Releases: NordicESMhub/docker-climate-notebook
Version 1.4 Galaxy Climate JupyterLab
Version 1.3 Galaxy Climate JupyterLab
- Base image is now scipy notebook so that we can have pangeo notebook by default.
- Remove additional kernels (julia, R) as there were not specific to climate (no specific packages).
- Created a new container with updated versions of packages for Pangeo, cesm and esmvaltool.
Interactive Climate Notebook (Galaxy Version 0.2)
Interactive Climate Notebook (Galaxy Version 0.2)
The Climate Notebook is based on Jupyter an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.
Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to do the heavy lifting and data reduction steps in Galaxy and the plotting and more interactive part on smaller datasets in Jupyter.
You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
You can import data into the notebook via a predefined get() function and write results back to Galaxy with a put() function.
The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science. The list of packages is based on what is available
on the Pangeo platform and Pangeo stacks.
Core scipy packages: numpy, scipy, matplotlib, pandas, xarray, sparse and sympy
Data science: scikit-image, scikit-learn, dask-ml, tensorflow, keras, pytorch-cpu, dask_labextension
Visualization: holoviews, panel, geoviews, hvplot, geoviews, datashader, seaborn, altair, descartes, folium, vega,
vega_datasets, palettable, cmocean,plotly, psy-maps, psy-reg, psyplot, psyplot-gui, psy-maps, psy-reg,
geopy, branca
System Message: WARNING/2 (, line 22)
Block quote ends without a blank line; unexpected unindent.
Geospatial: iris, cartopy, basemap, basemap-data-hires, geopandas, rasterio, netcdf4, erddapy, pydap, h5py, h5netcdf, regionmask and rio-cogeo
Geoscience related: climlab, metpy, satpy, gsw, eofs, esmpy, xesmf, windspharm, rasterstats, geojsoncontour
Climate related: pyaerocom, cdo, cdsapi, cfgrib, cis. esmvaltool, nc-time-axis, nco
Intake related: intake, intake-xarray, intake-esm, fsspec and intake-stac
zarr related: zarr, numcodecs, python-blosc, lz4, gcsfs, s3fs, tiledb-py
jupyter related: ipyleaflet, papermill, jupytext, ipydatawidgets, sidecar
xarray related: xgcm, xrft, xhistogram, xlrd, xrviz, climpred, pytide, pyinterp
misc: python-wget, prefect, requests, pillow, pip, nbgitpuller, pysplit, biopython, bioblend and galaxy-ie-helpers
Optimised Galaxy Climate Analysis docker container
Same set of packages but it produces a slightly smaller docker container because several RUN commands were grouped together.
Galaxy Climate Analysis docker container
1.0 Added information specific to climate docker