Merge remote-tracking branch 'origin/main' into anvy-eval

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/testing.yml

@@ -1,5 +1,5 @@
  name: Continuous Integration
- 
+
  on:
    push:
      branches: [main]
@@ -17,15 +17,12 @@
 
  jobs:
    tests:
-     name: ${{ matrix.os }}, ${{ matrix.environment-file }}
+     name: ${{ matrix.os }}
      runs-on: ${{ matrix.os }}
      timeout-minutes: 30
      strategy:
        matrix:
-         os: [ubuntu-latest]
-         environment-file: [
-            ci/py311_simplification-latest.yaml,
-         ]
+         os: [ubuntu-latest, macos-latest, macos-14, windows-latest]
        fail-fast: false
 
      defaults:
@@ -37,41 +34,20 @@
          uses: actions/checkout@v4
          with:
            fetch-depth: 0 # Fetch all history for all branches and tags.
-
-       - name: setup micromamba
-         uses: mamba-org/setup-micromamba@v1
-         with:
-           environment-file: ${{ matrix.environment-file }}
-           micromamba-version: "latest"
 
-       # - must be editable install for current tests to pass
-       # - due to data & pathing; probably need to:
-       #    1. rethink current 'convenience' funcs;
-       #    2. move `data/` into `core/data/`
-       #    3. something else
-       - name: install package
-         run: "pip install -e .[tests]"
+       - name: Setup Pixi
+         uses: prefix-dev/setup-pixi@v0.8.1
+         with:
+            cache: true
+            environments: "tests"
 
-       - name: environment info
-         run: "micromamba info && micromamba list"
-
        - name: spatial versions
-         run: 'python -c "import geopandas; geopandas.show_versions();"'
-       
+         run: 'pixi run -e tests python -c "import geopandas; geopandas.show_versions();"'
+
        - name: run tests
-         run: |
-           pytest \
-           core/ \
-           --verbose \
-           -r a \
-           --numprocesses logical \
-           --color yes \
-           --cov core \
-           --cov-append \
-           --cov-report term-missing \
-           --cov-report xml . \
-           --env_type ${{ matrix.environment-file }}
-       
+         run:
+           pixi run -e tests pytest -v -r a -n logical --color yes --cov code --cov-append --cov-report term-missing --cov-report xml .
+
        - name: codecov
          uses: codecov/codecov-action@v4
          with:

.gitignore

@@ -162,4 +162,7 @@ cython_debug/
 # Other stuff
 .DS_Store
 data/*/temp-parenx/*
-*.qgz
+*.qgz
+# pixi environments
+.pixi
+*.egg-info

README.md

@@ -18,10 +18,10 @@ The curated & tested code base for the project & publication, including:
 Parameterized notebooks.
 
 * `/preprocessing/`: workflows used to preprocess [raw data](https://github.com/martinfleis/urban-block-artifacts) (clipping and removing degree 2 nodes)
-* `/methods/`: exploration of different simplification methods, including the new method proposed here, `sgeop`
+* `/methods/`: exploration of different simplification methods, including the new method proposed here, `neatnet`
 * `/evaluation/`: comparative evaluation of each simplification method
 * `/usecases/`: collection of use cases
-* `/typology/`: exploration of different types of face artifacts, foundational to the `sgeop` algorithm
+* `/typology/`: exploration of different types of face artifacts, foundational to the `neatnet` algorithm
 * `/archive/`: archived notebooks
 
 ### `./data/`
@@ -88,11 +88,30 @@ Demonstration visualizations on specific types of urban form.
     * `roandabout.mp4`
   * `points.json` - use case locations
 
-### `environment.yml`
+### Reproducible environment
 
-Install and activate the `conda` (or mamba) environment, which creates an environment name `simplification`:
+This project uses reproducible multi-platform environments using [Pixi](https://pixi.sh). To create an environment able to run all the code in the repository, clone the repository and install the locked environment using:
 
+```sh
+pixi install
 ```
-conda env create -f environment.yml
-conda activate simplification
+
+#### Development
+
+To install the development environment allowing testing:
+
+```sh
+pixi install -e tests
+```
+
+If you would like to run the tests, use the `tests` Pixi environment:
+
+```sh
+pixi run -e tests pytest
 ```
+
+Installing pre-commit hook to the env:
+
+```sh
+pixi run pre-commit install
+```

core/algorithms/artifacts.py

@@ -10,13 +10,13 @@
 import shapely
 from esda import shape
 from libpysal import graph
-from scipy import sparse
-from sgeop.geometry import (
+from neatnet.geometry import (
     _is_within,
     snap_to_targets,
     voronoi_skeleton,
 )
-from sgeop.nodes import weld_edges
+from neatnet.nodes import weld_edges
+from scipy import sparse
 
 logger = logging.getLogger(__name__)
 

core/algorithms/simplify.py

@@ -6,16 +6,16 @@
 import numpy as np
 import pandas as pd
 from libpysal import graph
-from scipy import sparse
-from sgeop.continuity import continuity, get_stroke_info
-from sgeop.nodes import (
+from neatnet.continuity import continuity, get_stroke_info
+from neatnet.nodes import (
     _status,
     consolidate_nodes,
     fix_topology,
     induce_nodes,
     remove_false_nodes,
     split,
 )
+from scipy import sparse
 
 from .artifacts import (
     get_artifacts,

core/algorithms/triangles.py

@@ -1,7 +1,7 @@
 import geopandas as gpd
 import pandas as pd
 import shapely
-from sgeop.geometry import _is_within
+from neatnet.geometry import _is_within
 from tqdm.auto import tqdm
 
 

core/tests/test_utils.py

@@ -21,7 +21,7 @@ def test_read_sample_data():
 parenx_voronoi_records = [42_302, 9_569, 16_844, 29_446, 15_516, 14_242, 35_694]
 parenx_skeletonize_records = [44_294, 9_561, 17_469, 30_641, 16_075, 14_784, 37_557]
 osmnx_records = [43_451, 15_770, 24_025, 37_954, 21_755, 17_704, 30_156]
-sgeop_records = [39_489, 8_229, 13_587, 29_028, 12_395, 11_059, 16_298]
+neatnet_records = [39_489, 8_229, 13_587, 29_028, 12_395, 11_059, 16_298]
 
 
 @pytest.mark.parametrize("city, n_records", zip(cities, osm_records, strict=True))
@@ -123,12 +123,12 @@ def test_read_parenx_skeletonize(city, n_records):
     assert gdf_1.crs == gdf_2.crs == pytest.epsg_4326
 
 
-@pytest.mark.parametrize("city, n_records", zip(cities, sgeop_records, strict=True))
-def test_read_sgeop(city, n_records):
+@pytest.mark.parametrize("city, n_records", zip(cities, neatnet_records, strict=True))
+def test_read_neatnet(city, n_records):
     fua = core.utils.city_fua[city]
 
-    gdf_1 = core.utils.read_sgeop(fua, pytest.epsg_4326)
-    gdf_2 = core.utils.read_sgeop(core.utils.fua_city[fua], pytest.epsg_4326)
+    gdf_1 = core.utils.read_neatnet(fua, pytest.epsg_4326)
+    gdf_2 = core.utils.read_neatnet(core.utils.fua_city[fua], pytest.epsg_4326)
 
     geopandas.testing.assert_geodataframe_equal(gdf_1, gdf_2)
 

core/tests/test_viz_h3_hex.py

@@ -1,6 +1,5 @@
 import pytest
 from matplotlib.testing.decorators import image_comparison
-from matplotlib.testing.exceptions import ImageComparisonFailure
 
 import core
 
@@ -14,10 +13,6 @@ def test_viz_h3_hex_plot_aoi(grid_8_auckland):
     core.viz.h3_hex.plot_aoi(grid_8_auckland, "Auckland", 8)
 
 
-@pytest.mark.xfail(
-    reason="Needs updated Manual & Parenx -- See GH#131.",
-    raises=ImageComparisonFailure,
-)
 @image_comparison(
     baseline_images=["test_viz_h3_hex_plot_analysis.png"],
     style="mpl20",
@@ -60,10 +55,6 @@ def setup_method(
         self._m = "manual"
         self._p = "parenx-voronoi"
 
-    @pytest.mark.xfail(
-        reason="Needs updated Manual & Parenx -- See GH#131.",
-        raises=ImageComparisonFailure,
-    )
     @image_comparison(
         baseline_images=["test_viz_h3_hex_plot_cell_loc_id.png"], style="mpl20", tol=tol
     )
@@ -79,10 +70,6 @@ def test_loc_id(self):
             self._p,
         )
 
-    @pytest.mark.xfail(
-        reason="Needs updated Manual & Parenx -- See GH#131.",
-        raises=ImageComparisonFailure,
-    )
     @image_comparison(
         baseline_images=["test_viz_h3_hex_plot_cell_hex_id.png"],
         style="mpl20",

core/utils.py

@@ -17,7 +17,7 @@
     "read_cityseer",
     "read_osmnx",
     "read_parenx",
-    "read_sgeop",
+    "read_neatnet",
     "graph_size",
     "load_usecases",
     "make_grid",
@@ -128,11 +128,11 @@ def read_parenx(
     )
 
 
-def read_sgeop(fua: int, proj_crs: str | int | pyproj.CRS) -> geopandas.GeoDataFrame:
-    """Read in prepared sgeop data."""
+def read_neatnet(fua: int, proj_crs: str | int | pyproj.CRS) -> geopandas.GeoDataFrame:
+    """Read in prepared neatnet data."""
 
     return (
-        geopandas.read_parquet(_fua_path(fua, "sgeop"))
+        geopandas.read_parquet(_fua_path(fua, "neatnet"))
         .explode(ignore_index=True, index_parts=False)
         .to_crs(proj_crs)
     )

notebooks/archive/simplification_api.ipynb

@@ -19,7 +19,7 @@
     "import warnings\n",
     "\n",
     "import folium\n",
-    "import sgeop\n",
+    "import neatnet\n",
     "\n",
     "from core import utils"
    ]
@@ -57,8 +57,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# # Get the logger for sgeop.simplify\n",
-    "# logger = logging.getLogger('sgeop.simplify')\n",
+    "# # Get the logger for neatnet.simplify\n",
+    "# logger = logging.getLogger('neatnet.simplify')\n",
     "# logger.setLevel(logging.DEBUG)\n",
     "\n",
     "# # Set the logging format\n",
@@ -118,7 +118,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "new_roads = sgeop.simplify_network(roads)"
+    "new_roads = neatnet.simplify_network(roads)"
    ]
   },
   {