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The landing page serving as the entrance to PAVICS
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update nb output for Thredds v5 #77

Open tlvu opened 6 months ago

tlvu commented 6 months ago

Only merge if https://github.com/bird-house/birdhouse-deploy/pull/413 can be merged.

This is mostly to have a nice notebook diff.

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 0 _
  Notebook cell execution failed
  Cell 0: Cell outputs differ

  Input:
  from siphon.catalog import TDSCatalog

  url = "https://boreas.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip5/ouranos/cb-oura-1.0/catalog.xml"  # TEST_USE_PROD_DATA

  # Create Catalog
  cat = TDSCatalog(url)

  # List of datasets
  print(f"Number of datasets: {len(cat.datasets)}")

  # Access mechanisms - here we are interested in OPENDAP, a data streaming protocol
  cds = cat.datasets[0]
  print(f"Access URLs: {tuple(cds.access_urls.keys())}")

  Traceback:
   mismatch 'stdout'

   assert reference_output == test_output failed:

    "Number of da...cdfSubset')\n" == "Number of da...cdfSubset')\n"
    Skipping 43 identical leading characters in diff, use -v to show
    Skipping 50 identical trailing characters in diff, use -v to show
    - erver', 'OpenDAP', 'NC
    ?           ^^^
    + erver', 'OPENDAP', 'NC
    ?           ^^^

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 2 _
  Notebook cell execution failed
  Cell 2: Cell outputs differ

  Input:
  # Extract a subset of the file

  # Again, this only creates an in-memory representation of the data
  sub = ds.pr.sel(time="2050").sel(lon=-80, lat=46, method="nearest")

  # The data is only downloaded when we actuall need it for a computation.
  sub.mean(keep_attrs=True).compute()

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '<xarray.Data...[256  16  16]' == '<xarray.Data...[256  16  16]'
    Skipping 238 identical trailing characters in diff, use -v to show
      <xarray.DataArray 'pr' ()>
    - array(4.372211e-05, dty
    + array(3.975487e-05, dty

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 3 _
  Notebook cell execution failed
  Cell 3: Cell outputs differ

  Input:
  rcp45_data = [cat.datasets[x] for x in cat.datasets if "rcp45" in x]
  rcp45_data

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '[day_NorESM1...50-2100.ncml]' == '[day_ACCESS1...50-2100.ncml]'
    Skipping 66 identical trailing characters in diff, use -v to show
    - [day_ACCESS1-3_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    ?      ^^^  ^  ^
    + [day_NorESM1-M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    ?      ^^^  ^  ^
    +  day_MPI-ESM-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_IPSL-CM5B-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_IPSL-CM5A-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_INM-CM4_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_HadGEM2-CC_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_GFDL-ESM2M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_CanESM2_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_CMCC-CMS_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
       day_BNU-ESM_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_CMCC-CMS_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_CanESM2_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_GFDL-ESM2M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_HadGEM2-CC_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_INM-CM4_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_IPSL-CM5A-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_IPSL-CM5B-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_MPI-ESM-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_NorESM1-M_historic
    ?      ^^^  ^  ^
    +  day_ACCESS1-3_historic
    ?      ^^^  ^  ^

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 5 _
  Notebook cell execution failed
  Cell 5: Cell outputs differ

  Input:
  datasets = {}
  for r in ["rcp45", "rcp85"]:
      expected = 11
      datasets[r] = get_ncfilelist(r, expected, url)

  # Display search results
  display(datasets["rcp45"])
  display(datasets["rcp85"])

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '[day_NorESM1...50-2100.ncml]' == '[day_ACCESS1...50-2100.ncml]'
    Skipping 66 identical trailing characters in diff, use -v to show
    - [day_ACCESS1-3_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    ?      ^^^  ^  ^
    + [day_NorESM1-M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    ?      ^^^  ^  ^
    +  day_MPI-ESM-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_IPSL-CM5B-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_IPSL-CM5A-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_INM-CM4_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_HadGEM2-CC_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_GFDL-ESM2M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_CanESM2_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    +  day_CMCC-CMS_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
       day_BNU-ESM_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_CMCC-CMS_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_CanESM2_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_GFDL-ESM2M_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_HadGEM2-CC_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_INM-CM4_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_IPSL-CM5A-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_IPSL-CM5B-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_MPI-ESM-LR_historical+rcp45_r1i1p1_na10kgrid_qm-moving-50bins-detrend_1950-2100.ncml,
    -  day_NorESM1-M_historic
    ?      ^^^  ^  ^
    +  day_ACCESS1-3_historic
    ?      ^^^  ^  ^

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-2Subsetting.ipynb::Cell 0 _
  Notebook cell execution failed
  Cell 0: Cell outputs differ

  Input:
  import warnings

  import xarray as xr
  from IPython.display import display  # Fancy representation of xarray objects
  from siphon.catalog import TDSCatalog

  warnings.simplefilter("ignore")
  url = "https://boreas.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip5/ouranos/cb-oura-1.0/catalog.xml"  # TEST_USE_PROD_DATA

  # Create Catalog
  cat = TDSCatalog(url)

  # DAP link for this demo
  ds_url = cat.datasets[0].access_urls["OPENDAP"]

  # xarray.Dataset
  ds = xr.open_dataset(ds_url, chunks=dict(time=256 * 2, lon=32, lat=32))
  display(ds)
  a = ds.tasmin.isel(time=0).plot(figsize=(10, 4))

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '<xarray.Data...id:       NCC' == '<xarray.Data...    ACCESS1-3'
    Skipping 50 identical leading characters in diff, use -v to show
    -  time: 55152)
    ?            -
    +  time: 55115)
    ?           +
      Coordinates:
        * lat      (lat) float32 66.62 66.54 66.46 66.37 ... 40.29 40.21 40.12 40.04
        * lon      (lon) float32 -120.8 -120.7 -120.6 -120.5 ... -54.63 -54.55 -54.46
    -   * time     (time) datetime64[ns]/DATE/1950-01-02 ... 2100-12-31
    +   * time     (time) object/DATE/TIME/.../DATE/00:00:00
      Data variables:
          tasmin   (time, lat, lon) float32 dask.array<chunksize=(512, 32, 32), meta=np.ndarray>
          tasmax   (time, lat, lon) float32 dask.array<chunksize=(512, 32, 32), meta=np.ndarray>
          pr       (time, lat, lon) float32 dask.array<chunksize=(512, 32, 32), meta=np.ndarray>
    - Attributes: (12/27)
    ?                  ^
    + Attributes: (12/26)
    ?                  ^
          Conventions:                CF-1.5
          title:                      Ouranos standard ensemble of bias-adjusted cl...
    -     history:                    CMIP5 compliant file produced from raw ACCESS...
    +     history:                    DATE_TIME_TZ CMOR rewrote data to com...
          institution:                Ouranos Consortium on Regional Climatology an...
    -     source:                     ACCESS1-3 2011. Atmosphere: AGCM v1.0 (N96 gr...
    -     driving_model:              ACCESS1-3
    +     source:                     NorESM1-M 2011  atmosphere: CAM-Oslo (CAM4-Os...
    +     driving_experiment:         historical,rcp85
          ...                         ...
    +     frequency:                  day
          modeling_realm:             atmos
          target_dataset:             CANADA : ANUSPLIN interpolated Canada daily 3...
          target_dataset_references:  CANADA : https://doi.org/10.1175/2011BAMS3132...
    -     driving_institution:        Commonwealth Scientific and Industrial Resear...
    +     driving_institution:        Norwegian Climate Centre
    -     driving_institute_id:       CSIRO-BOM
    ?                                  ^^^^^^^^^
    +     driving_institute_id:       NCC
    ?                                 + ^
    -     driving_model_id:           ACCESS1-3

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-2Subsetting.ipynb::Cell 1 _
  Notebook cell execution failed
  Cell 1: Cell outputs differ

  Input:
  from clisops.core import subset

  lon = [-75.4, -85, -65.5]  # Longitude
  lat = [46.67, 41, 55.3]  # Latitude

  ds_gridpoint = subset.subset_gridpoint(ds, lon=lon, lat=lat)
  display(ds_gridpoint)

  # Plot first year of tasmax data
  a = ds_gridpoint.tasmax.isel(time=slice(0, 365)).plot.line(x="time", figsize=(10, 4))

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '<xarray.Data...id:       NCC' == '<xarray.Data...    ACCESS1-3'
    Skipping 39 identical leading characters in diff, use -v to show
    -  time: 55152)
    ?            -
    +  time: 55115)
    ?           +
      Coordinates:
          lat      (site) float32 46.71 41.04 55.29
          lon      (site) float32 -75.38 -84.96 -65.46
    -   * time     (time) datetime64[ns]/DATE/1950-01-02 ... 2100-12-31
    +   * time     (time) object/DATE/TIME/.../DATE/00:00:00
      Dimensions without coordinates: site
      Data variables:
          tasmin   (time, site) float32 dask.array<chunksize=(512, 3), meta=np.ndarray>
          tasmax   (time, site) float32 dask.array<chunksize=(512, 3), meta=np.ndarray>
          pr       (time, site) float32 dask.array<chunksize=(512, 3), meta=np.ndarray>
    - Attributes: (12/27)
    ?                  ^
    + Attributes: (12/26)
    ?                  ^
          Conventions:                CF-1.5
          title:                      Ouranos standard ensemble of bias-adjusted cl...
    -     history:                    CMIP5 compliant file produced from raw ACCESS...
    +     history:                    DATE_TIME_TZ CMOR rewrote data to com...
          institution:                Ouranos Consortium on Regional Climatology an...
    -     source:                     ACCESS1-3 2011. Atmosphere: AGCM v1.0 (N96 gr...
    -     driving_model:              ACCESS1-3
    +     source:                     NorESM1-M 2011  atmosphere: CAM-Oslo (CAM4-Os...
    +     driving_experiment:         historical,rcp85
          ...                         ...
    +     frequency:                  day
          modeling_realm:             atmos
          target_dataset:             CANADA : ANUSPLIN interpolated Canada daily 3...
          target_dataset_references:  CANADA : https://doi.org/10.1175/2011BAMS3132...
    -     driving_institution:        Commonwealth Scientific and Industrial Resear...
    +     driving_institution:        Norwegian Climate Centre
    -     driving_institute_id:       CSIRO-BOM
    ?                                  ^^^^^^^^^
    +     driving_institute_id:       NCC
    ?                                 + ^
    -     driving_model_id:           ACCESS1-3

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-2Subsetting.ipynb::Cell 3 _
  Notebook cell execution failed
  Cell 3: Cell outputs differ

  Input:
  # Specify the longitude and latitude boundaries
  lon_bnds = [-80.5, -60.2]
  lat_bnds = [44, 55]

  ds1 = subset.subset_bbox(ds, lon_bnds=lon_bnds, lat_bnds=lat_bnds)
  display(ds1)

  # Plot a map of first timestep
  a = ds1.tasmax.isel(time=0).plot()

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '<xarray.Data...id:       NCC' == '<xarray.Data...    ACCESS1-3'
    Skipping 50 identical leading characters in diff, use -v to show
    -  time: 55152)
    ?            -
    +  time: 55115)
    ?           +
      Coordinates:
        * lat      (lat) float32 54.96 54.87 54.79 54.71 ... 44.29 44.21 44.12 44.04
        * lon      (lon) float32 -80.46 -80.38 -80.3 -80.21 ... -60.38 -60.3 -60.21
    -   * time     (time) datetime64[ns]/DATE/1950-01-02 ... 2100-12-31
    +   * time     (time) object/DATE/TIME/.../DATE/00:00:00
      Data variables:
          tasmin   (time, lat, lon) float32 dask.array<chunksize=(512, 20, 28), meta=np.ndarray>
          tasmax   (time, lat, lon) float32 dask.array<chunksize=(512, 20, 28), meta=np.ndarray>
          pr       (time, lat, lon) float32 dask.array<chunksize=(512, 20, 28), meta=np.ndarray>
    - Attributes: (12/27)
    ?                  ^
    + Attributes: (12/26)
    ?                  ^
          Conventions:                CF-1.5
          title:                      Ouranos standard ensemble of bias-adjusted cl...
    -     history:                    CMIP5 compliant file produced from raw ACCESS...
    +     history:                    DATE_TIME_TZ CMOR rewrote data to com...
          institution:                Ouranos Consortium on Regional Climatology an...
    -     source:                     ACCESS1-3 2011. Atmosphere: AGCM v1.0 (N96 gr...
    -     driving_model:              ACCESS1-3
    +     source:                     NorESM1-M 2011  atmosphere: CAM-Oslo (CAM4-Os...
    +     driving_experiment:         historical,rcp85
          ...                         ...
    +     frequency:                  day
          modeling_realm:             atmos
          target_dataset:             CANADA : ANUSPLIN interpolated Canada daily 3...
          target_dataset_references:  CANADA : https://doi.org/10.1175/2011BAMS3132...
    -     driving_institution:        Commonwealth Scientific and Industrial Resear...
    +     driving_institution:        Norwegian Climate Centre
    -     driving_institute_id:       CSIRO-BOM
    ?                                  ^^^^^^^^^
    +     driving_institute_id:       NCC
    ?                                 + ^
    -     driving_model_id:           ACCESS1-3

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-2Subsetting.ipynb::Cell 6 _
  Notebook cell execution failed
  Cell 6: Cell outputs differ

  Input:
  # Align data to a starting year
  ds_sub = subset.subset_time(ds, start_date="1981")
  print(
      f"Subset time using start_date only\nstart: {ds_sub.time.min().values};\tend: {ds_sub.time.max().values}\n"
  )

  # Select a temporal slice
  ds_sub = subset.subset_time(ds, start_date="1981-08-05", end_date="2084-06-15")
  print(
      f"Subset time using both start_date & end_date\nstart: {ds_sub.time.min().values};\tend: {ds_sub.time.max().values}"
  )

  Traceback:
   mismatch 'stdout'

   assert reference_output == test_output failed:

    'Subset time ...TE/00:00:00\n' == 'Subset time ...0.000000000\n'
      Subset time using start_date only
    - start: 1981-01-01T00:00:00.000000000; end: 2100-12-31T00:00:00.000000000
    + start:/DATE/00:00:00; end:/DATE/00:00:00

      Subset time using both start_date & end_date
    - start: 1981-08-05T00:00:00.000000000; end: 2084-06-15T00:00:00.000000000
    + start:/DATE/00:00:00; end:/DATE/00:00:00

  _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb::Cell 0 _
  Notebook cell execution failed
  Cell 0: Cell outputs differ

  Input:
  import os

  os.environ["USE_PYGEOS"] = "0"  # force use Shapely with GeoPandas

  import warnings

  import numba

  warnings.simplefilter("ignore", category=numba.core.errors.NumbaDeprecationWarning)

  import geopandas as gpd
  import matplotlib.pyplot as plt
  import xarray as xr
  from clisops.core import subset
  from dask.diagnostics import ProgressBar
  from siphon.catalog import TDSCatalog
  from xclim import atmos

  warnings.simplefilter("ignore")
  # TODO change address
  url = "https://boreas.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip5/ouranos/cb-oura-1.0/catalog.xml"  # TEST_USE_PROD_DATA

  # Create Catalog
  cat = TDSCatalog(url)

  # Subset over the Gasp�� peninsula in eastern Quebec
  gaspe = gpd.GeoDataFrame.from_file(
      "/notebook_dir/pavics-homepage/tutorial_data/gaspesie_mrc.geojson"
  )
  ds = subset.subset_shape(
      xr.open_dataset(cat.datasets[0].access_urls["OPENDAP"], chunks=dict(time=256)),
      shape=gpd.GeoDataFrame(geometry=gaspe.buffer(0.05)),
  )

  # What we see here is only a representation of the full content, the entire data set hasn't been loaded.
  display(ds)

  # plot of single day tasmin
  a = ds.tasmin.isel(time=0).plot(figsize=(10, 4))

  Traceback:
   mismatch 'text/plain'

   assert reference_output == test_output failed:

    '<xarray.Data...    EPSG:4326' == '<xarray.Data...    EPSG:4326'
    Skipping 48 identical leading characters in diff, use -v to show
    -  time: 55152)
    ?            -
    +  time: 55115)
    ?           +
      Coordinates:
        * lat      (lat) float32 49.29 49.21 49.12 49.04 ... 48.12 48.04 47.96 47.87
        * lon      (lon) float32 -67.71 -67.63 -67.55 -67.46 ... -64.3 -64.21 -64.13
    -   * time     (time) datetime64[ns]/DATE/1950-01-02 ... 2100-12-31
    +   * time     (time) object/DATE/TIME/.../DATE/00:00:00
      Data variables:
          tasmin   (time, lat, lon) float32 dask.array<chunksize=(256, 18, 44), meta=np.ndarray>
          tasmax   (time, lat, lon) float32 dask.array<chunksize=(256, 18, 44), meta=np.ndarray>
          pr       (time, lat, lon) float32 dask.array<chunksize=(256, 18, 44), meta=np.ndarray>
          crs      int64 1
    - Attributes: (12/28)
    ?                  ^
    + Attributes: (12/27)
    ?                  ^
          Conventions:                CF-1.5
          title:                      Ouranos standard ensemble of bias-adjusted cl...
    -     history:                    CMIP5 compliant file produced from raw ACCESS...
    +     history:                    DATE_TIME_TZ CMOR rewrote data to com...
          institution:                Ouranos Consortium on Regional Climatology an...
    -     source:                     ACCESS1-3 2011. Atmosphere: AGCM v1.0 (N96 gr...
    -     driving_model:              ACCESS1-3
    +     source:                     NorESM1-M 2011  atmosphere: CAM-Oslo (CAM4-Os...
    +     driving_experiment:         historical,rcp85
          ...                         ...
    +     modeling_realm:             atmos
          target_dataset:             CANADA : ANUSPLIN interpolated Canada daily 3...
          target_dataset_references:  CANADA : https://doi.org/10.1175/2011BAMS3132...
    -     driving_institution:        Commonwealth Scientific and Industrial Resear...
    +     driving_institution:        Norwegian Climate Centre
    -     driving_institute_id:       CSIRO-BOM
    ?                                  ^^^^^^^^
    +     driving_institute_id:       NCC
    ?                                 + ^
    -     driving_model_id:           ACCESS1-3
          crs:                        EPSG:4326
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tlvu commented 6 months ago

Most of the graphs are different, weird.