Update paper.md

Fixing typo in web browser editor

Taweret/mix/bivariate_linear.py

@@ -625,6 +625,16 @@ def train(self,
         result : bilby posterior object
             object returned by the bilby sampler
         '''
+        import platform
+        i
+        if platform.system() == 'Darwin':
+            if 'threads' in kwargs_for_sampler.keys(
+            ) and kwargs_for_sampler['threads'] > 1:
+                import warnings
+                import multiprocessing
+                warnings.warn("'threads' detected in `kwargs` on Darwin." +
+                              " Setting `start_method` fot `fork`")
+                multiprocessing.set_start_method('fork')
 
         prior = self._prior
         if prior is None:

docs/run_to_rebuild_tawret_rst.sh

@@ -1,5 +1,5 @@
 cd source/
-sphinx-apidoc -f -E --implicit-namespaces -l -o . ../../Taweret
+sphinx-apidoc -f -E --implicit-namespaces -l -o . ../Taweret
 cd ..
 make clean html
 open build/html/Taweret.html

docs/source/Taweret.core.rst

@@ -1,27 +1,31 @@
 Taweret.core namespace
 ======================
 
+.. py:module:: Taweret.core
+
 Submodules
 ----------
 
+
 .. automodule:: Taweret.core.base_mixer
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 
 .. automodule:: Taweret.core.base_model
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-.. automodule:: Taweret.core.trees_setup
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
-.. automodule:: Taweret.core.wrappers
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. automodule:: Taweret.core.trees_setup
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 
+.. automodule:: Taweret.core.wrappers
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Taweret.mix.rst

@@ -1,22 +1,25 @@
 Taweret.mix namespace
 =====================
 
+.. py:module:: Taweret.mix
+
 Submodules
 ----------
 
+
 .. automodule:: Taweret.mix.bivariate_linear
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-.. automodule:: Taweret.mix.gaussian
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
-.. automodule:: Taweret.mix.trees
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. automodule:: Taweret.mix.gaussian
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 
+.. automodule:: Taweret.mix.trees
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Taweret.models.rst

@@ -1,22 +1,25 @@
 Taweret.models namespace
 ========================
 
+.. py:module:: Taweret.models
+
 Submodules
 ----------
 
+
 .. automodule:: Taweret.models.coleman_models
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-.. automodule:: Taweret.models.polynomial_models
-    :members:
-    :undoc-members:
-    :show-inheritance:
 
-.. automodule:: Taweret.models.samba_models
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. automodule:: Taweret.models.polynomial_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 
+.. automodule:: Taweret.models.samba_models
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Taweret.rst

@@ -5,17 +5,18 @@ Subpackages
 -----------
 
 .. toctree::
+   :maxdepth: 4
 
-    Taweret.core
-    Taweret.mix
-    Taweret.models
-    Taweret.sampler
-    Taweret.utils
+   Taweret.core
+   Taweret.mix
+   Taweret.models
+   Taweret.sampler
+   Taweret.utils
 
 Module contents
 ---------------
 
 .. automodule:: Taweret
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Taweret.sampler.rst

@@ -1,12 +1,13 @@
 Taweret.sampler namespace
 =========================
 
+.. py:module:: Taweret.sampler
+
 Submodules
 ----------
 
-.. automodule:: Taweret.sampler.likelihood_wrappers
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 
+.. automodule:: Taweret.sampler.likelihood_wrappers
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Taweret.utils.rst

@@ -1,12 +1,13 @@
 Taweret.utils namespace
 =======================
 
+.. py:module:: Taweret.utils
+
 Submodules
 ----------
 
-.. automodule:: Taweret.utils.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 
+.. automodule:: Taweret.utils.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -17,6 +17,7 @@ Welcome to Bayesian Model Mixing with Taweret!
    :caption: Installation:
 
    installation
+   macos_users
 
 .. toctree::
    :maxdepth: 4

docs/source/macos_users.rst

@@ -0,0 +1,15 @@
+MacOS Users
+===========
+
+To run the `bilby` examples using the `ptemcee` module, you will need to make \ 
+to run the following commands at the beginning of your notebook
+
+.. code-block:: python
+    
+    import multiprocssing
+    multiprocessing.set_start_method('fork')
+
+There is currently an `issue <https://git.ligo.org/lscsoft/bilby/-/issues/722>`_ open on the `bilby` \
+repository that will address this automatically in the future.\
+For now, you will recieve a warning whenever you use `ptemcee` with more than one `thread`, even if you have set the start method.
+We will remove this warning once `bilby` patches their bug.

joss_paper/paper.md

@@ -83,9 +83,9 @@ where $p(Y_0 \mid x_0, Y, \mathcal{M}_k)$ represents the predictive density of a
 setup, a key challenge is defining $w_k(x)$---the functional
 relationship between the inputs and the weights.
 
-![Schematic of Bayesian model mixing. Each model has region of paramtere space where it has a high
+![Schematic of Bayesian model mixing. Each model has region of parameter space where it has a high
 fidelity, but all models are meant to describe the same phenomenon. To obtain a model that works
-well for all of parameter space, we combine them using Bayesian model mixing methods](bmm_schematic.pdf){#fig:bmm_schematic width="\\textwidth"}
+well for all of parameter space, we combine them using Bayesian model mixing methods.](bmm_schematic.pdf){#fig:bmm_schematic width="\\textwidth"}
 
 This work introduces `Taweret`, a Python package for Bayesian model
 mixing that includes three novel approaches for combining models, each