Merge branch 'develop' of https://github.com/stan-dev/cmdstanpy into develop

Author: mitzimorris

.github/workflows/main.yml

@@ -53,7 +53,7 @@ jobs:
 
       - name: Install dependencies (python)
         run: |
-          pip install --upgrade pip wheel
+          python -m pip install --upgrade pip wheel
           pip install -r requirements.txt
           pip install -r requirements-test.txt
           pip install codecov

.github/workflows/release.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Install dependencies (python)
         run: |
-          pip install --upgrade pip wheel twine codecov sphinx nbsphinx ipython ipykernel pydata-sphinx-theme requests sphinx-copybutton matplotlib
+          python -m pip install --upgrade pip wheel twine codecov sphinx nbsphinx ipython ipykernel pydata-sphinx-theme requests sphinx-copybutton matplotlib
           pip install -r requirements.txt
           pip install -e .
 

cmdstanpy/model.py

@@ -1175,10 +1175,13 @@ def sample(
                     " force_one_process_per_chain to True"
                 )
 
-            if not runset._check_retcodes():
-                msg = 'Error during sampling:\n{}'.format(runset.get_err_msgs())
-                msg = '{}Command and output files:\n{}'.format(
-                    msg, runset.__repr__()
+            errors = runset.get_err_msgs()
+            if errors or not runset._check_retcodes():
+                msg = (
+                    f'Error during sampling:\n{errors}\n'
+                    + f'Command and output files:\n{repr(runset)}\n'
+                    + 'Consider re-running with show_console=True if the above'
+                    + ' output is unclear!'
                 )
                 raise RuntimeError(msg)
 
@@ -1317,12 +1320,13 @@ def generate_quantities(
                         show_console=show_console,
                     )
 
-            if not runset._check_retcodes():
-                msg = 'Error during generate_quantities:\n{}'.format(
-                    runset.get_err_msgs()
-                )
-                msg = '{}Command and output files:\n{}'.format(
-                    msg, runset.__repr__()
+            errors = runset.get_err_msgs()
+            if errors:
+                msg = (
+                    f'Error during generate_quantities:\n{errors}\n'
+                    + f'Command and output files:\n{repr(runset)}\n'
+                    + 'Consider re-running with show_console=True if the above'
+                    + ' output is unclear!'
                 )
                 raise RuntimeError(msg)
             quantities = CmdStanGQ(runset=runset, mcmc_sample=mcmc_fit)

docsrc/community.rst

@@ -0,0 +1,27 @@
+Community
+=========
+
+This page highlights community projects that involve CmdStanPy. Check them out!
+
+Project templates
+-----------------
+
+Templates are a great way to piggy back on other users' work, saving you time
+when you start a new project.
+
+- `cookiecutter-cmdstanpy-analysis
+  <https://github.com/teddygroves/cookiecutter-cmdstanpy-analysis>`_ A
+  cookiecutter template for cmdstanpy-based statistical analysis projects.
+
+Software
+--------
+
+- `Prophet <https://github.com/facebook/prophet>`_ A procedure for forecasting
+  time series data based on an additive model where non-linear trends are fit
+  with yearly, weekly, and daily seasonality, plus holiday effects.
+
+- `ArviZ <https://github.com/arviz-devs/arviz>`_ A Python package (with a `Julia
+  interface <https://julia.arviz.org/stable/>`_) for exploratory analysis of
+  Bayesian models. Includes functions for posterior analysis, data storage,
+  model checking, comparison and diagnostics.
+

docsrc/index.rst

@@ -29,6 +29,7 @@ set of model, data, and posterior estimates.
    hello_world
    workflow
    examples
+   community
    api
 
 :ref:`genindex`