Version 0.1.0 Release

Update the changelog for version0.1.0 release

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
+- Jerome Kelleher