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Update the list of classes and functions in each module.
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@pwcazenave
pwcazenave committed May 7, 2019
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Expand Up @@ -47,6 +47,8 @@ Provides
- `utm_from_lonlat`
- `lonlat_from_utm`
- `british_national_grid_to_lonlat`
- `lonlat_decimal_from_degminsec`
- `lonlat_decimal_from_degminsec_wco`

* `ctd` - interrogate an SQLite data base of CTD casts.
- `CTD` - class to hold a range of time series data from many different CTD formats we (PML) encounter.
Expand All @@ -59,6 +61,7 @@ Provides
- `scalar2vector`
- `vector2scalar`
- `residual_flow`
- `progressive_vectors`
- `vorticity`
- `ebb_flood`
- `principal_axis`
Expand All @@ -70,15 +73,18 @@ Provides
- `Domain.horizontal_transect_nodes`
- `Domain.horizontal_transect_elements`
- `Domain.calculate_areas`
- `mp_interp_func`
- `OpenBoundary` - class to handle model open boundaries.
- `OpenBoundary.add_sponge_layer`
- `OpenBoundary.add_tpxo_tides`
- `OpenBoundary.add_nested_forcing`
- `read_sms_mesh`
- `read_fvcom_mesh`
- `read_smesh_mesh`
- `read_mike_mesh`
- `read_gmsh_mesh`
- `read_smesh_mesh`
- `read_fvcom_obc`
- `parse_obc_sections`
- `read_sms_cst`
- `write_sms_mesh`
- `write_sms_bathy`
Expand Down Expand Up @@ -106,6 +112,7 @@ Provides
- `grid_metrics`
- `control_volumes`
- `node_control_area`
- `clockwise`
- `element_control_area`
- `unstructured_grid_volume`
- `unstructured_grid_depths`
Expand All @@ -117,6 +124,21 @@ Provides
- `reduce_triangulation`
- `getcrossectiontriangles`
- `isintriangle`
- `subset_domain`
- `model_exterior`
- `fvcom2ugrid`
- `point_in_pixel`
- `node_to_centre`
- `Graph` - class to hold an unstructured grid as a graph
- `ReducedFVCOMdist` - class to query a grid graph for distance-based metrics
- `GraphFVCOMdepth` - class to query a grid graph for depth-based metrics

* `interpolate` - a class to handle interpolation between unstructured and regular grids.
- `mask_to_fvcom`
- `mask_to_fvcom_meshgrid`
- `MPIRegularInterpolateWorker`
- `MPIRegularInterpolateWorker.InitialiseGrid`
- `MPIRegularInterpolateWorker.InterpolateRegular`

* `ocean` - a number of routines to convert between combinations of temperature, salinity, pressure, depth and density.
- `pressure2depth`
Expand All @@ -141,23 +163,43 @@ Provides
- `calculate_rhum`

* `plot` - plotting class for FVCOM outputs.
- `Depth` - for plotting vertical slices
- `Depth.plot_slice`
- `Time` - for plotting timer series of data
- `Time.plot_line`
- `Time.plot_scatter`
- `Time.plot_quiver`
- `Time.plot_surface`
- `Plotter` - for plotting horizontal maps
- `Plotter.plot_field`
- `Plotter.plot_quiver`
- `Plotter.plot_lines`
- `Plotter.remove_line_plots`
- `Plotter.plot_scatter`
- `Plotter.plot_streamlines`
- `CrossPlotter` - for plotting cross-sections
- `CrossPlotter.cross_section_init`
- `CrossPlotter.plot_pcolor_field`
- `CrossPlotter.plot_quiver`
- `MPIWorker` - for plotting in parallel with MPI
- `MPIWorker.plot_field`
- `MPIWorker.plot_streamlines`
- `Player` - for interactive animation of horizontal maps
- `plot_domain` - to quickly plot a FileReader.
- `colourbar_extension`
- `cm2inch`

* `preproc` - class for creating input files for FVCOM model runs.
- `Model` - hold everything needed to generate new model inputs
- `Model.write_grid`
- `Model.write_coriolis`
- `Model.add_bed_roughness`
- `Model.write_bed_roughness`
- `Model.interp_sst_assimilation`
- `Model.write_sstgrd`
- `Model.interp_ady`
- `Model.interp_ady_climatology`
- `Model.write_adygrd`
- `Model.add_sigma_coordinates`
- `Model.sigma_generalized`
- `Model.sigma_geometric`
Expand All @@ -173,24 +215,98 @@ Provides
- `Model.write_river_forcing`
- `Model.write_river_namelist`
- `Model.read_nemo_rivers`
- `Model.read_ea_river_temperature_climatology`
- `Model.add_probes`
- `Model.write_probes`
- `Model.add_stations`
- `Model.write_stations`
- `Model.add_nests`
- `Model.add_nests_harmonics`
- `Model.add_nests_regular`
- `Model.avg_nest_force_vel`
- `Model.load_nested_forcing`
- `Model.write_nested_forcing`
- `Model.add_obc_types`
- `Model.write_obc`
- `Model.add_groundwater`
- `Model.write_groundwater`
- `Model.read_regular`
- `Model.subset_existing_nest`
- `Model.load_elevtide`
- `Model.write_tsobc`
- `NameListEntry` - class for holding entries in a NameList class
- `NameListEntry.string`
- `NameListEntry.tolist`
- `NameList` - class for creating FVCOM model namelists
- `NameList.index`
- `NameList.value`
- `NameList.update`
- `NameList.update_nudging`
- `NameList.update_nesting_interval`
- `NameList.valid_nesting_timescale`
- `NameList.update_ramp`
- `NameList.write_model_namelist`
- `write_model_namelist`
- `Nest` - class for holding nested OpenBoudnary objects
- `Nest.add_level`
- `Nest.add_weights`
- `Nest.add_tpxo_tides`
- `Nest.add_nested_forcing`
- `Nest.add_fvcom_tides`
- `Nest.avg_nest_force_vel`
- `WriteForcing` - actually a fairly generic class to write netCDFs with a concise syntax
- `WriteForcing.add_variable`
- `WriteForcing.write_fvcom_time`
- `RegularReader` - like `PyFVCOM.read.FileReader`, but for regularly gridded data.
- `read_regular` - load multiple regularly gridded files.
- `HYCOMReader` - like `PyFVCOM.read.FileReader`, but for HYCOM data.
- `read_hycom` - load multiple regularly gridded files.
- `RegularReader` - like `PyFVCOM.read.FileReader`, but for regularly gridded data
- `RegularReader.closest_element`
- `RegularReader.closest_node`
- `read_regular` - load multiple regularly gridded files
- `HYCOMReader` - like `PyFVCOM.read.FileReader`, but for HYCOM data
- `HYCOMReader.load_data`
- `read_hycom` - load multiple regularly gridded files
- `NEMOReader` - like `RegularReader`, but specifically for NEMO outputs
- `NEMOReader.load`
- `NemoRestartRegularReader`
- `Regular2DReader`
- `Restart` - class to interact/modify FVCOM restart files
- `Restart.replace_variable`
- `Restart.replace_variable_with_regular`
- `Restart.write_restart`
- `Restart.read_regular`

* `read` - parse the netCDF model output and extract a subset of the variables.
- `FileReader`
- `MFileReader`
- `FileReaderFromDict`
- `FileReader` - read in FVCOM outputs
- `FileReader.add`
- `FileReader.subtract`
- `FileReader.multiply`
- `FileReader.divide`
- `FileReader.power`
- `FileReader.load_data`
- `FileReader.closest_time`
- `FileReader.grid_volume`
- `FileReader.total_volume_var`
- `FileReader.avg_volume_var`
- `FileReader.time_to_index`
- `FileReader.time_average`
- `FileReader.add_river_flow
- `FileReader.to_excel`
- `FileReader.to_csv`
- `read_nesting_nodes`
- `apply_mask`
- `MFileReader` - read in multiple FVCOM outputs
- `SubDomainReader` - subset a model domain in space
- `SubDomainReader.add_evap_precip`
- `SubDomainReader.add_river_data`
- `SubDomainReader.aopen_integral`
- `SubDomainReader.volume_integral`
- `SubDomainReader.surface_integral`
- `time_to_index`
- `FileReaderFromDict` - have a go at converting from `ncread` output to `FileReader` format
- `ncwrite`
- `ncread`
- `ncread` - read netCDF data to a dictionary
- `read_probes`
- `write_probes`
- `WriteFVCOM` - write a FileReader object to a netCDF file in FVCOM format

* `stats` - some basic statistics tools.
- `calculate_regression`
Expand Down Expand Up @@ -224,55 +340,63 @@ Provides
- `lanczos` - As above, but not a class.

* `utilities` - general utilities (including time utilities)
- `general.PassiveStore` - our template class for lots of other classes
- `general.fix_range`
- `general.ind2sub`
- `general.flatten_list`
- `general.split_string`
- `general.ObjectFromDict`
- `general.clean_html`
- `general.cart2pol`
- `general.pol2cart`
- `time.julian_day`
- `time.gregorian_date`
- `time.overlap`
- `time.common_time`
- `time.make_signal`
- `time.ramped_signal`

* `validation` - post-processing and validation utilities. Some of these are currently incomplete.
- `validation_db`
- `validation_db.execute_sql`
- `validation_db.create_table`
- `validation_db.insert_into_table`
- `validation_db.select_qry`
- `validation_db.table_exists`
- `validation_db.close_conn`
- `ValidationDB`
- `ValidationDB.execute_sql`
- `ValidationDB.create_table`
- `ValidationDB.insert_into_table`
- `ValidationDB.select_qry`
- `ValidationDB.table_exists`
- `ValidationDB.close_conn`
- `dt_to_epochsec`
- `epochsec_to_dt`
- `plot_map`
- `plot_tides`
- `db_tide`
- `db_tide.make_bodc_tables`
- `db_tide.insert_tide_file`
- `db_tide.get_tidal_series`
- `db_tide.get_gauge_locations`
- `db_tide.get_nearest_gauge_id`
- `bodc_annual_tide_file`
- `db_wco`
- `db_wco.make_wco_tables`
- `db_wco.insert_CTD_file`
- `db_wco.insert_buoy_file`
- `db_wco.insert_CTD_dir`
- `db_wco.insert_csv_file`
- `db_wco.get_observations`
- `WCO_obs_file`
- `csv_formatted`
- `comp_data`
- `comp_data.retrieve_file_data`
- `comp_data.retrieve_obs_data`
- `comp_data.get_comp_data_interpolated`
- `comp_data.comp_data_nearest`
- `comp_data.model_closest_time`
- `comp_data_filereader`
- `comp_data_filereader.retrieve_file_data`
- `comp_data_filereader.model_closest_time`
- `comp_data_probe`
- `comp_data_probe.retrieve_file_data`
- `ICES_comp`
- `ICES_comp.get_var_comp`
- `TideDB`
- `TideDB.make_bodc_tables`
- `TideDB.insert_tide_file`
- `TideDB.get_tidal_series`
- `TideDB.get_gauge_locations`
- `TideDB.get_nearest_gauge_id`
- `BODCAnnualTideFile`
- `WCODB`
- `WCODB.make_wco_tables`
- `WCODB.insert_CTD_file`
- `WCODB.insert_buoy_file`
- `WCODB.insert_CTD_dir`
- `WCODB.insert_csv_file`
- `WCODB.get_observations`
- `WCOParseFile`
- `CSVFormatter`
- `CompareData`
- `CompareData.retrieve_file_data`
- `CompareData.retrieve_obs_data`
- `CompareData.get_comp_data_interpolated`
- `CompareData.comp_data_nearest`
- `CompareData.model_closest_time`
- `CompareDataFileReader`
- `CompareDataFileReader.retrieve_file_data`
- `CompareDataFileReader.model_closest_time`
- `CompareDataProbe`
- `CompareDataProbe.retrieve_file_data`
- `CompareICES`
- `CompareICES.get_var_comp`

Examples
--------
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