Colocation cleanup and update dev version number

docs/api.rst

@@ -88,7 +88,7 @@ Ungridded data
 Co-located data
 ^^^^^^^^^^^^^^^
 
-.. automodule:: pyaerocom.colocateddata
+.. automodule:: pyaerocom.colocation.colocated_data
    :members:
    :undoc-members:
 
@@ -112,20 +112,20 @@ Co-location routines
 High-level co-location engine
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: pyaerocom.colocation_auto
+.. automodule:: pyaerocom.colocation.colocator
    :members:
 
-.. automodule:: pyaerocom.colocation_setup
+.. automodule:: pyaerocom.colocation.colocation_setup
    :members:
 
 Low-level co-location functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: pyaerocom.colocation
+.. automodule:: pyaerocom.colocation.colocation_utils
    :members:
    :undoc-members:
 
-.. automodule:: pyaerocom.colocation_3d
+.. automodule:: pyaerocom.colocation.colocation_3d
    :members:
    :undoc-members:
 

pyaerocom/__init__.py

@@ -46,9 +46,10 @@
 from .stationdata import StationData
 from .griddeddata import GriddedData
 from .ungriddeddata import UngriddedData
+from .colocation.colocated_data import ColocatedData
+from .colocation.colocator import Colocator
+from .colocation.colocation_setup import ColocationSetup
 from .filter import Filter
-from .colocateddata import ColocatedData
-from .colocation_auto import ColocationSetup, Colocator
 from .tstype import TsType
 from .time_resampler import TimeResampler
 from .io.helpers import search_data_dir_aerocom

pyaerocom/aeroval/_processing_base.py

@@ -3,8 +3,8 @@
 from pyaerocom._lowlevel_helpers import TypeValidator
 from pyaerocom.aeroval import EvalSetup
 from pyaerocom.aeroval.experiment_output import ExperimentOutput
-from pyaerocom.colocation_auto import Colocator
-from pyaerocom.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocator import Colocator
 
 
 class HasConfig:

pyaerocom/aeroval/coldatatojson_helpers.py

@@ -12,12 +12,12 @@
 import pandas as pd
 import xarray as xr
 
+from pyaerocom import ColocatedData, TsType
 from pyaerocom._warnings import ignore_warnings
 from pyaerocom.aeroval.exceptions import ConfigError, TrendsError
 from pyaerocom.aeroval.fairmode_stats import fairmode_stats
 from pyaerocom.aeroval.helpers import _get_min_max_year_periods, _period_str_to_timeslice
 from pyaerocom.aeroval.json_utils import read_json, round_floats, write_json
-from pyaerocom.colocateddata import ColocatedData
 from pyaerocom.config import ALL_REGION_NAME
 from pyaerocom.exceptions import DataCoverageError, TemporalResolutionError
 from pyaerocom.helpers import start_stop
@@ -26,7 +26,6 @@
 from pyaerocom.stats.stats import _init_stats_dummy, calculate_statistics
 from pyaerocom.trends_engine import TrendsEngine
 from pyaerocom.trends_helpers import _get_season_from_months
-from pyaerocom.tstype import TsType
 
 logger = logging.getLogger(__name__)
 

pyaerocom/aeroval/setupclasses.py

@@ -33,7 +33,7 @@
     check_if_year,
 )
 from pyaerocom.aeroval.json_utils import read_json, set_float_serialization_precision, write_json
-from pyaerocom.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocation_setup import ColocationSetup
 
 logger = logging.getLogger(__name__)
 

pyaerocom/aeroval/superobs_engine.py

@@ -4,9 +4,9 @@
 import numpy as np
 import xarray as xr
 
+from pyaerocom import ColocatedData
 from pyaerocom.aeroval._processing_base import HasColocator, ProcessingEngine
 from pyaerocom.aeroval.coldatatojson_engine import ColdataToJsonEngine
-from pyaerocom.colocateddata import ColocatedData
 from pyaerocom.helpers import get_lowest_resolution
 
 logger = logging.getLogger(__name__)

pyaerocom/colocation_3d.py → pyaerocom/colocation/colocation_3d.py

@@ -14,15 +14,6 @@
 
 from pyaerocom import __version__ as pya_ver
 from pyaerocom import const
-from pyaerocom.colocateddata import ColocatedData
-from pyaerocom.colocation import (
-    _colocate_site_data_helper,
-    _colocate_site_data_helper_timecol,
-    _regrid_gridded,
-    check_time_ival,
-    check_ts_type,
-    resolve_var_name,
-)
 from pyaerocom.exceptions import (
     DataUnitError,
     DimensionOrderError,
@@ -34,6 +25,16 @@
 from pyaerocom.helpers import make_datetime_index
 from pyaerocom.tstype import TsType
 
+from .colocated_data import ColocatedData
+from .colocation_utils import (
+    _colocate_site_data_helper,
+    _colocate_site_data_helper_timecol,
+    _regrid_gridded,
+    check_time_ival,
+    check_ts_type,
+    resolve_var_name,
+)
+
 logger = logging.getLogger(__name__)
 
 

pyaerocom/colocation.py → pyaerocom/colocation/colocation_utils.py

@@ -12,7 +12,6 @@
 
 from pyaerocom import __version__ as pya_ver
 from pyaerocom import const
-from pyaerocom.colocateddata import ColocatedData
 from pyaerocom.exceptions import (
     DataUnitError,
     DimensionOrderError,
@@ -31,7 +30,8 @@
 )
 from pyaerocom.time_resampler import TimeResampler
 from pyaerocom.tstype import TsType
-from pyaerocom.variable import Variable
+
+from .colocated_data import ColocatedData
 
 logger = logging.getLogger(__name__)
 

pyaerocom/colocation_auto.py → pyaerocom/colocation/colocator.py

@@ -15,14 +15,11 @@
 
 from pyaerocom import const
 from pyaerocom._lowlevel_helpers import chk_make_subdir
-from pyaerocom.colocateddata import ColocatedData
-from pyaerocom.colocation import (
+from pyaerocom.colocation.colocation_utils import (
     colocate_gridded_gridded,
     colocate_gridded_ungridded,
     correct_model_stp_coldata,
 )
-from pyaerocom.colocation_3d import ColocatedDataLists, colocate_vertical_profile_gridded
-from pyaerocom.colocation_setup import ColocationSetup
 from pyaerocom.exceptions import ColocationError, ColocationSetupError, DataCoverageError
 from pyaerocom.helpers import (
     get_lowest_resolution,
@@ -34,6 +31,10 @@
 from pyaerocom.io.helpers import get_all_supported_ids_ungridded
 from pyaerocom.io.mscw_ctm.reader import ReadMscwCtm
 
+from .colocated_data import ColocatedData
+from .colocation_3d import ColocatedDataLists, colocate_vertical_profile_gridded
+from .colocation_setup import ColocationSetup
+
 logger = logging.getLogger(__name__)
 
 

pyaerocom/combine_vardata_ungridded.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from pyaerocom._lowlevel_helpers import invalid_input_err_str
-from pyaerocom.colocation import _colocate_site_data_helper
+from pyaerocom.colocation.colocation_utils import _colocate_site_data_helper
 from pyaerocom.geodesy import find_coord_indices_within_distance
 from pyaerocom.helpers import sort_ts_types
 from pyaerocom.obs_io import ObsVarCombi

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "pyaerocom"
-version = "0.19.0"
+version = "0.20.dev0"
 authors = [{ name = "MET Norway" }]
 description = "pyaerocom model evaluation software"
 classifiers = [

tests/fixtures/collocated_data.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pandas as pd
 import pytest
-import xarray as xr
 
 from pyaerocom import ColocatedData, Filter
 from pyaerocom.config import ALL_REGION_NAME

tests/plot/test_mapping.py

@@ -6,7 +6,7 @@
 from matplotlib.figure import Figure
 
 from pyaerocom import GriddedData
-from pyaerocom.colocateddata import ColocatedData
+from pyaerocom.colocation.colocated_data import ColocatedData
 from pyaerocom.config import ALL_REGION_NAME
 from pyaerocom.exceptions import DataDimensionError
 from pyaerocom.plot.config import ColorTheme, get_color_theme

tests/test_colocation.py

@@ -5,8 +5,8 @@
 from cf_units import Unit
 
 from pyaerocom import GriddedData, const, helpers
-from pyaerocom.colocateddata import ColocatedData
-from pyaerocom.colocation import (
+from pyaerocom.colocation.colocated_data import ColocatedData
+from pyaerocom.colocation.colocation_utils import (
     _colocate_site_data_helper,
     _colocate_site_data_helper_timecol,
     _regrid_gridded,

tests/test_colocation_3d.py

@@ -5,7 +5,10 @@
 import pytest
 
 from pyaerocom import GriddedData
-from pyaerocom.colocation_3d import ColocatedDataLists, colocate_vertical_profile_gridded
+from pyaerocom.colocation.colocation_3d import (
+    ColocatedDataLists,
+    colocate_vertical_profile_gridded,
+)
 from pyaerocom.io.read_earlinet import ReadEarlinet
 from tests.fixtures.data_access import TEST_DATA
 

tests/test_colocation_auto.py

@@ -5,8 +5,8 @@
 from pydantic import ValidationError
 
 from pyaerocom import ColocatedData, GriddedData, UngriddedData, const
-from pyaerocom.colocation_auto import Colocator
-from pyaerocom.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocator import Colocator
 from pyaerocom.config import ALL_REGION_NAME
 from pyaerocom.exceptions import ColocationError, ColocationSetupError
 from pyaerocom.io.aux_read_cubes import add_cubes

tests/test_colocation_setup.py

@@ -4,7 +4,7 @@
 from pydantic import ValidationError
 
 from pyaerocom import const
-from pyaerocom.colocation_setup import ColocationSetup
+from pyaerocom.colocation.colocation_setup import ColocationSetup
 from pyaerocom.config import ALL_REGION_NAME
 
 COL_OUT_DEFAULT = Path(const.OUTPUTDIR) / "colocated_data"