.. SURFEX Python API documentation master file, created by
   auto_sphinx.py on Fri May  3 13:42:55 2024
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

PYSURFEX documentation
=============================================

.. toctree::
   :maxdepth: 3
   :caption: Contents:

.. include::  README.rst
.. include::  docs/example.rst

Classes
---------------------------------------------
.. autoclass:: pysurfex.namelist_legacy.BaseNamelist
.. autoclass:: pysurfex.namelist_legacy.Namelist
.. autoclass:: pysurfex.observation.Observation
.. autoclass:: pysurfex.file.SurfexIO
.. autoclass:: pysurfex.file.SurfexSurfIO
.. autoclass:: pysurfex.file.PGDFile
.. autoclass:: pysurfex.file.PREPFile
.. autoclass:: pysurfex.file.SURFFile
.. autoclass:: pysurfex.file.SurfexFileVariable
.. autoclass:: pysurfex.file.AsciiSurfexFile
.. autoclass:: pysurfex.file.NCSurfexFile
.. autoclass:: pysurfex.file.FaSurfexFile
.. autoclass:: pysurfex.file.SurfFileTypeExtension
.. autoclass:: pysurfex.file.NetCDFSurfexFile
.. autoclass:: pysurfex.file.TexteSurfexFile
.. autoclass:: pysurfex.file.ForcingFileNetCDF
.. autoclass:: pysurfex.titan.QualityControl
.. autoclass:: pysurfex.titan.Plausibility
.. autoclass:: pysurfex.titan.FirstGuess
.. autoclass:: pysurfex.titan.Fraction
.. autoclass:: pysurfex.titan.Sct
.. autoclass:: pysurfex.titan.Buddy
.. autoclass:: pysurfex.titan.Climatology
.. autoclass:: pysurfex.titan.Redundancy
.. autoclass:: pysurfex.titan.Blacklist
.. autoclass:: pysurfex.titan.DomainCheck
.. autoclass:: pysurfex.titan.NoMeta
.. autoclass:: pysurfex.titan.QCDataSet
.. autoclass:: pysurfex.titan.TitanDataSet
.. autoclass:: pysurfex.titan.Departure
.. autoclass:: pysurfex.read.ReadData
.. autoclass:: pysurfex.read.ConvertedInput
.. autoclass:: pysurfex.read.ConstantValue
.. autoclass:: pysurfex.read.Converter
.. autoclass:: pysurfex.cmd_parsing.LoadFromFile
.. autoclass:: pysurfex.grib.Grib
.. autoclass:: pysurfex.grib.Grib2Variable
.. autoclass:: pysurfex.configuration.Configuration
.. autoclass:: pysurfex.configuration.ConfigurationFromHarmonie
.. autoclass:: pysurfex.configuration.ConfigurationFromHarmonieAndConfigFile
.. autoclass:: pysurfex.configuration.ConfigurationFromTomlFile
.. autoclass:: pysurfex.forcing.SurfexForcing
.. autoclass:: pysurfex.forcing.SurfexNetCDFForcing
.. autoclass:: pysurfex.forcing.SurfexOutputForcing
.. autoclass:: pysurfex.forcing.NetCDFOutput
.. autoclass:: pysurfex.forcing.AsciiOutput
.. autoclass:: pysurfex.bufr.BufrObservationSet
.. autoclass:: pysurfex.pseudoobs.SentinelObservationSet
.. autoclass:: pysurfex.pseudoobs.CryoclimObservationSet
.. autoclass:: pysurfex.obs.ObservationSet
.. autoclass:: pysurfex.obs.NetatmoObservationSet
.. autoclass:: pysurfex.obs.MetFrostObservations
.. autoclass:: pysurfex.obs.JsonObservationSet
.. autoclass:: pysurfex.obs.ObservationFromTitanJsonFile
.. autoclass:: pysurfex.timeseries.TimeSeries
.. autoclass:: pysurfex.timeseries.TimeSeriesFromConverter
.. autoclass:: pysurfex.namelist.NamelistGenerator
.. autoclass:: pysurfex.variable.Variable
.. autoclass:: pysurfex.binary_input_legacy.PgdInputData
.. autoclass:: pysurfex.binary_input_legacy.PrepInputData
.. autoclass:: pysurfex.binary_input_legacy.OfflineInputData
.. autoclass:: pysurfex.binary_input_legacy.InlineForecastInputData
.. autoclass:: pysurfex.binary_input_legacy.SodaInputData
.. autoclass:: pysurfex.geo.Geo
.. autoclass:: pysurfex.geo.SurfexGeo
.. autoclass:: pysurfex.geo.ConfProj
.. autoclass:: pysurfex.geo.LonLatVal
.. autoclass:: pysurfex.geo.Cartesian
.. autoclass:: pysurfex.geo.LonLatReg
.. autoclass:: pysurfex.geo.IGN
.. autoclass:: pysurfex.run.BatchJob
.. autoclass:: pysurfex.run.SURFEXBinary
.. autoclass:: pysurfex.run.PerturbedOffline
.. autoclass:: pysurfex.run.Masterodb
.. autoclass:: pysurfex.fa.Fa
.. autoclass:: pysurfex.platform_deps.SystemFilePaths
.. autoclass:: pysurfex.platform_deps.SystemFilePathsFromFile
.. autoclass:: pysurfex.interpolation.Interpolation
.. autoclass:: pysurfex.interpolation.ObsOperator
.. autoclass:: pysurfex.ecoclimap.ExternalSurfexInputFile
.. autoclass:: pysurfex.ecoclimap.Ecoclimap
.. autoclass:: pysurfex.ecoclimap.EcoclimapSG
.. autoclass:: pysurfex.netcdf.Netcdf
.. autoclass:: pysurfex.netcdf.Axis
.. autoclass:: pysurfex.netcdf.NetCDFReadVariable
.. autoclass:: pysurfex.netcdf.NetCDFFileVariable
.. autoclass:: pysurfex.obsoul.ObservationDataSetFromObsoul
.. autoclass:: pysurfex.obsoul.ObservationDataSetFromObsoulFile
.. autoclass:: pysurfex.binary_input.InputDataToSurfexBinaries
.. autoclass:: pysurfex.binary_input.OutputDataFromSurfexBinaries
.. autoclass:: pysurfex.binary_input.JsonOutputData
.. autoclass:: pysurfex.binary_input.JsonOutputDataFromFile
.. autoclass:: pysurfex.binary_input.JsonInputData
.. autoclass:: pysurfex.binary_input.JsonInputDataFromFile
.. autoclass:: pysurfex.binary_input.InputDataFromNamelist

Class methods
---------------------------------------------
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.prolog
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.set_pgd_namelist
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.set_offline_namelist
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.set_soda_namelist
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.epilog
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.override
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.set_direct_data_namelist
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.capitalize_namelist_dict
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.lower_case_namelist_dict
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.merge_namelist_dicts
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.ascii2nml
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.ascii_file2nml
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.nml2ascii
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.merge_json_namelist_file
.. automethod:: pysurfex.namelist_legacy.BaseNamelist.get_namelist
.. automethod:: pysurfex.namelist_legacy.Namelist.prolog
.. automethod:: pysurfex.namelist_legacy.Namelist.set_pgd_namelist
.. automethod:: pysurfex.namelist_legacy.Namelist.set_offline_namelist
.. automethod:: pysurfex.namelist_legacy.Namelist.prepare_offline_perturbation
.. automethod:: pysurfex.namelist_legacy.Namelist.set_obs
.. automethod:: pysurfex.namelist_legacy.Namelist.set_soda_namelist
.. automethod:: pysurfex.namelist_legacy.Namelist.epilog
.. automethod:: pysurfex.namelist_legacy.Namelist.override
.. automethod:: pysurfex.namelist_legacy.Namelist.sub
.. automethod:: pysurfex.namelist_legacy.Namelist.delete
.. automethod:: pysurfex.namelist_legacy.Namelist.get_filetype_from_suffix
.. automethod:: pysurfex.namelist_legacy.Namelist.set_direct_data_namelist
.. automethod:: pysurfex.namelist_legacy.Namelist.capitalize_namelist_dict
.. automethod:: pysurfex.namelist_legacy.Namelist.lower_case_namelist_dict
.. automethod:: pysurfex.namelist_legacy.Namelist.merge_namelist_dicts
.. automethod:: pysurfex.namelist_legacy.Namelist.ascii2nml
.. automethod:: pysurfex.namelist_legacy.Namelist.ascii_file2nml
.. automethod:: pysurfex.namelist_legacy.Namelist.nml2ascii
.. automethod:: pysurfex.namelist_legacy.Namelist.merge_json_namelist_file
.. automethod:: pysurfex.namelist_legacy.Namelist.get_namelist
.. automethod:: pysurfex.observation.Observation.print_obs
.. automethod:: pysurfex.observation.Observation.vectors2obs
.. automethod:: pysurfex.observation.Observation.obs2vectors
.. automethod:: pysurfex.observation.Observation.format_lon
.. automethod:: pysurfex.observation.Observation.format_lat
.. automethod:: pysurfex.observation.Observation.get_pos_from_stid
.. automethod:: pysurfex.observation.Observation.get_stid_from_stationlist
.. automethod:: pysurfex.file.SurfexIO.__init__
.. automethod:: pysurfex.file.SurfexIO.field
.. automethod:: pysurfex.file.SurfexIO.points
.. automethod:: pysurfex.file.SurfexIO.interpolate_field
.. automethod:: pysurfex.file.SurfexSurfIO.symlink_input
.. automethod:: pysurfex.file.SurfexSurfIO.copy_input
.. automethod:: pysurfex.file.SurfexSurfIO.archive_output_file
.. automethod:: pysurfex.file.SurfexFileVariable.print_var
.. automethod:: pysurfex.file.AsciiSurfexFile.__init__
.. automethod:: pysurfex.file.AsciiSurfexFile.get_geo
.. automethod:: pysurfex.file.AsciiSurfexFile.read
.. automethod:: pysurfex.file.AsciiSurfexFile.field
.. automethod:: pysurfex.file.AsciiSurfexFile.points
.. automethod:: pysurfex.file.NCSurfexFile.__init__
.. automethod:: pysurfex.file.NCSurfexFile.get_geo
.. automethod:: pysurfex.file.NCSurfexFile.field
.. automethod:: pysurfex.file.NCSurfexFile.points
.. automethod:: pysurfex.file.FaSurfexFile.__init__
.. automethod:: pysurfex.file.FaSurfexFile.field
.. automethod:: pysurfex.file.FaSurfexFile.points
.. automethod:: pysurfex.file.SurfFileTypeExtension.__init__
.. automethod:: pysurfex.file.NetCDFSurfexFile.__init__
.. automethod:: pysurfex.file.NetCDFSurfexFile.read
.. automethod:: pysurfex.file.NetCDFSurfexFile.field
.. automethod:: pysurfex.file.NetCDFSurfexFile.points
.. automethod:: pysurfex.file.TexteSurfexFile.__init__
.. automethod:: pysurfex.file.TexteSurfexFile.read
.. automethod:: pysurfex.file.TexteSurfexFile.field
.. automethod:: pysurfex.file.TexteSurfexFile.points
.. automethod:: pysurfex.file.ForcingFileNetCDF.__init__
.. automethod:: pysurfex.file.ForcingFileNetCDF.read_field
.. automethod:: pysurfex.file.ForcingFileNetCDF.field
.. automethod:: pysurfex.file.ForcingFileNetCDF.points
.. automethod:: pysurfex.titan.QualityControl.__init__
.. automethod:: pysurfex.titan.QualityControl.set_input
.. automethod:: pysurfex.titan.QualityControl.test
.. automethod:: pysurfex.titan.QualityControl.set_flags
.. automethod:: pysurfex.titan.Plausibility.__init__
.. automethod:: pysurfex.titan.Plausibility.set_input
.. automethod:: pysurfex.titan.Plausibility.test
.. automethod:: pysurfex.titan.FirstGuess.set_input
.. automethod:: pysurfex.titan.FirstGuess.test
.. automethod:: pysurfex.titan.Fraction.set_input
.. automethod:: pysurfex.titan.Fraction.test
.. automethod:: pysurfex.titan.Sct.set_input
.. automethod:: pysurfex.titan.Sct.test
.. automethod:: pysurfex.titan.Buddy.test
.. automethod:: pysurfex.titan.Climatology.__init__
.. automethod:: pysurfex.titan.Climatology.set_input
.. automethod:: pysurfex.titan.Climatology.test
.. automethod:: pysurfex.titan.Redundancy.__init__
.. automethod:: pysurfex.titan.Redundancy.set_input
.. automethod:: pysurfex.titan.Redundancy.test
.. automethod:: pysurfex.titan.Blacklist.__init__
.. automethod:: pysurfex.titan.Blacklist.set_input
.. automethod:: pysurfex.titan.Blacklist.test
.. automethod:: pysurfex.titan.DomainCheck.__init__
.. automethod:: pysurfex.titan.DomainCheck.set_input
.. automethod:: pysurfex.titan.DomainCheck.test
.. automethod:: pysurfex.titan.NoMeta.__init__
.. automethod:: pysurfex.titan.NoMeta.set_input
.. automethod:: pysurfex.titan.NoMeta.test
.. automethod:: pysurfex.titan.QCDataSet.get_stid_index
.. automethod:: pysurfex.titan.QCDataSet.get_pos_index
.. automethod:: pysurfex.titan.QCDataSet.perform_tests
.. automethod:: pysurfex.titan.QCDataSet.write_output
.. automethod:: pysurfex.titan.TitanDataSet.__init__
.. automethod:: pysurfex.titan.TitanDataSet.perform_tests
.. automethod:: pysurfex.titan.Departure.__init__
.. automethod:: pysurfex.titan.Departure.get_departure
.. automethod:: pysurfex.titan.Departure.get_values
.. automethod:: pysurfex.read.ReadData.__init__
.. automethod:: pysurfex.read.ReadData.read_time_step
.. automethod:: pysurfex.read.ReadData.print_info
.. automethod:: pysurfex.read.ConvertedInput.__init__
.. automethod:: pysurfex.read.ConvertedInput.read_time_step
.. automethod:: pysurfex.read.ConvertedInput.print_info
.. automethod:: pysurfex.read.ConstantValue.__init__
.. automethod:: pysurfex.read.ConstantValue.read_time_step
.. automethod:: pysurfex.read.ConstantValue.print_info
.. automethod:: pysurfex.read.Converter.__init__
.. automethod:: pysurfex.read.Converter.print_info
.. automethod:: pysurfex.read.Converter.create_variable
.. automethod:: pysurfex.read.Converter.mslp2ps
.. automethod:: pysurfex.read.Converter.read_time_step
.. automethod:: pysurfex.cmd_parsing.LoadFromFile.__call__
.. automethod:: pysurfex.grib.Grib.__init__
.. automethod:: pysurfex.grib.Grib.field
.. automethod:: pysurfex.grib.Grib.read_geo_info
.. automethod:: pysurfex.grib.Grib.read_field_in_message
.. automethod:: pysurfex.grib.Grib.points
.. automethod:: pysurfex.grib.Grib.__init__
.. automethod:: pysurfex.grib.Grib.is_accumulated
.. automethod:: pysurfex.grib.Grib.matches
.. automethod:: pysurfex.grib.Grib.print_keys
.. automethod:: pysurfex.grib.Grib.generate_grib_id
.. automethod:: pysurfex.grib.Grib2Variable.__init__
.. automethod:: pysurfex.grib.Grib2Variable.matches
.. automethod:: pysurfex.grib.Grib2Variable.is_accumulated
.. automethod:: pysurfex.grib.Grib2Variable.print_keys
.. automethod:: pysurfex.grib.Grib2Variable.generate_grib_id
.. automethod:: pysurfex.configuration.Configuration.__init__
.. automethod:: pysurfex.configuration.Configuration.dump_json
.. automethod:: pysurfex.configuration.Configuration.update_setting
.. automethod:: pysurfex.configuration.ConfigurationFromHarmonie.__init__
.. automethod:: pysurfex.configuration.ConfigurationFromHarmonieAndConfigFile.__init__
.. automethod:: pysurfex.configuration.ConfigurationFromTomlFile.__init__
.. automethod:: pysurfex.forcing.SurfexForcing.__init__
.. automethod:: pysurfex.forcing.SurfexNetCDFForcing.__init__
.. automethod:: pysurfex.forcing.SurfexOutputForcing.__init__
.. automethod:: pysurfex.forcing.SurfexOutputForcing._check_sanity
.. automethod:: pysurfex.forcing.SurfexOutputForcing.write_forcing
.. automethod:: pysurfex.forcing.NetCDFOutput.write_forcing
.. automethod:: pysurfex.forcing.NetCDFOutput._define_forcing
.. automethod:: pysurfex.forcing.NetCDFOutput.finalize
.. automethod:: pysurfex.forcing.AsciiOutput.write_forcing
.. automethod:: pysurfex.forcing.AsciiOutput._define_forcing
.. automethod:: pysurfex.forcing.AsciiOutput.finalize
.. automethod:: pysurfex.bufr.BufrObservationSet.td2rh
.. automethod:: pysurfex.bufr.BufrObservationSet.inside_window
.. automethod:: pysurfex.obs.ObservationSet.__init__
.. automethod:: pysurfex.obs.ObservationSet.get_stid_index
.. automethod:: pysurfex.obs.ObservationSet.get_pos_index
.. automethod:: pysurfex.obs.ObservationSet.get_obs
.. automethod:: pysurfex.obs.ObservationSet.matching_obs
.. automethod:: pysurfex.obs.ObservationSet.points
.. automethod:: pysurfex.obs.ObservationSet.write_json_file
.. automethod:: pysurfex.obs.JsonObservationSet.__init__
.. automethod:: pysurfex.obs.ObservationFromTitanJsonFile.__init__
.. automethod:: pysurfex.timeseries.TimeSeries.__init__
.. automethod:: pysurfex.timeseries.TimeSeries.write_json
.. automethod:: pysurfex.namelist.NamelistGenerator.__init__
.. automethod:: pysurfex.namelist.NamelistGenerator.flatten_config
.. automethod:: pysurfex.namelist.NamelistGenerator._flatten_dict_gen
.. automethod:: pysurfex.namelist.NamelistGenerator.namelist_blocks
.. automethod:: pysurfex.namelist.NamelistGenerator.get_namelist
.. automethod:: pysurfex.namelist.NamelistGenerator.check_nml_setting
.. automethod:: pysurfex.namelist.NamelistGenerator.concistency
.. automethod:: pysurfex.namelist.NamelistGenerator.get_filetype_from_suffix
.. automethod:: pysurfex.namelist.NamelistGenerator.assemble_namelist
.. automethod:: pysurfex.namelist.NamelistGenerator.write
.. automethod:: pysurfex.namelist.NamelistGenerator.flatten_list
.. automethod:: pysurfex.namelist.NamelistGenerator.find_num
.. automethod:: pysurfex.variable.Variable.__init__
.. automethod:: pysurfex.variable.Variable.get_filename
.. automethod:: pysurfex.variable.Variable.get_filehandler
.. automethod:: pysurfex.variable.Variable.read_var_field
.. automethod:: pysurfex.variable.Variable.read_var_points
.. automethod:: pysurfex.variable.Variable.set_var
.. automethod:: pysurfex.variable.Variable.read_variable
.. automethod:: pysurfex.variable.Variable.print_variable_info
.. automethod:: pysurfex.variable.Variable.deaccumulate
.. automethod:: pysurfex.variable.Variable.get_basetime
.. automethod:: pysurfex.variable.Variable.rotate_geographic_wind
.. automethod:: pysurfex.binary_input_legacy.PgdInputData.__init__
.. automethod:: pysurfex.binary_input_legacy.OfflineInputData.__init__
.. automethod:: pysurfex.binary_input_legacy.InlineForecastInputData.__init__
.. automethod:: pysurfex.binary_input_legacy.SodaInputData.set_input_observations
.. automethod:: pysurfex.binary_input_legacy.SodaInputData.set_input_sea_assimilation
.. automethod:: pysurfex.binary_input_legacy.SodaInputData.set_input_vertical_soil_oi
.. automethod:: pysurfex.geo.Geo.__init__
.. automethod:: pysurfex.geo.Geo.identifier
.. automethod:: pysurfex.geo.Geo.is_identical
.. automethod:: pysurfex.geo.Geo.write_proj_info
.. automethod:: pysurfex.geo.SurfexGeo.__init__
.. automethod:: pysurfex.geo.SurfexGeo.update_namelist
.. automethod:: pysurfex.geo.SurfexGeo.subset
.. automethod:: pysurfex.geo.ConfProj.__init__
.. automethod:: pysurfex.geo.ConfProj.update_namelist
.. automethod:: pysurfex.geo.ConfProj.subset
.. automethod:: pysurfex.geo.LonLatVal.__init__
.. automethod:: pysurfex.geo.LonLatVal.update_namelist
.. automethod:: pysurfex.geo.LonLatVal.subset
.. automethod:: pysurfex.geo.Cartesian.__init__
.. automethod:: pysurfex.geo.Cartesian.update_namelist
.. automethod:: pysurfex.geo.Cartesian.subset
.. automethod:: pysurfex.geo.LonLatReg.__init__
.. automethod:: pysurfex.geo.LonLatReg.update_namelist
.. automethod:: pysurfex.geo.LonLatReg.subset
.. automethod:: pysurfex.geo.IGN.__init__
.. automethod:: pysurfex.geo.IGN.get_coord
.. automethod:: pysurfex.geo.IGN.ign_mask
.. automethod:: pysurfex.geo.IGN.update_namelist
.. automethod:: pysurfex.geo.IGN.subset
.. automethod:: pysurfex.run.BatchJob.__init__
.. automethod:: pysurfex.run.BatchJob.run
.. automethod:: pysurfex.run.SURFEXBinary.__init__
.. automethod:: pysurfex.run.Masterodb.archive_output
.. automethod:: pysurfex.fa.Fa.__init__
.. automethod:: pysurfex.fa.Fa.field
.. automethod:: pysurfex.fa.Fa.points
.. automethod:: pysurfex.platform_deps.SystemFilePaths.__init__
.. automethod:: pysurfex.platform_deps.SystemFilePaths.substitute_string
.. automethod:: pysurfex.platform_deps.SystemFilePathsFromFile.__init__
.. automethod:: pysurfex.interpolation.Interpolation.__init__
.. automethod:: pysurfex.interpolation.Interpolation.interpolate
.. automethod:: pysurfex.interpolation.Interpolation.rotate_wind_to_geographic
.. automethod:: pysurfex.interpolation.Interpolation.distance
.. automethod:: pysurfex.interpolation.Interpolation.alpha_grid_rot
.. automethod:: pysurfex.interpolation.ObsOperator.__init__
.. automethod:: pysurfex.interpolation.ObsOperator.get_obs_value
.. automethod:: pysurfex.interpolation.ObsOperator.is_in_grid
.. automethod:: pysurfex.interpolation.ObsOperator.obs2vectors
.. automethod:: pysurfex.ecoclimap.ExternalSurfexInputFile.__init__
.. automethod:: pysurfex.ecoclimap.Ecoclimap.__init__
.. automethod:: pysurfex.ecoclimap.Ecoclimap.set_input
.. automethod:: pysurfex.ecoclimap.Ecoclimap.set_bin_files
.. automethod:: pysurfex.ecoclimap.EcoclimapSG.__init__
.. automethod:: pysurfex.ecoclimap.EcoclimapSG.set_bin_files
.. automethod:: pysurfex.ecoclimap.EcoclimapSG.set_input
.. automethod:: pysurfex.ecoclimap.EcoclimapSG.parse_fnames
.. automethod:: pysurfex.netcdf.Netcdf.__init__
.. automethod:: pysurfex.netcdf.Netcdf.field
.. automethod:: pysurfex.netcdf.Netcdf.points
.. automethod:: pysurfex.netcdf.NetCDFReadVariable.__init__
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.__init__
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.axis_types
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.dim_names
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.units
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.lats
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.lons
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.datetimes
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.times
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.members
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.levels
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.is_level
.. automethod:: pysurfex.netcdf.NetCDFFileVariable.check_input_to_soda_dimensions
.. automethod:: pysurfex.binary_input.InputDataToSurfexBinaries.__init__
.. automethod:: pysurfex.binary_input.InputDataToSurfexBinaries.prepare_input
.. automethod:: pysurfex.binary_input.OutputDataFromSurfexBinaries.__init__
.. automethod:: pysurfex.binary_input.OutputDataFromSurfexBinaries.archive_files
.. automethod:: pysurfex.binary_input.JsonOutputData.__init__
.. automethod:: pysurfex.binary_input.JsonOutputData.archive_files
.. automethod:: pysurfex.binary_input.JsonOutputDataFromFile.__init__
.. automethod:: pysurfex.binary_input.JsonOutputDataFromFile.archive_files
.. automethod:: pysurfex.binary_input.JsonInputData.__init__
.. automethod:: pysurfex.binary_input.JsonInputData.prepare_input
.. automethod:: pysurfex.binary_input.JsonInputData.add_data
.. automethod:: pysurfex.binary_input.JsonInputDataFromFile.__init__
.. automethod:: pysurfex.binary_input.JsonInputDataFromFile.prepare_input
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.__init__
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.get_nml_value2
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.get_nml_value
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.get_nml_value_from_string
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.substitute
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.read_macro_setting
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.extend_macro
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.process_macro
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.matching_value
.. automethod:: pysurfex.binary_input.InputDataFromNamelist.process_data
.. automethod:: pysurfex.binary_input.InputDataFromNamelist._process_data

Methods
---------------------------------------------
.. autofunction:: pysurfex.file.guess_file_format
.. autofunction:: pysurfex.titan.define_quality_control
.. autofunction:: pysurfex.titan.merge_json_qc_data_sets
.. autofunction:: pysurfex.cli.get_geo_and_config_from_cmd
.. autofunction:: pysurfex.cli.run_first_guess_for_oi
.. autofunction:: pysurfex.cli.run_masterodb
.. autofunction:: pysurfex.cli.run_surfex_binary
.. autofunction:: pysurfex.cli.run_gridpp
.. autofunction:: pysurfex.cli.run_titan
.. autofunction:: pysurfex.cli.run_oi2soda
.. autofunction:: pysurfex.cli.run_hm2pysurfex
.. autofunction:: pysurfex.cli.set_geo_from_stationlist
.. autofunction:: pysurfex.cli.sentinel_obs
.. autofunction:: pysurfex.cli.qc2obsmon
.. autofunction:: pysurfex.cli.prep
.. autofunction:: pysurfex.cli.plot_points
.. autofunction:: pysurfex.cli.plot_field
.. autofunction:: pysurfex.cli.pgd
.. autofunction:: pysurfex.cli.perturbed_offline
.. autofunction:: pysurfex.cli.offline
.. autofunction:: pysurfex.cli.cli_oi2soda
.. autofunction:: pysurfex.cli.cli_modify_forcing
.. autofunction:: pysurfex.cli.cli_merge_qc_data
.. autofunction:: pysurfex.cli.masterodb
.. autofunction:: pysurfex.cli.hm2pysurfex
.. autofunction:: pysurfex.cli.gridpp
.. autofunction:: pysurfex.cli.dump_environ
.. autofunction:: pysurfex.cli.first_guess_for_oi
.. autofunction:: pysurfex.cli.cryoclim_pseudoobs
.. autofunction:: pysurfex.cli.create_namelist
.. autofunction:: pysurfex.cli.create_lsm_file_assim
.. autofunction:: pysurfex.cli.create_forcing
.. autofunction:: pysurfex.cli.bufr2json
.. autofunction:: pysurfex.cli.obs2json
.. autofunction:: pysurfex.cli.cli_set_domain
.. autofunction:: pysurfex.cli.cli_set_geo_from_obs_set
.. autofunction:: pysurfex.cli.cli_set_geo_from_stationlist
.. autofunction:: pysurfex.cli.cli_shape2ign
.. autofunction:: pysurfex.cli.soda
.. autofunction:: pysurfex.cli.titan
.. autofunction:: pysurfex.cmd_parsing.parse_args_create_forcing
.. autofunction:: pysurfex.cmd_parsing.parse_args_modify_forcing
.. autofunction:: pysurfex.cmd_parsing.parse_args_qc2obsmon
.. autofunction:: pysurfex.cmd_parsing.parse_args_dump_environ
.. autofunction:: pysurfex.cmd_parsing.parse_args_first_guess_for_oi
.. autofunction:: pysurfex.cmd_parsing.parse_args_masterodb
.. autofunction:: pysurfex.cmd_parsing.parse_args_surfex_binary
.. autofunction:: pysurfex.cmd_parsing.parse_args_create_namelist
.. autofunction:: pysurfex.cmd_parsing.parse_args_gridpp
.. autofunction:: pysurfex.cmd_parsing.parse_args_titan
.. autofunction:: pysurfex.cmd_parsing.parse_args_oi2soda
.. autofunction:: pysurfex.cmd_parsing.parse_args_lsm_file_assim
.. autofunction:: pysurfex.cmd_parsing.parse_args_hm2pysurfex
.. autofunction:: pysurfex.cmd_parsing.parse_args_bufr2json
.. autofunction:: pysurfex.cmd_parsing.parse_args_obs2json
.. autofunction:: pysurfex.cmd_parsing.parse_args_plot_points
.. autofunction:: pysurfex.cmd_parsing.parse_args_plot_field
.. autofunction:: pysurfex.cmd_parsing.get_variables_from_args
.. autofunction:: pysurfex.cmd_parsing.parse_args_set_geo_from_obs_set
.. autofunction:: pysurfex.cmd_parsing.parse_args_set_geo_from_stationlist
.. autofunction:: pysurfex.cmd_parsing.parse_args_merge_qc_data
.. autofunction:: pysurfex.cmd_parsing.parse_timeseries2json
.. autofunction:: pysurfex.cmd_parsing.parse_cryoclim_pseudoobs
.. autofunction:: pysurfex.cmd_parsing.variable_parser
.. autofunction:: pysurfex.cmd_parsing.parse_sentinel_obs
.. autofunction:: pysurfex.cmd_parsing.parse_args_shape2ign
.. autofunction:: pysurfex.cmd_parsing.parse_set_domain
.. autofunction:: pysurfex.forcing.write_formatted_array
.. autofunction:: pysurfex.forcing.run_time_loop
.. autofunction:: pysurfex.forcing.set_forcing_config
.. autofunction:: pysurfex.forcing.modify_forcing
.. autofunction:: pysurfex.obsmon.open_db
.. autofunction:: pysurfex.obsmon.close_db
.. autofunction:: pysurfex.obsmon.create_db
.. autofunction:: pysurfex.obsmon.populate_usage_db
.. autofunction:: pysurfex.obsmon.rmse
.. autofunction:: pysurfex.obsmon.absbias
.. autofunction:: pysurfex.obsmon.mean
.. autofunction:: pysurfex.obsmon.calculate_statistics
.. autofunction:: pysurfex.obsmon.populate_obsmon_db
.. autofunction:: pysurfex.obsmon.write_obsmon_sqlite_file
.. autofunction:: pysurfex.geo.get_geo_object
.. autofunction:: pysurfex.geo.set_domain
.. autofunction:: pysurfex.geo.shape2ign
.. autofunction:: pysurfex.run.create_working_dir
.. autofunction:: pysurfex.run.clean_working_dir
.. autofunction:: pysurfex.input_methods.get_datasources
.. autofunction:: pysurfex.datetime_utils.as_datetime
.. autofunction:: pysurfex.datetime_utils.as_datetime_string
.. autofunction:: pysurfex.datetime_utils.offsetaware
.. autofunction:: pysurfex.datetime_utils.as_timedelta
.. autofunction:: pysurfex.datetime_utils.fromtimestamp
.. autofunction:: pysurfex.datetime_utils.utcfromtimestamp
.. autofunction:: pysurfex.datetime_utils.isdatetime
.. autofunction:: pysurfex.datetime_utils.as_datetime_args
.. autofunction:: pysurfex.interpolation.fill_field
.. autofunction:: pysurfex.interpolation.grid2points
.. autofunction:: pysurfex.interpolation.inside_grid
.. autofunction:: pysurfex.interpolation.sum_neighbour_points
.. autofunction:: pysurfex.util.merge_toml_env
.. autofunction:: pysurfex.util.merge_toml_env_from_files
.. autofunction:: pysurfex.util.deep_update
.. autofunction:: pysurfex.util.remove_existing_file
.. autofunction:: pysurfex.util.parse_filepattern
.. autofunction:: pysurfex.netcdf.read_first_guess_netcdf_file
.. autofunction:: pysurfex.netcdf.oi2soda
.. autofunction:: pysurfex.netcdf.read_cryoclim_nc
.. autofunction:: pysurfex.netcdf.read_sentinel_nc

* :ref: `README`

Indices and tables
==================

* :ref:`genindex`
* :ref:`search`