more cleanup

Author: mitzimorris

cmdstanpy/model.py

@@ -1303,14 +1303,13 @@ def _run_cmdstan(
             )
             while proc.poll() is None:
                 if proc.stdout is not None:
-                    lines = proc.stdout.readlines()
-                    for line in lines:
-                        fd_out.write(line)
-                        line = line.strip()
-                        if show_console and len(line) > 1:
-                            print('chain {}: {}'.format(idx + 1, line))
-                        if show_progress and progress_hook is not None:
-                            progress_hook(line)
+                    line = proc.stdout.readline()
+                    fd_out.write(line)
+                    line = line.strip()
+                    if show_console and len(line) > 1:
+                        print('chain {}: {}'.format(idx + 1, line))
+                    if show_progress and progress_hook is not None:
+                        progress_hook(line)
             if show_progress and progress_hook is not None:
                 progress_hook("Done")
 

cmdstanpy/utils.py

@@ -961,12 +961,11 @@ def do_command(
         )
         while proc.poll() is None:
             if proc.stdout is not None:
-                lines = proc.stdout.readlines()
-                for line in lines:
-                    if fd_out is not None:
-                        fd_out.write(line)
-                    if pbar is not None:
-                        pbar(line.strip())
+                line = proc.stdout.readline()
+                if fd_out is not None:
+                    fd_out.write(line)
+                if pbar is not None:
+                    pbar(line.strip())
 
         stdout, _ = proc.communicate()
         if stdout:

cmdstanpy_tutorial.ipynb

@@ -308,15 +308,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "import pandas as pd\n",
-    "\n",
     "vars = fit.stan_variables()\n",
     "for (k,v) in vars.items():\n",
-    "    print(k, v.shape)\n",
-    "\n",
-    "thetas = fit.stan_variable(var='theta')\n",
-    "pd.DataFrame(data=thetas).plot.density()"
+    "    print(k, v.shape)"
    ]
   },
   {