Fix/rust ubuntu issue

.github/workflows/cd.yml

@@ -0,0 +1,30 @@
+name: cd
+
+on:
+  push:
+    tags:
+      - '**'
+
+jobs:
+  pypi_binwheels:
+    uses: ecmwf/reusable-workflows/.github/workflows/cd-pypi-binwheel.yml@feat/rust_wheels_with_clang
+    secrets: inherit
+    with:
+      platforms: "['ubuntu-latest','macos-latest','windows-latest']"
+      pyversions: "['38','39','310','311','312','313']"
+      env_vars: |
+        {
+          "USE_RUST": "1",
+          "SETUPTOOLS_RUST_CARGO_PROFILE": "release"
+        }
+
+  pypi_purepython:
+    needs: pypi_binwheels
+    uses: ecmwf/reusable-workflows/.github/workflows/cd-pypi.yml@feat/rust_wheels_with_clang
+    secrets: inherit
+    with:
+      env_vars: |
+        {
+          "USE_RUST": "0",
+          "SETUPTOOLS_RUST_CARGO_PROFILE": "release"
+        }

.github/workflows/ci.yaml → .github/workflows/ci.yml

@@ -1,19 +1,9 @@
-name: ci
 on:
-  # Trigger the workflow on push to master or develop, except tag creation
   push:
-    branches:
-      - 'main'
-      - 'develop'
-  # Trigger the workflow on pull request
-  pull_request: ~
-  # Trigger the workflow manually
-  workflow_dispatch: ~
-  # Trigger after public PR approved for CI
-  pull_request_target:
-    types: [labeled]
-  release:
-    types: [created]
+    branches: [ "main", "develop" ]
+  pull_request:
+    branches: [ "main", "develop" ]
+
 jobs:
   qa:
     name: qa
@@ -28,7 +18,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ inputs.python_version }}
+          python-version: '3.12'
 
       - name: Install Python Dependencies
         run: |
@@ -42,10 +32,10 @@ jobs:
 
       - name: Check flake8
         run: flake8 .
-  test:
-    name: test
-    needs:
-      - qa
+
+  test-purepython:
+    env:
+      USE_RUST: "0"
     strategy:
       fail-fast: false
       matrix:
@@ -62,8 +52,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
-      - name: Install eccodes and Dependencies
-        id: install-dependencies
+
+      - name: Install eccodes
+        id: install-ecbuild
         uses: ecmwf/build-package@v2
         with:
           self_build: false
@@ -75,21 +66,16 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ inputs.python_version }}
+          python-version: '3.12'
 
-      - name: Install Python Dependencies
+      - name: Install setuptools
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
-          python -m pip install pytest pytest-cov
-          python -m pip install -r requirements.txt 
-          python -m pip install -r ./tests/requirements_test.txt
+          python -m pip install --upgrade pip setuptools
 
-      - name: Verify Source Distribution
-        shell: bash -eux {0}
+      - name: Install Polytope
         run: |
-          python setup.py sdist
-          python -m pip install dist/*
+          python -m pip install -v .[test]
+
       - name: Run Tests with Repository Code
         env:
           LD_LIBRARY_PATH: ${{ steps.install-dependencies.outputs.lib_path }}
@@ -102,25 +88,62 @@ jobs:
         uses: codecov/codecov-action@v4
         with:
           files: coverage.xml
-  deploy:
-    needs: test
-    if: ${{ github.event_name == 'release' }}
-    name: Upload to Pypi
-    runs-on: ubuntu-24.04
+
+  test-rust:
+    env:
+      USE_RUST: "1"
+    strategy:
+      fail-fast: false
+      matrix:
+        name:
+          - ubuntu-22.04
+          - macos-latest
+        include:
+          - name: ubuntu-22.04
+            os: ubuntu-22.04
+            compiler_fc: gfortran
+          - name: macos-latest
+            os: macos-latest
+            compiler_fc: gfortran-12
+    runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+
+      - name: Install eccodes and Dependencies
+        id: install-dependencies
+        uses: ecmwf/build-package@v2
         with:
-          python-version: '3.8'
-      - name: Install dependencies
+          self_build: false
+          dependencies: |
+            ecmwf/ecbuild@develop
+            MathisRosenhauer/libaec@master
+            ecmwf/eccodes@develop
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install setuptools
         run: |
-          python -m pip install --upgrade pip
-          pip install build twine
-      - name: Build and publish
+          python -m pip install --upgrade pip setuptools
+
+      - name: Install rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install Polytope
+        run: |
+          python -m pip install -v .[test]
+
+      - name: Run Tests with Repository Code
         env:
-          TWINE_USERNAME: "__token__"
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+          LD_LIBRARY_PATH: ${{ steps.install-dependencies.outputs.lib_path }}
+        shell: bash -eux {0}
         run: |
-          python -m build
-          twine upload dist/*
+          DYLD_LIBRARY_PATH=${{ env.LD_LIBRARY_PATH }} python -m pytest -m "not fdb" tests --cov=./ --cov-report=xml
+          python -m coverage report
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: coverage.xml

.github/workflows/test-pypi.yml

@@ -0,0 +1,31 @@
+name: test-cd
+
+on:
+  pull_request:
+    branches: [ "main", "develop" ]
+
+jobs:
+  pypi_binwheels:
+    uses: ecmwf/reusable-workflows/.github/workflows/cd-pypi-binwheel.yml@feat/rust_wheels_with_clang
+    secrets: inherit
+    with:
+      platforms: "['ubuntu-latest','macos-latest']" #",'windows-latest']"
+      pyversions: "['38','39','310','311','312']"
+      testpypi: true
+      env_vars: |
+        {
+          "USE_RUST": "1",
+          "SETUPTOOLS_RUST_CARGO_PROFILE": "release"
+        }
+
+  pypi_purepython:
+    needs: pypi_binwheels
+    uses: ecmwf/reusable-workflows/.github/workflows/cd-pypi.yml@feat/rust_wheels_with_clang
+    secrets: inherit
+    with:
+      testpypi: true
+      env_vars: |
+        {
+          "USE_RUST": "0",
+          "SETUPTOOLS_RUST_CARGO_PROFILE": "release"
+        }

.gitignore

@@ -1,23 +1,40 @@
 *.py[cod]
 *.swp
-**/__pycache__
-.vscode
-polytope.egg-info
-.pytest_cache
+*.grib
+*.gif
+*.html
+*.req
 *.prof
 *.idx
 *.grib
 *.xml
-site
+*.pstats
+*.profile
+*.egg-info
+*.json
+*.txt
+*.gz
+*.so
+
 .coverage
-*.grib
-*.gif
-*.html
+.mypy_cache
+.vscode
+.pytest_cache
+
+__pycache__/
+.ipynb_checkpoints/
+
+_version.py
+target/
+dist/
+build/
+
+Cargo.lock
+.DS_Store
+
+site
 example_eo
 example_mri
-.mypy_cache
-*.req
-polytope_python.egg-info
 new_test_venv_polytope
 new_venv_polytope
 polytope_venv
@@ -26,6 +43,11 @@ new_updated_numpy_venv
 newest-polytope-venv
 serializedTree
 new_polytope_venv
+newest-polytope-venv
+new_polytope_venv
+polytope_feature/datacube/quadtree/target
+venv_python3_11
+venv_gj_iterator
 *.json
 venv_python3_11
 *.txt

Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "polytope-python"
+version = "0.0.0" # placeholder
+edition = "2021"
+
+[dependencies]
+pyo3 = { version = "0.20", features = ["extension-module"] }
+qhull = { git = "https://github.com/LucaCiucci/qhull-rs" }
+rayon = "1.8"
+
+[lib]
+name = "quadtree"
+path = "rust/lib.rs"
+crate-type = ["cdylib"]

Makefile

@@ -1,6 +1,3 @@
-init:
-	pip install -r requirements.txt
-
 testk:
 	python3 -m pytest -vsrA tests/* -k $(filter-out $@, $(MAKECMDGOALS)) -W ignore::DeprecationWarning -W ignore::FutureWarning --log-cli-level=DEBUG
 

examples/3D_shipping_route.py

@@ -6,9 +6,9 @@
 import numpy as np
 from earthkit import data
 
-from polytope.engine.hullslicer import HullSlicer
-from polytope.polytope import Polytope, Request
-from polytope.shapes import Ellipsoid, Path, Select
+from polytope_feature.engine.hullslicer import HullSlicer
+from polytope_feature.polytope import Polytope, Request
+from polytope_feature.shapes import Ellipsoid, Path, Select
 
 
 class Test:

examples/3D_shipping_route_wave_model.py

@@ -4,10 +4,10 @@
 import pytest
 from eccodes import codes_grib_find_nearest, codes_grib_new_from_file
 
-from polytope.datacube.backends.fdb import FDBDatacube
-from polytope.engine.hullslicer import HullSlicer
-from polytope.polytope import Polytope, Request
-from polytope.shapes import Ellipsoid, Path, Select
+from polytope_feature.datacube.backends.fdb import FDBDatacube
+from polytope_feature.engine.hullslicer import HullSlicer
+from polytope_feature.polytope import Polytope, Request
+from polytope_feature.shapes import Ellipsoid, Path, Select
 from tests.helper_functions import download_test_data
 
 

examples/4D_flight_path.py

@@ -4,10 +4,10 @@
 from earthkit import data
 from PIL import Image
 
-from polytope.datacube.backends.xarray import XArrayDatacube
-from polytope.engine.hullslicer import HullSlicer
-from polytope.polytope import Polytope, Request
-from polytope.shapes import Box, Path, Select
+from polytope_feature.datacube.backends.xarray import XArrayDatacube
+from polytope_feature.engine.hullslicer import HullSlicer
+from polytope_feature.polytope import Polytope, Request
+from polytope_feature.shapes import Box, Path, Select
 
 
 class Test:

examples/country_slicing.py

@@ -4,10 +4,10 @@
 from earthkit import data
 from shapely.geometry import shape
 
-from polytope.datacube.backends.xarray import XArrayDatacube
-from polytope.engine.hullslicer import HullSlicer
-from polytope.polytope import Polytope, Request
-from polytope.shapes import Polygon, Select, Union
+from polytope_feature.datacube.backends.xarray import XArrayDatacube
+from polytope_feature.engine.hullslicer import HullSlicer
+from polytope_feature.polytope import Polytope, Request
+from polytope_feature.shapes import Polygon, Select, Union
 
 
 class Test:

examples/cyclic_route_around_earth.py

@@ -3,10 +3,10 @@
 import numpy as np
 from earthkit import data
 
-from polytope.datacube.backends.xarray import XArrayDatacube
-from polytope.engine.hullslicer import HullSlicer
-from polytope.polytope import Polytope, Request
-from polytope.shapes import Box, PathSegment, Select
+from polytope_feature.datacube.backends.xarray import XArrayDatacube
+from polytope_feature.engine.hullslicer import HullSlicer
+from polytope_feature.polytope import Polytope, Request
+from polytope_feature.shapes import Box, PathSegment, Select
 
 
 class Test: