From 64a28306dc2ba1a63015163bcccb0139331e85c6 Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Fri, 18 Apr 2025 15:35:05 -0400 Subject: [PATCH 1/8] remove requirements.txt in favor of listings in pyproject.toml --- requirements.txt | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index d317ce1..0000000 --- a/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -numpy -rasterio -fiona -affine -scipy -rasterstats From 8c3cac7118428aa96157b9c4ea503e53fe694000 Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Sat, 14 Mar 2026 20:35:33 -0400 Subject: [PATCH 2/8] rewrite core functionality in rust --- .github/workflows/build-and-publish.yml | 59 +- .github/workflows/test-with-coverage.yml | 9 +- .github/workflows/test.yml | 6 +- .gitignore | 250 +++++++- Cargo.lock | 619 +++++++++++++++++++ Cargo.toml | 15 + pyproject.toml | 15 +- src/distance.rs | 69 +++ src/distancerasters/main.py | 66 +- src/distancerasters/utils.py | 7 +- src/haversine.rs | 30 + src/lib.rs | 50 ++ uv.lock | 753 +++++++++++++++++++++++ 13 files changed, 1854 insertions(+), 94 deletions(-) create mode 100644 Cargo.lock create mode 100644 Cargo.toml create mode 100644 src/distance.rs create mode 100644 src/haversine.rs create mode 100644 src/lib.rs create mode 100644 uv.lock diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml index 4503982..61c06e9 100644 --- a/.github/workflows/build-and-publish.yml +++ b/.github/workflows/build-and-publish.yml @@ -6,41 +6,64 @@ on: - master jobs: + build-wheels: + name: Build wheels on ${{ matrix.os }} 🚧 + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + steps: + - uses: actions/checkout@v4 + - uses: PyO3/maturin-action@v1 + with: + command: build + args: --release --out dist + - uses: actions/upload-artifact@v4 + with: + name: wheels-${{ matrix.os }} + path: dist + + build-sdist: + name: Build source distribution 🚧 + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: PyO3/maturin-action@v1 + with: + command: sdist + args: --out dist + - uses: actions/upload-artifact@v4 + with: + name: sdist + path: dist + publish: name: Publish 🚀 + needs: [build-wheels, build-sdist] runs-on: ubuntu-latest - env: - VERSION: null - steps: - - uses: actions/checkout@v2 - - name: Set up Python 🐍 - uses: actions/setup-python@v2 + - uses: actions/download-artifact@v4 with: - python-version: 3.x - - name: Install dependencies ⚙️ - run: | - python -m pip install --upgrade pip - pip install build - - name: Get version + path: dist + merge-multiple: true + - name: Get version from Cargo.toml run: | - cat setup.cfg | grep "version = " | awk '{print "VERSION="$(NF)}' >> $GITHUB_ENV - - name: Build a binary wheel and a source tarball 🚧 - run: python -m build --sdist --wheel --outdir dist/ . + VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)"/\1/') + echo "VERSION=$VERSION" >> $GITHUB_ENV - name: Validate release tag run: | if [ "${GITHUB_REF#refs/tags/}" != "${VERSION}" ]; then exit 1; fi - name: Publish to Test PyPI 📦 if: contains(env.VERSION, 'a') - uses: pypa/gh-action-pypi-publish@v1.4.2 + uses: pypa/gh-action-pypi-publish@v1 with: user: __token__ password: ${{ secrets.TEST_PYPI_API_TOKEN }} - repository_url: https://test.pypi.org/legacy/ + repository-url: https://test.pypi.org/legacy/ - name: Publish to PyPI 📦 if: | !contains(env.VERSION, 'a') - uses: pypa/gh-action-pypi-publish@v1.4.2 + uses: pypa/gh-action-pypi-publish@v1 with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/test-with-coverage.yml b/.github/workflows/test-with-coverage.yml index 128818c..f81912b 100644 --- a/.github/workflows/test-with-coverage.yml +++ b/.github/workflows/test-with-coverage.yml @@ -17,13 +17,15 @@ jobs: uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + - name: Install Rust 🦀 + uses: dtolnay/rust-toolchain@stable - name: Install dependencies ⚙️ run: | sudo apt-get update sudo apt-get install libgdal-dev python -m pip install --upgrade pip - pip install . - pip install pytest pytest-cov shapely build geopandas + pip install maturin pytest pytest-cov shapely geopandas numpy rasterio fiona affine rasterstats + maturin develop --release - name: Test with pytest ✅ run: | pytest --cov=distancerasters @@ -35,6 +37,3 @@ jobs: run: | pip install coveralls coveralls - - name: Try building a binary wheel and a source tarball 🚧 - run: | - python -m build --sdist --wheel --outdir dist/ . diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 073ef4f..954cab8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -15,11 +15,13 @@ jobs: uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + - name: Install Rust 🦀 + uses: dtolnay/rust-toolchain@stable - name: Install dependencies ⚙️ run: | python -m pip install --upgrade pip - pip install . - pip install pytest pytest-cov shapely geopandas + pip install maturin pytest pytest-cov shapely geopandas numpy rasterio fiona affine rasterstats + maturin develop --release - name: Test with pytest ✅ run: | pytest --cov=distancerasters diff --git a/.gitignore b/.gitignore index 6f9aef5..7fdd2d6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,13 +1,249 @@ *.pyc *.tif.aux.xml *.tif -build/* -dist/* -.DS_Store -MANIFEST -*.egg-info -htmlcov + .coverage tests/* !tests/*.py -examples/*.tif \ No newline at end of file +examples/*.tif + +.DS_Store + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[codz] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +# Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# uv.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +# poetry.lock +# poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +# pdm.lock +# pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +# pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# Redis +*.rdb +*.aof +*.pid + +# RabbitMQ +mnesia/ +rabbitmq/ +rabbitmq-data/ + +# ActiveMQ +activemq-data/ + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +# .idea/ + +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ + +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. 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"7e6cc098ea4d3bd6246687de65af3f920c430e236bee1e3bf2e441463f08a02f" +dependencies = [ + "proc-macro2", + "quote", + "syn", +] diff --git a/Cargo.toml b/Cargo.toml new file mode 100644 index 0000000..a008801 --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,15 @@ +[package] +name = "distancerasters" +version = "0.5.0" +edition = "2024" +license = "BSD-3-Clause" + +[lib] +name = "_distancerasters" +crate-type = ["cdylib"] + +[dependencies] +pyo3 = { version = "0.28.2", features = ["extension-module"] } +numpy = "0.28" +kiddo = "5.2.4" +rayon = "1.11.0" diff --git a/pyproject.toml b/pyproject.toml index 0bb74f9..d4734f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["setuptools>=42", "wheel"] -build-backend = "setuptools.build_meta" +requires = ["maturin>=1.0,<2.0"] +build-backend = "maturin" [project] authors = [{ name = "Seth Goodman", email = "sgoodman@aiddata.wm.edu" }] @@ -8,7 +8,7 @@ classifiers = ["Programming Language :: Python :: 3"] keywords = ["raster", "distance", "spatial"] license = { text = "BSD 3-Clause License" } name = "distancerasters" -version = "0.3.3" +version = "0.5.0" description = "Generate distance raster using arbitrary sets of spatial features" readme = "README.md" requires-python = ">= 3.9" @@ -17,9 +17,7 @@ dependencies = [ "rasterio", "fiona", "affine", - "scipy>=1.6.0", "rasterstats", - "tqdm", ] [project.urls] @@ -30,5 +28,12 @@ issues = "https://github.com/sgoodm/python-distance-rasters/issues" dev = [ "coverage>=7.6.4", "geopandas>=1.0.1", + "maturin>=1.12.6", "pytest>=8.3.3", + "shapely", ] + +[tool.maturin] +features = ["pyo3/extension-module"] +module-name = "distancerasters._distancerasters" +python-source = "src" diff --git a/src/distance.rs b/src/distance.rs new file mode 100644 index 0000000..f2d28f8 --- /dev/null +++ b/src/distance.rs @@ -0,0 +1,69 @@ +use kiddo::{KdTree, SquaredEuclidean}; +use rayon::prelude::*; + +use crate::haversine; + +/// Calculate distances from every pixel in an (nrows x ncols) grid to the +/// nearest point in `indices`. +/// +/// `indices` is a slice of (row, col) pairs (as f64) where the conditional is true. +/// `affine_params`, if provided, is (pixel_size, xmin, ymax) and triggers +/// geographic distance conversion (haversine, output in meters). +/// Without affine_params, raw Euclidean pixel distance is returned. +/// +/// Returns a flat Vec of length nrows * ncols (row-major). +pub fn calculate_distances( + indices: &[[f64; 2]], + nrows: usize, + ncols: usize, + affine_params: Option<(f64, f64, f64)>, +) -> Vec { + if indices.is_empty() { + return vec![f64::INFINITY; nrows * ncols]; + } + + // kiddo's KdTree requires (point, content) pairs; we store the index as content + let mut tree: KdTree = KdTree::new(); + for (i, point) in indices.iter().enumerate() { + tree.add(point, i as u64); + } + + let tree_ref = &tree; + let result: Vec = (0..nrows) + .into_par_iter() + .flat_map_iter(|r| { + (0..ncols).map(move |c| { + let query = [r as f64, c as f64]; + let nearest = tree_ref.nearest_one::(&query); + let nearest_idx = nearest.item as usize; + let nearest_point = indices[nearest_idx]; + let min_dist = nearest.distance.sqrt(); + + match affine_params { + Some((pixel_size, xmin, ymax)) => { + let km_dist = if (c as f64) == nearest_point[1] { + // Same column: purely vertical, simple conversion + min_dist * pixel_size * 111.321 + } else { + let p1 = haversine::index_to_coords( + r as f64, c as f64, pixel_size, xmin, ymax, + ); + let p2 = haversine::index_to_coords( + nearest_point[0], + nearest_point[1], + pixel_size, + xmin, + ymax, + ); + haversine::haversine(p1, p2) + }; + km_dist * 1000.0 + } + None => min_dist, + } + }) + }) + .collect(); + + result +} diff --git a/src/distancerasters/main.py b/src/distancerasters/main.py index 147feb6..d832cfa 100644 --- a/src/distancerasters/main.py +++ b/src/distancerasters/main.py @@ -1,13 +1,10 @@ import time -from itertools import product import numpy as np from affine import Affine -from scipy.spatial import KDTree -from tqdm import tqdm -from .utils import (calc_haversine_distance, convert_index_to_coords, - export_raster) +from distancerasters._distancerasters import calculate_distances +from .utils import export_raster class DistanceRaster(object): @@ -36,27 +33,18 @@ def __init__(self, raster_array, affine=None, conditional=None, output_path=None if affine is None and output_path is not None: raise Exception("Affine is required for output") - pixel_size = None - if affine is not None: - pixel_size = affine[0] - if conditional is None: conditional = self.default_conditional elif not callable(conditional): raise Exception("Conditional must be function") - self.conditional = conditional self.raster_array = raster_array - self.pixel_size = pixel_size self.affine = affine - self.progress_bar = progress_bar - self.tree = None self.dist_array = None - self._build_tree() self._calculate_distance() if output_path is not None: @@ -67,51 +55,21 @@ def default_conditional(self, rarray): return rarray == 1 - def _build_tree(self, tree_type='kdtree'): - # kd-tree instance - # https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.KDTree.html - t_start = time.time() - if tree_type == "kdtree": - self.tree = KDTree(data=np.array(np.where(self.conditional(self.raster_array))).T, leafsize=64) - print("Tree build time: {0} seconds".format(round(time.time() - t_start, 4))) - - def _calculate_distance(self): - - nrows, ncols = self.raster_array.shape - self.dist_array = np.empty(self.raster_array.shape, dtype=float) - t_start = time.time() + mask = self.conditional(self.raster_array) + indices = np.array(np.where(mask)).T.astype(np.float64) + print("Tree build time: {} seconds".format(round(time.time() - t_start, 4))) - row_col_iterable = product(range(nrows), range(ncols)) - - for r, c in tqdm(row_col_iterable, total=nrows*ncols, disable=(not self.progress_bar)): - cur_index = (r, c) - min_dist, min_index = self.tree.query([cur_index]) - min_dist = min_dist[0] - min_index = self.tree.data[min_index[0]] - - if self.affine is not None: - if cur_index[1] == min_index[1]: - # columns are same meaning nearest is either vertical or self. - # no correction needed, just convert to km - dd_min_dist = min_dist * self.pixel_size - km_min_dist = dd_min_dist * 111.321 - - else: - km_min_dist = calc_haversine_distance( - convert_index_to_coords(cur_index, self.affine), - convert_index_to_coords(min_index, self.affine), - ) - - val = km_min_dist * 1000 - - else: - val = min_dist + nrows, ncols = self.raster_array.shape - self.dist_array[r][c] = val + affine_params = None + if self.affine is not None: + affine_params = (float(self.affine[0]), float(self.affine[2]), float(self.affine[5])) - print("Distance calc run time: {0} seconds".format(round(time.time() - t_start, 4))) + t_start = time.time() + self.dist_array = calculate_distances(indices, nrows, ncols, affine_params) + print("Distance calc run time: {} seconds".format(round(time.time() - t_start, 4))) def output_raster(self, output_path): diff --git a/src/distancerasters/utils.py b/src/distancerasters/utils.py index 6391e4f..e5c08c6 100644 --- a/src/distancerasters/utils.py +++ b/src/distancerasters/utils.py @@ -1,12 +1,13 @@ import os import math +import os from warnings import warn -import fiona + +import numpy as np import rasterio -from rasterio import features from affine import Affine +from rasterio import features from rasterstats.io import read_features -import numpy as np def rasterize( diff --git a/src/haversine.rs b/src/haversine.rs new file mode 100644 index 0000000..0cf3f58 --- /dev/null +++ b/src/haversine.rs @@ -0,0 +1,30 @@ +/// Calculate haversine distance between two points. +/// +/// Points are in (longitude, latitude) format. +/// Returns distance in kilometers. +pub fn haversine(p1: (f64, f64), p2: (f64, f64)) -> f64 { + let (lon1, lat1) = p1; + let (lon2, lat2) = p2; + + let radius: f64 = 6371.0; + + let delta_lat = (lat2 - lat1).to_radians(); + let delta_lon = (lon2 - lon1).to_radians(); + + let a = (delta_lat / 2.0).sin().powi(2) + + lat1.to_radians().cos() * lat2.to_radians().cos() * (delta_lon / 2.0).sin().powi(2); + + let c = 2.0 * a.sqrt().atan2((1.0 - a).sqrt()); + + radius * c +} + +/// Convert 2D array indices to geographic coordinates. +/// +/// Takes row and column indices along with affine parameters +/// and returns (longitude, latitude) of the pixel centroid. +pub fn index_to_coords(r: f64, c: f64, pixel_size: f64, xmin: f64, ymax: f64) -> (f64, f64) { + let lon = xmin + pixel_size * (0.5 + c); + let lat = ymax - pixel_size * (0.5 + r); + (lon, lat) +} diff --git a/src/lib.rs b/src/lib.rs new file mode 100644 index 0000000..c5630ec --- /dev/null +++ b/src/lib.rs @@ -0,0 +1,50 @@ +mod distance; +mod haversine; + +use numpy::{PyArray2, PyReadonlyArray2}; +use pyo3::prelude::*; + +/// Calculate distances from every pixel to the nearest feature pixel. +/// +/// Args: +/// indices: numpy array of shape (N, 2) with (row, col) pairs where condition is true +/// nrows: number of rows in the raster +/// ncols: number of columns in the raster +/// affine_params: optional tuple of (pixel_size, xmin, ymax) for geographic distance +/// +/// Returns: +/// numpy array of shape (nrows, ncols) with distances +#[pyfunction] +fn calculate_distances<'py>( + py: Python<'py>, + indices: PyReadonlyArray2<'py, f64>, + nrows: usize, + ncols: usize, + affine_params: Option<(f64, f64, f64)>, +) -> Bound<'py, PyArray2> { + let indices_array = indices.as_array(); + + // Convert numpy array to Vec of [f64; 2] + let points: Vec<[f64; 2]> = indices_array + .rows() + .into_iter() + .map(|row| [row[0], row[1]]) + .collect(); + + let result = py.detach(|| distance::calculate_distances(&points, nrows, ncols, affine_params)); + + PyArray2::from_vec2( + py, + &result + .chunks(ncols) + .map(|c: &[f64]| c.to_vec()) + .collect::>(), + ) + .expect("Failed to create output array") +} + 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actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} 🐍 - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install Rust 🦀 - uses: dtolnay/rust-toolchain@stable - - name: Install dependencies ⚙️ - run: | - sudo apt-get update - sudo apt-get install libgdal-dev - python -m pip install --upgrade pip - pip install maturin pytest pytest-cov shapely geopandas numpy rasterio fiona affine rasterstats - maturin develop --release - - name: Test with pytest ✅ - run: | - pytest --cov=distancerasters - - name: Coveralls 👖 - if: matrix.python-version == '3.13' - env: - COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} - GITHUB_TOKEN: $COVERALLS_REPO_TOKEN - run: | - pip install coveralls - coveralls + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Set up Python ${{ matrix.python-version }} 🐍 + run: uv python install ${{ matrix.python-version }} + - name: Install Rust 🦀 + uses: dtolnay/rust-toolchain@stable + - name: Install dependencies ⚙️ + run: | + sudo apt-get update + sudo apt-get install libgdal-dev + uv sync + uv run maturin develop --release + - name: Test with pytest ✅ + run: | + uv run pytest --cov=distancerasters + - name: Coveralls 👖 + if: matrix.python-version == '3.13' + env: + COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} + GITHUB_TOKEN: $COVERALLS_REPO_TOKEN + run: | + uv run coveralls diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 954cab8..e64a61c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -10,19 +10,20 @@ jobs: python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} 🐍 - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install Rust 🦀 - uses: dtolnay/rust-toolchain@stable - - name: Install dependencies ⚙️ - run: | - python -m pip install --upgrade pip - pip install maturin pytest pytest-cov shapely geopandas numpy rasterio fiona affine rasterstats - maturin develop --release - - name: Test with pytest ✅ - run: | - pytest --cov=distancerasters + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Set up Python ${{ matrix.python-version }} 🐍 + run: uv python install ${{ matrix.python-version }} + - name: Install Rust 🦀 + uses: dtolnay/rust-toolchain@stable + - name: Install dependencies ⚙️ + run: | + sudo apt-get update + sudo apt-get install libgdal-dev + uv sync + uv run maturin develop --release + - name: Test with pytest ✅ + run: | + uv run pytest --cov=distancerasters diff --git a/pyproject.toml b/pyproject.toml index d4734f8..5c08759 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,9 +27,11 @@ issues = "https://github.com/sgoodm/python-distance-rasters/issues" [dependency-groups] dev = [ "coverage>=7.6.4", + "coveralls", "geopandas>=1.0.1", "maturin>=1.12.6", 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'3.14' env: COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} GITHUB_TOKEN: $COVERALLS_REPO_TOKEN diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e64a61c..52f8fb6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"] steps: - uses: actions/checkout@v4 @@ -26,4 +26,3 @@ jobs: - name: Test with pytest ✅ run: | uv run pytest --cov=distancerasters - From cde323f6dd70fae9720f6a3ad088393b78d88100 Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Thu, 19 Mar 2026 16:18:39 -0400 Subject: [PATCH 5/8] code formatting and comments --- src/distance.rs | 13 +++++++++---- src/distancerasters/__init__.py | 2 +- src/distancerasters/main.py | 24 +++++++++++++++++------- src/distancerasters/utils.py | 8 +------- src/haversine.rs | 3 ++- src/lib.rs | 5 ++++- 6 files changed, 34 insertions(+), 21 deletions(-) diff --git a/src/distance.rs b/src/distance.rs index f2d28f8..abf5cd5 100644 --- a/src/distance.rs +++ b/src/distance.rs @@ -22,27 +22,33 @@ pub fn calculate_distances( return vec![f64::INFINITY; nrows * ncols]; } - // kiddo's KdTree requires (point, content) pairs; we store the index as content + // Build a 2-D k-d tree from the input points for fast nearest-neighbor lookups. + // Each entry stores the point's position and its index into `indices`. let mut tree: KdTree = KdTree::new(); for (i, point) in indices.iter().enumerate() { tree.add(point, i as u64); } + // Iterate over every pixel in parallel (one thread per row via rayon). + // For each pixel, find the closest input point and compute the distance. let tree_ref = &tree; let result: Vec = (0..nrows) .into_par_iter() .flat_map_iter(|r| { (0..ncols).map(move |c| { + // Look up the nearest input point to this pixel in the k-d tree let query = [r as f64, c as f64]; let nearest = tree_ref.nearest_one::(&query); let nearest_idx = nearest.item as usize; let nearest_point = indices[nearest_idx]; let min_dist = nearest.distance.sqrt(); + // If affine params are provided, convert pixel distance to + // geographic distance (meters) using the haversine formula. + // Otherwise, return raw Euclidean distance in pixel units. match affine_params { Some((pixel_size, xmin, ymax)) => { let km_dist = if (c as f64) == nearest_point[1] { - // Same column: purely vertical, simple conversion min_dist * pixel_size * 111.321 } else { let p1 = haversine::index_to_coords( @@ -57,13 +63,12 @@ pub fn calculate_distances( ); haversine::haversine(p1, p2) }; - km_dist * 1000.0 + km_dist * 1000.0 // convert km → meters } None => min_dist, } }) }) .collect(); - result } diff --git a/src/distancerasters/__init__.py b/src/distancerasters/__init__.py index f58a5b8..b08a690 100644 --- a/src/distancerasters/__init__.py +++ b/src/distancerasters/__init__.py @@ -1,3 +1,3 @@ # -*- coding: utf-8 -*- from .main import DistanceRaster -from .utils import rasterize, export_raster +from .utils import export_raster, rasterize diff --git a/src/distancerasters/main.py b/src/distancerasters/main.py index d832cfa..4a1bd3e 100644 --- a/src/distancerasters/main.py +++ b/src/distancerasters/main.py @@ -4,12 +4,19 @@ from affine import Affine from distancerasters._distancerasters import calculate_distances + from .utils import export_raster class DistanceRaster(object): - - def __init__(self, raster_array, affine=None, conditional=None, output_path=None, progress_bar=False): + def __init__( + self, + raster_array, + affine=None, + conditional=None, + output_path=None, + progress_bar=False, + ): """build distance array from raster array Args @@ -50,11 +57,9 @@ def __init__(self, raster_array, affine=None, conditional=None, output_path=None if output_path is not None: self.output_raster(output_path) - def default_conditional(self, rarray): return rarray == 1 - def _calculate_distance(self): t_start = time.time() mask = self.conditional(self.raster_array) @@ -65,12 +70,17 @@ def _calculate_distance(self): affine_params = None if self.affine is not None: - affine_params = (float(self.affine[0]), float(self.affine[2]), float(self.affine[5])) + affine_params = ( + float(self.affine[0]), + float(self.affine[2]), + float(self.affine[5]), + ) t_start = time.time() self.dist_array = calculate_distances(indices, nrows, ncols, affine_params) - print("Distance calc run time: {} seconds".format(round(time.time() - t_start, 4))) - + print( + "Distance calc run time: {} seconds".format(round(time.time() - t_start, 4)) + ) def output_raster(self, output_path): export_raster(self.dist_array, self.affine, output_path) diff --git a/src/distancerasters/utils.py b/src/distancerasters/utils.py index e5c08c6..a5dc50e 100644 --- a/src/distancerasters/utils.py +++ b/src/distancerasters/utils.py @@ -1,4 +1,3 @@ -import os import math import os from warnings import warn @@ -81,7 +80,6 @@ def rasterize( and isinstance(shape, tuple) and len(shape) == 2 ): - if pixel_size is not None and pixel_size != affine[0]: warn("Ignoring `pixel_size` provided due to valid affine and shape input.") @@ -99,7 +97,6 @@ def rasterize( else: raise Exception("Must provide either pixel_size and bounds or affine and shape") - features_iter = read_features(vectors, layer) if attribute is None: @@ -115,7 +112,6 @@ def rasterize( if feat["geometry"] is not None ] - rv_array = features.rasterize( feats, out_shape=shape, @@ -133,7 +129,6 @@ def rasterize( def export_raster(raster, affine, path, out_dtype="float64", nodata=None): - if not rasterio.dtypes.check_dtype(out_dtype): raise ValueError("out_dtype not recognized by rasterio") @@ -163,8 +158,7 @@ def export_raster(raster, affine, path, out_dtype="float64", nodata=None): def get_affine_and_shape(bounds, pixel_size): - """Get affine and shape from bounds and pixel size - """ + """Get affine and shape from bounds and pixel size""" try: pixel_size = float(pixel_size) except: diff --git a/src/haversine.rs b/src/haversine.rs index 0cf3f58..d1b3152 100644 --- a/src/haversine.rs +++ b/src/haversine.rs @@ -1,11 +1,12 @@ /// Calculate haversine distance between two points. /// /// Points are in (longitude, latitude) format. -/// Returns distance in kilometers. +/// Returns haversine distance between given points p1 and p2. pub fn haversine(p1: (f64, f64), p2: (f64, f64)) -> f64 { let (lon1, lat1) = p1; let (lon2, lat2) = p2; + // Mean radius of the Earth in km let radius: f64 = 6371.0; let delta_lat = (lat2 - lat1).to_radians(); diff --git a/src/lib.rs b/src/lib.rs index c5630ec..57213d1 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -24,15 +24,17 @@ fn calculate_distances<'py>( ) -> Bound<'py, PyArray2> { let indices_array = indices.as_array(); - // Convert numpy array to Vec of [f64; 2] + // Convert numpy's row views into owned [f64; 2] arrays to pass into Rust functions let points: Vec<[f64; 2]> = indices_array .rows() .into_iter() .map(|row| [row[0], row[1]]) .collect(); + // py.detach() releases the GIL so Rayon's parallel threads can run freely let result = py.detach(|| distance::calculate_distances(&points, nrows, ncols, affine_params)); + // Reshape the flat result vec back into a 2D numpy array (nrows × ncols) PyArray2::from_vec2( py, &result @@ -43,6 +45,7 @@ fn calculate_distances<'py>( .expect("Failed to create output array") } +// register this as a Python extension module named `_distancerasters`. #[pymodule] fn _distancerasters(m: &Bound<'_, PyModule>) -> PyResult<()> { m.add_function(wrap_pyfunction!(calculate_distances, m)?)?; From dc2a4c24c7483cfd03412cc413ab70bcf1533d65 Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Fri, 20 Mar 2026 12:54:26 -0400 Subject: [PATCH 6/8] fix current version of package --- pyproject.toml | 2 +- uv.lock | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5c08759..f565d2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ classifiers = ["Programming Language :: Python :: 3"] keywords = ["raster", "distance", "spatial"] license = { text = "BSD 3-Clause License" } name = "distancerasters" -version = "0.5.0" +version = "0.4.0" description = "Generate distance raster using arbitrary sets of spatial features" readme = "README.md" requires-python = ">= 3.9" diff --git a/uv.lock b/uv.lock index 5dcafa8..4166948 100644 --- a/uv.lock +++ b/uv.lock @@ -306,7 +306,7 @@ wheels = [ [[package]] name = "distancerasters" -version = "0.5.0" +version = "0.4.0" source = { editable = "." } dependencies = [ { name = "affine" }, @@ -427,7 +427,7 @@ name = "importlib-metadata" version = "6.7.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "zipp", marker = "python_full_version < '3.11'" }, + { name = "zipp", marker = "python_full_version < '3.10'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/a3/82/f6e29c8d5c098b6be61460371c2c5591f4a335923639edec43b3830650a4/importlib_metadata-6.7.0.tar.gz", hash = "sha256:1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4", size = 53569, upload-time = "2023-06-18T21:44:35.024Z" } wheels = [ From 9d11e7a8b01b2232c33035a1b699d5b8ab88d65f Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Fri, 20 Mar 2026 13:11:07 -0400 Subject: [PATCH 7/8] format build and publish Action, fix pypi-publish version --- .github/workflows/build-and-publish.yml | 86 ++++++++++++------------- 1 file changed, 43 insertions(+), 43 deletions(-) diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml index 61c06e9..4ccf907 100644 --- a/.github/workflows/build-and-publish.yml +++ b/.github/workflows/build-and-publish.yml @@ -13,57 +13,57 @@ jobs: matrix: os: [ubuntu-latest, macos-latest, windows-latest] steps: - - uses: actions/checkout@v4 - - uses: PyO3/maturin-action@v1 - with: - command: build - args: --release --out dist - - uses: actions/upload-artifact@v4 - with: - name: wheels-${{ matrix.os }} - path: dist + - uses: actions/checkout@v4 + - uses: PyO3/maturin-action@v1 + with: + command: build + args: --release --out dist + - uses: actions/upload-artifact@v4 + with: + name: wheels-${{ matrix.os }} + path: dist build-sdist: name: Build source distribution 🚧 runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: PyO3/maturin-action@v1 - with: - command: sdist - args: --out dist - - uses: actions/upload-artifact@v4 - with: - name: sdist - path: dist + - uses: actions/checkout@v4 + - uses: PyO3/maturin-action@v1 + with: + command: sdist + args: --out dist + - uses: actions/upload-artifact@v4 + with: + name: sdist + path: dist publish: name: Publish 🚀 needs: [build-wheels, build-sdist] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v4 - with: - path: dist - merge-multiple: true - - name: Get version from Cargo.toml - run: | - VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)"/\1/') - echo "VERSION=$VERSION" >> $GITHUB_ENV - - name: Validate release tag - run: | - if [ "${GITHUB_REF#refs/tags/}" != "${VERSION}" ]; then exit 1; fi - - name: Publish to Test PyPI 📦 - if: contains(env.VERSION, 'a') - uses: pypa/gh-action-pypi-publish@v1 - with: - user: __token__ - password: ${{ secrets.TEST_PYPI_API_TOKEN }} - repository-url: https://test.pypi.org/legacy/ - - name: Publish to PyPI 📦 - if: | - !contains(env.VERSION, 'a') - uses: pypa/gh-action-pypi-publish@v1 - with: - user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} + - uses: actions/download-artifact@v4 + with: + path: dist + merge-multiple: true + - name: Get version from Cargo.toml + run: | + VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)"/\1/') + echo "VERSION=$VERSION" >> $GITHUB_ENV + - name: Validate release tag + run: | + if [ "${GITHUB_REF#refs/tags/}" != "${VERSION}" ]; then exit 1; fi + - name: Publish to Test PyPI 📦 + if: contains(env.VERSION, 'a') + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository-url: https://test.pypi.org/legacy/ + - name: Publish to PyPI 📦 + if: | + !contains(env.VERSION, 'a') + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} From 9f4d607c6350e715482b5021ed950160059770e3 Mon Sep 17 00:00:00 2001 From: Jacob Hall Date: Fri, 20 Mar 2026 13:33:15 -0400 Subject: [PATCH 8/8] remove progress_bar option entirely --- src/distancerasters/main.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/distancerasters/main.py b/src/distancerasters/main.py index 4a1bd3e..404ebea 100644 --- a/src/distancerasters/main.py +++ b/src/distancerasters/main.py @@ -15,7 +15,6 @@ def __init__( affine=None, conditional=None, output_path=None, - progress_bar=False, ): """build distance array from raster array