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Merge pull request #1483 from lesserwhirls/docs
Documentation updates
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‎docs/src/site/_data/sidebars/netcdfJavaTutorial_sidebar.yml‎

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- title: netCDF-Java Reference Docs
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output: web, pdf
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folderitems:
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- title: ArrayStructures
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url: /arraystructures_ref.html
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output: web, pdf
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- title: BUFR Files
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url: /bufr_processing.html
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output: web, pdf
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- title: BUFR Tables
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url: /bufr_tables.html
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output: web, pdf
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- title: CDM File Types
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url: /file_types.html
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output: web, pdf
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- title: CDM Calendar Date Handling
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url: /cdm_calendar_date_time_ref.html
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output: web, pdf
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- title: CDM Disk Caching
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url: /disk_caching.html
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output: web, pdf
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- title: CDMRemote
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url: /cdmremote.html
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output: web, pdf
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- title: CDMRemote Feature Datasets
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url: /cdmremote_feature_datasets.html
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output: web, pdf
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- title: CDM to NetCDF Mapping
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url: /cdm_netcdf_mapping.html
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output: web, pdf
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- title: CDM - OPeNDAP Interface
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url: /cdm_opendap_interface.html
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output: web, pdf
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- title: NetCDF4 Compound Attributes
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url: /cdm_netcdf_mapping.html
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output: web, pdf
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- output: web, pdf
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subfolders:
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- title: More API
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output: web, pdf
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subfolderitems:
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- title: ArrayStructures
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url: /arraystructures_ref.html
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output: web, pdf
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- title: CDM Calendar Date Handling
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url: /cdm_calendar_date_time_ref.html
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output: web, pdf
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- title: CDM Disk Caching
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url: /disk_caching.html
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output: web, pdf
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- title: Dataset URLs
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url: /dataset_urls.html
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output: web, pdf
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- title: Forecast Model Run Collection
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url: /fmrc_ref.html
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output: web, pdf
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- title: netCDF C Library
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url: /netcdf4_c_library.html
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output: web, pdf
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- title: PointFeature Reference
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url: /pointfeature_ref.html
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output: web, pdf
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- title: Standard Horizontal Coordinate Transforms
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url: /std_horizonal_coord_transforms.html
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output: web, pdf
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- title: Unidata Defined System Properties
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url: /systemproperties.html
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output: web, pdf
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- title: Common Data Model Mappings
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output: web, pdf
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subfolderitems:
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- title: CDM to NetCDF Mapping
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url: /cdm_netcdf_mapping.html
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output: web, pdf
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- title: CDM - OPeNDAP Interface
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url: /cdm_opendap_interface.html
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output: web, pdf
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- title: Conventions
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output: web, pdf
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subfolderitems:
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- title: CF DSG Encoding Table
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url: /cf_dsg_encoding_ref.html
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output: web, pdf
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- title: Coordinate Attribute Convention
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url: /coord_attr_conv.html
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output: web, pdf
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- title: Data Formats
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output: web, pdf
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subfolderitems:
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- title: CDM File Types
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url: /file_types.html
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output: web, pdf
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- title: BUFR Files
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url: /bufr_processing.html
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output: web, pdf
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- title: BUFR Tables
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url: /bufr_tables.html
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output: web, pdf
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- title: GRIB Files in CDM
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url: /grib_files_cdm.html
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output: web, pdf
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- title: GRIB Tables in CDM
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url: /grib_tables.html
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output: web, pdf
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- title: GRIB Collection Specification
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url: /grib_feature_collections_ref.html
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output: web, pdf
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- title: Reading Zarr
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url: /reading_zarr.html
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output: web, pdf
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- title: Remote Access
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output: web, pdf
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subfolderitems:
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- title: Read CDM files over HTTP
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url: /read_over_http.html
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output: web, pdf
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- title: CDMRemote
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url: /cdmremote.html
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output: web, pdf
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- title: CDMRemote Feature Datasets
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url: /cdmremote_feature_datasets.html
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output: web, pdf
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- title: NC Stream
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url: /ncstream.html
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output: web, pdf
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- title: NC Stream Grammar
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url: /ncstream_grammar.html
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output: web, pdf
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- title: NetCDF Subset Service
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external_url: https://docs.unidata.ucar.edu/tds/current/userguide/netcdf_subset_service_ref.html
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output: web, pdf
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- title: NcML
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output: web, pdf
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subfolderitems:
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- title: NcML Overview
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url: /ncml_overview.html
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output: web, pdf
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- title: NcML Cookbook
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url: /ncml_cookbook.html
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output: web, pdf
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- title: Annotated Schema for NcML
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url: /annotated_ncml_schema.html
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output: web, pdf
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- title: CDM Utility Programs
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url: /cdm_utility_programs.html
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output: web, pdf
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- title: CF DSG Encoding Table
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url: /cf_dsg_encoding_ref.html
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output: web, pdf
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- title: Coordinate Attribute Convention
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url: /coord_attr_conv.html
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output: web, pdf
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- title: Dataset URLs
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url: /dataset_urls.html
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output: web, pdf
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- title: Forecast Model Run Collection
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url: /fmrc_ref.html
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output: web, pdf
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- title: GRIB Files in CDM
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url: /grib_files_cdm.html
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output: web, pdf
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- title: GRIB Tables in CDM
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url: /grib_tables.html
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output: web, pdf
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- title: GRIB Collection Specification
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url: /grib_feature_collections_ref.html
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output: web, pdf
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- title: NcML Overview
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url: /ncml_overview.html
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output: web, pdf
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- title: NcML Cookbook
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url: /ncml_cookbook.html
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output: web, pdf
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- title: Annotated Schema for NcML
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url: /annotated_ncml_schema.html
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output: web, pdf
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- title: NC Stream
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url: /ncstream.html
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output: web, pdf
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- title: NC Stream Grammar
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url: /ncstream_grammar.html
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output: web, pdf
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- title: netCDF-Java and TDS Doc Guide
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url: /doc_guide.html
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output: web, pdf
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- title: NetCDF Subset Service
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external_url: https://docs.unidata.ucar.edu/tds/current/userguide/netcdf_subset_service_ref.html
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output: web, pdf
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- title: netCDF C Library
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url: /netcdf4_c_library.html
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output: web, pdf
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- title: PointFeature Reference
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url: /pointfeature_ref.html
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output: web, pdf
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- title: Read CDM files over HTTP
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url: /read_over_http.html
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output: web, pdf
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- title: Reading Zarr
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url: /reading_zarr.html
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output: web, pdf
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- title: Standard Horizontal Coordinate Transforms
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url: /std_horizonal_coord_transforms.html
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output: web, pdf
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- title: ToolsUI Reference
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url: /toolsui_ref.html
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output: web, pdf
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- title: Unidata Defined System Properties
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url: /systemproperties.html
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- title: netCDF-Java and TDS Doc Guide
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url: /doc_guide.html
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‎docs/src/site/pages/netcdfJava/GribFilesCdm.md‎

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A GRIB file is an unordered collection of GRIB records.
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A GRIB record consists of a single 2D (x, y) slice of data.
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The CDM library reads a GRIB file and creates a 2, 3,4, or 5 dimension Variable (time, ensemble, z, y, x), by finding the records with the same parameter, with different time / level / ensemble coordinates.
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This amounts to [guessing the dataset schema](https://www.unidata.ucar.edu/blogs/developer/en/entry/dataset_schemas_are_lost_in){:target="_blank"} and the intent of the data provider, and is unfortunately a bit arbitrary.
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This amounts to [guessing the dataset schema](https://www.unidata.ucar.edu/blogs/developer/entry/dataset_schemas_are_lost_in){:target="_blank"} and the intent of the data provider, and is unfortunately a bit arbitrary.
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Most of our testing is against the NCEP operational models from the [IDD](https://www.unidata.ucar.edu/projects/index.html#idd){:target="_blank"}, and so are influenced by those.
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Deciding how to group the GRIB records into CDM Variables is one of the main source of problems.
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It uses the following GRIB fields to construct a unique variable.

‎docs/src/site/pages/netcdfJava/Upgrade.md‎

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Point release notes:
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* [5.7.0](https://github.com/Unidata/netcdf-java/releases/tag/v5.7.0){:target="_blank"} (_2025-01-06_)
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5.7.x adds support for a service provider interface for applying enhancements by NSF Unidata summer intern Leo Matak (see https://www.unidata.ucar.edu/blogs/developer/en/entry/extensible-ncml-for-ai-ml for more information!).
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5.7.x adds support for a service provider interface for applying enhancements by NSF Unidata summer intern Leo Matak (see https://www.unidata.ucar.edu/blogs/developer/entry/extensible-ncml-for-ai-ml for more information!).
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BUFR support has been enhanced to include multi-category messages thanks to an external contribution from github user @Yaqiang!
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Please see the release notes on GitHub for more details on additions, enhancements, and bug fixes.
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Much of the work in 5.4.x is focused on establishing a public API.
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We now publish two sets of javadocs - [with](../javadoc-with-deprecations/){:target="_blank"} and [without deprecations](../javadoc/){:target="_blank"}.
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For more information about these efforts and why this work is being done, please visit ([link](https://www.unidata.ucar.edu/blogs/developer/en/entry/netcdf-java-looking-ahead){:target="_blank"}).
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For more information about these efforts and why this work is being done, please visit ([link](https://www.unidata.ucar.edu/blogs/developer/entry/netcdf-java-looking-ahead){:target="_blank"}).
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Only those classes and methods outlined in the javadocs [without deprecations](../javadoc/) will exist in the next major release of netCDF-Java (`v6.0`).
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For more information about the changes in this release, please visit the [netCDF-Java github wiki](https://github.com/Unidata/netcdf-java/wiki#public-api-details){:target="_blank"}.

‎docs/src/site/pages/netcdfJava/faq.md‎

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#### Q: What is the relationship of NetCDF with HDF5?
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The netCDF-4 file format is built on top of the <a href="http://www.hdfgroup.org/HDF5/">HDF5 file format</a>. NetCDF adds shared dimensions, so it is unfortunately not a strict subset of HDF5. Gory details are here: <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimensions_scales">Part 1</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scale2">Part 2</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scales_part_3">Part 3</a>.
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The netCDF-4 file format is built on top of the <a href="http://www.hdfgroup.org/HDF5/">HDF5 file format</a>. NetCDF adds shared dimensions, so it is unfortunately not a strict subset of HDF5. Gory details are here: <a href="https://www.unidata.ucar.edu/blogs/developer/entry/dimensions_scales">Part 1</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/entry/dimension_scale2">Part 2</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scales_part_3">Part 3</a>.
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HDF5 is a very complicated format, and we do not plan to write a pure Java version for writing netCDF4 files (we do have a pure Java version for reading both HDF5 and netCDF-4). You must use the JNI interface to the [netCDF C library](netcdf4_c_library.html).
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‎docs/src/site/pages/netcdfJava_tutorial/cdmdatasets/writing_netcdf.md‎

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#### Writing to a netCDF-4 file with compression (version 4.5)
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The main use of netCDF-4 is to get the performance benefits from compression, and possibly from chunking
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([why it matters](https://www.unidata.ucar.edu/blogs/developer/en/entry/chunking_data_why_it_matters)).
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([why it matters](https://www.unidata.ucar.edu/blogs/developer/entry/chunking_data_why_it_matters)).
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By default, the Java library will use the default chunking algorithm to write chunked and compressed netcdf-4 files.
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To control chunking and compression settings, you must create a `Nc4Chunking` object and pass it into `NetcdfFormatWriter.createNewNetcdf4`:
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