Merge pull request #240 from lnccbrown/239-reorganize-documentation

Documentation reorganization and various bug fixes
lnccbrown · Jul 26, 2023 · 0c54135 · 0c54135
2 parents 01f0cd9 + 54da8c8
commit 0c54135
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diff --git a/.gitignore b/.gitignore
@@ -69,4 +69,4 @@ docs/site
 site/
 
 # folders in the repository
-notebooks/
+/notebooks
diff --git a/README.md b/README.md
@@ -42,7 +42,7 @@ pip install git+https://github.com/lnccbrown/HSSM.git
 ```
 
 You will need optional dependencies to use JAX-based samplers and graph the models.
-Please refer to our [installation guide](https://lnccbrown.github.io/HSSM/installation/)
+Please refer to our [installation guide](https://lnccbrown.github.io/HSSM/getting_started/installation/)
 for more detailed instructions.
 
 **Note**: Possible solutions to any issues with installations with hssm can be located [here](https://github.com/lnccbrown/HSSM/discussions). We recommend leveraging an environment manager with Python 3.9~3.11 to prevent any problems with dependencies during the installation process. Please note that hssm is tested for python 3.9, 3.10, 3.11. Use other python versions with caution.
@@ -82,8 +82,8 @@ model = hssm.HSSM(
 model.sample()
 ```
 
-To quickly get started with HSSM, please follow [this tutorial](https://lnccbrown.github.io/HSSM/tutorial_notebooks/no_execute/getting_started/).
-For a deeper dive into HSSM, please follow [our main tutorial](https://lnccbrown.github.io/HSSM/tutorial_notebooks/no_execute/main_tutorial/).
+To quickly get started with HSSM, please follow [this tutorial](https://lnccbrown.github.io/HSSM/getting_started/getting_started/).
+For a deeper dive into HSSM, please follow [our main tutorial](https://lnccbrown.github.io/HSSM/tutorials/main_tutorial/).
 
 ## License
 

diff --git a/docs/api_defaults.md → docs/api/defaults.md b/docs/api_defaults.md → docs/api/defaults.md
diff --git a/docs/api_distribution_utils.md → docs/api/distribution_utils.md b/docs/api_distribution_utils.md → docs/api/distribution_utils.md
diff --git a/docs/api_hssm.md → docs/api/hssm.md b/docs/api_hssm.md → docs/api/hssm.md
diff --git a/docs/api_likelihoods.md → docs/api/likelihoods.md b/docs/api_likelihoods.md → docs/api/likelihoods.md
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,15 @@
 
 ## 0.1.x
 
+### 0.1.3
+
+- Added the ability to specify `inf`s in bounds.
+- Fixed an issue where `nuts_numpyro` sampler fails with regression and lapse distribution.
+- Defaults to `nuts_numpyro` sampler with `approx_differentiable` likelihoods and `jax` backend.
+- Added a `hssm.show_defaults()` convenience function to print out default configs.
+- Added default `blackbox` likelihoods for `ddm` and `ddm_sdv` models.
+- Various under-the-hood documentation improvements.
+
 ### 0.1.2
 
 - Improved numerical stability of `analytical` likelihoods.