diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 0ae4e97..8665054 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -16,8 +16,8 @@ on: - 'docs/**' - '*' env: - GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_23.1 + GALAXY_FORK: usegalaxy-eu + GALAXY_BRANCH: release_23.1_europe GALAXY_COPERNICUS_CDSAPIRC_KEY: ${{ secrets.GALAXY_COPERNICUS_CDSAPIRC_KEY }} COPERNICUS_CDSAPIRC_KEY_FILE: ${{ secrets.COPERNICUS_CDSAPIRC_KEY_FILE }} MAX_CHUNKS: 4 diff --git a/tools/netcdf2zarr/.shed.yml b/tools/netcdf2zarr/.shed.yml new file mode 100644 index 0000000..47c8758 --- /dev/null +++ b/tools/netcdf2zarr/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Climate Analysis +description: netCDF to Zarr conversion +homepage_url: https://docs.xarray.dev/en/latest/generated/xarray.Dataset.to_zarr.html +long_description: | + This tool is a wrapper for converting netCDF data into Zarr. +name: netcdf2zarr +owner: climate +remote_repository_url: https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/netcdf2zarr +type: unrestricted diff --git a/tools/netcdf2zarr/README.md b/tools/netcdf2zarr/README.md new file mode 100644 index 0000000..461b6fa --- /dev/null +++ b/tools/netcdf2zarr/README.md @@ -0,0 +1,5 @@ + +# netCDF to Zarr conversion + +This tool allows you to generate NC Zarr from a netCDF file. + diff --git a/tools/netcdf2zarr/test-data/output.dat b/tools/netcdf2zarr/test-data/output.dat new file mode 100644 index 0000000..e69de29 diff --git a/tools/netcdf2zarr/test-data/output.nc b/tools/netcdf2zarr/test-data/output.nc new file mode 100644 index 0000000..2e06aa9 Binary files /dev/null and b/tools/netcdf2zarr/test-data/output.nc differ diff --git a/tools/netcdf2zarr/test-data/output.zarr/.zattrs b/tools/netcdf2zarr/test-data/output.zarr/.zattrs new file mode 100644 index 0000000..5a7b079 --- /dev/null +++ b/tools/netcdf2zarr/test-data/output.zarr/.zattrs @@ -0,0 +1,9 @@ +{ + "ANALYSIS": "Europe, 20210616+[0H_0H]", + "history": "Model ENSEMBLE ANALYSIS", + "institution": "Data produced by Meteo France", + "project": "MACC-RAQ (http://macc-raq.gmes-atmosphere.eu)", + "source": "Data from ENSEMBLE model", + "summary": "ENSEMBLE model hourly ANALYSIS of NO2 concentration at the Surface from 20210616+[0H_0H] on Europe", + "title": "NO2 Air Pollutant ANALYSIS at the Surface" +} \ No newline at end of file diff --git a/tools/netcdf2zarr/test-data/output.zarr/.zgroup b/tools/netcdf2zarr/test-data/output.zarr/.zgroup new file mode 100644 index 0000000..3b7daf2 --- /dev/null +++ b/tools/netcdf2zarr/test-data/output.zarr/.zgroup @@ -0,0 +1,3 @@ +{ + "zarr_format": 2 +} \ No newline at end of file diff --git a/tools/netcdf2zarr/test-data/output.zarr/.zmetadata b/tools/netcdf2zarr/test-data/output.zarr/.zmetadata new file mode 100644 index 0000000..7a421f0 --- /dev/null +++ b/tools/netcdf2zarr/test-data/output.zarr/.zmetadata @@ -0,0 +1,163 @@ +{ + "metadata": { + ".zattrs": { + "ANALYSIS": "Europe, 20210616+[0H_0H]", + "history": "Model ENSEMBLE ANALYSIS", + "institution": "Data produced by Meteo France", + "project": "MACC-RAQ (http://macc-raq.gmes-atmosphere.eu)", + "source": "Data from ENSEMBLE model", + "summary": "ENSEMBLE model hourly ANALYSIS of NO2 concentration at the Surface from 20210616+[0H_0H] on Europe", + "title": "NO2 Air Pollutant ANALYSIS at the Surface" + }, + ".zgroup": { + "zarr_format": 2 + }, + "latitude/.zarray": { + "chunks": [ + 1 + ], + "compressor": { + "blocksize": 0, + "clevel": 5, + "cname": "lz4", + "id": "blosc", + "shuffle": 1 + }, + "dtype": " + Rewrite a netCDF to Zarr + + topic_3318 + + + operation_0335 + + + python + zarr + xarray + netcdf4 + dask + cftime + + + + + + + + + + + + + + + + + + + + + + + @article{hoyer2017xarray, + title = {xarray: {N-D} labeled arrays and datasets in {Python}}, + author = {Hoyer, S. and J. Hamman}, + journal = {Journal of Open Research Software}, + volume = {5}, + number = {1}, + year = {2017}, + publisher = {Ubiquity Press}, + doi = {10.5334/jors.148}, + url = {http://doi.org/10.5334/jors.148} + } + + +