chore(CI/CD): bump version 0.7.5 -> 0.7.6 (#463)

* chore(CI/CD): bump version 0.7.5 -> 0.7.6

* docs: update CHANGELOG.md

* chore: remove geopandas datasets from tests

* chore: apply refurb suggestions

* chore: change test typing

* chore: set minimal versions for dependencies

* chore: bumped scipy version

* chore: remove pytest-xdist dependency

* chore: set minimal versions for dependencies

* ci: change pdm groups installation

* chore: change lightning fabrik import

* chore: bumped pytorch-lightning and pytest versions

* chore: bumped kaleido and plotly version

* chore: bumped pillow version

* chore: bumped pillow version

* chore: bumped h3ronpy version

* chore: set minimal versions for dependencies

* chore: bumped mapclassify version

* chore: bumped mapclassify version

* chore: bumped scikit-learn version

* chore: bumped scikit-learn version

* chore: bumped folium and spherical-geometry version

* chore: bumped topojson version

* chore: set minimal versions for dependencies

* chore: bump scikit learn and scipy versions

* chore: add numpy divide error ignore

---------

Co-authored-by: Kamil Raczycki <[email protected]>

.github/workflows/ci-dev.yml

@@ -69,7 +69,7 @@ jobs:
       - name: Regenerate lock with environment markers
         run: pdm lock --update-reuse --strategy inherit_metadata
       - name: Generate requirements.txt
-        run: pdm export --no-default -G osm -G voronoi -G gtfs -G plotting -G torch -dG docs -dG visualization -f requirements -o requirements.txt
+        run: pdm export --no-default -G all -dG docs -dG visualization -f requirements -o requirements.txt
       - name: Install dependencies
         run: pip install --no-deps -r requirements.txt
       - name: Install nbconvert dependency

.github/workflows/ci-prod.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Regenerate lock with environment markers
         run: pdm lock --update-reuse --strategy inherit_metadata
       - name: Generate requirements.txt
-        run: pdm export --no-default -G osm -G voronoi -G gtfs -G plotting -G torch -dG docs -dG visualization -f requirements -o requirements.txt
+        run: pdm export --no-default -G all -dG docs -dG visualization -f requirements -o requirements.txt
       - name: Install dependencies
         run: pip install --no-deps -r requirements.txt
       - name: Install nbconvert dependency

.github/workflows/generate-dev-docs.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Regenerate lock with environment markers
         run: pdm lock --update-reuse --strategy inherit_metadata
       - name: Generate requirements.txt
-        run: pdm export --no-default -G docs -G visualization -f requirements -o requirements.txt
+        run: pdm export --no-default -dG docs -dG visualization -f requirements -o requirements.txt
       - name: Install dependencies
         run: pip install --no-deps -r requirements.txt
       - name: Install nbconvert dependency

.github/workflows/manual_tests.yml

@@ -30,9 +30,9 @@ jobs:
       - name: Install pdm
         run: pip install pdm
       - name: Generate lock with newest dependencies
-        run: pdm lock --lockfile pdm.newest.lock --strategy no_cross_platform -G osm -G voronoi -G gtfs -G plotting -G torch -dG test
+        run: pdm lock --lockfile pdm.newest.lock --strategy no_cross_platform -G all -dG test
       - name: Install srai and tests dependencies
-        run: pdm install --lockfile pdm.newest.lock -G osm -G voronoi -G gtfs -G plotting -G torch -dG test --skip=post_install
+        run: pdm install --lockfile pdm.newest.lock -G all -dG test --skip=post_install
       - name: Run tests with pytest
         run: pdm run pytest -v --durations=20 tests
 
@@ -56,8 +56,8 @@ jobs:
       - name: Install pdm
         run: pip install pdm
       - name: Generate lock with oldest dependencies
-        run: pdm lock --lockfile pdm.oldest.lock --strategy no_cross_platform,direct_minimal_versions -G osm -G voronoi -G gtfs -G plotting -G torch -dG test
+        run: pdm lock --lockfile pdm.oldest.lock --strategy no_cross_platform,direct_minimal_versions -G all -dG test
       - name: Install srai and tests dependencies
-        run: pdm install --lockfile pdm.oldest.lock -G osm -G voronoi -G gtfs -G plotting -G torch -dG test --skip=post_install
+        run: pdm install --lockfile pdm.oldest.lock -G all -dG test --skip=post_install
       - name: Run tests with pytest
         run: pdm run pytest -v --durations=20 tests

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.7.6] - 2024-08-29
+
 ### Fixed
 
 - Changed a typo in the `BASE_OSM_GROUPS_FILTER` (implemented by [@starsep](https://github.com/starsep)).
@@ -290,7 +292,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Intersection Joiner
 - Geoparquet Loader
 
-[Unreleased]: https://github.com/kraina-ai/srai/compare/0.7.5...HEAD
+[Unreleased]: https://github.com/kraina-ai/srai/compare/0.7.6...HEAD
+
+[0.7.6]: https://github.com/kraina-ai/srai/compare/0.7.5...0.7.6
 
 [0.7.5]: https://github.com/kraina-ai/srai/compare/0.7.4...0.7.5
 

CITATION.cff

@@ -30,7 +30,7 @@ keywords:
   - geospatial
   - spatial-analysis
 license: Apache-2.0
-version: 0.7.5
+version: 0.7.6
 date-released: '2022-11-23'
 preferred-citation:
   type: conference-paper

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "srai"
-version = "0.7.5"
+version = "0.7.6"
 description = "A set of python modules for geospatial machine learning and data mining"
 authors = [
     { name = "Piotr Gramacki", email = "[email protected]" },
@@ -12,18 +12,17 @@ authors = [
 dependencies = [
     "pandas",
     "geopandas>=0.6",
-    "shapely>=2",
+    "shapely>=2.0.1",
     "h3>=4.0.0b1",
     "numpy>=1.26.0",
-    "geoparquet",
-    "pyfunctional",
+    "pyfunctional>=1.0.0",
     "pyarrow>=13.0.0",
-    "topojson",
+    "topojson>=1.6",
     "tqdm>=4.42.0",
     "s2>=0.1.9",
     "typeguard>=3.0.0",
     "requests",
-    "h3ronpy>=0.18.0",
+    "h3ronpy>=0.20.1",
     "osmnx>=1.3.0",
 ]
 requires-python = ">=3.9"
@@ -59,25 +58,26 @@ Changelog = "https://github.com/kraina-ai/srai/blob/main/CHANGELOG.md"
 
 # pdm add -G osm <library>
 osm = [
-    "overpass",
-    "pillow",
+    "overpass>=0.7",
+    "pillow>=8.0.0",
     "beautifulsoup4",
     "quackosm>=0.9.1",
 ]
 # pdm add -G voronoi <library>
-voronoi = ["pymap3d", "haversine", "scipy", "spherical-geometry"]
+voronoi = ["pymap3d>=3.0.0", "haversine>=2.0.0", "scipy>=1.10.0", "spherical-geometry>=1.3.2"]
 # pdm add -G gtfs <library>
 gtfs = ["gtfs-kit"]
 # pdm add -G plotting <library>
 plotting = [
-    "folium",
-    "mapclassify",
+    "folium>=0.14.0",
+    "mapclassify>=2.4.0",
+    "scikit-learn>=1.2.0",
     "matplotlib>=3.2.0",
-    "plotly",
-    "kaleido<=0.2.1",
+    "plotly>=4.6.0",
+    "kaleido<=0.2.1,>=0.2.0",
 ] # kaleido<=0.2.1 because installation breaks on 0.2.1.post1
 # pdm add -G torch <library>
-torch = ["pytorch-lightning", "torch"]
+torch = ["pytorch-lightning>=2.0.0", "torch"]
 all = ["srai[osm,voronoi,gtfs,plotting,torch]"]
 
 
@@ -94,17 +94,15 @@ dev = ["bumpver", "types-requests"]
 lint = ["pre-commit", "mypy", "docformatter[tomli]", "ruff"]
 # pdm add -dG test <library>
 test = [
-    "pytest>=7.0.0",
+    "pytest>=8.0.0",
     "tox-pdm>=0.7.2",
     "pytest-mock>=3.3.0",
     "requests-mock>=1.12.1",
     "pytest-check>=2.3.1",
     "pytest-parametrization>=2022.2.1",
     "pytest-doctestplus>=1.2.1",
-    "pytest-xdist",
-    "pyogrio",
-    "six",
-    "pytest-snapshot",
+    "six>=1.9.0",
+    "pytest-snapshot>=0.9.0",
 ]
 # pdm add -dG visualization <library>
 visualization = ["keplergl", "matplotlib"]
@@ -119,7 +117,7 @@ docs = [
     "mkdocs-gen-files",
     "mkdocs-awesome-pages-plugin",
     "mike>=1,<2",
-    "scikit-learn",
+    "scikit-learn>=1.2.0",
     "umap-learn",
 ]
 # performance = ["scalene"]
@@ -192,7 +190,7 @@ close-quotes-on-newline = true
 wrap-one-line = true
 
 [tool.bumpver]
-current_version = "0.7.5"
+current_version = "0.7.6"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "chore(CI/CD): bump version {old_version} -> {new_version}"
 commit = true

srai/__init__.py

@@ -10,4 +10,4 @@
 for complete documentation.
 """
 
-__version__ = "0.7.5"
+__version__ = "0.7.6"

srai/regionalizers/_spherical_voronoi.py

@@ -57,12 +57,13 @@ def _generate_sphere_parts() -> None:
         POINT_LEFT = (0.0, -1.0, 0.0)  # LON: -90; LAT: 0
         POINT_RIGHT = (0.0, 1.0, 0.0)  # LON: 90; LAT: 0
 
-        SPHERE_PARTS = [
-            SphericalPolygon([POINT_FRONT, POINT_TOP, POINT_BACK, POINT_RIGHT, POINT_FRONT]),
-            SphericalPolygon([POINT_FRONT, POINT_RIGHT, POINT_BACK, POINT_BOTTOM, POINT_FRONT]),
-            SphericalPolygon([POINT_FRONT, POINT_BOTTOM, POINT_BACK, POINT_LEFT, POINT_FRONT]),
-            SphericalPolygon([POINT_FRONT, POINT_LEFT, POINT_BACK, POINT_TOP, POINT_FRONT]),
-        ]
+        with np.errstate(invalid="ignore"):
+            SPHERE_PARTS = [
+                SphericalPolygon([POINT_FRONT, POINT_TOP, POINT_BACK, POINT_RIGHT, POINT_FRONT]),
+                SphericalPolygon([POINT_FRONT, POINT_RIGHT, POINT_BACK, POINT_BOTTOM, POINT_FRONT]),
+                SphericalPolygon([POINT_FRONT, POINT_BOTTOM, POINT_BACK, POINT_LEFT, POINT_FRONT]),
+                SphericalPolygon([POINT_FRONT, POINT_LEFT, POINT_BACK, POINT_TOP, POINT_FRONT]),
+            ]
         SPHERE_PARTS_BOUNDING_BOXES = [
             box(minx=0, miny=0, maxx=180, maxy=90),
             box(minx=0, miny=-90, maxx=180, maxy=0),
@@ -185,7 +186,11 @@ def generate_voronoi_regions(
 
         regions_parts: dict[int, list[tuple[int, list[EdgeHash]]]] = {}
 
-        for region_id, sphere_part_id, spherical_polygon_points in spherical_polygons_parts:
+        for (
+            region_id,
+            sphere_part_id,
+            spherical_polygon_points,
+        ) in spherical_polygons_parts:
             if region_id not in regions_parts:
                 regions_parts[region_id] = []
 
@@ -326,7 +331,9 @@ def _parse_multiprocessing_activation_threshold(
     return multiprocessing_activation_threshold
 
 
-def _parse_geodataframe_seeds(gdf: gpd.GeoDataFrame) -> tuple[list[Point], list[Hashable]]:
+def _parse_geodataframe_seeds(
+    gdf: gpd.GeoDataFrame,
+) -> tuple[list[Point], list[Hashable]]:
     """Transform GeoDataFrame into list of Points with index."""
     seeds_wgs84 = gdf.to_crs(crs=WGS84_CRS)
     region_ids: list[Hashable] = []

srai/regionalizers/administrative_boundary_regionalizer.py

@@ -11,6 +11,7 @@
 from typing import Any, Optional, Union
 
 import geopandas as gpd
+import numpy as np
 import topojson as tp
 from shapely import union
 from shapely.geometry import GeometryCollection, MultiPolygon, Point, Polygon
@@ -188,7 +189,8 @@ def transform(self, gdf: gpd.GeoDataFrame) -> gpd.GeoDataFrame:
             empty_region = self._generate_empty_region(mask=gdf_wgs84, regions_gdf=regions_gdf)
             if not empty_region.is_empty:
                 regions_gdf.loc[
-                    AdministrativeBoundaryRegionalizer.EMPTY_REGION_NAME, GEOMETRY_COLUMN
+                    AdministrativeBoundaryRegionalizer.EMPTY_REGION_NAME,
+                    GEOMETRY_COLUMN,
                 ] = empty_region
 
         return regions_gdf
@@ -205,7 +207,9 @@ def _generate_regions_from_all_geometries(
 
         with tqdm(desc="Loading boundaries: 0", total=len(all_geometries)) as pbar:
             for geometry in all_geometries:
-                if not geometry.covered_by(unary_geometry):
+                with np.errstate(invalid="ignore"):
+                    is_covered = geometry.covered_by(unary_geometry)
+                if not is_covered:
                     query = self._generate_query_for_single_geometry(geometry)
                     boundaries_list = self._query_overpass(query)
                     for boundary in boundaries_list:
@@ -366,7 +370,9 @@ def _check_intersects_with_points(
         )
 
     def _calculate_intersection_area_fraction(
-        self, region_geometry: BaseGeometry, clipping_polygon_area: Optional[BaseGeometry]
+        self,
+        region_geometry: BaseGeometry,
+        clipping_polygon_area: Optional[BaseGeometry],
     ) -> float:
         """Calculate intersection area fraction to check if it's big enough."""
         if clipping_polygon_area is None or clipping_polygon_area.is_empty:

tests/embedders/geovex/test_embedder.py

@@ -187,7 +187,7 @@ def test_embedder_save_load() -> None:
         assert isinstance(loaded_embedder._model, GeoVexModel)
 
         # safely clean up tmp_models directory
-        os.remove(tmp_models_dir / "test_model" / "model.pt")
-        os.remove(tmp_models_dir / "test_model" / "config.json")
+        (tmp_models_dir / "test_model" / "model.pt").unlink()
+        (tmp_models_dir / "test_model" / "config.json").unlink()
         os.rmdir(tmp_models_dir / "test_model")
         os.rmdir(tmp_models_dir)

tests/embedders/geovex/test_model.py

@@ -9,7 +9,7 @@
 import pandas as pd
 import pytest
 import torch
-from lightning_fabric import seed_everything
+from pytorch_lightning import seed_everything
 
 from srai.embedders.geovex.embedder import GeoVexEmbedder
 from srai.embedders.geovex.model import GeoVexModel

tests/loaders/osm_way_loader/test_osm_way_loader.py

@@ -240,7 +240,7 @@ def test_contract(
     area_gdf = request.getfixturevalue(area_gdf_fixture)
     nodes_expected_len, edges_expected_len = expected_result or (None, None)
 
-    def patched_graph_from_polygon(f_name: str, *args, **kwargs) -> Any:  # type: ignore
+    def patched_graph_from_polygon(f_name: Optional[str], *args, **kwargs) -> Any:  # type: ignore
         if f_name == "type_error":
             raise TypeError
         elif f_name == "empty_overpass_response":
@@ -254,7 +254,7 @@ def patched_graph_from_polygon(f_name: str, *args, **kwargs) -> Any:  # type: ig
                 raise osmnx._errors.EmptyOverpassResponse
 
         files_path = Path(__file__).parent / "test_files"
-        file_name = f_name + ".pkl"
+        file_name = (f_name or "") + ".pkl"
         file_path = files_path / file_name
 
         with file_path.open("rb") as f:

tests/regionalizers/conftest.py

@@ -122,8 +122,9 @@ def gdf_earth_poles(earth_poles) -> gpd.GeoDataFrame:
 @pytest.fixture  # type: ignore
 def gdf_poland() -> gpd.GeoDataFrame:
     """Get Poland GeoDataFrame."""
-    world = gpd.read_file(gpd.datasets.get_path("naturalearth_lowres"))
-    area = world[world.name == "Poland"]
+    area = gpd.read_file(
+        "https://raw.githubusercontent.com/johan/world.geo.json/master/countries/POL.geo.json"
+    )
     return area