vector2dggs 0.6.0__tar.gz → 0.6.1__tar.gz

{vector2dggs-0.6.0 → vector2dggs-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vector2dggs
-Version: 0.6.0
+Version: 0.6.1
 Summary: CLI DGGS indexer for vector geospatial data
 Home-page: https://github.com/manaakiwhenua/vector2dggs
 License: LGPL-3.0-or-later
@@ -9,27 +9,27 @@ Author: James Ardo
 Author-email: ardoj@landcareresearch.co.nz
 Maintainer: Richard Law
 Maintainer-email: lawr@landcareresearch.co.nz
-Requires-Python: >=3.10,<4.0
+Requires-Python: >=3.11,<4.0
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: GIS
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Requires-Dist: click (>=8.1.3,<9.0.0)
+Requires-Dist: click (>=8.1.7,<9.0.0)
 Requires-Dist: click-log (>=0.4.0,<0.5.0)
-Requires-Dist: dask (>=2023.3.0,<2024.0.0)
-Requires-Dist: dask-geopandas (>=0.3.0,<0.4.0)
-Requires-Dist: gdal (>=3.8.0,<4.0.0)
-Requires-Dist: geopandas (>=0.12.2,<0.13.0)
+Requires-Dist: dask (>=2024.8.0,<2025.0.0)
+Requires-Dist: dask-geopandas (>=0.4.1,<0.5.0)
+Requires-Dist: gdal (==3.8.4)
+Requires-Dist: geopandas (>=1.0.1,<2.0.0)
 Requires-Dist: h3pandas (>=0.2.6,<0.3.0)
-Requires-Dist: psycopg2 (>=2.9.6,<3.0.0)
-Requires-Dist: pyarrow (>=14.0.1,<15.0.0)
-Requires-Dist: pygeos (>=0.13,<0.14)
-Requires-Dist: pyproj (>=3.5.0,<4.0.0)
-Requires-Dist: sqlalchemy (>=2.0.10,<3.0.0)
-Requires-Dist: tqdm (>=4.65.0,<5.0.0)
+Requires-Dist: numpy (<2)
+Requires-Dist: psycopg2 (>=2.9.9,<3.0.0)
+Requires-Dist: pyarrow (>=17.0.0,<18.0.0)
+Requires-Dist: pyproj (>=3.6.1,<4.0.0)
+Requires-Dist: shapely (>=2.0.5,<3.0.0)
+Requires-Dist: sqlalchemy (>=2.0.32,<3.0.0)
+Requires-Dist: tqdm (>=4.66.5,<5.0.0)
 Project-URL: Repository, https://github.com/manaakiwhenua/vector2dggs
 Description-Content-Type: text/markdown
 
@@ -159,6 +159,8 @@ In brief, to get started:
 
 If you run `poetry install`, the CLI tool will be aliased so you can simply use `vector2dggs` rather than `poetry run vector2dggs`, which is the alternative if you do not `poetry install`.
 
+Alternaively, it is also possible to isntall using pip with `pip install -e .`, and bypass Poetry.
+
 #### Code formatting
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
@@ -187,14 +189,14 @@ vector2dggs h3 -v DEBUG -id ogc_fid -r 9 -p 5 -t 4 --overwrite -tbl topo50_lake
   title={{vector2dggs}},
   author={Ardo, James and Law, Richard},
   url={https://github.com/manaakiwhenua/vector2dggs},
-  version={0.6.0},
+  version={0.6.1},
   date={2023-04-20}
 }
 ```
 
 APA/Harvard
 
-> Ardo, J., & Law, R. (2023). vector2dggs (0.6.0) [Computer software]. https://github.com/manaakiwhenua/vector2dggs
+> Ardo, J., & Law, R. (2023). vector2dggs (0.6.1) [Computer software]. https://github.com/manaakiwhenua/vector2dggs
 
 [![manaakiwhenua-standards](https://github.com/manaakiwhenua/vector2dggs/workflows/manaakiwhenua-standards/badge.svg)](https://github.com/manaakiwhenua/manaakiwhenua-standards)
 

{vector2dggs-0.6.0 → vector2dggs-0.6.1}/README.md

@@ -124,6 +124,8 @@ In brief, to get started:
 
 If you run `poetry install`, the CLI tool will be aliased so you can simply use `vector2dggs` rather than `poetry run vector2dggs`, which is the alternative if you do not `poetry install`.
 
+Alternaively, it is also possible to isntall using pip with `pip install -e .`, and bypass Poetry.
+
 #### Code formatting
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
@@ -152,13 +154,13 @@ vector2dggs h3 -v DEBUG -id ogc_fid -r 9 -p 5 -t 4 --overwrite -tbl topo50_lake
   title={{vector2dggs}},
   author={Ardo, James and Law, Richard},
   url={https://github.com/manaakiwhenua/vector2dggs},
-  version={0.6.0},
+  version={0.6.1},
   date={2023-04-20}
 }
 ```
 
 APA/Harvard
 
-> Ardo, J., & Law, R. (2023). vector2dggs (0.6.0) [Computer software]. https://github.com/manaakiwhenua/vector2dggs
+> Ardo, J., & Law, R. (2023). vector2dggs (0.6.1) [Computer software]. https://github.com/manaakiwhenua/vector2dggs
 
 [![manaakiwhenua-standards](https://github.com/manaakiwhenua/vector2dggs/workflows/manaakiwhenua-standards/badge.svg)](https://github.com/manaakiwhenua/manaakiwhenua-standards)

{vector2dggs-0.6.0 → vector2dggs-0.6.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "vector2dggs"
-version = "0.6.0"
+version = "0.6.1"
 description = "CLI DGGS indexer for vector geospatial data"
 authors = ["James Ardo <ardoj@landcareresearch.co.nz>"]
 maintainers = ["Richard Law <lawr@landcareresearch.co.nz>"]
@@ -15,20 +15,21 @@ classifiers = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.10"
-gdal = "^3.8.0"
-geopandas = "^0.12.2"
+python = "^3.11"
+gdal = "3.8.4"
+geopandas = "^1.0.1"
 h3pandas = "^0.2.6"
-dask-geopandas = "^0.3.0"
-dask = "^2023.3.0"
-click = "^8.1.3"
-tqdm = "^4.65.0"
+dask-geopandas = "^0.4.1"
+dask = "^2024.8.0"
+click = "^8.1.7"
+tqdm = "^4.66.5"
 click-log = "^0.4.0"
-pyarrow = "^14.0.1"
-pygeos = "^0.13"
-pyproj = "^3.5.0"
-sqlalchemy = "^2.0.10"
-psycopg2 = "^2.9.6"
+pyarrow = "^17.0.0"
+pyproj = "^3.6.1"
+sqlalchemy = "^2.0.32"
+psycopg2 = "^2.9.9"
+shapely = "^2.0.5"
+numpy = "<2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.2"

vector2dggs-0.6.1/vector2dggs/__init__.py

@@ -0,0 +1 @@
+__version__: str = "0.6.1"

{vector2dggs-0.6.0 → vector2dggs-0.6.1}/vector2dggs/h3.py

@@ -11,8 +11,6 @@ from typing import Union
 from urllib.parse import urlparse
 import warnings
 
-os.environ["USE_PYGEOS"] = "0"
-
 import click
 import click_log
 import dask.dataframe as dd
@@ -69,8 +67,8 @@ def polyfill(
     output_directory: str,
 ) -> None:
     """
-    Reads a geoparquet, performs H3 polyfilling (for polygons),
-    linetracing (for linestrings), and writes out to parquet.
+    Reads a geoparquet, performs H3 polyfilling (for Polygon),
+    linetracing (for LineString), and writes out to parquet.
     """
     df = gpd.read_parquet(pq_in).reset_index().drop(columns=[spatial_sort_col])
     if len(df.index) == 0:
@@ -215,7 +213,7 @@ def _index(
         # Remove all attributes except the geometry
         df = df.loc[:, ["geometry"]]
 
-    LOGGER.info("Watch out for ninjas! (Cutting polygons)")
+    LOGGER.info("Cutting large geometries")
     with tqdm(total=df.shape[0]) as pbar:
         for index, row in df.iterrows():
             df.loc[index, "geometry"] = GeometryCollection(
@@ -242,7 +240,7 @@ def _index(
                 (frame.geometry.geom_type != "Polygon")
                 & (frame.geometry.geom_type != "LineString")
             ],  # NB currently points and other types are lost; in principle, these could be indexed
-            "message": "Dropping non-polygonal geometries",
+            "message": "Dropping unsupported geometries",
         },
     ]
     for condition in drop_conditions:
@@ -342,7 +340,7 @@ def _index(
     required=False,
     default=None,
     type=int,
-    help="Set the coordinate reference system (CRS) used for cutting large polygons (see `--cur-threshold`). Defaults to the same CRS as the input. Should be a valid EPSG code.",
+    help="Set the coordinate reference system (CRS) used for cutting large geometries (see `--cur-threshold`). Defaults to the same CRS as the input. Should be a valid EPSG code.",
     nargs=1,
 )
 @click.option(
@@ -351,7 +349,7 @@ def _index(
     required=True,
     default=5000,
     type=int,
-    help="Cutting up large polygons into smaller pieces based on a target length. Units are assumed to match the input CRS units unless the `--cut_crs` is also given, in which case units match the units of the supplied CRS.",
+    help="Cutting up large geometries into smaller geometries based on a target length. Units are assumed to match the input CRS units unless the `--cut_crs` is also given, in which case units match the units of the supplied CRS.",
     nargs=1,
 )
 @click.option(

{vector2dggs-0.6.0 → vector2dggs-0.6.1}/vector2dggs/katana.py

@@ -11,13 +11,20 @@ Redistribution and use in source and binary forms, with or without modification,
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
 
-from shapely.geometry import box, Polygon, MultiPolygon, GeometryCollection
+from shapely.geometry import (
+    box,
+    Polygon,
+    MultiPolygon,
+    LineString,
+    MultiLineString,
+    GeometryCollection,
+)
 from shapely.validation import explain_validity, make_valid
 
 
 def katana(geometry, threshold, count=0) -> GeometryCollection:
     """
-    Split a polygon into two parts across it's shortest dimension.
+    Split a geometry into two parts across its shortest dimension.
     Invalid input `geometry` will silently be made valid (if possible).
     """
     if geometry is None:
@@ -53,7 +60,7 @@ def katana(geometry, threshold, count=0) -> GeometryCollection:
         if not isinstance(c, GeometryCollection):
             c = GeometryCollection([c])
         for e in c.geoms:
-            if isinstance(e, (Polygon, MultiPolygon)):
+            if isinstance(e, (Polygon, MultiPolygon, LineString, MultiLineString)):
                 result.extend(katana(e, threshold, count + 1))
     if count > 0:
         return result

vector2dggs-0.6.0/setup.py

@@ -1,46 +0,0 @@
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-packages = \
-['vector2dggs']
-
-package_data = \
-{'': ['*']}
-
-install_requires = \
-['click-log>=0.4.0,<0.5.0',
- 'click>=8.1.3,<9.0.0',
- 'dask-geopandas>=0.3.0,<0.4.0',
- 'dask>=2023.3.0,<2024.0.0',
- 'gdal>=3.8.0,<4.0.0',
- 'geopandas>=0.12.2,<0.13.0',
- 'h3pandas>=0.2.6,<0.3.0',
- 'psycopg2>=2.9.6,<3.0.0',
- 'pyarrow>=14.0.1,<15.0.0',
- 'pygeos>=0.13,<0.14',
- 'pyproj>=3.5.0,<4.0.0',
- 'sqlalchemy>=2.0.10,<3.0.0',
- 'tqdm>=4.65.0,<5.0.0']
-
-entry_points = \
-{'console_scripts': ['vector2dggs = vector2dggs.cli:main']}
-
-setup_kwargs = {
-    'name': 'vector2dggs',
-    'version': '0.6.0',
-    'description': 'CLI DGGS indexer for vector geospatial data',
-    'long_description': '# vector2dggs\n\n[![pypi](https://img.shields.io/pypi/v/vector2dggs?label=vector2dggs)](https://pypi.org/project/vector2dggs/)\n\nPython-based CLI tool to index raster files to DGGS in parallel, writing out to Parquet.\n\nThis is the vector equivalent of [raster2dggs](https://github.com/manaakiwhenua/raster2dggs).\n\nCurrently only supports H3 DGGS, and probably has other limitations since it has been developed for a specific internal use case, though it is intended as a general-purpose abstraction. Contributions, suggestions, bug reports and strongly worded letters are all welcome.\n\nCurrently only supports polygons; but both coverages (strictly non-overlapping polygons), and sets of polygons that do/may overlap, are supported. Overlapping polygons are captured by ensuring that DGGS cell IDs may be non-unique (repeated) in the output.\n\n![Example use case for vector2dggs, showing parcels indexed to a high H3 resolution](./docs/imgs/vector2dggs-example.png "Example use case for vector2dggs, showing parcels indexed to a high H3 resolution")\n\n## Installation\n\n```bash\npip install vector2dggs\n```\n\n## Usage\n\n```bash\nvector2dggs h3 --help\nUsage: vector2dggs h3 [OPTIONS] VECTOR_INPUT OUTPUT_DIRECTORY\n\n  Ingest a vector dataset and index it to the H3 DGGS.\n\n  VECTOR_INPUT is the path to input vector geospatial data. OUTPUT_DIRECTORY\n  should be a directory, not a file or database table, as it will instead be\n  the write location for an Apache Parquet data store.\n\nOptions:\n  -v, --verbosity LVL             Either CRITICAL, ERROR, WARNING, INFO or\n                                  DEBUG  [default: INFO]\n  -r, --resolution [0|1|2|3|4|5|6|7|8|9|10|11|12|13|14|15]\n                                  H3 resolution to index  [required]\n  -pr, --parent_res [0|1|2|3|4|5|6|7|8|9|10|11|12|13|14|15]\n                                  H3 Parent resolution for the output\n                                  partition. Defaults to resolution - 6\n  -id, --id_field TEXT            Field to use as an ID; defaults to a\n                                  constructed single 0...n index on the\n                                  original feature order.\n  -k, --keep_attributes           Retain attributes in output. The default is\n                                  to create an output that only includes H3\n                                  cell ID and the ID given by the -id field\n                                  (or the default index ID).\n  -ch, --chunksize INTEGER        The number of rows per index partition to\n                                  use when spatially partioning. Adjusting\n                                  this number will trade off memory use and\n                                  time.  [default: 50; required]\n  -s, --spatial_sorting [hilbert|morton|geohash]\n                                  Spatial sorting method when perfoming\n                                  spatial partitioning.  [default: hilbert]\n  -crs, --cut_crs INTEGER         Set the coordinate reference system (CRS)\n                                  used for cutting large polygons (see `--cur-\n                                  threshold`). Defaults to the same CRS as the\n                                  input. Should be a valid EPSG code.\n  -c, --cut_threshold INTEGER     Cutting up large polygons into smaller\n                                  pieces based on a target length. Units are\n                                  assumed to match the input CRS units unless\n                                  the `--cut_crs` is also given, in which case\n                                  units match the units of the supplied CRS.\n                                  [default: 5000; required]\n  -t, --threads INTEGER           Amount of threads used for operation\n                                  [default: 7]\n  -tbl, --table TEXT              Name of the table to read when using a\n                                  spatial database connection as input\n  -g, --geom_col TEXT             Column name to use when using a spatial\n                                  database connection as input  [default:\n                                  geom]\n  --tempdir PATH                  Temporary data is created during the\n                                  execution of this program. This parameter\n                                  allows you to control where this data will\n                                  be written.\n  -o, --overwrite\n  --version                       Show the version and exit.\n  --help                          Show this message and exit.\n```\n\n## Visualising output\n\nOutput is in the Apache Parquet format, a directory with one file per partition.\n\nFor a quick view of your output, you can read Apache Parquet with pandas, and then use h3-pandas and geopandas to convert this into a GeoPackage or GeoParquet for visualisation in a desktop GIS, such as QGIS. The Apache Parquet output is indexed by an ID column (which you can specify), so it should be ready for two intended use-cases:\n- Joining attribute data from the original feature-level data onto computer DGGS cells.\n- Joining other data to this output on the H3 cell ID. (The output has a column like `h3_\\d{2}`, e.g. `h3_09` or `h3_12` according to the target resolution.)\n\nGeoparquet output (hexagon boundaries):\n\n```python\n>>> import pandas as pd\n>>> import h3pandas\n>>> g = pd.read_parquet(\'./output-data/nz-property-titles.12.parquet\').h3.h3_to_geo_boundary()\n>>> g\n                  title_no                                           geometry\nh3_12                                                                        \n8cbb53a734553ff  NA94D/635  POLYGON ((174.28483 -35.69315, 174.28482 -35.6...\n8cbb53a734467ff  NA94D/635  POLYGON ((174.28454 -35.69333, 174.28453 -35.6...\n8cbb53a734445ff  NA94D/635  POLYGON ((174.28416 -35.69368, 174.28415 -35.6...\n8cbb53a734551ff  NA94D/635  POLYGON ((174.28496 -35.69329, 174.28494 -35.6...\n8cbb53a734463ff  NA94D/635  POLYGON ((174.28433 -35.69335, 174.28432 -35.6...\n...                    ...                                                ...\n8cbb53a548b2dff  NA62D/324  POLYGON ((174.30249 -35.69369, 174.30248 -35.6...\n8cbb53a548b61ff  NA62D/324  POLYGON ((174.30232 -35.69402, 174.30231 -35.6...\n8cbb53a548b11ff  NA57C/785  POLYGON ((174.30140 -35.69348, 174.30139 -35.6...\n8cbb53a548b15ff  NA57C/785  POLYGON ((174.30161 -35.69346, 174.30160 -35.6...\n8cbb53a548b17ff  NA57C/785  POLYGON ((174.30149 -35.69332, 174.30147 -35.6...\n\n[52736 rows x 2 columns]\n>>> g.to_parquet(\'./output-data/parcels.12.geo.parquet\')\n```\n\n### For development\n\nIn brief, to get started:\n\n- Install [Poetry](https://python-poetry.org/docs/basic-usage/)\n- Install [GDAL](https://gdal.org/)\n    - If you\'re on Windows, `pip install gdal` may be necessary before running the subsequent commands.\n    - On Linux, install GDAL 3.6+ according to your platform-specific instructions, including development headers, i.e. `libgdal-dev`.\n- Create the virtual environment with `poetry init`. This will install necessary dependencies.\n- Subsequently, the virtual environment can be re-activated with `poetry shell`.\n\nIf you run `poetry install`, the CLI tool will be aliased so you can simply use `vector2dggs` rather than `poetry run vector2dggs`, which is the alternative if you do not `poetry install`.\n\n#### Code formatting\n\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\nPlease run `black .` before committing.\n\n## Example commands\n\nWith a local GPKG:\n\n```bash\nvector2dggs h3 -v DEBUG -id title_no -r 12 -o ~/Downloads/nz-property-titles.gpkg ~/Downloads/nz-property-titles.parquet\n\n```\n\nWith a PostgreSQL/PostGIS connection:\n\n```bash\nvector2dggs h3 -v DEBUG -id ogc_fid -r 9 -p 5 -t 4 --overwrite -tbl topo50_lake postgresql://user:password@host:port/db ./topo50_lake.parquet\n```\n\n## Citation\n\n```bibtex\n@software{vector2dggs,\n  title={{vector2dggs}},\n  author={Ardo, James and Law, Richard},\n  url={https://github.com/manaakiwhenua/vector2dggs},\n  version={0.6.0},\n  date={2023-04-20}\n}\n```\n\nAPA/Harvard\n\n> Ardo, J., & Law, R. (2023). vector2dggs (0.6.0) [Computer software]. https://github.com/manaakiwhenua/vector2dggs\n\n[![manaakiwhenua-standards](https://github.com/manaakiwhenua/vector2dggs/workflows/manaakiwhenua-standards/badge.svg)](https://github.com/manaakiwhenua/manaakiwhenua-standards)\n',
-    'author': 'James Ardo',
-    'author_email': 'ardoj@landcareresearch.co.nz',
-    'maintainer': 'Richard Law',
-    'maintainer_email': 'lawr@landcareresearch.co.nz',
-    'url': 'https://github.com/manaakiwhenua/vector2dggs',
-    'packages': packages,
-    'package_data': package_data,
-    'install_requires': install_requires,
-    'entry_points': entry_points,
-    'python_requires': '>=3.10,<4.0',
-}
-
-
-setup(**setup_kwargs)

vector2dggs-0.6.0/vector2dggs/__init__.py

@@ -1 +0,0 @@
-__version__: str = "0.6.0"