MNT: pin xtensor, fix RTD, update pixi conf (#176)

benbovy · web-flow · commit 33c288b665a6 · 2025-06-13T14:08:37.000+02:00
* pin xtensor in ci dev conda environments

* doc: try fix RTD builds

* ci: remove ubuntu 20.04 from py test matrix

* pixi: add cxx-compiler and update lockfile

* ci: try fix mypy

I don't have any error locally.

* ci python wheels: bump upload-artifact action v4

* update cibuildwheels config

Can now build natively on MacOS arm64.

* ci workflow typo

* try fix ci wheels on macos

* add github integration (dependabot, release, codecov)

* ci tests: bump pixi action version

* ci build wheels: re-deactivate numba tests for py313

* ci: fix pixi (update pixi lock file)
diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -0,0 +1,12 @@
+codecov:
+  notify:
+    after_n_builds: 3
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 5%
+    patch:
+      default:
+        informational: true
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      dependencies:
+        patterns:
+          - "*"
diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci
diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
@@ -21,35 +21,52 @@ jobs:
       - name: Upload SDist
         uses: actions/upload-artifact@v4
         with:
-          path: dist/*.tar.gz
+          name: release-sdist
+          path: ./dist/*.tar.gz
+          retention-days: 30
 
   build_wheels:
     name: Build wheel (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        include:
+        - os: ubuntu-latest
+          arch: x86_64
+        - os: windows-2019
+          arch: AMD64
+          msvc_arch: x64
+        - os: macos-13
+          arch: x86_64
+          cmake_osx_architectures: x86_64
+          macosx_deployment_target: 10.13
+        - os: macos-14
+          arch: arm64
+          cmake_osx_architectures: arm64
+          macosx_deployment_target: 14.0
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21
+        uses: pypa/cibuildwheel@v2.22
         env:
           # skip PyPy and muslinux (for now)
           CIBW_SKIP: "pp* *musllinux*"
-          # skip 32-bits platforms on linux and windows
-          CIBW_ARCHS_LINUX: "auto64"
-          CIBW_ARCHS_WINDOWS: "auto64"
-          # macos: opt-in cross-compile on arm64
-          CIBW_ARCHS_MACOS: "x86_64 arm64"
-          CIBW_TEST_SKIP: "*_arm64 *_universal2:arm64"
+          CIBW_ARCHS: ${{ matrix.arch }}
+          # need also to redefine here some environment vars defined in pyprojet.toml
+          CIBW_ENVIRONMENT_MACOS:
+            MACOSX_DEPLOYMENT_TARGET=${{ matrix.macosx_deployment_target }}
+            CMAKE_OSX_ARCHITECTURES='${{ matrix.cmake_osx_architectures }}'
+            SKBUILD_CMAKE_ARGS='-DFS_DOWNLOAD_XTENSOR_PYTHON=ON'
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          path: wheelhouse/*.whl
+          name: release-${{ matrix.os }}-${{ matrix.arch }}
+          path: ./wheelhouse/*.whl
+          retention-days: 5
 
   upload_all:
     needs: [build_wheels, make_sdist]
@@ -62,7 +79,8 @@ jobs:
       - name: Get dist files
         uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: release-*
+          merge-multiple: true
           path: dist
 
       - name: Publish on PyPI
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -63,7 +63,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-20.04", "ubuntu-latest", "macos-latest", "windows-latest"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.10", "3.11", "3.12"]
     steps:
       - name: Checkout repo
@@ -114,7 +114,7 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - uses: prefix-dev/setup-pixi@v0.8.1
+      - uses: prefix-dev/setup-pixi@v0.8.10
         with:
           pixi-version: v0.40.1
           cache: true
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -13,5 +13,6 @@ conda:
 
 sphinx:
   fail_on_warning: true
+  configuration: doc/source/conf.py
 
 formats: []
diff --git a/doc/environment.yml b/doc/environment.yml
@@ -5,7 +5,7 @@ dependencies:
   - python=3.11
   - breathe
   - cmake
-  - xtensor-python
+  - xtensor-python>=0.27,<0.28
   - pybind11
   - scikit-build-core
   - numpy
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -2,7 +2,7 @@ name: fastscapelib-dev
 channels:
   - conda-forge
 dependencies:
-  - xtensor
+  - xtensor>=0.25,<0.26
   - cmake
   - gtest
   - benchmark
diff --git a/environment-python-dev.yml b/environment-python-dev.yml
@@ -5,7 +5,7 @@ dependencies:
   - python>=3.10
   - numpy
   - numba
-  - xtensor-python
+  - xtensor-python>=0.27,<0.28
   - pybind11
   - cmake
   - scikit-build-core
diff --git a/pixi.lock b/pixi.lock
diff --git a/pixi.toml b/pixi.toml
@@ -24,6 +24,7 @@ xtensor = ">=0.24,<0.26"
 cmake = ">=3.31.4,<4"
 ninja = ">=1.12.1,<2"
 make = ">=4.4.1,<5"
+cxx-compiler = ">=1.9.0,<1.10.0"
 
 [feature.cpp.dependencies]
 eigen = ">=3.4.0,<4"
diff --git a/pyproject.toml b/pyproject.toml
@@ -46,14 +46,14 @@ test-command = "pytest {project}/python/fastscapelib/tests"
 build-verbosity = 1
 
 [[tool.cibuildwheel.overrides]]
-# TODO: remove when numba supports python 3.13
+# keep this override: will be useful for next versions of Python
+# (Numba support always come with a delay)
+# TODO: activate numba tests for py313
+# (still some failing test with jitclass in macos arm64, issue seems in numba)
 select = "cp3{10,11,12}-*"
 inherit.test-requires = "append"
 test-requires = ["numba"]
 
-[tool.cibuildwheel.macos]
-environment = {SKBUILD_CMAKE_ARGS='-DFS_DOWNLOAD_XTENSOR_PYTHON=ON', MACOSX_DEPLOYMENT_TARGET=10.13}
-
 [tool.isort]
 profile = "black"
 skip_gitignore = true
diff --git a/python/fastscapelib/flow/numba/flow_kernel.py b/python/fastscapelib/flow/numba/flow_kernel.py
@@ -23,6 +23,7 @@
 
 import numba as nb
 import numpy as np
+import numpy.typing as npt
 from numba.experimental.jitclass import _box  # type: ignore[missing-imports]
 
 from fastscapelib.flow import (
@@ -970,6 +971,8 @@ def apply_flow_kernel(
     if kernel.node_data_init:
         kernel.node_data_init(node_data, data.jitclass_obj)
 
+    indices: npt.NDArray[np.uint64]
+
     if wrapped_kernel.apply_dir == FlowGraphTraversalDir.ANY:
         indices = np.arange(0, flow_graph.size, 1, dtype=np.uint64)
     elif wrapped_kernel.apply_dir == FlowGraphTraversalDir.BREADTH_UPSTREAM:
