ctlab/GADMA issues and pull requests

#98 - Bump actions/download-artifact from 4.1.4 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 18 days ago - 1 comment
Labels: dependencies, github_actions

#97 - How to estimate population parameters for best log models?

Issue - State: open - Opened by lmarieslava 2 months ago - 1 comment

#96 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

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

#95 - folding question (gene copies vs diploid sample size)

Issue - State: closed - Opened by jdlozier 4 months ago - 6 comments

#94 - Model with no population split?

Issue - State: open - Opened by kristinaleilani 5 months ago - 3 comments

#93 - Automatically check for args option when gadma.optimize_ga is using

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

#92 - Lower bound of split in inference of model with structure

Issue - State: closed - Opened by Enricobazzi 8 months ago - 9 comments

#91 - When to use Split fractions = False?

Issue - State: closed - Opened by kristinaleilani 10 months ago - 3 comments

#90 - how to modify the plot?

Issue - State: open - Opened by nicolashazzi23 10 months ago - 1 comment

#89 - running test on installation issue (yaml?)

Issue - State: closed - Opened by jdlozier 11 months ago - 4 comments

#88 - Update README.md

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

#87 - Final estimates for parameters

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

#86 - facilitating 3 population model convergence

Issue - State: open - Opened by steigeec about 1 year ago - 12 comments

#85 - Add documentation about migration rates

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

#84 - TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'

Issue - State: closed - Opened by btmartin721 about 1 year ago - 19 comments

#83 - Error when using BO

Issue - State: closed - Opened by btmartin721 about 1 year ago - 11 comments

#82 - Installing gadma on Macs with the M1 chip

Issue - State: open - Opened by burbrink over 1 year ago - 13 comments

#81 - Specifying the number of time periods (final structure) for a single population

Issue - State: closed - Opened by mrml500 over 1 year ago - 1 comment

#80 - bootstrap for linked SNPs

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

#79 - Installation problem

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

#78 - Estimating current Ne population

Issue - State: closed - Opened by AudeCaizergues almost 2 years ago - 5 comments

#77 - Check why tests fail with new moments engine

Issue - State: open - Opened by noscode about 2 years ago
Labels: bug

#76 - mapping values are not allowed here

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

#75 - Add documentation about sequence length as dict

Issue - State: closed - Opened by noscode about 2 years ago
Labels: enhancement

#74 - Adding machine learning (ML) models for fast prediction in GADMA

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

#73 - Keyerror

Issue - State: closed - Opened by AudeCaizergues over 2 years ago - 11 comments

#72 - refactor(fsc2_engine): replaced `NoReturn` annotations with `None`

Pull Request - State: closed - Opened by cafuneandchill over 2 years ago

#71 - Folded SFS

Issue - State: closed - Opened by deboraycb over 2 years ago - 6 comments

#70 - IndexError: string index out of range

Issue - State: closed - Opened by anubhabkhan over 2 years ago - 7 comments

#69 - New engine: fastsimcoal2

Pull Request - State: closed - Opened by cafuneandchill over 2 years ago

#68 - Using linear extrapolation in dadi

Issue - State: closed - Opened by AudeCaizergues over 2 years ago - 12 comments
Labels: enhancement

#67 - MomentsLD — ValueError: Can specify only recombination or bp bins, not both

Issue - State: closed - Opened by James-S-Santangelo over 2 years ago - 3 comments
Labels: bug

#66 - Error - Set Nanc value for translation

Issue - State: closed - Opened by alexsanyum over 2 years ago - 3 comments

#65 - dadi code for 3 population model

Issue - State: closed - Opened by SamWittwer almost 3 years ago - 4 comments

#64 - Error running gadma

Issue - State: closed - Opened by SamWittwer almost 3 years ago - 5 comments

#63 - Missed update on the main output for demographic inference of one population with structure [1]

Issue - State: closed - Opened by noscode almost 3 years ago
Labels: bug

#62 - current state of adding fastsimcoal2 engine

Pull Request - State: closed - Opened by iam28th about 3 years ago

#61 - Add custom model specification with GADMA as a library

Issue - State: open - Opened by noscode about 3 years ago
Labels: enhancement

#60 - Add citations at the end or at the begining of GADMA run

Issue - State: closed - Opened by noscode about 3 years ago
Labels: enhancement

#59 - Moments ld engine

Pull Request - State: closed - Opened by stanislavzlp about 3 years ago - 1 comment

#58 - The error for custom model and relative parameters set to True

Issue - State: closed - Opened by noscode about 3 years ago
Labels: bug

#57 - Wrong output for one population with [1] structure

Issue - State: closed - Opened by noscode about 3 years ago
Labels: bug

#56 - failed to generate code

Issue - State: closed - Opened by alexsanyum about 3 years ago - 12 comments

#55 - Coalescent Model and Engine

Pull Request - State: closed - Opened by n8ron over 3 years ago

#54 - Add support for fastsimcoal2 SFS data format

Pull Request - State: closed - Opened by iam28th over 3 years ago - 1 comment

#53 - Inbreeding

Pull Request - State: closed - Opened by stanislavzlp over 3 years ago - 1 comment

#52 - Translation coalescent demographic model

Pull Request - State: closed - Opened by n8ron over 3 years ago - 1 comment

#51 - Mask migration error

Issue - State: closed - Opened by DeondeJager over 3 years ago - 4 comments

#50 - global optimizer falls with an error

Issue - State: closed - Opened by dingearteom over 3 years ago - 1 comment

#49 - Add DemographicVariable

Pull Request - State: closed - Opened by n8ron over 3 years ago

#48 - Addition to previous commit and PR

Pull Request - State: closed - Opened by noscode almost 4 years ago

#47 - New fixes

Pull Request - State: closed - Opened by noscode almost 4 years ago - 1 comment

#46 - Fix version error in gadma and error when running from command line

Pull Request - State: closed - Opened by noscode almost 4 years ago - 1 comment

#45 - Fix issues with version

Pull Request - State: closed - Opened by noscode almost 4 years ago

#44 - Add github actions for pypi sync

Pull Request - State: closed - Opened by noscode almost 4 years ago

#43 - Fix #42 and sorting function in utils

Pull Request - State: closed - Opened by noscode almost 4 years ago

#42 - Units of time out by factor of 10

Issue - State: closed - Opened by iracooke almost 4 years ago - 3 comments

#41 - Fix error when folded SFS is used

Pull Request - State: closed - Opened by noscode almost 4 years ago

#40 - Add num_init_const option

Pull Request - State: closed - Opened by noscode almost 4 years ago

#39 - Change timeout function to work on windows and fix translation

Pull Request - State: closed - Opened by noscode almost 4 years ago

#38 - Add timeout in Inference.optimize_ga and fix some bugs in local optim…

Pull Request - State: closed - Opened by noscode almost 4 years ago - 1 comment

#37 - New tests

Pull Request - State: closed - Opened by noscode almost 4 years ago - 1 comment

#36 - Ffx docs failing

Pull Request - State: closed - Opened by noscode almost 4 years ago

#35 - Fix jupyter notebooks generation in docs

Pull Request - State: closed - Opened by noscode almost 4 years ago

#34 - Jupyter notebooks are shown incorrectly in the documentation

Issue - State: closed - Opened by noscode almost 4 years ago

#33 - Mistake in manual re migration rates?

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

#32 - Add tests for engines

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#31 - Add changelogs in documentation

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#30 - Add new checks for probabilities in selection of GA

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#29 - Add new tests and fixes

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#28 - Add extension with migration masks to restrict migrations manually

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#27 - Add migration masks to restrict migrations manually

Pull Request - State: closed - Opened by noscode about 4 years ago

#26 - Add migration masks to restrict migrations manually

Pull Request - State: closed - Opened by noscode about 4 years ago

#25 - Fix ZeroDivisionError when Nanc is zero (Issue #23).

Pull Request - State: closed - Opened by noscode about 4 years ago - 1 comment

#24 - restrict the number of migration

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

#23 - ZeroDivisionError

Issue - State: closed - Opened by silvewheat about 4 years ago - 6 comments

#22 - Try to fix docs

Pull Request - State: closed - Opened by noscode about 4 years ago

#21 - Fix tests failure

Pull Request - State: closed - Opened by noscode about 4 years ago

#20 - Fix pep8

Pull Request - State: closed - Opened by noscode about 4 years ago

#19 - Move pandas to optional dependency

Pull Request - State: closed - Opened by noscode about 4 years ago

#18 - Fix test run without moments

Pull Request - State: closed - Opened by noscode about 4 years ago

#17 - Fix paths for test data

Pull Request - State: closed - Opened by noscode about 4 years ago

#16 - New version of GADMA

Pull Request - State: closed - Opened by noscode about 4 years ago

#15 - Fix pep8

Pull Request - State: closed - Opened by noscode about 4 years ago

#14 - Fix bugs and add new version in setup.py

Pull Request - State: closed - Opened by noscode about 4 years ago

#13 - New docs

Pull Request - State: closed - Opened by noscode about 4 years ago

#12 - Fix docs

Pull Request - State: closed - Opened by noscode about 4 years ago

#11 - Remove old docs

Pull Request - State: closed - Opened by noscode about 4 years ago

#10 - Docs update for 2nd version

Pull Request - State: closed - Opened by noscode about 4 years ago

#9 - Theta0, popt, and divergence Times

Issue - State: closed - Opened by btmartin721 about 4 years ago - 7 comments

#8 - Finding theta and calculating theta (determining L)

Issue - State: closed - Opened by DeondeJager over 4 years ago - 8 comments

#7 - Custom Model Upper Lower Bounds Issue

Issue - State: closed - Opened by btmartin721 over 4 years ago - 1 comment

#6 - sciPy error: dimension mismatch

Issue - State: closed - Opened by PazhenkovaEA over 4 years ago

#5 - Error when trying to plot from best_logLL_model_moments_code.py

Issue - State: closed - Opened by Mills33 over 4 years ago - 10 comments

#4 - IndexError when No migrations : True

Issue - State: closed - Opened by alexnater about 5 years ago - 1 comment

#3 - Estimating Theta0?

Issue - State: closed - Opened by Sh1ne111 over 5 years ago - 1 comment

#2 - example Error

Issue - State: closed - Opened by Sh1ne111 over 5 years ago - 5 comments

#1 - Unzip .egg file by default

Pull Request - State: closed - Opened by isheshukov over 5 years ago

GitHub / ctlab/GADMA issues and pull requests