Add PAVICS homepage notebooks to Jenkins testsuite #29
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To fix this error in Jenkins:
```
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb::Cell 1 _
Notebook cell execution failed
Cell 1: Cell outputs differ
Input:
freq = 'YS'
print(f'calculating yearly output using freq="{freq}"')
with ProgressBar():
out = atmos.tx_days_above(tasmax=ds.tasmax, thresh='27 degC', freq=freq) # Yearly frequency
# Average over spatial domain and plot time-series
fig1 = plt.figure(figsize=(20,4))
plt.subplot(1,2,1)
out.mean(dim=['lon','lat'], keep_attrs=True).plot()
plt.title('spatial mean')
# Calculate a 30 year climatology and plot a map
plt.subplot(1,2,2)
subset.subset_time(out, start_date='1981', end_date='2010').mean(dim='time', keep_attrs=True).plot()
plt.title('1981-2010 mean')
display()
Traceback:
mismatch 'stdout'
assert reference_output == test_output failed:
'calculating ...one | 1.0s\n' == 'calculating ...one | 1.0s\n'
Skipping 94 identical leading characters in diff, use -v to show
- mpleted | 18.0s
+ mpleted | 1min 47.7s
[########################################] | 100% Completed |100% Done | 1.0s
```
This is of type `application/javascript` which should already be ignored by default (https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/3806e67e7ad46c915797f483a373780c36f8a8f6/conftest.py#L3) Not sure why have to force ignore here but don't have time to investigate.
For error:
```
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 1 _
Notebook cell execution failed
Cell 1: Cell outputs differ
Input:
import xarray as xr
# This does not download the entire dataset, just the metadata and attributes describing the content.
ds = xr.open_dataset(cds.access_urls["OPENDAP"], chunks='auto')
# What we see here is an in-memory representation of the full content, the actual data is still on the server.
ds
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data...id: NCC' == '<xarray.Data...id: NCC'
Skipping 357 identical leading characters in diff, use -v to show
Skipping 792 identical trailing characters in diff, use -v to show
- hunksize=(7693, 40, 109), meta=np.ndarray>
? ^^^ ^ ^^^
+ hunksize=(323, 320, 323), meta=np.ndarray>
? ^^ ^^ ^^^
- tasmax (time, lat, lon) float32 dask.array<chunksize=(7693, 40, 109), meta=np.ndarray>
? ^^^ ^ ^^^
+ tasmax (time, lat, lon) float32 dask.array<chunksize=(323, 320, 323), meta=np.ndarray>
? ^^ ^^ ^^^
- pr (time, lat, lon) float32 dask.array<chunksize=(7693, 40, 109), meta=n
? ^^^ ^ ^^^
+ pr (time, lat, lon) float32 dask.array<chunksize=(323, 320, 323), meta=n
? ^^ ^^ ^^^
```
For error:
```
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb::Cell 3 _
Notebook cell execution failed
Cell 3: Cell outputs differ
Input:
with xclim.set_options(metadata_locales=['fr']):
out_fr = atmos.tx_days_above(tasmax=ds.tasmax,
thresh = '27 degC',
freq='YS')
out_fr
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data...ent_fr: ' == '<xarray.Data...ent_fr: '
Skipping 537 identical leading characters in diff, use -v to show
Skipping 370 identical trailing characters in diff, use -v to show
- ys_above: TX_DAYS_ABOVE(tasma...
+ ys_above: tx_days_above(tasma...
```
For errors:
```
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-4Ensembles.ipynb::Cell 0 _
Notebook cell execution failed
Cell 0: Cell outputs differ
Input:
from xclim import ensembles as xens
from clisops.core import subset
from pathlib import Path
import matplotlib.pyplot as plt
import warnings
import logging
logging.getLogger().disabled = True
warnings.simplefilter("ignore")
output = '/notebook_dir/writable-workspace/tmp/tutorial3/output'
infolder = Path(output)
# Create a list of rcp 4.5 files (n=11)
ncfiles = [d for d in infolder.glob('tx_days_above*QS-DEC*rcp45*.nc')]
#Create an ensemble dataset from the 11 simulations
ds_ens = xens.create_ensemble(ncfiles)
display(ds_ens)
# Plot time series of single grid point
lon = -66
lat = 48.5
ds1 = subset.subset_gridpoint(ds_ens, lon=lon, lat=lat)
# plot summer season
ds1.tx_days_above.sel(time=ds1['time.season']=='JJA').plot.line(figsize=(10,5), x='time' ,linewidth=0.5)
#plt.title('RCP 4.5 individuals runs : ')
display()
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data... EPSG:4326' == '<xarray.Data... EPSG:4326'
Skipping 678 identical leading characters in diff, use -v to show
- DATE_TIME_TZ CMOR rewrote data to com...
+ MOHC pp to CMOR/NetCDF convertor (version 1.1...
institution: Ouranos Consortium on Regional Climatology an...
- source: NorESM1-M 2011 atmosphere: CAM-Oslo (CAM4-Os...
+ source: HadGEM2-CC (2011) atmosphere: HadGAM2(N96L60)...
- driving_model: NorESM1-M
? ^^^ - ^ ^
+ driving_model: HadGEM2-CC
? ^^^^ ^ ^^
... ...
modeling_realm: atmos
target_dataset: CANADA : ANUSPLIN interpolated Canada daily 3...
target_dataset_references: CANADA : https://doi.org/10.1175/2011BAMS3132...
- driving_institution: Norwegian Climate Centre
? ^^^^ ^ ^^^ ----
+ driving_institution: Met Office Hadley Centre
? ^ ^^^^^ ++++ ^ +
- driving_institute_id: NCC
? ^^
+ driving_institute_id: MOHC
? ^^^
crs: EPSG:4326
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-4Ensembles.ipynb::Cell 1 _
Notebook cell execution failed
Cell 1: Cell outputs differ
Input:
# Calculate percentiles
ds_perc = xens.ensemble_percentiles(ds_ens, values=[10, 50, 90], split=False)
display(ds_perc)
# compare with indiviudual runs
sel1 = ds1.tx_days_above.sel(time=ds1['time.season']=='JJA')
sel1.plot.line(label='individual runs',color=[0.6, .6 , .6],figsize=(10,5),x='time' ,linewidth=0.5)
perc1 = subset.subset_gridpoint(ds_perc,
lon=lon, lat=lat).tx_days_above.sel(time=ds_perc['time.season']=='JJA')
# plot uncertainty bounds
plt.fill_between(color='b',label="RCP 4.5 : 10th - 90th percentile",
x=perc1.time.values, y1=perc1.sel(percentiles=10),
y2=perc1.sel(percentiles=90), alpha=0.2)
# plot median
perc1.sel(percentiles=50).plot(label="RCP 4.5 : 50th percentile",
color='b', linewidth=.85, )
# combine legend entries for individual runs
handles, labels = plt.gca().get_legend_handles_labels()
by_label = dict(zip(labels, handles))
plt.legend(by_label.values(), by_label.keys())
plt.title('Summer tx_days_above : RCP 4.5 ensembles percentiles vs individual runs')
display()
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data...ersion 1.1...' == '<xarray.Data... EPSG:4326'
Skipping 507 identical leading characters in diff, use -v to show
- utes: (12/33)
? ^^
+ utes: (12/28)
? ^^
- units: days
- cell_methods: time: maximum within days time: sum over days
- xclim_history: DATE_TIME_TZ CMOR rewrote data to com...
- standard_name: number_of_days_with_air_temperature_above_thr...
- long_name: Number of days with tmax > 27 degc
- description: Seasonal number of days where daily maximum t...
+ Conventions: CF-1.5
+ title: Ouranos standard ensemble of bias-adjusted cl...
+ history: MOHC pp to CMOR/NetCDF convertor (version 1.1...
+ institution: Ouranos Consortium on Regional Climatology an...
+ source: HadGEM2-CC (2011) atmosphere: HadGAM2(N96L60)...
+ driving_model: HadGEM2-CC
... ...
- modeling_realm: atmos
target_dataset: CANADA : ANUSPLIN interpolated Canada daily 3...
target_dataset_references: CANADA : https://doi.org/10.1175/2011BAMS3132...
- driving_institution: Norwegian Climate Centre
? ^^^^ ^ ^^^ ----
+ driving_institution: Met Office Hadley Centre
? ^ ^^^^^ ++++ ^ +
- driving_institute_id: NCC
? ^^
+ driving_institute_id: MOHC
? ^^^
- crs: EPSG:4326
+ crs: EPSG:4326
? +
+ xclim_history: MOHC pp to CMOR/NetCDF convertor (version 1.1...
```
For errors:
```
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-5Visualization.ipynb::Cell 1 _
Notebook cell execution failed
Cell 1: Cell outputs differ
Input:
# 30 year means and delta calculations
window = 30
d30yAvg = ds_ens.rolling(year=window).mean()
d30yAvg = d30yAvg.isel(year=slice(window-1,None)) # Select from the first full windowed mean
# Select every horizons in 10 y intervals
d30yAvg = d30yAvg.sel(year=(d30yAvg.year.values%10==0))
horizons = xr.DataArray([f'{yr - 29}-{yr}' for yr in d30yAvg.year.values], dims=dict(year=d30yAvg.year))
d30yAvg = d30yAvg.assign_coords(horizon=horizons)
# Calculate deltas
ref = d30yAvg.sel(year=(d30yAvg.horizon=='1981-2010')).squeeze()
for v in d30yAvg.data_vars:
with xr.set_options(keep_attrs=True):
d30yAvg[f"{v}_delta"]= d30yAvg[v] - ref[v]
for a in ['description', 'long_name']:
d30yAvg[f"{v}_delta"].attrs[a] = f"{d30yAvg[f'{v}_delta'].attrs[a]} : delta vs 1981-2010"
# Calculate percentiles on 30y normals
d30yAvg_ens = xens.ensemble_percentiles(d30yAvg, split=False).load()
display(d30yAvg_ens)
map1 = d30yAvg_ens.tx_mean.hvplot.quadmesh(cmap='Spectral_r', geo=True,tiles='EsriImagery', framewise=False, frame_width=400)
map1
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data...entiles on...' == '<xarray.Data... EPSG:4326'
Skipping 956 identical leading characters in diff, use -v to show
+ ttributes:
+ xclim_history: [DATE_TIME] : Computation of the percentiles on...
- ttributes: (12/35)
- long_name: Mean daily maximum temperature
- standard_name: air_temperature
- units: ��C
- _ChunkSizes: [256 16 16]
- grid_mapping: crs
- cell_methods: time: maximum within days time: mean over days
- ... ...
- modeling_realm: atmos
- target_dataset: CANADA : ANUSPLIN interpolated Canada daily 3...
- target_dataset_references: CANADA : https://doi.org/10.1175/2011BAMS3132...
- driving_institution: Norwegian Climate Centre
- driving_institute_id: NCC
- crs: EPSG:4326
_ PAVICS-landing-add-pavics-homepage-notebooks-to-jenkins-testsuite/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-5Visualization.ipynb::Cell 5 _
Notebook cell execution failed
Cell 5: Cell outputs differ
Input:
rolling = pn.widgets.FloatInput(value=30, step=10, start=10, end=30, width=50)
rolling1 = pn.Column(pn.pane.Markdown('Smoothing'),rolling)
## Time-series plot
@pn.depends(vars.param.value, regions.param.value, seasons.param.value, rolling.param.value)
def plot_region_ts(v=vars.param.value, reg=regions.param.value, s=seasons.param.value,
wind=rolling.param.value):
colors = dict(rcp45="#0000FF",rcp85="#FF0000")
plt1 = None
wind = max(wind,1)
for r in reg_ts.rcp.values:
if plt1 is None:
plt1 = reg_ts.rolling(year=wind, center=True, min_periods=1).mean(dim='year')\
.sel(geom=reg, season=s, rcp=r).hvplot.area(title=f"{reg} {s}", width=800,
height=300, x='year', y= f"{v}_p10", y2= f"{v}_p90",
color=colors[r], alpha=0.3, line_alpha=.1,
label=f"RCP {r[-2:].replace('5','.5')}")
plt1 = plt1 * reg_ts.rolling(year=wind, center=True, min_periods=1).mean(dim='year')\
.sel(geom=reg, season=s, rcp=r).hvplot.line(x='year', y= f"{v}_p50", color=colors[r],
alpha=0.7, label=f"RCP {r[-2:].replace('5','.5')}")
else:
plt1 = plt1 * reg_ts.rolling(year=wind, center=True, min_periods=1).mean(dim='year')\
.sel(geom=reg, season=s, rcp=r).hvplot.area(x='year', y=v + '_p10', y2= v + '_p90',
color=colors[r], alpha=0.3, line_alpha=.1, label=f"RCP {r[-2:].replace('5','.5')}")
plt1 = plt1 * reg_ts.rolling(year=wind, center=True, min_periods=1).mean(dim='year')\
.sel(geom=reg, season=s, rcp=r).hvplot.line(x='year', y= f"{v}_p50", color=colors[r],
alpha=0.7, label=f"RCP {r[-2:].replace('5','.5')}")
for vv in ['_p10','_p90']:
plt1 = plt1 * reg_ts.rolling(year=wind, center=True, min_periods=1).mean(dim='year')\
.sel(geom=reg, season=s, rcp=r).hvplot.line(x='year', y= f"{v}{vv}", color=colors[r],
line_width=0.1, alpha=0.3, label=f"RCP {r[-2:].replace('5','.5')}")
title = pn.pane.Markdown(f"### {s} {reg_ts[f'{v}_p50'].attrs['long_name'].lower()} \
({reg_ts[f'{v}_p50'].attrs['units'].lower()})<br/><br/>")
return pn.Column(pn.Row(plt1.opts(legend_position='top_left'), rolling1))
## Table summary
@pn.depends(vars.param.value, regions.param.value, hors.param.value, delta.param.value)
def create_table(v = vars.param.value, r=regions.param.value, h=hors.param.value, delta_flag=delta.param.value):
title1 = f"Summary : {r} {h}"
var_cols = var_cols = [vv for vv in df.columns if v in vv]
if delta_flag:
var_cols = [vv for vv in var_cols if 'delta' in vv]
title1 = f"{title1} (delta vs 1981-2010)"
else:
var_cols = [vv for vv in var_cols if 'delta' not in vv]
out = df[var_cols].iloc[(df.index.get_level_values('horizon') == h)&(df.index.get_level_values('region') == r)]
return(out.sort_values(['season']).round(decimals=1).hvplot.table(title=title1, width=800, dynamic=True))
pn.Column(pn.pane.Markdown('# A simple PAVICS dashboard'), map1, regions1, plot_region_ts, create_table)
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'Column\n ...ion(function)' == 'Column\n ...ion(function)'
Skipping 806 identical leading characters in diff, use -v to show
- 41-2070', width=200)
+ 41-2070', value_throttled='2041-2070', width=200)
[5] Column
[0] Markdown(str)
[1] Checkbox()
[2] Column
[0] Markdown(str)
[1] Select(options=['Avignon', 'Bonaventure',...], value='Avignon')
[3] ParamFunction(function)
[4] ParamFunction(function)
```
They use too much .ncml which means too much .nc files to replicate to test servers.
…utside of Ouranos Since we use data from prod, test servers outside of Ouranos do not have acess to port 8083 so will fail. All prod Thredds access much go through port 443.
tlogan2000
approved these changes
Jul 6, 2021
tlvu
added a commit
to Ouranosinc/PAVICS-e2e-workflow-tests
that referenced
this pull request
Jul 6, 2021
…to-jenkins-testsuite Add PAVICS homepage notebooks to Jenkins testsuite and new Jupyter env build # Overview - Add PAVICS homepage notebooks to Jenkins testsuite and those notebooks enabled by default. - Also released new Jupyter build for the homepage notebook. Only `unzip` is newly added to the Jupyter env. No other update. Matching required notebook changes PR Ouranosinc/PAVICS-landing#29 Matching PAVICS PR deployment change to test this PR bird-house/birdhouse-deploy#180 Matching PR to update pavics-landing deployment config bird-house/birdhouse-deploy-ouranos#12 ## Other Changes - Add new ability to force link to stay on `pavics.ouranos.ca` in notebooks. Pavics homepage notebooks use a lot of .ncml so it was too much of .nc files to replicated to all the test servers. ## Related Issue / Discussion - Homepage notebooks are also deployed on Binder under `tutorial-notebooks`. They are already previously deployed to Jupyter env outside of `tutorial-notebooks` so it is kept as-is - There is a stable interface between the homepage notebooks and Jenkins for setup the layout the notebooks requires. The stable interface means future layout changes will be transparent to Jenkins. ## Additional Information - Test passing against prod Pavics: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/add-pavics-homepage-notebooks-to-jenkins-testsuite/13/console - Test passing against my dev server: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/add-pavics-homepage-notebooks-to-jenkins-testsuite/14/console - Test passing against CRIM server to test remote server and ensure the IAC pipeline will also work: https://daccs-jenkins.crim.ca/job/PAVICS-e2e-workflow-tests/job/add-pavics-homepage-notebooks-to-jenkins-testsuite/3/console (one failure unrelated).
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Various changes so the notebooks pass Jenkins:
.ncml(and.nc) files to replicate to all the test serversSee each commit description for more detailed info.
Not regenerating all the .html files since the code change is really minimal (adding comments and one line switch the Thredds url from direct url to behind twitcher).
Matching PR that actually add the homepage notebooks to Jenkins: Ouranosinc/PAVICS-e2e-workflow-tests#79