Merge remote-tracking branch 'upstream/main' into gh26406

Author: mdhaber

.circleci/config.yml

@@ -54,29 +54,22 @@ jobs:
           command: |
             python3.11 -m venv venv
             . venv/bin/activate
-            pip install --progress-bar=off -r requirements/test_requirements.txt
+            pip install --progress-bar=off -r requirements/test_requirements.txt \
+               -r requirements/build_requirements.txt \
+               -r requirements/ci_requirements.txt
             # get newer, pre-release versions of critical packages
-            pip install --progress-bar=off --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple -r requirements/doc_requirements.txt
+            pip install --progress-bar=off --pre -r requirements/doc_requirements.txt
             # then install numpy HEAD, which will override the version installed above
-            pip install . --config-settings=setup-args="-Dallow-noblas=true"
-
-      - run:
-          name: create release notes
-          command: |
-            . venv/bin/activate
-            VERSION=$(pip show numpy | grep Version: | cut -d ' ' -f 2 | cut -c 1-5)
-            towncrier build --version $VERSION --yes
-            ./tools/ci/test_all_newsfragments_used.py
+            spin build --with-scipy-openblas=64
 
       - run:
           name: build devdocs w/ref warnings
           command: |
             . venv/bin/activate
-            cd doc
             # Don't use -q, show warning summary"
-            SPHINXOPTS="-n" make -e html
-            if [[ $(find build/html -type f | wc -l) -lt 1000 ]]; then
-                echo "doc build failed: build/html is empty"
+            SPHINXOPTS="-W -n" spin docs
+            if [[ $(find doc/build/html -type f | wc -l) -lt 1000 ]]; then
+                echo "doc build failed: doc/build/html is empty"
                 exit -1
             fi
 
@@ -95,14 +88,17 @@ jobs:
      #      destination: neps
 
       - run:
-          name: run doctests on documentation
+          name: check doctests
           command: |
             . venv/bin/activate
-            # Note: keep these two checks separate, because they seem to
-            # influence each other through changing global state (e.g., via
-            # `np.polynomial.set_default_printstyle`)
-            python tools/refguide_check.py --rst
-            python tools/refguide_check.py --doctests
+            spin check-docs -v
+            spin check-tutorials -v
+            # Currently, this does two checks not done by check-docs:
+            #  - validates ReST blocks (via validate_rst_syntax)
+            #  - checks that all of a module's `__all__` is reflected in the
+            #    module-level docstring autosummary
+            echo calling python tools/refguide_check.py -v
+            python tools/refguide_check.py -v
 
       - persist_to_workspace:
           root: ~/repo

.editorconfig

@@ -6,3 +6,21 @@ indent_size = 4
 indent_style = space
 max_line_length = 80
 trim_trailing_whitespace = true
+
+[*.{py,pyi,pxd}]
+# https://peps.python.org/pep-0008/
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.py]
+# Keep in sync with `tools/lint_diff.ini` and `tools/linter.py`
+# https://pycodestyle.pycqa.org/en/latest/intro.html#configuration
+max_line_length = 88
+
+[*.pyi]
+# https://typing.readthedocs.io/en/latest/guides/writing_stubs.html#style-guide
+max_line_length = 130

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -56,7 +56,7 @@ body:
     label: "Runtime Environment:"
     description: |
       1. Install `threadpoolctl` (e.g. with `pip` or `conda`)
-      2. Paste the output of `import numpy; print(numpy.show_runtime())`.
+      2. Paste the output of `import numpy; numpy.show_runtime()`.
 
       Note: Only valid for NumPy 1.24 or newer.
   validations:

.github/ISSUE_TEMPLATE/typing.yml

@@ -0,0 +1,68 @@
+name: Static Typing
+description: Report an issue with the NumPy typing hints.
+title: "TYP: <Please write a comprehensive title after the 'TYP: ' prefix>"
+labels: [Static typing]
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      Thank you for taking the time to report this issue.
+      Please make sure that this issue hasn't already been reported before.
+
+- type: textarea
+  attributes:
+    label: "Describe the issue:"
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Reproduce the code example:"
+    description: >
+      A short code example that reproduces the error in your type-checker. It
+      should be self-contained, i.e., can be run as-is via e.g.
+      `mypy myproblem.py` or `pyright myproblem.py`.
+    placeholder: |
+      import numpy as np
+      import numpy.typing as npt
+      << your code here >>
+    render: python
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Error message:"
+    description: >
+      Please include all relevant error messages from your type-checker or IDE.
+    render: shell
+
+- type: textarea
+  attributes:
+    label: "Python and NumPy Versions:"
+    description: >
+      Output from `import sys, numpy; print(numpy.__version__); print(sys.version)`.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Type-checker version and settings:"
+    description: >
+      Please include the exact version of the type-checker you are using.
+      Popular (static) type checkers include Mypy, Pyright / Pylance, Pytype,
+      Pyre, PyCharm, etc.
+      Also include the full CLI command used to run the type-checker, and
+      all of the relevant configuration options.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Additional typing packages."
+    description: |
+      If you are using `typing-extensions` or typing-stub packages, please
+      list their versions here.
+  validations:
+    required: false

.github/pr-prefix-labeler.yml

@@ -1,15 +1,16 @@
 "API": "30 - API"
 "BENCH": "28 - Benchmark"
-"BUG": "00 - Bug"
 "BLD": "36 - Build"
+"BUG": "00 - Bug"
 "DEP": "07 - Deprecation"
 "DEV": "16 - Development"
 "DOC": "04 - Documentation"
 "ENH": "01 - Enhancement"
 "MAINT": "03 - Maintenance"
+"MNT": "03 - Maintenance"
+"REL": "14 - Release"
 "REV": "34 - Reversion"
 "STY": "03 - Maintenance"
 "TST": "05 - Testing"
-"REL": "14 - Release"
-"WIP": "25 - WIP"
 "TYP": "static typing"
+"WIP": "25 - WIP"

.github/workflows/codeql.yml

@@ -45,7 +45,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@cdcdbb579706841c47f7063dda365e292e5cad7a # v2.13.4
+        uses: github/codeql-action/init@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -55,7 +55,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@cdcdbb579706841c47f7063dda365e292e5cad7a # v2.13.4
+        uses: github/codeql-action/autobuild@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -68,6 +68,6 @@ jobs:
       #   ./location_of_script_within_repo/buildscript.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@cdcdbb579706841c47f7063dda365e292e5cad7a # v2.13.4
+        uses: github/codeql-action/analyze@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
         with:
           category: "/language:${{matrix.language}}"

.github/workflows/cygwin.yml

@@ -62,7 +62,7 @@ jobs:
           cd tools
           /usr/bin/python3.9 -m pytest --pyargs numpy -n2 -m "not slow"
       - name: Upload wheel if tests fail
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
         if: failure()
         with:
           name: numpy-cygwin-wheel

.github/workflows/dependency-review.yml

@@ -17,4 +17,4 @@ jobs:
       - name: 'Checkout Repository'
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@0c155c5e8556a497adf53f2c18edabf945ed8e70 # v4.3.2
+        uses: actions/dependency-review-action@5a2ce3f5b92ee19cbb1541a4984c76d921601d7c # v4.3.4

.github/workflows/emscripten.yml

@@ -6,10 +6,7 @@ on:
       - main
       - maintenance/**
   # Note: this workflow gets triggered on the same schedule as the
-  # wheels.yml workflow, with the exception that this workflow runs
-  # the test suite for the Pyodide wheel too, prior to uploading it.
-  #
-  # Run on schedule to upload to Anaconda.org
+  # wheels.yml workflow to upload WASM wheels to Anaconda.org.
   schedule:
     #        ┌───────────── minute (0 - 59)
     #        │  ┌───────────── hour (0 - 23)
@@ -35,92 +32,53 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-permissions:
-  contents: read # to fetch code (actions/checkout)
 
 jobs:
   build-wasm-emscripten:
+    permissions:
+      contents: read  # to fetch code (actions/checkout)
     name: Build NumPy distribution for Pyodide
     runs-on: ubuntu-22.04
     # To enable this workflow on a fork, comment out:
     if: github.repository == 'numpy/numpy'
-    env:
-      PYODIDE_VERSION: 0.25.1
-      # PYTHON_VERSION and EMSCRIPTEN_VERSION are determined by PYODIDE_VERSION.
-      # The appropriate versions can be found in the Pyodide repodata.json
-      # "info" field, or in Makefile.envs:
-      # https://github.com/pyodide/pyodide/blob/main/Makefile.envs#L2
-      PYTHON_VERSION: 3.11.3
-      EMSCRIPTEN_VERSION: 3.1.46
-      NODE_VERSION: 18
     steps:
       - name: Checkout NumPy
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11  # v4.1.1
         with:
           submodules: recursive
-          # This input shall fetch tags without the need to fetch the
-          # entire VCS history, see https://github.com/actions/checkout#usage
           fetch-tags: true
 
-      - name: Set up Python ${{ env.PYTHON_VERSION }}
-        id: setup-python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
+      - uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b  # v2.21.3
+        env:
+          CIBW_PLATFORM: pyodide
 
-      - name: Set up Emscripten toolchain
-        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
+      - name: Upload wheel artifact(s)
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882  # v4.4.3
         with:
-          version: ${{ env.EMSCRIPTEN_VERSION }}
-          actions-cache-folder: emsdk-cache
-
-      - name: Install pyodide-build
-        run: pip install "pydantic<2" pyodide-build==${{ env.PYODIDE_VERSION }}
-
-      - name: Find installation for pyodide-build
-        shell: python
-        run: |
-          import os
-          import pyodide_build
-          from pathlib import Path
-
-          pyodide_build_path = Path(pyodide_build.__file__).parent
-
-          env_file = os.getenv('GITHUB_ENV')
-
-          with open(env_file, "a") as myfile:
-              myfile.write(f"PYODIDE_BUILD_PATH={pyodide_build_path}\n")
-
-      - name: Build NumPy for Pyodide
-        run: |
-          pyodide build -Cbuild-dir=build -Csetup-args="--cross-file=$PWD/tools/ci/emscripten/emscripten.meson.cross" -Csetup-args="-Dblas=none" -Csetup-args="-Dlapack=none"
-
-      - name: Set up Node.js
-        uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4.0.2
+          name: cp312-pyodide_wasm32
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  # Push to https://anaconda.org/scientific-python-nightly-wheels/numpy
+  # WARNING: this job will overwrite any existing WASM wheels.
+  upload-wheels:
+    name: Upload NumPy WASM wheels to Anaconda.org
+    runs-on: ubuntu-22.04
+    permissions: {}
+    needs: [build-wasm-emscripten]
+    if: >-
+      (github.repository == 'numpy/numpy') &&
+      (github.event_name == 'workflow_dispatch' && github.event.inputs.push_wheels == 'true') ||
+      (github.event_name == 'schedule')
+    steps:
+      - name: Download wheel artifact(s)
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16  # v4.1.8
         with:
-          node-version: ${{ env.NODE_VERSION }}
-
-      - name: Set up Pyodide virtual environment
-        run: |
-          pyodide venv .venv-pyodide
-          source .venv-pyodide/bin/activate
-          pip install dist/*.whl
-          pip install -r requirements/emscripten_test_requirements.txt
-
-      - name: Test NumPy for Pyodide
-        run: |
-          source .venv-pyodide/bin/activate
-          cd ..
-          pytest --pyargs numpy -m "not slow"
+          path: wheelhouse/
+          merge-multiple: true
 
-        # Push to https://anaconda.org/scientific-python-nightly-wheels/numpy
-        # WARNING: this job will overwrite any existing WASM wheels.
       - name: Push to Anaconda PyPI index
-        if: >-
-          (github.repository == 'numpy/numpy') &&
-          (github.event_name == 'workflow_dispatch' && github.event.inputs.push_wheels == 'true') ||
-          (github.event_name == 'schedule')
-        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # v0.5.0
+        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b  # v0.6.1
         with:
-          artifacts_path: dist/
+          artifacts_path: wheelhouse/
           anaconda_nightly_upload_token: ${{ secrets.NUMPY_NIGHTLY_UPLOAD_TOKEN }}