Era5 notebook #200
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Era5 notebook #200
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Salem seems to be failing to parse CRS of the shapefile now, even though it worked yesterday. @huard can you test and see if it works for you? Do you have an ETA on when we'll be able to do this type of operation on the server side (as we'll eventually replace the code in these workbooks to use the methods on the server)? Thanks! |
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Working on it. |
tlvu
added a commit
to Ouranosinc/PAVICS-e2e-workflow-tests
that referenced
this pull request
Mar 10, 2020
…tebooks docker: add regionmask and salem for Era5 Raven notebooks, removed jupyter_bokeh jupyter_bokeh (the extension, not the package) was removed due to this issue bokeh/jupyter_bokeh#93 Era5 Raven notebook PR: Ouranosinc/raven#200 Noticeable rather large Jupyter env changes: ```diff < - birdy=v0.6.5=py_0 > - birdy=v0.6.6=py_0 < - bokeh=1.4.0=py36_0 > - bokeh==2.0.0 # from pip recursive dependencies (we get newer version by not explicitly get from conda !) < - esgf-compute-api=2.2.1=py_2 > - esgf-compute-api=2.2.3=py_0 < - jupyterlab=1.2.5=py_0 > - jupyterlab=2.0.1=py_0 < - owslib=0.19.0=py_2 > - owslib=0.19.1=py_0 < - pandas=0.25.3=py36hb3f55d8_0 > - pandas=1.0.1=py37hb3f55d8_0 < - python=3.6.7=h357f687_1006 > - python=3.7.6=h357f687_4_cpython > - regionmask=0.5.0=py_1 < - xarray=0.14.1=py_1 > - xarray=0.15.0=py_0 < - dask==2.9.2 > - dask==2.12.0 > - salem==0.2.4 < - xclim==0.13.0 > - xclim==0.14.0 ``` Full conda env export Diff: [200120-200309-conda-env-export.diff.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4309639/200120-200309-conda-env-export.diff.txt) ```diff 10c10 < - alembic=1.3.2=py_0 --- > - alembic=1.4.1=py_0 14,16c14,16 < - beautifulsoup4=4.8.2=py36_0 < - birdy=v0.6.5=py_0 < - bleach=3.1.0=py_0 --- > - beautifulsoup4=4.8.2=py37_0 > - birdy=v0.6.6=py_0 > - bleach=3.1.1=py_0 18d17 < - bokeh=1.4.0=py36_0 20c19 < - boost-cpp=1.70.0=h8e57a91_2 --- > - boost-cpp=1.72.0=h8e57a91_0 25,27c24,26 < - cartopy=0.17.0=py36h423102d_1009 < - cdat_info=8.2=py_6 < - cdtime=3.1.2=py36h1ac8016_8 --- > - cartopy=0.17.0=py37h39d8c00_1011 > - cdat_info=8.2=py_7 > - cdtime=3.1.3=py37h1ac8016_0 29c28 < - certifi=2019.11.28=py36_0 --- > - certifi=2019.11.28=py37_0 31c30 < - cffi=1.13.2=py36h8022711_0 --- > - cffi=1.14.0=py37hd463f26_0 33,34c32,33 < - cftime=1.0.4.2=py36hc1659b7_0 < - chardet=3.0.4=py36_1003 --- > - cftime=1.0.4.2=py37hc1659b7_0 > - chardet=3.0.4=py37_1003 40,42c39,41 < - coverage=5.0.3=py36h516909a_0 < - cryptography=2.8=py36h72c5cf5_1 < - curl=7.65.3=hf8cf82a_0 --- > - coverage=5.0.3=py37h516909a_0 > - cryptography=2.8=py37h72c5cf5_1 > - curl=7.68.0=hf8cf82a_0 45c44 < - decorator=4.4.1=py_0 --- > - decorator=4.4.2=py_0 51,55c50,54 < - entrypoints=0.3=py36_1000 < - esgf-compute-api=2.2.1=py_2 < - esmf=8.0.0=nompi_he6d0a24_4 < - esmpy=8.0.0=nompi_py36hf0e99fa_1 < - expat=2.2.5=he1b5a44_1004 --- > - entrypoints=0.3=py37_1000 > - esgf-compute-api=2.2.3=py_0 > - esmf=8.0.0=nompi_he6d0a24_5 > - esmpy=8.0.0=nompi_py37hf0e99fa_1 > - expat=2.2.9=he1b5a44_2 57c56 < - fiona=1.8.13=py36h900e953_0 --- > - fiona=1.8.13=py37h900e953_0 62c61 < - future=0.18.2=py36_0 --- > - future=0.18.2=py37_0 64,66c63,65 < - gdal=3.0.2=py36hbb6b9fb_7 < - genutil=8.2=py36hc1659b7_3 < - geopandas=0.6.2=py_0 --- > - gdal=3.0.4=py37hbb6b9fb_1 > - genutil=8.2=py37hc1659b7_3 > - geopandas=0.7.0=py_1 68c67 < - geotiff=1.5.1=hbd99317_7 --- > - geotiff=1.5.1=hcbe54f9_9 71,75c70,74 < - giflib=5.2.1=h516909a_1 < - gitdb2=2.0.6=py_0 < - gitpython=3.0.5=py_0 < - glib=2.58.3=py36h6f030ca_1002 < - gmp=6.2.0=he1b5a44_0 --- > - giflib=5.2.1=h516909a_2 > - gitdb=4.0.2=py_0 > - gitpython=3.1.0=py_0 > - glib=2.58.3=py37h6f030ca_1002 > - gmp=6.2.0=he1b5a44_2 77,78c76,77 < - gst-plugins-base=1.14.5=h0935bb2_0 < - gstreamer=1.14.5=h36ae1b5_0 --- > - gst-plugins-base=1.14.5=h0935bb2_2 > - gstreamer=1.14.5=h36ae1b5_2 82,86c81,85 < - idna=2.8=py36_1000 < - importlib_metadata=1.4.0=py36_0 < - ipykernel=5.1.3=py36h5ca1d4c_0 < - ipyleaflet=0.12.1=py36_0 < - ipython=7.11.1=py36h5ca1d4c_0 --- > - idna=2.9=py_1 > - importlib_metadata=1.5.0=py37_0 > - ipykernel=5.1.4=py37h5ca1d4c_0 > - ipyleaflet=0.12.3=py_1 > - ipython=7.13.0=py37h5ca1d4c_0 90,91c89,90 < - jedi=0.15.2=py36_0 < - jinja2=2.10.3=py_0 --- > - jedi=0.16.0=py37_0 > - jinja2=2.11.1=py_0 94,95c93,94 < - json5=0.8.5=py_0 < - jsonschema=3.2.0=py36_0 --- > - json5=0.9.0=py_0 > - jsonschema=3.2.0=py37_0 97,102c96,103 < - jupyter_client=5.3.4=py36_1 < - jupyter_console=5.1.0=py36_0 < - jupyter_core=4.6.1=py36_0 < - jupyter_server=0.1.1=py36_0 < - jupyterhub=1.0.0=py36_0 < - jupyterlab=1.2.5=py_0 --- > - jupyter_client=6.0.0=py_0 > - jupyter_console=6.0.0=py_0 > - jupyter_core=4.6.3=py37_0 > - jupyter_server=0.1.1=py37_0 > - jupyter_telemetry=0.0.5=py_0 > - jupyterhub=1.1.0=py37_2 > - jupyterhub-base=1.1.0=py37_2 > - jupyterlab=2.0.1=py_0 104c105 < - jupyterlab_server=1.0.6=py_0 --- > - jupyterlab_server=1.0.7=py_0 106c107 < - kiwisolver=1.1.0=py36hc9558a2_0 --- > - kiwisolver=1.1.0=py37hc9558a2_0 109c110,111 < - lazy-object-proxy=1.4.3=py36h516909a_0 --- > - lazy-object-proxy=1.4.3=py37h516909a_1 > - ld_impl_linux-64=2.33.1=h53a641e_8 113c115 < - libcf=1.0.3=py36hdee1361_5 --- > - libcf=1.0.3=py37hdee1361_5 115c117 < - libcurl=7.65.3=hda55be3_0 --- > - libcurl=7.68.0=hda55be3_0 122,123c124,125 < - libgdal=3.0.2=hbe56659_7 < - libgfortran-ng=7.3.0=hdf63c60_4 --- > - libgdal=3.0.4=h022d3c0_1 > - libgfortran-ng=7.3.0=hdf63c60_5 127c129 < - libkml=1.3.0=h4fcabce_1010 --- > - libkml=1.3.0=hb574062_1011 130c132 < - libnetcdf=4.7.3=nompi_h94020b1_100 --- > - libnetcdf=4.7.3=nompi_h9f9fd6a_101 133c135 < - libpq=12.1=hd9ab2ff_0 --- > - libpq=12.2=hae5116b_0 135,136c137,138 < - libspatialindex=1.9.3=he1b5a44_1 < - libspatialite=4.3.0a=h343d7df_1033 --- > - libspatialindex=1.9.3=he1b5a44_3 > - libspatialite=4.3.0a=hd318ce7_1035 145c147 < - libxkbcommon=0.9.1=hebb1f50_0 --- > - libxkbcommon=0.10.0=he1b5a44_0 148c150 < - lxml=4.4.2=py36h7ec2d77_0 --- > - lxml=4.5.0=py37h7ec2d77_0 151,153c153,155 < - markupsafe=1.1.1=py36h516909a_0 < - matplotlib=3.1.2=py36_1 < - matplotlib-base=3.1.2=py36h250f245_1 --- > - markupsafe=1.1.1=py37h516909a_0 > - matplotlib=3.2.0=1 > - matplotlib-base=3.2.0=py37h250f245_1 156,157c158,159 < - mistune=0.8.4=py36h516909a_1000 < - more-itertools=8.1.0=py_0 --- > - mistune=0.8.4=py37h516909a_1000 > - more-itertools=8.2.0=py_0 159,162c161,164 < - nbconvert=5.6.1=py36_0 < - nbdime=1.1.0=py36_0 < - nbformat=5.0.3=py_0 < - nbval=0.9.4=py_0 --- > - nbconvert=5.6.1=py37_0 > - nbdime=1.1.0=py37_0 > - nbformat=5.0.4=py_0 > - nbval=0.9.5=py_0 165c167 < - netcdf4=1.5.3=nompi_py36hd35fb8e_102 --- > - netcdf4=1.5.3=nompi_py37hd35fb8e_102 167,169c169,171 < - nodejs=13.6.0=h10a4023_0 < - notebook=6.0.2=py36_0 < - nspr=4.24=he1b5a44_0 --- > - nodejs=13.9.0=h10a4023_0 > - notebook=6.0.3=py37_0 > - nspr=4.25=he1b5a44_0 171c173 < - numpy=1.17.5=py36h95a1406_0 --- > - numpy=1.18.1=py37h95a1406_0 178,179c180,181 < - owslib=0.19.0=py_2 < - packaging=20.0=py_0 --- > - owslib=0.19.1=py_0 > - packaging=20.1=py_0 181,182c183,184 < - pandas=0.25.3=py36hb3f55d8_0 < - pandoc=2.9.1.1=0 --- > - pandas=1.0.1=py37hb3f55d8_0 > - pandoc=2.9.2=0 184,189c186,191 < - parso=0.5.2=py_0 < - pcre=8.43=he1b5a44_0 < - pexpect=4.7.0=py36_0 < - pickleshare=0.7.5=py36_1000 < - pillow=7.0.0=py36hefe7db6_0 < - pip=19.3.1=py36_0 --- > - parso=0.6.2=py_0 > - pcre=8.44=he1b5a44_0 > - pexpect=4.8.0=py37_0 > - pickleshare=0.7.5=py37_1000 > - pillow=7.0.0=py37hefe7db6_0 > - pip=20.0.2=py_2 191c193 < - pluggy=0.12.0=py_0 --- > - pluggy=0.13.0=py37_0 194,195c196,197 < - postgresql=12.1=hc63931a_0 < - proj=6.2.1=hc80f0dc_0 --- > - postgresql=12.2=hf1211e9_0 > - proj=6.3.1=hc80f0dc_1 197c199 < - prompt_toolkit=3.0.2=py_0 --- > - prompt_toolkit=2.0.10=py_0 201,203c203,205 < - pycparser=2.19=py36_1 < - pycurl=7.43.0.4=py36h16ce93b_0 < - pydap=3.2.2=py36_1000 --- > - pycparser=2.20=py_0 > - pycurl=7.43.0.5=py37h16ce93b_0 > - pydap=3.2.2=py37_1000 205c207 < - pygments=2.5.2=py_0 --- > - pygments=2.6.1=py_0 207,208c209,210 < - pykdtree=1.3.1=py36hc1659b7_1002 < - pyopenssl=19.1.0=py36_0 --- > - pykdtree=1.3.1=py37hc1659b7_1002 > - pyopenssl=19.1.0=py_1 210,212c212,214 < - pyproj=2.4.2.post1=py36h12732c1_0 < - pyqt=5.12.3=py36hcca6a23_1 < - pyrsistent=0.15.7=py36h516909a_0 --- > - pyproj=2.5.0=py37he3cd046_1 > - pyqt=5.12.3=py37hcca6a23_1 > - pyrsistent=0.15.7=py37h516909a_0 214,216c216,218 < - pysocks=1.7.1=py36_0 < - pytest=5.3.4=py36_0 < - python=3.6.7=h357f687_1006 --- > - pysocks=1.7.1=py37_0 > - pytest=5.3.5=py37_1 > - python=3.7.6=h357f687_4_cpython 218a221,222 > - python-json-logger=0.1.11=py_0 > - python_abi=3.7=1_cp37m 220,221c224 < - pyyaml=5.3=py36h516909a_0 < - pyzmq=18.1.1=py36h1768529_0 --- > - pyzmq=19.0.0=py37h1768529_0 223,224c226,228 < - qtconsole=4.6.0=py_0 < - rasterio=1.1.2=py36h900e953_0 --- > - qtconsole=4.7.1=py_0 > - qtpy=1.9.0=py_0 > - rasterio=1.1.3=py37h900e953_0 226,228c230,235 < - requests=2.22.0=py36_1 < - rtree=0.9.3=py36h7b0cdae_0 < - scipy=1.4.1=py36h921218d_0 --- > - regionmask=0.5.0=py_1 > - requests=2.23.0=py37_0 > - rtree=0.9.4=py37h7b0cdae_0 > - ruamel.yaml=0.16.6=py37h516909a_0 > - ruamel.yaml.clib=0.2.0=py37h516909a_0 > - scipy=1.4.1=py37h921218d_0 230,233c237,240 < - setuptools=45.1.0=py36_0 < - shapely=1.6.4=py36h5d51c17_1007 < - six=1.14.0=py36_0 < - smmap2=2.0.5=py_0 --- > - setuptools=46.0.0=py37_0 > - shapely=1.7.0=py37h5d51c17_0 > - six=1.14.0=py37_0 > - smmap=3.0.1=py_0 235,236c242,243 < - soupsieve=1.9.4=py36_0 < - sqlalchemy=1.3.12=py36h516909a_0 --- > - soupsieve=1.9.4=py37_0 > - sqlalchemy=1.3.13=py37h516909a_0 239c246 < - terminado=0.8.3=py36_0 --- > - terminado=0.8.3=py37_0 244,245c251,252 < - tornado=6.0.3=py36h516909a_0 < - traitlets=4.3.3=py36_0 --- > - tornado=6.0.4=py37h516909a_0 > - traitlets=4.3.3=py37_0 249c256 < - urllib3=1.25.7=py36_0 --- > - urllib3=1.25.7=py37_0 251,252c258,259 < - voila=0.1.20=py_0 < - vtk-cdat=8.2.0.8.2=py36_mesalibhead77ed_0 --- > - voila=0.1.21=py_0 > - vtk-cdat=8.2.0.8.2=py37_mesalibhead77ed_0 255c262 < - webob=1.8.5=py_0 --- > - webob=1.8.6=py_0 257,259c264,266 < - wheel=0.33.6=py36_0 < - widgetsnbextension=3.5.1=py36_0 < - wrapt=1.11.2=py36h516909a_0 --- > - wheel=0.34.2=py_1 > - widgetsnbextension=3.5.1=py37_0 > - wrapt=1.12.1=py37h516909a_0 261c268 < - xarray=0.14.1=py_1 --- > - xarray=0.15.0=py_0 275d281 < - yaml=0.2.2=h516909a_1 277c283 < - zipp=2.0.0=py_0 --- > - zipp=3.1.0=py_0 282c288,289 < - bottleneck==1.3.1 --- > - bokeh==2.0.0 > - bottleneck==1.3.2 284c291 < - cloudpickle==1.2.2 --- > - cloudpickle==1.3.0 286,287c293,294 < - dask==2.9.2 < - distributed==2.9.3 --- > - dask==2.12.0 > - distributed==2.12.0 293c300 < - markdown==3.1.1 --- > - markdown==3.2.1 295c302 < - msgpack==0.6.2 --- > - msgpack==1.0.0 297c304 < - pint==0.9 --- > - pint==0.11 299c306 < - psutil==5.6.7 --- > - psutil==5.7.0 301a309 > - pyyaml==5.3 304c312,313 < - scikit-learn==0.22.1 --- > - salem==0.2.4 > - scikit-learn==0.22.2.post1 308,309c317,319 < - xclim==0.13.0 < - zict==1.0.0 --- > - typing-extensions==3.7.4.1 > - xclim==0.14.0 > - zict==2.0.0 ``` Full new conda env export: [200309-conda-env-export.yml.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4309640/200309-conda-env-export.yml.txt) ``` name: birdy channels: - cdat - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=0_gnu - affine=2.3.0=py_0 - alembic=1.4.1=py_0 - async_generator=1.10=py_0 - attrs=19.3.0=py_0 - backcall=0.1.0=py_0 - beautifulsoup4=4.8.2=py37_0 - birdy=v0.6.6=py_0 - bleach=3.1.1=py_0 - blinker=1.4=py_1 - boltons=20.0.0=py_0 - boost-cpp=1.72.0=h8e57a91_0 - branca=0.3.1=py_0 - bzip2=1.0.8=h516909a_2 - ca-certificates=2019.11.28=hecc5488_0 - cairo=1.16.0=hfb77d84_1002 - cartopy=0.17.0=py37h39d8c00_1011 - cdat_info=8.2=py_7 - cdtime=3.1.3=py37h1ac8016_0 - cdutil=8.2=py_2 - certifi=2019.11.28=py37_0 - certipy=0.1.3=py_0 - cffi=1.14.0=py37hd463f26_0 - cfitsio=3.470=hb60a0a2_2 - cftime=1.0.4.2=py37hc1659b7_0 - chardet=3.0.4=py37_1003 - click=7.0=py_0 - click-plugins=1.1.1=py_0 - cligj=0.5.0=py_0 - colorama=0.4.3=py_0 - configurable-http-proxy=4.2.0=node13_he01fd0c_2 - coverage=5.0.3=py37h516909a_0 - cryptography=2.8=py37h72c5cf5_1 - curl=7.68.0=hf8cf82a_0 - cycler=0.10.0=py_2 - dbus=1.13.6=he372182_0 - decorator=4.4.2=py_0 - defusedxml=0.6.0=py_0 - descartes=1.1.0=py_4 - distarray=2.12.2=py_1 - docopt=0.6.2=py_1 - dv3d=8.2=py_0 - entrypoints=0.3=py37_1000 - esgf-compute-api=2.2.3=py_0 - esmf=8.0.0=nompi_he6d0a24_5 - esmpy=8.0.0=nompi_py37hf0e99fa_1 - expat=2.2.9=he1b5a44_2 - ffmpeg=4.2=h167e202_0 - fiona=1.8.13=py37h900e953_0 - fontconfig=2.13.1=h86ecdb6_1001 - freetype=2.10.0=he983fc9_1 - freexl=1.0.5=h14c3975_1002 - funcsigs=1.0.2=py_3 - future=0.18.2=py37_0 - g2clib=1.6.0=hf3f1b0b_9 - gdal=3.0.4=py37hbb6b9fb_1 - genutil=8.2=py37hc1659b7_3 - geopandas=0.7.0=py_1 - geos=3.8.0=he1b5a44_0 - geotiff=1.5.1=hcbe54f9_9 - gettext=0.19.8.1=hc5be6a0_1002 - ghostscript=9.22=hf484d3e_1001 - giflib=5.2.1=h516909a_2 - gitdb=4.0.2=py_0 - gitpython=3.1.0=py_0 - glib=2.58.3=py37h6f030ca_1002 - gmp=6.2.0=he1b5a44_2 - gnutls=3.6.5=hd3a4fd2_1002 - gst-plugins-base=1.14.5=h0935bb2_2 - gstreamer=1.14.5=h36ae1b5_2 - hdf4=4.2.13=hf30be14_1003 - hdf5=1.10.5=nompi_h3c11f04_1104 - icu=64.2=he1b5a44_1 - idna=2.9=py_1 - importlib_metadata=1.5.0=py37_0 - ipykernel=5.1.4=py37h5ca1d4c_0 - ipyleaflet=0.12.3=py_1 - ipython=7.13.0=py37h5ca1d4c_0 - ipython_genutils=0.2.0=py_1 - ipywidgets=7.5.1=py_0 - jasper=1.900.1=h07fcdf6_1006 - jedi=0.16.0=py37_0 - jinja2=2.11.1=py_0 - jpeg=9c=h14c3975_1001 - json-c=0.13.1=h14c3975_1001 - json5=0.9.0=py_0 - jsonschema=3.2.0=py37_0 - jupyter=1.0.0=py_2 - jupyter_client=6.0.0=py_0 - jupyter_console=6.0.0=py_0 - jupyter_core=4.6.3=py37_0 - jupyter_server=0.1.1=py37_0 - jupyter_telemetry=0.0.5=py_0 - jupyterhub=1.1.0=py37_2 - jupyterhub-base=1.1.0=py37_2 - jupyterlab=2.0.1=py_0 - jupyterlab_pygments=0.1.0=py_0 - jupyterlab_server=1.0.7=py_0 - kealib=1.4.10=h58c409b_1005 - kiwisolver=1.1.0=py37hc9558a2_0 - krb5=1.16.4=h2fd8d38_0 - lame=3.100=h14c3975_1001 - lazy-object-proxy=1.4.3=py37h516909a_1 - ld_impl_linux-64=2.33.1=h53a641e_8 - libblas=3.8.0=11_openblas - libcblas=3.8.0=11_openblas - libcdms=3.1.2=ha54dda3_8 - libcf=1.0.3=py37hdee1361_5 - libclang=9.0.1=default_hde54327_0 - libcurl=7.68.0=hda55be3_0 - libdap4=3.20.4=hd3bb157_0 - libdrs=3.1.2=h9b7ed86_9 - libdrs_f=3.1.2=h322d3c2_5 - libedit=3.1.20170329=hf8c457e_1001 - libffi=3.2.1=he1b5a44_1006 - libgcc-ng=9.2.0=h24d8f2e_2 - libgdal=3.0.4=h022d3c0_1 - libgfortran-ng=7.3.0=hdf63c60_5 - libgomp=9.2.0=h24d8f2e_2 - libiconv=1.15=h516909a_1005 - libidn2=2.3.0=h516909a_0 - libkml=1.3.0=hb574062_1011 - liblapack=3.8.0=11_openblas - libllvm9=9.0.1=hc9558a2_0 - libnetcdf=4.7.3=nompi_h9f9fd6a_101 - libopenblas=0.3.6=h6e990d7_6 - libpng=1.6.37=hed695b0_0 - libpq=12.2=hae5116b_0 - libsodium=1.0.17=h516909a_0 - libspatialindex=1.9.3=he1b5a44_3 - libspatialite=4.3.0a=hd318ce7_1035 - libssh2=1.8.2=h22169c7_2 - libstdcxx-ng=9.2.0=hdf63c60_2 - libtiff=4.1.0=hc3755c2_3 - libunistring=0.9.10=h14c3975_0 - libuuid=2.32.1=h14c3975_1000 - libuv=1.34.0=h516909a_0 - libwebp=1.0.2=h56121f0_5 - libxcb=1.13=h14c3975_1002 - libxkbcommon=0.10.0=he1b5a44_0 - libxml2=2.9.10=hee79883_0 - libxslt=1.1.33=h31b3aaa_0 - lxml=4.5.0=py37h7ec2d77_0 - lz4-c=1.8.3=he1b5a44_1001 - mako=1.1.0=py_0 - markupsafe=1.1.1=py37h516909a_0 - matplotlib=3.2.0=1 - matplotlib-base=3.2.0=py37h250f245_1 - mechanicalsoup=0.12.0=py_0 - mesalib=18.3.1=h590aaf7_0 - mistune=0.8.4=py37h516909a_1000 - more-itertools=8.2.0=py_0 - munch=2.5.0=py_0 - nbconvert=5.6.1=py37_0 - nbdime=1.1.0=py37_0 - nbformat=5.0.4=py_0 - nbval=0.9.5=py_0 - ncurses=6.1=hf484d3e_1002 - netcdf-fortran=4.5.2=nompi_h09cde99_103 - netcdf4=1.5.3=nompi_py37hd35fb8e_102 - nettle=3.4.1=h1bed415_1002 - nodejs=13.9.0=h10a4023_0 - notebook=6.0.3=py37_0 - nspr=4.25=he1b5a44_0 - nss=3.47=he751ad9_0 - numpy=1.18.1=py37h95a1406_0 - oauthlib=3.0.1=py_0 - olefile=0.46=py_0 - openblas=0.3.6=h6e990d7_6 - openh264=1.8.0=hdbcaa40_1000 - openjpeg=2.3.1=h981e76c_3 - openssl=1.1.1d=h516909a_0 - owslib=0.19.1=py_0 - packaging=20.1=py_0 - pamela=1.0.0=py_0 - pandas=1.0.1=py37hb3f55d8_0 - pandoc=2.9.2=0 - pandocfilters=1.4.2=py_1 - parso=0.6.2=py_0 - pcre=8.44=he1b5a44_0 - pexpect=4.8.0=py37_0 - pickleshare=0.7.5=py37_1000 - pillow=7.0.0=py37hefe7db6_0 - pip=20.0.2=py_2 - pixman=0.38.0=h516909a_1003 - pluggy=0.13.0=py37_0 - poppler=0.67.0=h14e79db_8 - poppler-data=0.4.9=1 - postgresql=12.2=hf1211e9_0 - proj=6.3.1=hc80f0dc_1 - prometheus_client=0.7.1=py_0 - prompt_toolkit=2.0.10=py_0 - pthread-stubs=0.4=h14c3975_1001 - ptyprocess=0.6.0=py_1001 - py=1.8.1=py_0 - pycparser=2.20=py_0 - pycurl=7.43.0.5=py37h16ce93b_0 - pydap=3.2.2=py37_1000 - pyepsg=0.4.0=py_0 - pygments=2.6.1=py_0 - pyjwt=1.7.1=py_0 - pykdtree=1.3.1=py37hc1659b7_1002 - pyopenssl=19.1.0=py_1 - pyparsing=2.4.6=py_0 - pyproj=2.5.0=py37he3cd046_1 - pyqt=5.12.3=py37hcca6a23_1 - pyrsistent=0.15.7=py37h516909a_0 - pyshp=2.1.0=py_0 - pysocks=1.7.1=py37_0 - pytest=5.3.5=py37_1 - python=3.7.6=h357f687_4_cpython - python-dateutil=2.8.1=py_0 - python-editor=1.0.4=py_0 - python-json-logger=0.1.11=py_0 - python_abi=3.7=1_cp37m - pytz=2019.3=py_0 - pyzmq=19.0.0=py37h1768529_0 - qt=5.12.5=hd8c4c69_1 - qtconsole=4.7.1=py_0 - qtpy=1.9.0=py_0 - rasterio=1.1.3=py37h900e953_0 - readline=8.0=hf8c457e_0 - regionmask=0.5.0=py_1 - requests=2.23.0=py37_0 - rtree=0.9.4=py37h7b0cdae_0 - ruamel.yaml=0.16.6=py37h516909a_0 - ruamel.yaml.clib=0.2.0=py37h516909a_0 - scipy=1.4.1=py37h921218d_0 - send2trash=1.5.0=py_0 - setuptools=46.0.0=py37_0 - shapely=1.7.0=py37h5d51c17_0 - six=1.14.0=py37_0 - smmap=3.0.1=py_0 - snuggs=1.4.7=py_0 - soupsieve=1.9.4=py37_0 - sqlalchemy=1.3.13=py37h516909a_0 - sqlite=3.30.1=hcee41ef_0 - tbb=2018.0.5=h2d50403_0 - terminado=0.8.3=py37_0 - testpath=0.4.4=py_0 - threddsclient=0.4.2=py_0 - tiledb=1.7.0=hcde45ca_2 - tk=8.6.10=hed695b0_0 - tornado=6.0.4=py37h516909a_0 - traitlets=4.3.3=py37_0 - traittypes=0.2.1=py_1 - tzcode=2019a=h516909a_1002 - udunits2=2.2.27.6=h4e0c4b3_1001 - urllib3=1.25.7=py37_0 - vcs=8.2=py_2 - voila=0.1.21=py_0 - vtk-cdat=8.2.0.8.2=py37_mesalibhead77ed_0 - wcwidth=0.1.8=py_0 - webencodings=0.5.1=py_1 - webob=1.8.6=py_0 - wget=1.20.1=h22169c7_0 - wheel=0.34.2=py_1 - widgetsnbextension=3.5.1=py37_0 - wrapt=1.12.1=py37h516909a_0 - x264=1!152.20180806=h14c3975_0 - xarray=0.15.0=py_0 - xerces-c=3.2.2=h8412b87_1004 - xorg-kbproto=1.0.7=h14c3975_1002 - xorg-libice=1.0.10=h516909a_0 - xorg-libsm=1.2.3=h84519dc_1000 - xorg-libx11=1.6.9=h516909a_0 - xorg-libxau=1.0.9=h14c3975_0 - xorg-libxdmcp=1.1.3=h516909a_0 - xorg-libxext=1.3.4=h516909a_0 - xorg-libxrender=0.9.10=h516909a_1002 - xorg-renderproto=0.11.1=h14c3975_1002 - xorg-xextproto=7.3.0=h14c3975_1002 - xorg-xproto=7.0.31=h14c3975_1007 - xz=5.2.4=h14c3975_1001 - zeromq=4.3.2=he1b5a44_2 - zipp=3.1.0=py_0 - zlib=1.2.11=h516909a_1006 - zstd=1.4.4=h3b9ef0a_1 - pip: - astunparse==1.6.3 - bokeh==2.0.0 - bottleneck==1.3.2 - cdms2==3.1.4 - cloudpickle==1.3.0 - colour==0.1.5 - dask==2.12.0 - distributed==2.12.0 - fsspec==0.6.2 - geojson==2.5.0 - heapdict==1.0.1 - joblib==0.14.1 - locket==0.2.0 - markdown==3.2.1 - mpld3==0.3 - msgpack==1.0.0 - partd==1.1.0 - pint==0.11 - pixiedust==1.1.18 - psutil==5.7.0 - pyqt5-sip==4.19.18 - pyqtwebengine==5.12.1 - pyyaml==5.3 - regrid2==3.1.4 - requests-magpie==0.1.1 - salem==0.2.4 - scikit-learn==0.22.2.post1 - sortedcontainers==2.1.0 - tblib==1.6.0 - toolz==0.10.0 - typing-extensions==3.7.4.1 - xclim==0.14.0 - zict==2.0.0 prefix: /usr/local/envs/birdy ```
tlvu
added a commit
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Mar 10, 2020
… salem for Era5 Raven notebooks See PR Ouranosinc/PAVICS-e2e-workflow-tests#36 or commit Ouranosinc/PAVICS-e2e-workflow-tests@f916bea jupyter_bokeh (the extension, not the package) was removed due to this issue bokeh/jupyter_bokeh#93 Era5 Raven notebook PR: Ouranosinc/raven#200 Noticeable rather large Jupyter env changes: ```diff < - birdy=v0.6.5=py_0 > - birdy=v0.6.6=py_0 < - bokeh=1.4.0=py36_0 > - bokeh==2.0.0 # from pip recursive dependencies (we get newer version by not explicitly get from conda !) < - esgf-compute-api=2.2.1=py_2 > - esgf-compute-api=2.2.3=py_0 < - jupyterlab=1.2.5=py_0 > - jupyterlab=2.0.1=py_0 < - owslib=0.19.0=py_2 > - owslib=0.19.1=py_0 < - pandas=0.25.3=py36hb3f55d8_0 > - pandas=1.0.1=py37hb3f55d8_0 < - python=3.6.7=h357f687_1006 > - python=3.7.6=h357f687_4_cpython > - regionmask=0.5.0=py_1 < - xarray=0.14.1=py_1 > - xarray=0.15.0=py_0 < - dask==2.9.2 > - dask==2.12.0 > - salem==0.2.4 < - xclim==0.13.0 > - xclim==0.14.0 ``` Full conda env export Diff: [200120-200309-conda-env-export.diff.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4309639/200120-200309-conda-env-export.diff.txt) Full new conda env export: [200309-conda-env-export.yml.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4309640/200309-conda-env-export.yml.txt)
huard
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Mar 10, 2020
tlvu
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Mar 10, 2020
Some noticeable change: Ouranosinc/raven#200
This was referenced Mar 10, 2020
tlvu
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Mar 13, 2020
jupyter docker: upgrade birdy, pin pandas and geopandas for Era5 Raven notebooks This is to productize all the manual `pip install --user` we had to do to demo Era5 Raven notebook PR: Ouranosinc/raven#200 Latest birdy 0.6.9 is working flawlessly with existing old Finch 0.2.7 and existing recently released Raven 0.10.0. See Jenkins run http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/install-birdy-from-source/9/console for Finch testing. Raven test done manually. So I'll release this Jupyter env so at least the Raven notebooks works without manually hacking the Jupyter env. Old Finch is not broken anymore so no regression there. birdy updated for Raven, then for Finch. Pinning of pandas and geopandas is due to salem not supporting geopandas >= 0.7 as in this issue fmaussion/salem#152 so can unpin once there are new release of salem. scikit-image was also need by Raven notebook `gridded_data_subset.ipynb`. The ipyleaflet marker do not display in Raven `Region_selection.ipynb` but can be moved and its coordinate can be extracted. Not sure why, maybe relate to jupyter-widgets/ipyleaflet#91. Possibly also due to the freshly released jupyterlab-2.0 but downgrading jupyterlab means downgrading all the other jupyter extensions we used, too much work to just fix one broken extension so did not follow that road. The marker was working fine in the previous image `pavics/workflow-tests:200120` which had jupyterlab-1.2.5 which further support the theory that jupyterlab-2.0 broke it. Noticeable Jupyter env changes: ```diff < - birdy=v0.6.6=py_0 > - birdhouse-birdy==0.6.9 (install from Pypi instead of Conda to fix DockerHub failure !) < - geopandas=0.7.0=py_1 > - geopandas=0.6.2=py_0 < - pandas=1.0.1=py37hb3f55d8_0 > - pandas=0.25.3=py37hb3f55d8_0 > - scikit-image=0.16.2=py37hb3f55d8_0 ``` Full conda env export Diff: [200309-200310-conda-env-export.diff.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4315141/200309-200310-conda-env-export.diff.txt) [200310-200312-conda-env-export.diff.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4326073/200310-200312-conda-env-export.diff.txt) [200309-200312-conda-env-export.diff.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4326058/200309-200312-conda-env-export.diff.txt) ```diff 15d14 < - birdy=v0.6.6=py_0 18d16 < - boltons=20.0.0=py_0 28c26 < - certifi=2019.11.28=py37_0 --- > - certifi=2019.11.28=py37hc8dfbb8_1 36a35 > - cloudpickle=1.3.0=py_0 39c38 < - coverage=5.0.3=py37h516909a_0 --- > - coverage=5.0.3=py37h8f50634_1 42a42,43 > - cytoolz=0.10.1=py37h516909a_0 > - dask-core=2.12.0=py_0 60d60 < - funcsigs=1.0.2=py_3 65,66c65,66 < - geopandas=0.7.0=py_1 < - geos=3.8.0=he1b5a44_0 --- > - geopandas=0.6.2=py_0 > - geos=3.8.0=he1b5a44_1 81a82 > - imageio=2.8.0=py_0 97c98 < - jupyter_console=6.0.0=py_0 --- > - jupyter_console=6.1.0=py_0 106,107c107,108 < - kealib=1.4.10=h58c409b_1005 < - kiwisolver=1.1.0=py37hc9558a2_0 --- > - kealib=1.4.12=hec59c27_0 > - kiwisolver=1.1.0=py37h99015e2_1 138c139 < - libspatialite=4.3.0a=hd318ce7_1035 --- > - libspatialite=4.3.0a=hd318ce7_1036 153c154 < - markupsafe=1.1.1=py37h516909a_0 --- > - markupsafe=1.1.1=py37h8f50634_1 162c163 < - nbdime=1.1.0=py37_0 --- > - nbdime=2.0.0=py37hc8dfbb8_0 168a170 > - networkx=2.4=py_1 173c175 < - numpy=1.18.1=py37h95a1406_0 --- > - numpy=1.18.1=py37h8960a57_0 183c185 < - pandas=1.0.1=py37hb3f55d8_0 --- > - pandas=0.25.3=py37hb3f55d8_0 223a226 > - pywavelets=1.1.1=py37hc1659b7_0 234a238 > - scikit-image=0.16.2=py37hb3f55d8_0 237,239c241,243 < - setuptools=46.0.0=py37_0 < - shapely=1.7.0=py37h5d51c17_0 < - six=1.14.0=py37_0 --- > - setuptools=46.0.0=py37hc8dfbb8_2 > - shapely=1.7.0=py37hb106bac_1 > - six=1.14.0=py_1 243c247 < - sqlalchemy=1.3.13=py37h516909a_0 --- > - sqlalchemy=1.3.15=py37h8f50634_1 251,252c255,257 < - tornado=6.0.4=py37h516909a_0 < - traitlets=4.3.3=py37_0 --- > - toolz=0.10.0=py_0 > - tornado=6.0.4=py37h8f50634_1 > - traitlets=4.3.3=py37hc8dfbb8_1 266d270 < - wrapt=1.12.1=py37h516909a_0 287a292 > - birdhouse-birdy==0.6.9 288a294 > - boltons==20.0.0 291d296 < - cloudpickle==1.3.0 293d297 < - dask==2.12.0 295a300 > - funcsigs==1.0.2 316d320 < - toolz==0.10.0 317a322 > - wrapt==1.12.1 ``` Full new conda env export: [200310-conda-env-export.yml.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4315142/200310-conda-env-export.yml.txt) [200312-conda-env-export.yml.txt](https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/files/4326061/200312-conda-env-export.yml.txt) ``` name: birdy channels: - cdat - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=0_gnu - affine=2.3.0=py_0 - alembic=1.4.1=py_0 - async_generator=1.10=py_0 - attrs=19.3.0=py_0 - backcall=0.1.0=py_0 - beautifulsoup4=4.8.2=py37_0 - bleach=3.1.1=py_0 - blinker=1.4=py_1 - boost-cpp=1.72.0=h8e57a91_0 - branca=0.3.1=py_0 - bzip2=1.0.8=h516909a_2 - ca-certificates=2019.11.28=hecc5488_0 - cairo=1.16.0=hfb77d84_1002 - cartopy=0.17.0=py37h39d8c00_1011 - cdat_info=8.2=py_7 - cdtime=3.1.3=py37h1ac8016_0 - cdutil=8.2=py_2 - certifi=2019.11.28=py37hc8dfbb8_1 - certipy=0.1.3=py_0 - cffi=1.14.0=py37hd463f26_0 - cfitsio=3.470=hb60a0a2_2 - cftime=1.0.4.2=py37hc1659b7_0 - chardet=3.0.4=py37_1003 - click=7.0=py_0 - click-plugins=1.1.1=py_0 - cligj=0.5.0=py_0 - cloudpickle=1.3.0=py_0 - colorama=0.4.3=py_0 - configurable-http-proxy=4.2.0=node13_he01fd0c_2 - coverage=5.0.3=py37h8f50634_1 - cryptography=2.8=py37h72c5cf5_1 - curl=7.68.0=hf8cf82a_0 - cycler=0.10.0=py_2 - cytoolz=0.10.1=py37h516909a_0 - 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libclang=9.0.1=default_hde54327_0 - libcurl=7.68.0=hda55be3_0 - libdap4=3.20.4=hd3bb157_0 - libdrs=3.1.2=h9b7ed86_9 - libdrs_f=3.1.2=h322d3c2_5 - libedit=3.1.20170329=hf8c457e_1001 - libffi=3.2.1=he1b5a44_1006 - libgcc-ng=9.2.0=h24d8f2e_2 - libgdal=3.0.4=h022d3c0_1 - libgfortran-ng=7.3.0=hdf63c60_5 - libgomp=9.2.0=h24d8f2e_2 - libiconv=1.15=h516909a_1005 - libidn2=2.3.0=h516909a_0 - libkml=1.3.0=hb574062_1011 - liblapack=3.8.0=11_openblas - libllvm9=9.0.1=hc9558a2_0 - libnetcdf=4.7.3=nompi_h9f9fd6a_101 - libopenblas=0.3.6=h6e990d7_6 - libpng=1.6.37=hed695b0_0 - libpq=12.2=hae5116b_0 - libsodium=1.0.17=h516909a_0 - libspatialindex=1.9.3=he1b5a44_3 - libspatialite=4.3.0a=hd318ce7_1036 - libssh2=1.8.2=h22169c7_2 - libstdcxx-ng=9.2.0=hdf63c60_2 - libtiff=4.1.0=hc3755c2_3 - libunistring=0.9.10=h14c3975_0 - libuuid=2.32.1=h14c3975_1000 - libuv=1.34.0=h516909a_0 - libwebp=1.0.2=h56121f0_5 - libxcb=1.13=h14c3975_1002 - libxkbcommon=0.10.0=he1b5a44_0 - libxml2=2.9.10=hee79883_0 - libxslt=1.1.33=h31b3aaa_0 - 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qt=5.12.5=hd8c4c69_1 - qtconsole=4.7.1=py_0 - qtpy=1.9.0=py_0 - rasterio=1.1.3=py37h900e953_0 - readline=8.0=hf8c457e_0 - regionmask=0.5.0=py_1 - requests=2.23.0=py37_0 - rtree=0.9.4=py37h7b0cdae_0 - ruamel.yaml=0.16.6=py37h516909a_0 - ruamel.yaml.clib=0.2.0=py37h516909a_0 - scikit-image=0.16.2=py37hb3f55d8_0 - scipy=1.4.1=py37h921218d_0 - send2trash=1.5.0=py_0 - setuptools=46.0.0=py37hc8dfbb8_2 - shapely=1.7.0=py37hb106bac_1 - six=1.14.0=py_1 - smmap=3.0.1=py_0 - snuggs=1.4.7=py_0 - soupsieve=1.9.4=py37_0 - sqlalchemy=1.3.15=py37h8f50634_1 - sqlite=3.30.1=hcee41ef_0 - tbb=2018.0.5=h2d50403_0 - terminado=0.8.3=py37_0 - testpath=0.4.4=py_0 - threddsclient=0.4.2=py_0 - tiledb=1.7.0=hcde45ca_2 - tk=8.6.10=hed695b0_0 - toolz=0.10.0=py_0 - tornado=6.0.4=py37h8f50634_1 - traitlets=4.3.3=py37hc8dfbb8_1 - traittypes=0.2.1=py_1 - tzcode=2019a=h516909a_1002 - udunits2=2.2.27.6=h4e0c4b3_1001 - urllib3=1.25.7=py37_0 - vcs=8.2=py_2 - voila=0.1.21=py_0 - vtk-cdat=8.2.0.8.2=py37_mesalibhead77ed_0 - wcwidth=0.1.8=py_0 - webencodings=0.5.1=py_1 - webob=1.8.6=py_0 - wget=1.20.1=h22169c7_0 - wheel=0.34.2=py_1 - widgetsnbextension=3.5.1=py37_0 - x264=1!152.20180806=h14c3975_0 - xarray=0.15.0=py_0 - xerces-c=3.2.2=h8412b87_1004 - xorg-kbproto=1.0.7=h14c3975_1002 - xorg-libice=1.0.10=h516909a_0 - xorg-libsm=1.2.3=h84519dc_1000 - xorg-libx11=1.6.9=h516909a_0 - xorg-libxau=1.0.9=h14c3975_0 - xorg-libxdmcp=1.1.3=h516909a_0 - xorg-libxext=1.3.4=h516909a_0 - xorg-libxrender=0.9.10=h516909a_1002 - xorg-renderproto=0.11.1=h14c3975_1002 - xorg-xextproto=7.3.0=h14c3975_1002 - xorg-xproto=7.0.31=h14c3975_1007 - xz=5.2.4=h14c3975_1001 - zeromq=4.3.2=he1b5a44_2 - zipp=3.1.0=py_0 - zlib=1.2.11=h516909a_1006 - zstd=1.4.4=h3b9ef0a_1 - pip: - astunparse==1.6.3 - birdhouse-birdy==0.6.9 - bokeh==2.0.0 - boltons==20.0.0 - bottleneck==1.3.2 - cdms2==3.1.4 - colour==0.1.5 - distributed==2.12.0 - fsspec==0.6.2 - funcsigs==1.0.2 - geojson==2.5.0 - heapdict==1.0.1 - joblib==0.14.1 - locket==0.2.0 - markdown==3.2.1 - mpld3==0.3 - msgpack==1.0.0 - partd==1.1.0 - pint==0.11 - pixiedust==1.1.18 - psutil==5.7.0 - pyqt5-sip==4.19.18 - pyqtwebengine==5.12.1 - pyyaml==5.3 - regrid2==3.1.4 - requests-magpie==0.1.1 - salem==0.2.4 - scikit-learn==0.22.2.post1 - sortedcontainers==2.1.0 - tblib==1.6.0 - typing-extensions==3.7.4.1 - wrapt==1.12.1 - xclim==0.14.0 - zict==2.0.0 prefix: /usr/local/envs/birdy ```
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Aug 17, 2023
* Added notebooks showing how to work with ERA5, NRCan and CANOPEX data * Using NcML links for ERA5 and NRCan * bumpversion Co-authored-by: David Huard <huard.david@ouranos.ca>
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Overview
This PR includes a few notebooks, with one particular notebook "WF_FromShapefileToStreamflow.ipynb" that allows users to select the dataset (ERA5/NRCAN) and hydrological model (GR4JCN/HMETS/MOHYSE/HBVEC) and perform a complete simulation starting from just a shapefile.
The code makes use of WPS services to extract properties from within the shapefile (area, centroid lat/long, elevation) required to run RAVEN. It then uses the boundaries to extract the gridded data source selected and takes the spatial average of the points falling within the contour. The hydrological model is parameterized and run, providing streamflow stats and graphs.
Current limitations are:
1- Works for North America but West of 0° will be problematic for ERA5 due to 0:360° longitude scheme. Right now is hardcoded as longitude-360.
2- HBVEC and GR4JCN return an error due to the rain_snow_separation that seems to not be coded.
3- No streamflow provided, therefore calibration is not an option. Parameters are fixed and no NSE diagnostics are returned.
4- Had to install python package "salem", Don't know how to force that to be done automatically for future users during the deployment.
Also other notebooks are present in the PR that I wish to continue improving but are not necessarily required in the master at this stage...