From 7911c4152208ebee4b6b481b768229d15f159300 Mon Sep 17 00:00:00 2001 From: daikitag <48062118+daikitag@users.noreply.github.com> Date: Wed, 6 Mar 2024 23:41:07 +0000 Subject: [PATCH] Version 0.1.0 Release Update the changelog for version0.1.0 release --- CHANGELOG.md | 66 +++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 60 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4559cdd..781f4d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,59 @@ # Changelog +## [0.1.0] - 2024-03-XX + +### Changes from Version 0.0.1: + +- The output dataframe of `sim_trait` function is different, and the effect sizes are obtained after the frequency dependence architecture is used +- `sim_genetic` function is no longer supported, and users should be using `genetic_value` function instead +- `negative` input in exponential and gamma distribution trait models are no longer supported, and users should be using `random_sign` instead + +### Update: + +- Remove `num_causal` dependence on simulating effect sizes [#107](https://github.com/tskit-dev/tstrait/pull/107) +- Add options to simulate effect sizes from `random_sign` in fixed value trait model [#109](https://github.com/tskit-dev/tstrait/pull/109) +- Add frequency dependence architecture in `sim_trait` function [#111](https://github.com/tskit-dev/tstrait/pull/111) +- Implement `genetic_value` function to compute genetic values based on the trait dataframe [#112](https://github.com/tskit-dev/tstrait/pull/112) +- Rename `negative` in exponential and gamma distribution trait model as `random_sign`[#114](https://github.com/tskit-dev/tstrait/pull/114) +- Add option to input the causal site IDs, instead of randomly selecting them in `sim_phenotype` and `sim_trait` functions [#124](https://github.com/tskit-dev/tstrait/pull/124) +- Add `normalise_phenotypes` function to normalize the simulated phenotypes [#130](https://github.com/tskit-dev/tstrait/pull/130) +- Add delta degrees of freedom input in `normalise_phenotypes` function [#136](https://github.com/tskit-dev/tstrait/pull/136) +- Add `normalise_genetic_value` function to normalize the genetic values [#145](https://github.com/tskit-dev/tstrait/pull/145) + +### Fix: + +- Raise error when there are no individuals [#97](https://github.com/tskit-dev/tstrait/pull/97) +- Raise error when incorrect values are given in the `num_causal` argument [#99](https://github.com/tskit-dev/tstrait/pull/99) +- Remove `# pragma: no cover` in certain functions [#119](https://github.com/tskit-dev/tstrait/pull/119) +- Modify default input arguments of `sim_trait`, `sim_env` and `sim_phenotype` functions [#120](https://github.com/tskit-dev/tstrait/pull/120) +- Add `verification.py` for statistical tests [#129](https://github.com/tskit-dev/tstrait/pull/129) +- Add statistical tests against external simulators [#132](https://github.com/tskit-dev/tstrait/pull/132) +- Change the dtype of `trait_id` input in `genetic_value` function [#134](https://github.com/tskit-dev/tstrait/pull/134) +- Add density plot in `verification.py` [#138](https://github.com/tskit-dev/tstrait/pull/138) +- Add multithreading in `verification.py` [#139](https://github.com/tskit-dev/tstrait/pull/139) +- Conduct exact tests against AlphaSimR, simplePHENOTYPES and the simulation framework described in ARG-Needle paper in `verification.py` [#140](https://github.com/tskit-dev/tstrait/pull/140) + +### Documentation: + +- Modify introduction [#96](https://github.com/tskit-dev/tstrait/pull/96) +- Document ploidy [#98](https://github.com/tskit-dev/tstrait/pull/98) +- Documentation for the new `sim_trait` function [#115](https://github.com/tskit-dev/tstrait/pull/115) +- Documentation for `random_sign` input in trait distribution models [#122](https://github.com/tskit-dev/tstrait/pull/122) +- Modify phrasing in documentation [#123](https://github.com/tskit-dev/tstrait/pull/123) +- Documentation for specifying causal site IDs [#126](https://github.com/tskit-dev/tstrait/pull/126) +- Documentation for modifying the numericalization of genotypes [#133](https://github.com/tskit-dev/tstrait/pull/133) +- Modify the frequency dependence explanation in the documentation [#141](https://github.com/tskit-dev/tstrait/pull/141) +- Fix typo in documentation [#142](https://github.com/tskit-dev/tstrait/pull/142) + +### Contributors: + +- Jerome Kelleher +- Yan Wong +- Ben Jeffery +- Gertjan Bisschop +- Daiki Tagami + + ## [0.0.1] - 2023-09-05 ### Highlights: @@ -37,14 +91,14 @@ Test release of the package before releasing it to conda-forge ### Fix: -- Hide private functions and classes {pr}`73` -- Modify docstring explanations and examples {pr}`76` +- Hide private functions and classes [#73](https://github.com/tskit-dev/tstrait/pull/73) +- Modify docstring explanations and examples [#76](https://github.com/tskit-dev/tstrait/pull/76) ### Documentation: -- Create infrastructure for documentation {pr}`77` -- Build initial documentation {pr}`78` -- Add Changelog to documentation {pr}`79` +- Create infrastructure for documentation [#77](https://github.com/tskit-dev/tstrait/pull/77) +- Build initial documentation [#78](https://github.com/tskit-dev/tstrait/pull/78) +- Add Changelog to documentation [#79](https://github.com/tskit-dev/tstrait/pull/79) ### Contributors: @@ -60,4 +114,4 @@ Initial alpha release of the package. - Daiki Tagami - Gertjan Bisschop -- Jerome Kelleher \ No newline at end of file +- Jerome Kelleher