ago

#91 - Add plot 3d comparison and warnings for unsupported sample sizes

Pull Request - State: closed - Opened by tjstruck 10 months ago - 1 comment

#91 - Add plot 3d comparison and warnings for unsupported sample sizes

Pull Request - State: closed - Opened by tjstruck 10 months ago - 1 comment

#90 - plot pdf blank/empty

Issue - State: open - Opened by chapinkj 11 months ago - 4 comments

#89 - Update StatDM/DFE

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

#88 - Moved message about updating dadi for 3D models

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

#88 - Moved message about updating dadi for 3D models

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

#87 - Update global opt and Models.py for portik changes

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

#87 - Update global opt and Models.py for portik changes

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

#86 - Add Portik 2017 and Out of Africa models for donni compatibility

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

#85 - Functionality for dadi-cli to automatically make the directories

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

#85 - Functionality for dadi-cli to automatically make the directories

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

#84 - Misc updates for dadi-cli

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

#84 - Misc updates for dadi-cli

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

#83 - Better support for negative parameter bounds

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

#83 - Better support for negative parameter bounds

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

#82 - BestFit boundary update and -env.yml file dependency change for Issues #79 #78

Pull Request - State: closed - Opened by tjstruck over 1 year ago - 1 comment
Labels: enhancement

#81 - README and run_README.py updates for convergence flag

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

#80 - Update plot.md

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

#79 - Use bounds in BestFit

Issue - State: closed - Opened by RyanGutenkunst over 1 year ago - 2 comments
Labels: enhancement

#78 - Loosen dependency requirements

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

#77 - Convergence update

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

#76 - Readthedocs

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

#75 - Update plot

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

#74 - Terraform update

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

#73 - Remove email from dadi-cli

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

#72 - Snm fix for SimulateDM and GenerateCache

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

#71 - Update cloud-env.yml to install dadi-cli via conda-forge

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

#70 - Readme update

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

#69 - Bugfix _top_opts unittest

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

#68 - Update functions and tests for --bestfit-p0-file argument

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

#67 - Terraform update

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

#66 - Add ability to download fs and model file from HTML link

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

#65 - Update add_model_argument so --model not required for Plot

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

#64 - 1D DFE Plot Bugfix

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

#63 - Plot subcommand updates and bugfixes

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

#62 - Bugfixes for SimulateFS and updates for cache grid points

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

#61 - realSFS compatibility

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

#60 - Email

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

#59 - CLI returning ValueError

Issue - State: closed - Opened by andrewkern over 1 year ago - 5 comments

#58 - nlopt.RoundoffLimited error exception

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

#57 - nlopt.RoundoffLimited: NLopt roundoff-limited

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

#56 - Add pts_l_func usage for snm analysis

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

#55 - Add fix to not require boundaries when fitting a simple standard neutral model

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

#54 - InferDM with snm_1d

Issue - State: closed - Opened by bibionid over 1 year ago - 6 comments

#53 - nlopt.RoundoffLimited: NLopt roundoff-limited warning

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

#52 - different proportions from gamma and lognormal distributions

Issue - State: closed - Opened by xin-huang almost 2 years ago - 12 comments
Labels: question

#51 - Update conda environments

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

#50 - Update ValueError string formating incase it causes issues with some …

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

#49 - Pytest

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

#48 - removed fs_file variable and added support for uploading files in the…

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

#47 - Fix bugs caused by GitHub merging

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

#46 - Update tests

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

#45 - Update tests

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

#44 - Update main code for pytest branch

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

#43 - added support for auto running dadi-cli, added dadi-auto.tfvars for u…

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

#42 - Add option to choose work queue port with --port, default 9123

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

#41 - Fix bug in test_GenerateCache

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

#40 - Add doctrings

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

#39 - Robust tests of Work Queue functionality

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

#38 - Fix Work Queue InferDM and --optimizations

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

#37 - GPU support through Work Queue

Issue - State: open - Opened by RyanGutenkunst about 2 years ago
Labels: enhancement

#36 - Terraform

Pull Request - State: closed - Opened by sdavey about 2 years ago

#35 - Terraform

Pull Request - State: closed - Opened by sdavey about 2 years ago

#34 - Updated cuda support

Pull Request - State: closed - Opened by RyanGutenkunst about 2 years ago

#33 - Cuda

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

#32 - Revert "Cuda support"

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