Code works line-by-line in Spyder, but not when the whole script is run
I've installed pystan and am trying to verify that the installation has worked correctly.
When I go to the IPython console in Spyder and run the following code line by line, it generates the correct answer.
import pystan
model_code = 'parameters real y; model y ~ normal(0,1);'
model = pystan.StanModel(model_code=model_code)
y = model.sampling().extract()['y']
y.mean()
The line calling pystan.StanModel takes about 30 seconds, while the other lines execute instantaneously. In the end I get the right result (about 0, e.g. 0.01 or -0.01).
However, when I run the code as a single script in Spyder, it doesn't work, and instead the console just runs forever, doesn't produce a result, and I have to manually shut down Anaconda. Why is that?
python anaconda spyder stan pystan
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
add a comment |
I've installed pystan and am trying to verify that the installation has worked correctly.
When I go to the IPython console in Spyder and run the following code line by line, it generates the correct answer.
import pystan
model_code = 'parameters real y; model y ~ normal(0,1);'
model = pystan.StanModel(model_code=model_code)
y = model.sampling().extract()['y']
y.mean()
The line calling pystan.StanModel takes about 30 seconds, while the other lines execute instantaneously. In the end I get the right result (about 0, e.g. 0.01 or -0.01).
However, when I run the code as a single script in Spyder, it doesn't work, and instead the console just runs forever, doesn't produce a result, and I have to manually shut down Anaconda. Why is that?
python anaconda spyder stan pystan
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
(Spyder maintainer here) You probably need to addpystantoTools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.
– Carlos Cordoba
Nov 12 '18 at 23:17
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13
add a comment |
I've installed pystan and am trying to verify that the installation has worked correctly.
When I go to the IPython console in Spyder and run the following code line by line, it generates the correct answer.
import pystan
model_code = 'parameters real y; model y ~ normal(0,1);'
model = pystan.StanModel(model_code=model_code)
y = model.sampling().extract()['y']
y.mean()
The line calling pystan.StanModel takes about 30 seconds, while the other lines execute instantaneously. In the end I get the right result (about 0, e.g. 0.01 or -0.01).
However, when I run the code as a single script in Spyder, it doesn't work, and instead the console just runs forever, doesn't produce a result, and I have to manually shut down Anaconda. Why is that?
python anaconda spyder stan pystan
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
I've installed pystan and am trying to verify that the installation has worked correctly.
When I go to the IPython console in Spyder and run the following code line by line, it generates the correct answer.
import pystan
model_code = 'parameters real y; model y ~ normal(0,1);'
model = pystan.StanModel(model_code=model_code)
y = model.sampling().extract()['y']
y.mean()
The line calling pystan.StanModel takes about 30 seconds, while the other lines execute instantaneously. In the end I get the right result (about 0, e.g. 0.01 or -0.01).
However, when I run the code as a single script in Spyder, it doesn't work, and instead the console just runs forever, doesn't produce a result, and I have to manually shut down Anaconda. Why is that?
python anaconda spyder stan pystan
python anaconda spyder stan pystan
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
edited Nov 18 '18 at 22:40
user1205197
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
asked Nov 12 '18 at 5:10
user1205197user1205197
425820
425820
(Spyder maintainer here) You probably need to addpystantoTools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.
– Carlos Cordoba
Nov 12 '18 at 23:17
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13
add a comment |
(Spyder maintainer here) You probably need to addpystantoTools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.
– Carlos Cordoba
Nov 12 '18 at 23:17
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13
(Spyder maintainer here) You probably need to add
pystan to Tools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.– Carlos Cordoba
Nov 12 '18 at 23:17
(Spyder maintainer here) You probably need to add
pystan to Tools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.– Carlos Cordoba
Nov 12 '18 at 23:17
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13
add a comment |
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(Spyder maintainer here) You probably need to add
pystantoTools > Preferences > Python Interpreter > User Module Reloader > Set UMR excluded (not reloaded) modules. Please let me know if that works so we can exclude it by default.– Carlos Cordoba
Nov 12 '18 at 23:17
Unfortunately that didn't work. I added pystan, then restarted Anaconda and Spyder and checked that it was still added to UMR excluded. As before, the code works if executed line by line but when I run all the code as a single script nothing happens (aside from a lot of CPU noise) and I need to restart the kernel.
– user1205197
Nov 13 '18 at 12:13