This release comes with many new features, major improvements and a more stable API. Please see the individual points below for major changes.
New feature modules
Modules that contain new features. See [here](https://github.com/metno/pyaerocom/blob/master/changelog/diff_files_v080_v0100.md) for a list of all file modifications between version 0.8.0 and 0.10.0.
- **pyaerocom/combine_vardata_ungridded.py**: Colocation of ungridded data.
- **pyaerocom/helpers_landsea_masks.py**: Access and helpers for land-sea mask filtering.
- **pyaerocom/io/read_ghost.py**: reading routine for GHOST dataset.
- **pyaerocom/io/read_mscw_ctm.py**: Reading interface for EMEP data.
- **pyaerocom/molmasses.py**: helpers related to access of molecular masses for species.
- **pyaerocom/trends_engine.py**: Interface for computing trends using the method by [Mortier et al., 2020](https://acp.copernicus.org/articles/20/13355/2020/acp-20-13355-2020.html).
- **pyaerocom/web/helpers_evaluation_iface.py**: helper methods for conversion of `ColocatedData` to json files for [Aerocom Evaluation interface](https://aerocom-evaluation.met.no/main.php?project=aerocom&exp=glissetal-2020).
- **pyaerocom/web/helpers_trends_iface.py**: helper methods for conversion of `ColocatedData` to json files for [Aerocom trends interface](https://aerocom-trends.met.no/).
- **pyaerocom/web/utils.py**: High-level methods based on results from standard Aerocom analysis. Currently, this contains a method `compute_model_average_and_diversity` which can be used to compute ensemble median or mean modeldata (e.g. used to compute AEROCOM-MEDIAN and MEAN in [Gliss et al., 2020](https://acp.copernicus.org/preprints/acp-2019-1214/)).
- **pyaerocom/scripts/cli.py**: simple command line interface (currently very limited).
- **pyaerocom/scripts/highlevel_utils.py**: high-level functions used in CLI.
- **pyaerocom/testdata_access.py**: helpers related to initialization and access of pyaerocom testdata.
Updates related to supported observation data-sets and naming conventions
- Support for reading GHOST data.
- Support for reading of EMEP model data.
Below, relevant changes applied to already existing code are summarized.
Reading of data (`io` sub-package)
Reading of gridded data
- `ReadGridded` class
- Implement logic to apply constraint reading (i.e. read AOD where AE<0.5, read scattering where RH<40%, etc.). See input arg. `constraints` in `ReadGridded.read_var` and associated new class methods listed below.
- Improve flexibility related to multiple vert_code matches using new method get_vert_code in Variable class.
- Improve logic associated with resolving variable names for edge cases that include usage of alias variables and auxiliary reading of derived variables.
- Add new default auxiliary / derived variables: `sc550dryaer`, `concox`, `vmrox`, `fmf550aer`.
- New attrs. (incl. property decorators): `vars_provided`, `registered_var_patterns`.
- New methods: `reinit`, `check_constraint_valid`, `apply_read_constraint`, `__repr__`.
- **New**: Reading interface and support for EMEP file conventions (class `ReadMscvCtm`).
Reading of ungridded data
- `ReadUngridded`
- Add option `only_cached` in `read` method, to only read cached data e.g. when working offline.
- ReadUngridded can post compute variables with merge method combine.
- New attrs. (incl. property decorators): `data_dir`, `post_compute`
- New methods: `read_dataset_post`, `get_vars_supported`
- **NEW**: Reading interface for GHOST data (class `ReadGhost`).
- **read_ebas.oy** (`ReadEbas` and `ReadEbasOptions`)
- Introduced more reading options (e.g. related to shifting of wavelengths and assumed Angstrom Exponents used for shifting).
- **NOTE**: Before, data at wavelengths (wvl) within a tolerance of +/- 50nm were considered around the output wvl (e.g. 500-600nm for sc550aer) and were used as is (i.e. without converting the values to 550nm). Now, the column with wvl closest to the output wvl is used and the measurement data is shifted to the output wvl (e.g. 550nm) assuming a typical Angstrom Exponent (AE=1.5 for extinction and scattering, AAE=1 for absorption, [note also upcoming changes for next major release version 0.11.0](https://github.com/metno/pyaerocom/issues/285)).
- Remove `filelog` in `ReadEbas`.
- Resolve some issues related to old variable names and aliases.
- Implement unit check in column selection method `_find_best_data_column`.
- Add `framework` to output data.
- Added attrs. in `ReadEbas` (incl. property methods): `sqlite_database_file`, `file_dir`.
- `ReadUngriddedBase` (template metaclass for ungridded reading)
- allow to specify `dataset_path` (less dependency on server access, easier to work with local datasets)
- New attrs. (incl. property decorators): `data_id`
- New methods (implemented): `var_supported`
Further updates in `io` sub-package
- **cachehandler_ungridded.py** (`CacheHandlerUngridded` class)
- Modified to handle custom filenames (e.g. used in new method `UngriddedData.save_as`).
- New method `delete_all_cache_files`
- New option `force_use_outdated`
- Add method `get_ungridded_reader` in **io/utils.py**.
Data objects
- `GriddedData`
- Can be converted to xarray.
- More robust and flexible time-series extraction, e.g., constraints can be applied during temporal resampling (i.e. hierarchical `min_num_obs` or `how`).
- Improving automatic retrieval of lowest layer for profile data using CF attr. "positive".
- Method `mean` now uses area weighted mean by default.
- New methods: `years_avail`, `split_years`, `mean_at_coords`, `filter_altitude`, `filter_region`, `apply_region_mask`, `aerocom_savename`, `to_xarray`, `area_weighted_mean`
- `UngriddedData`
- Can be filtered by country names
- Can now be saved as pickled objects
- Create UngriddedData from StationData object(s)
- Colocation of UngriddedData is now possible (relevant code is in new module `combine_vardata_ungridded.py`)
- Support for wildcards in station data conversion methods.
- New attrs. (incl. decorators): `last_meta_idx`, `nonunique_station_names`, `countries_available`
- New methods: `from_station_data` (static method), `check_set_country`, `check_convert_var_units`, `filter_altitude`, `filter_region`, `apply_region_mask`, `colocate_vardata`, `save_as`, `from_cache` (static method).
- `ColocatedData`
- Implement method to compute regional time-series.
- Support automatic assignments of countries for each site.
- Support computation of area weighted statistics in `calc_statistics`.
- New attributes: `has_time_dim`, `has_latlon_dims`, `countries_available`, `country_codes_available`, `area_weights`
- New methods: `get_country_codes`, `calc_area_weights`, `flatten_latlondim_station_name`, `stack`, `unstack`, `check_set_countries`, `filter_altitude`, `apply_country_filter`, `set_zeros_nan`, `apply_region_mask`, `filter_region`, `get_regional_timeseries`
- `StationData`
- Computation of climatological time-series
- Improved handling of metadata access (`get_meta`) and merging of metadata
- `resample_timeseries` was renamed to `resample_time` (but old version still works.)
- new method `StationData.copy`
Colocation of data
Low-level colocation routines (`colocation.py`)
- Outliers in gridded/gridded colocation are now removed in original resolution.
- Gridded/gridded colocation now re-grids to the lowest of both resolutions.
- Add option resample_how, which can also be applied hierarchical, like `min_num_obs` (e.g. used to resample O3max).
- `resample_how` option in high level colocation routines.
- Option to use obs climatology for gridded / ungridded colocation.
- New helper method `correct_model_stp_coldata` in `colocation.py` which applies STP correction to a colocated data object containing obs at STP based on station altitude and temperature derived from ERA Interim data (BETA feature only working for 2010 data and with access to METNo infrastructure).
- Some bug fixes for certain edge cases.
High-level colocation routines (`colocation_auto.py`)
Affects classes `ColocationSetup` and `Colocator`
- Support new EMEP reading routine.
- Model and obsdata directories can be specified explicitly.
- Option `model_to_stp` (BETA feature which will not work in most cases, see above).
- New attrs. `obs_add_meta`, `resample_how`.
- New methods (`Colocator`): `read_model_data`, `read_ungridded`
Filtering of data
- Implement filtering of binary masks for `GriddedData`, `UngriddedData` and `ColocatedData`
- Harmonize API of spatial filtering in data classes (i.e. method `filter_region` that can handle rectangular and binary region masks)
- Automatic access to HTAP binary land-sea masks
- Handling of binary and rectangular regions in `Filter` class.
Other updates (in top-level modules)
- **config.py** (`Config` class)
- Major improvements and API changes, e.g. related to automatic setup and adding new data search directories and ungridded observations.
- In particular, attrs. `BASEDIR`, `MODELBASEDIR`, `OBSBASEDIR` are deprecated.
- Instead, methods `add_data_search_dir` and `add_ungridded_obs` can be used to register data locations.
- **geodesy.py**: new methods `calc_latlon_dists`, `find_coord_indices_within_distance`, `get_country_info_coords`.
- New methods in `helpers.py`, the most relevant ones are `extract_latlon_dataarray`, `make_dummy_cube_latlon`, `numpy_to_cube`, `sort_ts_types`, `calc_climatology`.
- New methods in `mathutils.py`: `weighted_sum`, `sum`, `weighted_mean`, `weighted_cov`, `weighted_corr`, `corr` (which were implemented in `calc_statistics`), `vmrx_to_concx`, `concx_to_vmrx`.
- New class `AerocomDataID` in **metastandards.py** (is used in `ReadGridded` to separate data ID into metadata based on AeroCom 3 conventions).
- New helper classes `ObsVarCombi` and `AuxInfoUngridded` in `obs_io.py`.
- `region.py`: New method `Region.plot` and support for binary regions.
- `TimeResampler`: implement handling of `how` to specify aggregating kernel (e.g. mean, max, min, std...).
- New and interactive tutorials, for details see [pyaerocom-tutorials repo](https://github.com/metno/pyaerocom-tutorials).
- **NEW**: colocation routine for ungridded data, the relevant code is in ne module `test_combine_vardata_ungridded.py`). NOTE: currently only implemented to create colocated `UngriddedData` objects, a routine that outputs `ColocatedData` object will come in v0.11.0.
- **tstype.py** (class `TsType`)
- Implement setter method for `mulfac`
- New attrs (incl. property decorators): `TO_NUMPY`, `RS_OFFSETS` (not in use), `TSTR_TO_CF`, `datetime64_str`, `timedelta64_str`, `cf_base_unit`, `next_lower`, `next_higher`
- New methods: `to_timedelta64`, `valid`, `to_numpy_freq`
- Rename method `to_pandas` to `to_pandas_freq`
- **variable.py**
- Define wildcard based lookup of default vertical codes for variable families (in `VarNameInfo`) and related class method `get_default_vert_code` (experimental)
- new helper function `get_emep_variables`
- `Variable` class
- New attrs (incl. property decorators): `var_name_aerocom`, `default_vert_code`, `var_name_input`, `is_3d`, `is_wavelength_dependent`, `is_dry`, `is_alias`
- New methods: `get_default_vert_code`, `__eq__`
- `VarCollection` class
- support adding new variables (in addition to the ones defined in an ini file)
- New methods: `add_var`, `get_var`
- **NEW** toplevel method `pyaerocom.initialise_testdata()`: checks access to testdataset and downloads it to directory *~/MyPyaerocom* if not available (or outdated).
Web processing tools (`web` sub-package)
- Better separation of modules and code for AerocomEvalation tools and AerosolTrends tools.
- Add support for auxiliary / derived obsdatasets in `web.helpers.ObsConfigEval`.
- New method to compute ensemble median or mean in **web/utils.py**.
Aerocom Evaluation tools
- Store a copy of the config file in experiment output directory.
- Option `weighted_stats` in `AerocomEvaluation` (if active, weighted statistics are applied to gridded/gridded colocated objects in heatmaps).
- Create json files for daily and monthly heat-maps.
- Support also country based regional statistics (`AerocomEvaluation.regions_how`)
- Regional time-series are now computed automatically for all regions.
- Support evaluation of diurnal (hourly data).
- utility function `compute_model_average_and_diversity` now also outputs fields for 1. and 3. quantiles (median) and std. (mean)
- New options `--onlyjson` and `--warnings` in CLI `pyaeroeval`.
- Improved robustness and flexibility of evaluation framework.
- New methods and attrs. in `AerocomEvaluation` class:
- Attrs: `only_json`, `weighted_stats`, `regions_how`, `region_groups`, `resample_how`, `all_obs_vars`, `iface_names`, `name_config_file`, `name_config_file_json`,
- Methods: `get_model_name`, `get_diurnal_only`, `read_model_data`, `read_ungridded_obsdata`,
Trends evaluation tools
No relevant changes here (only some refacturing).
Plotting (`plot` sub-package)
- New method `plot_nmb_map_colocateddata` in plot/mapping.py for plotting bias maps from `ColocatedData`
- Improve options in heatmap plot (**plot/heatmaps.py**) (i.e. smart automatic formatting of heatmap annotation if values span several orders of magnitude).
- Some bug fixes associated with automatic retrieval of colorbar levels (**io/helpers.py**).
- New method `init_multimap_grid` in **plot/mapping.py**
- Annotation fontsize in `plot_scatter` can now be controlled now via input arg `fontsize_annot`
Major API changes (not backwards compatible):
- Renamed class ReadSulphurAasEtAl to ReadAasEtal
- StationData.resample_timeseries is deprecated (but still works) and usage of new method resample_time is recommended
- Some AeroCom variables were renamed (e.g. scatc550aer -> sc550aer, absc550aer -> ac550aer, bscatc* -> bsc*, etc.)
Testing and CI
- Most tests now uses a publicly available test dataset.
- Implemented automatic CI testing in Github Actions.
- Add **conftest.py** for defining session wide test fixtures.
- Many more tests resulting in largely improved test coverage, [see here](https://github.com/metno/pyaerocom/blob/master/changelog/diff_files_v080_v0100.md).
Bug fixes
- Fix bug related to merging of `StationData` in case of overlapping time-series (issue [106](https://github.com/metno/pyaerocom/issues/106)).
- Fix bug in method `GriddedData.change_base_year`
- ReadEbas: Fixed bug related to column selection for wavelength range which identified data columns as valid if there was only one column match for var of interest.
- Fix minor bug in reordering of dimensions of GriddedData when one dimension definition was missing.
- Fix bug in GriddedData.crop due to time bounds not removed correctly.
- Fix bug related related to extraction of time interval in `GriddedData.sel` (see [here](https://github.com/metno/pyaerocom/issues/225) for details).
Upcoming changes
See [here](https://github.com/metno/pyaerocom/milestone/3) for a list of changes planned for the next upcoming release.