Fix external C++ doc

Author: WardBrian

cmdstanpy/model.py

@@ -541,7 +541,9 @@ def compile(
                     x for x in lines if x.startswith('Semantic error')
                 ]
                 exceptions = [
-                    x for x in lines if x.startswith('Uncaught exception')
+                    x
+                    for x in lines
+                    if 'Uncaught exception' in x or 'fatal error' in x
                 ]
                 if (
                     len(syntax_errors) > 0

cmdstanpy/stanfit/__init__.py

@@ -217,5 +217,5 @@ def from_csv(
             return None
     except (IOError, OSError, PermissionError) as e:
         raise ValueError(
-            'An error occured processing the CSV files:\n\t{}'.format(str(e))
+            'An error occurred processing the CSV files:\n\t{}'.format(str(e))
         ) from e

docsrc/conf.py

@@ -403,7 +403,7 @@ def emit(self, record):
     "CmdStanMCGQ": "~cmdstanpy.CmdStanMCGQ",
 }
 
-nbsphinx_allow_errors = True
+nbsphinx_allow_errors = False
 
 # Documents to append as an appendix to all manuals.
 # texinfo_appendices = []

docsrc/users-guide/examples/Using External C++.ipynb

@@ -19,7 +19,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {"nbsphinx": "hidden"},
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
    "outputs": [],
    "source": [
     "import os\n",
@@ -50,7 +52,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "raises-exception"
+    ]
+   },
    "outputs": [],
    "source": [
     "model_external.compile()"
@@ -66,7 +72,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "raises-exception"
+    ]
+   },
    "outputs": [],
    "source": [
     "model_external.compile(stanc_options={'allow-undefined':True})"
@@ -135,7 +145,8 @@
    "hash": "8765ce46b013071999fc1966b52035a7309a0da7551e066cc0f0fa23e83d4f60"
   },
   "kernelspec": {
-   "display_name": "Python 3.9.5 64-bit ('stan': conda)",
+   "display_name": "Python 3",
+   "language": "python",
    "name": "python3"
   },
   "language_info": {
@@ -149,9 +160,8 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.9.5"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docsrc/users-guide/examples/Variational Inference.ipynb

@@ -109,7 +109,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "raises-exception"
+    ]
+   },
    "outputs": [],
    "source": [
     "model_fail = CmdStanModel(stan_file='eta_should_fail.stan')\n",
@@ -172,7 +176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.9.5"
   }
  },
  "nbformat": 4,

docsrc/users-guide/examples/bernoulli_external.stan

@@ -0,0 +1,18 @@
+functions {
+  real make_odds(real theta);
+}
+data {
+  int<lower=0> N;
+  array[N] int<lower=0, upper=1> y;
+}
+parameters {
+  real<lower=0, upper=1> theta;
+}
+model {
+  theta ~ beta(1, 1); // uniform prior on interval 0, 1
+  y ~ bernoulli(theta);
+}
+generated quantities {
+  real odds;
+  odds = make_odds(theta);
+}