Closed nilshempelmann closed 4 years ago
nilshempelmann
commented
4 years ago @huard output_sanitize will be centralised in birdhouse-docs\docs\source\ ?
I removed the unittes testing the processes, they are now covered with the notebooks, is a double check necessary?
huard
commented
4 years ago Yes. unit tests can check various options. We could not be doing this for a notebook intended for documentation, which will describe only the most interesting functionality.
tlvu
commented
4 years ago
output_sanitizewill be centralised inbirdhouse-docs\docs\source\?
@nilshempelmann I can not find https://github.com/birdhouse-docs. Until we settle down on the more appropriate location of that file, can you not commit the file locally and curl it from its original location https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/raw/master/notebooks/output-sanitize.cfg? That's the repo with all the Jenkins infrastructure to run notebooks from multiples git repos.
nilshempelmann
commented
4 years ago
output_sanitizewill be centralised inbirdhouse-docs\docs\source\?@nilshempelmann I can not find https://github.com/birdhouse-docs. Until we settle down on the more appropriate location of that file, can you not commit the file locally and curl it from its original location https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/raw/master/notebooks/output-sanitize.cfg? That's the repo with all the Jenkins infrastructure to run notebooks from multiples git repos.
@tlvu Here is the top level birdhouse documentation: https://github.com/bird-house/birdhouse-docs/ and gues the right place for centalisation of output-sanitize.cfg.
nilshempelmann
commented
4 years ago Yes. unit tests can check various options. We could not be doing this for a notebook intended for documentation, which will describe only the most interesting functionality.
OK I see. Will took it back, also increase it with more functionality
nilshempelmann
commented
4 years ago @tlvu Thanks for the review. Still working on the notebooks tests. This needs to add to the output_sanitize.cfg:
assert reference_output == test_output failed:
'Metalink con..._subset.nc.\n' == 'Metalink con..._subset.nc.\n'
Metalink content-type detected.
Downloading to /tmp/tmpRANDOM/slp.2000_bbox_subset.nc.
+ Downloading to /tmp/tmpRANDOM/slp.2001_bbox_subset.nc.test-notebooks seems to fail due to the widgets in the notebooks:
~/anaconda3/envs/flyingpigeon/lib/python3.7/site-packages/birdy/client/notebook.py in monitor(execution, sleep)
47 Number of seconds to wait before each status check.
48 """
---> 49 progress = widgets.IntProgress(
50 value=0,
51 min=0,
AttributeError: 'NoneType' object has no attribute 'IntProgress'
@tlvu Thanks for the review. Still working on the notebooks tests. This needs to add to the output_sanitize.cfg:
assert reference_output == test_output failed: 'Metalink con..._subset.nc.\n' == 'Metalink con..._subset.nc.\n' Metalink content-type detected. Downloading to /tmp/tmpRANDOM/slp.2000_bbox_subset.nc. + Downloading to /tmp/tmpRANDOM/slp.2001_bbox_subset.nc.
@nilshempelmann looks like you need to make refresh-notebooks
tlvu
commented
4 years ago
test-notebooksseems to fail due to the widgets in the notebooks:~/anaconda3/envs/flyingpigeon/lib/python3.7/site-packages/birdy/client/notebook.py in monitor(execution, sleep) 47 Number of seconds to wait before each status check. 48 """ ---> 49 progress = widgets.IntProgress( 50 value=0, 51 min=0, AttributeError: 'NoneType' object has no attribute 'IntProgress'
@nilshempelmann I am not sure about this one. Notebooks requiring user interactive input need to have a default values for when those input are not there since the test is run non-interractively. Could this also be birdy/owslib/FP errors?
tlvu
commented
4 years ago I attempt to run make test-notebooks myself, and looks like it also run all the unit tests together with the notebooks, a bit un-expected.
I also have this error:
__________________________________________________ docs/source/notebooks/plot_indices.ipynb::Cell 6 __________________________________________________
Notebook cell execution failed
Cell 6: Cell execution caused an exception
Input:
# find ensemble files for one indice based on pr files:
tasInd_NER = [ tas_NER+f for f in listdir(tas_NER) if '.nc' in f ]
resource = [f for f in tasInd_NER if tas_indice in f ] # and '_yr_' in f
Traceback:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-7-17fa5defb2a2> in <module>
1 # find ensemble files for one indice based on pr files:
2
----> 3 tasInd_NER = [ tas_NER+f for f in listdir(tas_NER) if '.nc' in f ]
4
5
FileNotFoundError: [Errno 2] No such file or directory: '/home/nils/data/example_data/NER/'Don't forget to remove this hardcoded path on your machine once you're done.
tlvu
commented
4 years ago ________________________________________________ docs/source/notebooks/subset_processes.ipynb::Cell 0 ________________________________________________
Notebook cell execution failed
Cell 0: Cell execution caused an exception
Input:
# Import the WPS client and connect to the server
from birdy import WPSClient
import birdy
from os import environ
# To display Images from an url
from IPython.core.display import HTML
from IPython.display import Image
# Download files stored in a metalink
from metalink import download
import tempfile
# wait until WPS process is finished
import time
Traceback:
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-0b525ccfa987> in <module>
9
10 # Download files stored in a metalink
---> 11 from metalink import download
12 import tempfile
13
ModuleNotFoundError: No module named 'metalink' __________________________________________________ docs/source/notebooks/plot_indices.ipynb::Cell 1 __________________________________________________
Notebook cell execution failed
Cell 1: Cell outputs differ
Input:
# This cell is for server admnistration test purpose
# Ignore this cell and modify the following cell according to your needs
fp_server = environ.get('FYINGPIGEON_WPS_URL')
print(fp_server) # link to the flyingpigoen server
Traceback:
mismatch 'stdout'
assert reference_output == test_output failed:
'http://localhost:8093/wps\n' == 'None\n'
- None
+ http://localhost:8093/wpsShould be environ.get('WPS_URL', 'https://pavics.ouranos.ca/twitcher/ows/proxy/flyingpigeon')
nilshempelmann
commented
4 years ago
test-notebooksseems to fail due to the widgets in the notebooks:~/anaconda3/envs/flyingpigeon/lib/python3.7/site-packages/birdy/client/notebook.py in monitor(execution, sleep) 47 Number of seconds to wait before each status check. 48 """ ---> 49 progress = widgets.IntProgress( 50 value=0, 51 min=0, AttributeError: 'NoneType' object has no attribute 'IntProgress'@nilshempelmann I am not sure about this one. Notebooks requiring user interactive input need to have a default values for when those input are not there since the test is run non-interractively. Could this also be birdy/owslib/FP errors?
@huard @cehbrecht : progress=True for birdy in notebooks seems to fail in the test-notebooks. Any idea to solve the failure?
nilshempelmann
commented
4 years ago ________________________________________________ docs/source/notebooks/subset_processes.ipynb::Cell 0 ________________________________________________ Notebook cell execution failed Cell 0: Cell execution caused an exception Input: # Import the WPS client and connect to the server from birdy import WPSClient import birdy from os import environ # To display Images from an url from IPython.core.display import HTML from IPython.display import Image # Download files stored in a metalink from metalink import download import tempfile # wait until WPS process is finished import time Traceback: --------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) <ipython-input-1-0b525ccfa987> in <module> 9 10 # Download files stored in a metalink ---> 11 from metalink import download 12 import tempfile 13 ModuleNotFoundError: No module named 'metalink'
I installed metalink manually, since the pip installation failed
nilshempelmann
commented
4 years ago __________________________________________________ docs/source/notebooks/plot_indices.ipynb::Cell 1 __________________________________________________ Notebook cell execution failed Cell 1: Cell outputs differ Input: # This cell is for server admnistration test purpose # Ignore this cell and modify the following cell according to your needs fp_server = environ.get('FYINGPIGEON_WPS_URL') print(fp_server) # link to the flyingpigoen server Traceback: mismatch 'stdout' assert reference_output == test_output failed: 'http://localhost:8093/wps\n' == 'None\n' - None + http://localhost:8093/wpsShould be
environ.get('WPS_URL', 'https://pavics.ouranos.ca/twitcher/ows/proxy/flyingpigeon')
@tlvu Why? Should the birds be universal usable or tailord for pavics purposes?
nilshempelmann
commented
4 years ago I attempt to run
make test-notebooksmyself, and looks like it also run all the unit tests together with the notebooks, a bit un-expected.I also have this error:
__________________________________________________ docs/source/notebooks/plot_indices.ipynb::Cell 6 __________________________________________________ Notebook cell execution failed Cell 6: Cell execution caused an exception Input: # find ensemble files for one indice based on pr files: tasInd_NER = [ tas_NER+f for f in listdir(tas_NER) if '.nc' in f ] resource = [f for f in tasInd_NER if tas_indice in f ] # and '_yr_' in f Traceback: --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) <ipython-input-7-17fa5defb2a2> in <module> 1 # find ensemble files for one indice based on pr files: 2 ----> 3 tasInd_NER = [ tas_NER+f for f in listdir(tas_NER) if '.nc' in f ] 4 5 FileNotFoundError: [Errno 2] No such file or directory: '/home/nils/data/example_data/NER/'Don't forget to remove this hardcoded path on your machine once you're done.
@tlvu @cehbrecht So, we need a central place to store testdata.
huard
commented
4 years ago In birdy:
try:
import ipywidgets
except ImportError:
ipywidgets = None
warnings.warn('Jupyter Notebook is not supported. Please install *ipywidgets*.', IPythonWarning)ipywidget is probably not installed.
nilshempelmann
commented
4 years ago ipywidgets
@huard That was the trick !! test-notebooks passing.
nilshempelmann
commented
4 years ago Should be environ.get('WPS_URL', 'https://pavics.ouranos.ca/twitcher/ows/proxy/flyingpigeon')
@tlvu is there a way to avoid the hardcodes?
tlvu
commented
4 years ago Should be environ.get('WPS_URL', 'https://pavics.ouranos.ca/twitcher/ows/proxy/flyingpigeon')
@tlvu is there a way to avoid the hardcodes?
The hardcode is just to provide the default value when the environment var is not set. This is for the case when the notebook is used as tutorial by a real user.
When the notebook is used as a testing tool, that env var is set to the appropriate value or the string pavics.ouranos.ca is replaced with the real server.
So the hardcode so not cause any incompatibility and do not lock the user into only one specific server. Does that answer your concern @nilshempelmann ?
Overview
including make test-notebooks