refresh nbs, fix subset-user-input.ipynb #321
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```
_ pavics-sdi-fix_nbs_jupyter_alpha/docs/source/notebooks/climex.ipynb::Cell 5 __
Notebook cell execution failed
Cell 5: Cell outputs differ
Input:
ds = xr.open_dataset(
url, chunks=dict(realization=1, time=365, rlat=50 * 3, rlon=50 * 3)
)
xclim.set_options(check_missing="pct", missing_options={"pct": {"tolerance": 0.05}})
sdii = xclim.atmos.daily_pr_intensity(pr=ds.pr.sel(time="2000"))
sdii
Traceback:
Unexpected output fields from running code: {'stderr'}
_ pavics-sdi-fix_nbs_jupyter_alpha/docs/source/notebooks/climex.ipynb::Cell 8 __
Notebook cell execution failed
Cell 8: Cell outputs differ
Input:
# Subset over the Montreal gridpoint
ds = xr.open_dataset(url, chunks=dict(realization=1, time=365 * 50, rlon=25, rlat=25))
pt = subset_gridpoint(ds, lon=-73.69, lat=45.50)
print("Input dataset for Montreal :")
display(pt)
out = xclim.atmos.max_1day_precipitation_amount(pr=pt.pr, freq="YS")
print("Maximim 1-day precipitation `lazy` output ..")
out
Traceback:
Unexpected output fields from running code: {'stderr'}
```
for more information, see https://pre-commit.ci
Work-around for computationalmodelling/nbval#204 Have to use NBVAL_IGNORE_OUTPUT because the sanitize file seems to not be working in this case, see the issue above. ``` _ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 4 _ Notebook cell execution failed Cell 4: Cell outputs differ Input: ds_tgt.cf.plot.scatter(x="longitude", y="latitude", s=0.1) plt.title("Target regular grid"); Traceback: dissimilar number of outputs for key "text/plain"<<<<<<<<<<<< Reference outputs from ipynb file: <Figure size LENGTHxWIDTH with N Axes> ============ disagrees with newly computed (test) output: Text(0.5, 1.0, 'Target regular grid') <Figure size LENGTHxWIDTH with N Axes> >>>>>>>>>>>> _ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 6 _ Notebook cell execution failed Cell 6: Cell outputs differ Input: reg_bil = xe.Regridder(ds_in, ds_tgt, "bilinear") reg_bil # Show information about the regridding Traceback: Missing output fields from running code: {'stderr'} _ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 7 _ Notebook cell execution failed Cell 7: Cell outputs differ Input: # xesmf/frontend.py:476: FutureWarning: ``output_sizes`` should be given in the ``dask_gufunc_kwargs`` parameter. It will be removed as direct parameter in a future version. warnings.filterwarnings("ignore", category=FutureWarning) # Apply the regridding weights to the input sea ice concentration data sic_bil = reg_bil(ds_in.siconc) # Plot the results sic_bil.isel(time=0).plot(cmap=cmap) plt.title("Regridded sic data (Jan 2020)"); Traceback: dissimilar number of outputs for key "text/plain"<<<<<<<<<<<< Reference outputs from ipynb file: <Figure size LENGTHxWIDTH with N Axes> ============ disagrees with newly computed (test) output: Text(0.5, 1.0, 'Regridded sic data (Jan 2020)') <Figure size LENGTHxWIDTH with N Axes> >>>>>>>>>>>> _ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 20 _ Notebook cell execution failed Cell 20: Cell outputs differ Input: reg_mask_cons = xe.Regridder(ds_in_mask, ds_tgt_mask, "conservative") tasmin_mask_cons = reg_mask_cons(ds_in_mask.tasmin) fig, ax = plt.subplots(figsize=(6, 4)) tasmin_mask_cons.plot(cmap=cmap, ax=ax) ax.set_xlim(210, 320) ax.set_ylim(38, 86) ax.set_title("Conservative regridding without normalization - zoom on Canada") ax.annotate( "Some values are close to 0 Kelvins.\nCanada can get cold, but not that cold!", (280, 40), xytext=(1.3, 0.3), xycoords="data", textcoords="axes fraction", fontsize="x-large", arrowprops=dict(arrowstyle="->", connectionstyle="arc3, rad=-0.3"), ); Traceback: dissimilar number of outputs for key "text/plain"<<<<<<<<<<<< Reference outputs from ipynb file: <Figure size LENGTHxWIDTH with N Axes> ============ disagrees with newly computed (test) output: Text(1.3, 0.3, 'Some values are close to 0 Kelvins.\nCanada can get cold, but not that cold!') <Figure size LENGTHxWIDTH with N Axes> >>>>>>>>>>>> _ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 27 _ Notebook cell execution failed Cell 27: Cell outputs differ Input: # Now we can plot easily the results as a choropleth map! ax = shapes_data.plot( "tasmin", legend=True, legend_kwds={"label": "Minimal temperature 1993-05-20 [K]"} ) ax.set_ylabel("Latitude") ax.set_xlabel("Longitude"); Traceback: dissimilar number of outputs for key "text/plain"<<<<<<<<<<<< Reference outputs from ipynb file: <Figure size LENGTHxWIDTH with N Axes> ============ disagrees with newly computed (test) output: Text(0.5, 91.20243008191655, 'Longitude') <Figure size LENGTHxWIDTH with N Axes> >>>>>>>>>>>> ```
```
_ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/regridding.ipynb::Cell 6 _
Notebook cell execution failed
Cell 6: Cell outputs differ
Input:
reg_bil = xe.Regridder(ds_in, ds_tgt, "bilinear")
reg_bil # Show information about the regridding
Traceback:
Missing output fields from running code: {'stderr'}
```
for more information, see https://pre-commit.ci
Attempt to fix the following error:
```
_ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/climex.ipynb::Cell 5 _
Notebook cell execution failed
Cell 5: Cell outputs differ
Input:
ds = xr.open_dataset(
url, chunks=dict(realization=1, time=365, rlat=50 * 3, rlon=50 * 3)
)
xclim.set_options(check_missing="pct", missing_options={"pct": {"tolerance": 0.05}})
sdii = xclim.atmos.daily_pr_intensity(pr=ds.pr.sel(time="2000"))
sdii
Traceback:
Missing output fields from running code: {'stderr'}
_ pavics-sdi-fix_nbs_jupyter_alpha_refresh_output/docs/source/notebooks/climex.ipynb::Cell 8 _
Notebook cell execution failed
Cell 8: Cell outputs differ
Input:
# Subset over the Montreal gridpoint
ds = xr.open_dataset(url, chunks=dict(realization=1, time=365 * 50, rlon=25, rlat=25))
pt = subset_gridpoint(ds, lon=-73.69, lat=45.50)
print("Input dataset for Montreal :")
display(pt)
out = xclim.atmos.max_1day_precipitation_amount(pr=pt.pr, freq="YS")
print("Maximim 1-day precipitation `lazy` output ..")
out
Traceback:
Missing output fields from running code: {'stderr'}
```
for more information, see https://pre-commit.ci
tlvu
added a commit
to Ouranosinc/PAVICS-e2e-workflow-tests
that referenced
this pull request
May 9, 2024
…t xclim and ravenpy to smooth transition (#121) # Overview This new full build has latest of almost everything except `xclim` and `ravenpy` as intermediate step to smooth transition to `pandas` 2.2 freq strings changes. ## Changes - New: save conda env export, DockerHub build logs and Jenkins test result in the repo to track changes much more easily between releases - Jenkins: add `SAVE_RESULTING_NOTEBOOK_TIMEOUT` for slow notebooks or slow machine - Jupyter env changes: - add `conda-pack` so we can export the conda env outside of the docker image if need to run locally without docker - upgrade from Python 3.9 to 3.11 - Relevant changes (alphabetical order): ```diff - - birdy=0.8.4=pyh1a96a4e_0 + - birdhouse-birdy==0.8.7 # major upgrade from v2 to v3 - - bokeh=2.4.3=pyhd8ed1ab_3 + - bokeh=3.4.1=pyhd8ed1ab_0 - - cartopy=0.21.1=py39h6e7ad6e_0 + - cartopy=0.23.0=py311h320fe9a_0 - - cf_xarray=0.8.0=pyhd8ed1ab_0 + - cf_xarray=0.9.0=pyhd8ed1ab_0 - - cfgrib=0.9.10.4=pyhd8ed1ab_0 + - cfgrib=0.9.11.0=pyhd8ed1ab_0 - - cftime=1.6.2=py39h2ae25f5_1 + - cftime=1.6.3=py311h1f0f07a_0 - - climpred=2.3.0=pyhd8ed1ab_0 + - climpred=2.4.0=pyhd8ed1ab_0 - - clisops=0.9.6=pyh1a96a4e_0 + - clisops=0.13.0=pyhca7485f_0 - - dask=2023.5.1=pyhd8ed1ab_0 + - dask=2024.5.0=pyhd8ed1ab_0 - - geopandas=0.13.0=pyhd8ed1ab_0 + - geopandas=0.14.4=pyhd8ed1ab_0 - - hvplot=0.8.3=pyhd8ed1ab_0 + - hvplot=0.9.2=pyhd8ed1ab_0 - - numpy=1.23.5=py39h3d75532_0 + - numpy=1.24.4=py311h64a7726_0 - - numba=0.57.0=py39hb75a051_1 + - numba=0.59.1=py311h96b013e_0 # major upgrade from v1 to v2 - - pandas=1.3.5=py39hde0f152_0 + - pandas=2.1.4=py311h320fe9a_0 # major upgrade to v1 - - panel=0.14.4=pyhd8ed1ab_0 + - panel=1.4.2=pyhd8ed1ab_0 # major upgrade from v1 to v2 - - pydantic=1.10.8=py39hd1e30aa_0 + - pydantic=2.7.1=pyhd8ed1ab_0 # Python 3.9 to 3.11 - - python=3.9.16=h2782a2a_0_cpython + - python=3.11.6=hab00c5b_0_cpython - - raven-hydro=0.2.1=py39h8e2dbb5_1 + - raven-hydro=0.2.4=py311h64a4d7b_0 - - ravenpy=0.12.1=py39hf3d152e_0 + - ravenpy==0.13.1 - - rioxarray=0.14.1=pyhd8ed1ab_0 + - rioxarray=0.15.5=pyhd8ed1ab_0 - - roocs-utils=0.6.4=pyh1a96a4e_0 + - roocs-utils=0.6.8=pyhd8ed1ab_0 - - scipy=1.9.1=py39h8ba3f38_0 + - scipy=1.13.0=py311h517d4fd_1 - - xarray=2023.1.0=pyhd8ed1ab_0 + - xarray=2023.8.0=pyhd8ed1ab_0 - - xclim=0.43.0=py39hf3d152e_1 + - xclim=0.47.0=py311h38be061_0 - - xesmf=0.7.1=pyhd8ed1ab_0 + - xesmf=0.8.5=pyhd8ed1ab_0 - - xskillscore=0.0.24=pyhd8ed1ab_0 + - xskillscore=0.0.26=pyhd8ed1ab_0 + - xscen=0.8.2=pyhd8ed1ab_0 + - figanos==0.3.0 - - xncml==0.2 + - xncml==0.4.0 ``` ## Test - Deployed as "beta" image in production for bokeh visualization performance regression testing. - Manual test notebook https://github.com/Ouranosinc/PAVICS-landing/blob/master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-5Visualization.ipynb for bokeh visualization performance and it looks fine. - Jenkins build: - Default notebooks, all passed: https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/54792e6510adfcd1bb21e1bd31fdfa36c5c634e0/docker/saved_buildout/jenkins-buildlogs-default.txt - Raven notebooks, only known `HydroShare_integration.ipynb` failing: https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/931cfc924a147d07b59e88badff9f170e852a03b/docker/saved_buildout/jenkins-buildlogs-raven.txt ## Related Issue / Discussion - Matching notebook fixes: - Pavics-sdi: PR Ouranosinc/pavics-sdi#321 - Finch: PR url: None - PAVICS-landing: PR Ouranosinc/PAVICS-landing#78 - RavenPy: PR CSHS-CWRA/RavenPy#356 - Resolves Ouranosinc/PAVICS-landing#65 - Resolves Ouranosinc/PAVICS-landing#66 - Deployment to PAVICS: bird-house/birdhouse-deploy#453 - Jenkins-config changes for new notebooks: PR url: None - Other issues found while working on this one - computationalmodelling/nbval#204 - jupyterlab-contrib/jupyter-archive#132 - CSHS-CWRA/RavenPy#357 - CSHS-CWRA/RavenPy#361 - CSHS-CWRA/RavenPy#362 - Previous release: PR #134 ## Additional Information Full diff conda env export: 81deb99...931cfc9#diff-e8f2a6a53085ae29bb7cedc701c1d345a330651ae971555e85a5c005e94f4cd9 Full new conda env export: https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/931cfc924a147d07b59e88badff9f170e852a03b/docker/saved_buildout/conda-env-export.yml DockerHub build log https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/931cfc924a147d07b59e88badff9f170e852a03b/docker/saved_buildout/docker-buildlogs.txt
tlvu
approved these changes
May 9, 2024
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fixes pavics-sdi bugs noted here : https://github.com/Ouranosinc/pavics-jupyter-env-issues/issues/2, https://github.com/Ouranosinc/pavics-jupyter-env-issues/issues/6
Fix for Ouranosinc/PAVICS-e2e-workflow-tests#121