chore: idsse-554: create "sci" Python submodule (#53)

* create new Python submodule for code that uses numpy, shapely, or pyproj
* removing explicit version from docker pygrib so conda can figure out the version it needs
---------

Co-authored-by: michael.rabellino <[email protected]>

python/idsse_common/idsse/common/geo_image.py → python/idsse_common/idsse/common/sci/geo_image.py

@@ -20,10 +20,9 @@
 from PIL import Image
 from shapely import from_geojson, from_wkt, Geometry, LineString, MultiPolygon, Polygon
 
-
-from .grid_proj import GridProj
-from .utils import round_
-from .vectaster import geographic_to_pixel, rasterize
+from idsse.common.utils import round_
+from idsse.common.sci.grid_proj import GridProj
+from idsse.common.sci.vectaster import geographic_to_pixel, rasterize
 
 logger = logging.getLogger(__name__)
 

python/idsse_common/idsse/common/grid_proj.py → python/idsse_common/idsse/common/sci/grid_proj.py

@@ -21,7 +21,7 @@
 from pyproj.enums import TransformDirection
 
 from idsse.common.utils import round_values, RoundingParam
-from idsse.common.scientific_utils import coordinate_pairs_to_axes
+from idsse.common.sci.utils import coordinate_pairs_to_axes
 
 # type hints
 Scalar = Union[int, float, np.integer, np.float_]

python/idsse_common/idsse/common/vectaster.py → python/idsse_common/idsse/common/sci/vectaster.py

@@ -17,9 +17,9 @@
 import numpy
 from shapely import Geometry, LinearRing, LineString, MultiPolygon, Point, Polygon, from_wkt
 
-from idsse.common.grid_proj import GridProj
+from idsse.common.sci.grid_proj import GridProj
+from idsse.common.sci.utils import Pixel, Coord, Coords, coordinate_pairs_to_axes
 from idsse.common.utils import round_, round_values, RoundingMethod, RoundingParam
-from idsse.common.scientific_utils import Pixel, Coord, Coords, coordinate_pairs_to_axes
 
 logger = logging.getLogger(__name__)
 

python/idsse_common/test/test_geo_image.py → python/idsse_common/test/sci/test_geo_image.py

@@ -14,9 +14,9 @@
 import numpy
 from pytest import fixture, approx
 
-from idsse.common.geo_image import ColorPalette, GeoImage, normalize, scale_to_color_palette
-from idsse.common.grid_proj import GridProj
-from idsse.common.netcdf_io import read_netcdf
+from idsse.common.sci.geo_image import ColorPalette, GeoImage, normalize, scale_to_color_palette
+from idsse.common.sci.grid_proj import GridProj
+from idsse.common.sci.netcdf_io import read_netcdf
 
 
 @fixture
@@ -376,8 +376,8 @@ def test_color_palette_with_anchor():
 
 
 def test_add_all_states(proj):
-    current_path = os.path.dirname(os.path.realpath(__file__))
-    filename = os.path.join(current_path, 'resources', 'nbm_temp-202211111100-202211121300.nc')
+    filename = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'resources',
+                            'nbm_temp-202211111100-202211121300.nc')
     attrs, data = read_netcdf(filename)
     if attrs['data_order'] == 'latitude,longitude':
         data = numpy.transpose(data)

python/idsse_common/test/test_grid_proj.py → python/idsse_common/test/sci/test_grid_proj.py

@@ -18,7 +18,7 @@
 import numpy as np
 from pytest import approx, fixture, raises
 
-from idsse.common.grid_proj import GridProj
+from idsse.common.sci.grid_proj import GridProj
 from idsse.common.utils import round_, RoundingMethod
 
 

python/idsse_common/test/test_netcdf_io.py → python/idsse_common/test/sci/test_netcdf_io.py

@@ -16,15 +16,11 @@
 from pytest import fixture, approx
 from numpy import ndarray
 
-from idsse.common.netcdf_io import read_netcdf, read_netcdf_global_attrs, write_netcdf
+from idsse.common.sci.netcdf_io import read_netcdf, read_netcdf_global_attrs, write_netcdf
 
 
 # test data
-EXAMPLE_NETCDF_FILEPATH = os.path.join(
-    os.path.dirname(__file__),
-    'resources',
-    'gridstore55657865.nc'
-)
+EXAMPLE_NETCDF_FILEPATH = f'{os.path.dirname(__file__)}/../resources/gridstore55657865.nc'
 
 EXAMPLE_ATTRIBUTES = {
     'product': 'NBM.AWS.GRIB',

python/idsse_common/test/test_vectaster.py → python/idsse_common/test/sci/test_vectaster.py

@@ -16,8 +16,8 @@
 import numpy
 from pytest import fixture, MonkeyPatch
 
-from idsse.common.grid_proj import GridProj
-from idsse.common.vectaster import (geographic_to_pixel,
+from idsse.common.sci.grid_proj import GridProj
+from idsse.common.sci.vectaster import (geographic_to_pixel,
                                     geographic_linestring_to_pixel,
                                     geographic_point_to_pixel,
                                     geographic_polygon_to_pixel,
@@ -80,9 +80,9 @@ def test_geographic_to_pixel(monkeypatch: MonkeyPatch, grid_proj: GridProj):
     point_mock = Mock()
     line_string_mock = Mock()
     polygon_mock = Mock()
-    monkeypatch.setattr('idsse.common.vectaster.geographic_point_to_pixel', point_mock)
-    monkeypatch.setattr('idsse.common.vectaster.geographic_linestring_to_pixel', line_string_mock)
-    monkeypatch.setattr('idsse.common.vectaster.geographic_polygon_to_pixel', polygon_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.geographic_point_to_pixel', point_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.geographic_linestring_to_pixel', line_string_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.geographic_polygon_to_pixel', polygon_mock)
 
     _ = geographic_to_pixel(point, grid_proj)
     point_mock.assert_called_once_with(point, grid_proj, None)
@@ -172,9 +172,9 @@ def test_rasterize(monkeypatch: MonkeyPatch, grid_proj: GridProj):
     point_mock = Mock()
     linestring_mock = Mock()
     polygon_mock = Mock()
-    monkeypatch.setattr('idsse.common.vectaster.rasterize_point', point_mock)
-    monkeypatch.setattr('idsse.common.vectaster.rasterize_linestring', linestring_mock)
-    monkeypatch.setattr('idsse.common.vectaster.rasterize_polygon', polygon_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.rasterize_point', point_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.rasterize_linestring', linestring_mock)
+    monkeypatch.setattr('idsse.common.sci.vectaster.rasterize_polygon', polygon_mock)
 
     rasterize(point, grid_proj)
     point_mock.assert_called_once()