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diff --git a/_modules/torchtree/evolution/tree_likelihood.html b/_modules/torchtree/evolution/tree_likelihood.html
diff --git a/_modules/torchtree/evolution/tree_model.html b/_modules/torchtree/evolution/tree_model.html
diff --git a/_modules/torchtree/evolution/tree_model_flexible.html b/_modules/torchtree/evolution/tree_model_flexible.html
diff --git a/_modules/torchtree/evolution/tree_regression.html b/_modules/torchtree/evolution/tree_regression.html
diff --git a/_modules/torchtree/inference/hmc/adaptation.html b/_modules/torchtree/inference/hmc/adaptation.html
diff --git a/_modules/torchtree/inference/hmc/hamiltonian.html b/_modules/torchtree/inference/hmc/hamiltonian.html
diff --git a/_modules/torchtree/inference/hmc/hmc.html b/_modules/torchtree/inference/hmc/hmc.html
diff --git a/_modules/torchtree/inference/hmc/integrator.html b/_modules/torchtree/inference/hmc/integrator.html
diff --git a/_modules/torchtree/inference/hmc/operator.html b/_modules/torchtree/inference/hmc/operator.html
diff --git a/_modules/torchtree/inference/hmc/stan_adaptation.html b/_modules/torchtree/inference/hmc/stan_adaptation.html
diff --git a/_modules/torchtree/inference/mcmc/gmrf_block_updating.html b/_modules/torchtree/inference/mcmc/gmrf_block_updating.html
diff --git a/_modules/torchtree/inference/mcmc/mcmc.html b/_modules/torchtree/inference/mcmc/mcmc.html
diff --git a/_modules/torchtree/inference/mcmc/operator.html b/_modules/torchtree/inference/mcmc/operator.html
diff --git a/_modules/torchtree/inference/sampler.html b/_modules/torchtree/inference/sampler.html
diff --git a/_modules/torchtree/inference/utils.html b/_modules/torchtree/inference/utils.html
diff --git a/_modules/torchtree/nf/energy_functions.html b/_modules/torchtree/nf/energy_functions.html
diff --git a/_modules/torchtree/nf/flow.html b/_modules/torchtree/nf/flow.html
diff --git a/_modules/torchtree/nf/planar.html b/_modules/torchtree/nf/planar.html
diff --git a/_modules/torchtree/nf/realnvp.html b/_modules/torchtree/nf/realnvp.html
diff --git a/_modules/torchtree/nn/module.html b/_modules/torchtree/nn/module.html
diff --git a/_modules/torchtree/ops/dual_averaging.html b/_modules/torchtree/ops/dual_averaging.html
diff --git a/_modules/torchtree/ops/smooth.html b/_modules/torchtree/ops/smooth.html
diff --git a/_modules/torchtree/ops/welford.html b/_modules/torchtree/ops/welford.html
diff --git a/_modules/torchtree/optim/convergence.html b/_modules/torchtree/optim/convergence.html
diff --git a/_modules/torchtree/optim/lr_scheduler.html b/_modules/torchtree/optim/lr_scheduler.html
diff --git a/_modules/torchtree/optim/optimizer.html b/_modules/torchtree/optim/optimizer.html
diff --git a/_modules/torchtree/torchtree.html b/_modules/torchtree/torchtree.html
diff --git a/_modules/torchtree/variational/chi.html b/_modules/torchtree/variational/chi.html
diff --git a/_modules/torchtree/variational/kl.html b/_modules/torchtree/variational/kl.html
diff --git a/_modules/torchtree/variational/renyi.html b/_modules/torchtree/variational/renyi.html
diff --git a/_sources/autoapi/torchtree/_version/index.rst b/_sources/autoapi/torchtree/_version/index.rst
diff --git a/_sources/autoapi/torchtree/cli/advi/index.rst b/_sources/autoapi/torchtree/cli/advi/index.rst
@@ -1,15 +1,19 @@
-:py:mod:`torchtree.cli.advi`
-============================
+torchtree.cli.advi
+==================
 
 .. py:module:: torchtree.cli.advi
 
 
-Module Contents
----------------
+Attributes
+----------
+
+.. autoapisummary::
+
+   torchtree.cli.advi.logger
 
 
 Functions
-~~~~~~~~~
+---------
 
 .. autoapisummary::
 
@@ -37,22 +41,13 @@ Functions
    torchtree.cli.advi.build_advi
 
 
-
-Attributes
-~~~~~~~~~~
-
-.. autoapisummary::
-
-   torchtree.cli.advi.logger
-
+Module Contents
+---------------
 
 .. py:data:: logger
 
-   
-
 .. py:function:: create_variational_parser(subprasers)
 
-
 .. py:function:: create_tril(scales: torch.Tensor) -> torch.Tensor
 
    Create a 1 dimentional tensor containing a flatten tridiagonal matrix.
@@ -68,61 +63,41 @@ Attributes
 
 .. py:function:: create_fullrank_from_meanfield(params, path)
 
-
 .. py:function:: create_fullrank(var_id, json_object, arg)
 
-
 .. py:function:: create_flexible_variational(arg, json_object)
 
-
 .. py:function:: create_realnp_distribution(var_id: str, x, params: torch.Tensor)
 
-
 .. py:function:: create_realnvp(var_id, json_object, arg)
 
-
 .. py:function:: gather_parameters(json_object: dict, group_map: dict, parameters: dict)
 
-
 .. py:function:: apply_sigmoid_transformed(json_object, value=None)
 
-
 .. py:function:: apply_affine_transform(json_object, loc, scale)
 
-
 .. py:function:: apply_exp_transform(json_object)
 
-
 .. py:function:: apply_simplex_transform(json_object)
 
-
 .. py:function:: create_normal_distribution(var_id, x_unres, json_object, loc, scale)
 
-
 .. py:function:: create_gamma_distribution(var_id, x_unres, json_object, concentration, rate)
 
-
 .. py:function:: create_weibull_distribution(var_id, x_unres, json_object, scale, concentration)
 
-
 .. py:function:: create_meanfield(var_id: str, json_object: dict, distribution: str) -> tuple[list[str], list[str]]
 
-
 .. py:function:: apply_transforms_for_fullrank(var_id: str, json_object: Union[dict, list]) -> list[tuple[str, str, list]]
 
-
 .. py:function:: create_variational_model(id_, joint, arg) -> tuple[dict, list[str]]
 
-
 .. py:function:: create_advi(joint, variational, parameters, arg)
 
-
 .. py:function:: create_logger(id_, parameters, arg)
 
-
 .. py:function:: create_sampler(id_, var_id, parameters, arg)
 
-
 .. py:function:: build_advi(arg)
 
-
diff --git a/_sources/autoapi/torchtree/cli/argparse_utils/index.rst b/_sources/autoapi/torchtree/cli/argparse_utils/index.rst
@@ -1,15 +1,11 @@
-:py:mod:`torchtree.cli.argparse_utils`
-======================================
+torchtree.cli.argparse_utils
+============================
 
 .. py:module:: torchtree.cli.argparse_utils
 
 
-Module Contents
----------------
-
-
 Functions
-~~~~~~~~~
+---------
 
 .. autoapisummary::
 
@@ -19,10 +15,11 @@ Functions
    torchtree.cli.argparse_utils.list_or_int
 
 
+Module Contents
+---------------
 
 .. py:function:: zero_or_path(arg)
 
-
 .. py:function:: str_or_float(arg, choices)
 
    Used by argparse when the argument can be either a number or a string

diff --git a/_sources/autoapi/torchtree/cli/cli/index.rst b/_sources/autoapi/torchtree/cli/cli/index.rst
@@ -1,26 +1,22 @@
-:py:mod:`torchtree.cli.cli`
-===========================
+torchtree.cli.cli
+=================
 
 .. py:module:: torchtree.cli.cli
 
 
-Module Contents
----------------
-
-
 Functions
-~~~~~~~~~
+---------
 
 .. autoapisummary::
 
    torchtree.cli.cli.create_show_parser
    torchtree.cli.cli.main
 
 
+Module Contents
+---------------
 
 .. py:function:: create_show_parser(subprasers)
 
-
 .. py:function:: main()
 
-
diff --git a/_sources/autoapi/torchtree/cli/evolution/index.rst b/_sources/autoapi/torchtree/cli/evolution/index.rst
@@ -1,15 +1,20 @@
-:py:mod:`torchtree.cli.evolution`
-=================================
+torchtree.cli.evolution
+=======================
 
 .. py:module:: torchtree.cli.evolution
 
 
-Module Contents
----------------
+Attributes
+----------
+
+.. autoapisummary::
+
+   torchtree.cli.evolution.logger
+   torchtree.cli.evolution.COALESCENT_PIECEWISE
 
 
 Functions
-~~~~~~~~~
+---------
 
 .. autoapisummary::
 
@@ -53,37 +58,23 @@ Functions
    torchtree.cli.evolution.get_engine
 
 
-
-Attributes
-~~~~~~~~~~
-
-.. autoapisummary::
-
-   torchtree.cli.evolution.logger
-   torchtree.cli.evolution.COALESCENT_PIECEWISE
-
+Module Contents
+---------------
 
 .. py:data:: logger
 
-   
-
 .. py:data:: COALESCENT_PIECEWISE
    :value: ['piecewise-constant', 'piecewise-exponential', 'piecewise-linear', 'skyglide', 'skygrid', 'skyride']
 
-
 
 .. py:function:: create_evolution_parser(parser)
 
-
 .. py:function:: add_birth_death(parser)
 
-
 .. py:function:: add_coalescent(parser)
 
-
 .. py:function:: check_arguments(arg, parser)
 
-
 .. py:function:: distribution_type(arg, choices)
 
    Used by argparse for specifying distributions with optional
@@ -92,100 +83,68 @@ Attributes
 
 .. py:function:: run_tree_regression(arg, taxa)
 
-
 .. py:function:: create_tree_model(id_: str, taxa: dict, arg)
 
-
 .. py:function:: create_poisson_tree_likelihood(id_, taxa, arg)
 
-
 .. py:function:: create_tree_likelihood_single(id_, tree_model, branch_model, substitution_model, site_model, site_pattern)
 
-
 .. py:function:: create_tree_likelihood_general(trait: str, data_type: dict, taxa: torchtree.evolution.taxa.Taxa, arg)
 
-
 .. py:function:: create_tree_likelihood(id_, taxa, alignment, arg)
 
-
 .. py:function:: create_site_model(id_, arg, w=None)
 
-
 .. py:function:: create_site_model_srd06_mus(id_)
 
-
 .. py:function:: is_float(value)
 
-
 .. py:function:: create_branch_model(id_, tree_id, taxa_count, arg, rate_init=None)
 
-
 .. py:function:: build_alignment(file_name, data_type)
 
-
 .. py:function:: create_substitution_model(id_, model, arg)
 
-
 .. py:function:: create_site_pattern(id_, alignment, indices=None)
 
-
 .. py:function:: create_data_type(id_, arg)
 
-
 .. py:function:: create_general_data_type(id_, trait, taxa)
 
-
 .. py:function:: create_alignment(id_, taxa, arg)
 
-
 .. py:function:: create_taxa(id_, arg)
 
-
 .. py:function:: create_birth_death(birth_death_id, tree_id, arg)
 
-
 .. py:function:: create_constant_birth_death(birth_death_id, tree_id, arg)
 
-
 .. py:function:: create_bdsk(birth_death_id, tree_id, arg)
 
-
 .. py:function:: create_coalesent(id_, tree_id, taxa, arg)
 
-
 .. py:function:: create_substitution_model_priors(substmodel_id, model)
 
-
 .. py:function:: create_ucln_prior(branch_model_id)
 
-
 .. py:function:: parse_distribution(desc)
 
-
 .. py:function:: create_clock_prior(arg)
 
-
 .. py:function:: create_evolution_priors(taxa, arg)
 
-
 .. py:function:: create_time_tree_prior(taxa, arg)
 
-
 .. py:function:: create_bd_prior(id_, parameters)
 
-
 .. py:function:: create_constant_bd_prior(birth_death_id)
 
-
 .. py:function:: create_bdsk_prior(birth_death_id)
 
-
 .. py:function:: create_poisson_evolution_joint(taxa, arg)
 
-
 .. py:function:: create_evolution_joint(taxa, alignment, arg)
 
-
 .. py:function:: get_engine(arg)
 
    Import module or use cashed module if engine is specified in