Stubtest and related fixes

.editorconfig

@@ -11,9 +11,9 @@ indent_style = space
 trim_trailing_whitespace = true
 
 # 4 space indentation
-[*.{py, pyi, .md}]
+[*.{py,pyi,md}]
 indent_size = 4
 
 # 2 space indentation
-[*.{json, jsonc, yml, yaml}]
+[*.{json,jsonc,yml,yaml,toml}]
 indent_size = 2

.github/workflows/ci.yml

@@ -0,0 +1,61 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    timeout-minutes: 5
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: markdownlint
+        uses: DavidAnson/markdownlint-cli2-action@v16
+        with:
+          config: ".markdownlint.yaml"
+          globs: "**/*.md"
+
+      - name: install poetry
+        run: |
+          pipx install poetry
+          poetry config virtualenvs.create true --local
+          poetry config virtualenvs.in-project true --local
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: poetry
+
+      - name: poetry install
+        run: poetry install
+
+      - name: ruff check
+        run: poetry run ruff check --output-format=github
+
+      - name: basedpyright --verifytypes
+        run: poetry run basedpyright --ignoreexternal --verifytypes scipy-stubs
+
+      # TODO: don't continue on error
+      - name: basedmypy stubtest
+        run: poetry run stubtest --concise --mypy-config-file=pyproject.toml scipy
+        continue-on-error: true
+
+      # TODO: don't continue on error
+      - name: basedpyright --verifytypes
+        run: poetry run basedpyright --verifytypes scipy-stubs
+        continue-on-error: true
+
+      # TODO
+      # - uses: scientific-python/[email protected]
+      #   with:
+      #     plugins: sp-repo-review

.vscode/settings.json

@@ -5,6 +5,14 @@
   "[markdown]": {
     "editor.rulers": [88]
   },
+  "[toml]": {
+    "editor.rulers": [88],
+    "editor.tabSize": 4
+  },
   "git.branchProtection": ["master"],
-  "mypy-type-checker.args": ["--config-file=pyproject.toml"]
+  "mypy-type-checker.args": [
+    "--config-file=pyproject.toml"
+  ],
+  "yaml.format.printWidth": 88,
+  "prettier.printWidth": 88
 }

README.md

@@ -83,32 +83,33 @@ pip install scipy-stubs
 | Module                            | Stubs status    |
 |---------------------------------- |---------------- |
 | `scipy`                           | 1: skeleton     |
-| `scipy._lib`                      | 1: skeleton     |
-| `scipy._lib._uarray`              | 0: missing      |
+| `scipy._lib`                      | 2: partial      |
+| `scipy._lib.uarray`               | 2: ready        |
+| `scipy._lib.array_api_compat`     | 2: partial      |
 | `scipy.cluster`                   | 1: skeleton     |
 | `scipy.constants`                 | 3: ready        |
 | `scipy.datasets`                  | 1: skeleton     |
 | `scipy.fft`                       | 1: skeleton     |
-| `scipy.fft._pocketfft`            | 1: skeleton     |
+| `scipy.fft._pocketfft`            | 1: partial      |
 | `scipy.fftpack`                   | 1: skeleton     |
-| `scipy.integrate`                 | 1: skeleton     |
-| `scipy.integrate._ivp`            | 1: skeleton     |
-| `scipy.interpolate`               | 1: skeleton     |
+| `scipy.integrate`                 | 2: partial      |
+| `scipy.integrate._ivp`            | 1: partial      |
+| `scipy.interpolate`               | 2: partial      |
 | `scipy.io`                        | 1: skeleton     |
 | `scipy.io.arff`                   | 1: skeleton     |
-| `scipy.io.matlab`                 | 1: skeleton     |
+| `scipy.io.matlab`                 | 2: partial      |
 | `scipy.linalg`                    | 3: ready        |
 | `scipy.misc`                      | 0: missing      |
 | `scipy.ndimage`                   | 1: skeleton     |
 | `scipy.odr`                       | 1: skeleton     |
-| `scipy.optimize`                  | 1: skeleton     |
+| `scipy.optimize`                  | 2: partial      |
 | `scipy.optimize.cython_optimize`  | 0: missing      |
 | `scipy.optimize.zeros`            | 0: missing      |
-| `scipy.signal`                    | 1: skeleton     |
+| `scipy.signal`                    | 1: partial      |
 | `scipy.signal.windows`            | 1: skeleton     |
-| `scipy.sparse`                    | 1: skeleton     |
-| `scipy.sparse.csgraph`            | 1: skeleton     |
-| `scipy.sparse.linalg`             | 1: skeleton     |
+| `scipy.sparse`                    | 2: partial      |
+| `scipy.sparse.csgraph`            | 2: partial      |
+| `scipy.sparse.linalg`             | 2: partial      |
 | `scipy.spatial`                   | 2: partial      |
 | `scipy.spatial.distance`          | 3: ready        |
 | `scipy.special`                   | 3: ready        |

pyproject.toml

@@ -1,74 +1,72 @@
 [build-system]
-requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
-
+requires = ["poetry-core"]
 
 [tool.poetry]
-name = "scipy-stubs"
-version = "1.4.1.dev0"
-description = ""
 authors = ["Joren Hammudoglu <[email protected]>"]
-license = "BSD-3-Clause"
-readme = "README.md"
-packages = [{include = "scipy-stubs"}]
 classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Operating System :: OS Independent",
-    "Topic :: Scientific/Engineering",
-    "Typing :: Stubs Only",
-    "Typing :: Typed",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
+  "Development Status :: 3 - Alpha",
+  "Operating System :: OS Independent",
+  "Topic :: Scientific/Engineering",
+  "Typing :: Stubs Only",
+  "Typing :: Typed",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
-repository = "https://github.com/jorenham/scipy-stubs/"
+description = ""
 documentation = "https://github.com/jorenham/scipy-stubs?tab=readme-ov-file#scipy-stubs"
+license = "BSD-3-Clause"
+name = "scipy-stubs"
+packages = [{include = "scipy-stubs"}]
+readme = "README.md"
+repository = "https://github.com/jorenham/scipy-stubs/"
+version = "1.4.1.dev0"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jorenham/scipy-stubs/issues"
 "Changelog" = "https://github.com/jorenham/scipy-stubs/releases"
 
 [tool.poetry.dependencies]
-python = "^3.10.1"
 optype = "^0.6.1"
+python = "^3.10.1"
 scipy = "^1.14.1"
 
 [tool.poetry.group.lint.dependencies]
-ruff = "^0.6.2"
 basedmypy = "^2.6.0"
 basedpyright = "^1.17.1"
+ruff = "^0.6.2"
 
 [tool.poetry.group.dev.dependencies]
-pre-commit = "^3.8.0"
 poethepoet = "^0.27.0"
-
+pre-commit = "^3.8.0"
 
 [tool.mypy]
-warn_unused_ignores = true
-disallow_any_explicit = false  # no other way to type e.g. `np.float64 <: np.number[Any]`
 disable_bytearray_promotion = true
 disable_memoryview_promotion = true
-
+disallow_any_explicit = false  # no other way to type e.g. `float64 <: number[Any]`
+disallow_untyped_defs = false  # TODO
+disallow_incomplete_defs = false  # TODO
+warn_unused_ignores = true
 
 [tool.pyright]
 include = ["scipy-stubs"]
-stubPath = "."
-venvPath = "."
-venv = ".venv"
-pythonVersion = "3.10"
 pythonPlatform = "All"
+pythonVersion = "3.10"
+stubPath = "."
 typeCheckingMode = "strict"
+venv = ".venv"
+venvPath = "."
 
 deprecateTypingAliases = true
-reportPrivateUsage = false
 reportIgnoreCommentWithoutRule = true
 reportImplicitRelativeImport = true
 reportInvalidCast = true
+reportPrivateUsage = false
 reportUnnecessaryTypeIgnoreComment = true
 reportUnsafeMultipleInheritance = true
 
-
 [tool.ruff]
 builtins = ["reveal_locals", "reveal_type"]
 exclude = ["scipy-pyright", ".venv"]
@@ -82,26 +80,88 @@ src = ["scipy-stubs"]
 line-ending = "lf"
 skip-magic-trailing-comma = false
 
-
 [tool.ruff.lint]
+ignore = [
+  "E741",
+  "COM812", # ruff format compat
+  "ANN", # TODO
+]
 preview = true
-select = ["E", "W", "I", "UP", "ANN", "COM", "EXE", "ICN", "INP", "PYI", "Q", "TID", "TCH", "ERA", "PGH", "RUF"]
-extend-select = [
-    "PLC0105", "PLC0131", "PLC0132", "PLC0414",
-    "PLE0303", "PLE0304", "PLE0305", "PLE0307", "PLE0308", "PLE0309",
-    "PLE0604", "PLE0605", "PLE1132"
+select = [
+  "E",
+  "W",
+  "I",
+  "UP",
+  "ANN",
+  "COM",
+  "EXE",
+  "ICN",
+  "INP",
+  "PYI",
+  "Q",
+  "TID",
+  "TCH",
+  "ERA",
+  "PGH",
+  "RUF",
+  "PLC0105",
+  "PLC0131",
+  "PLC0132",
+  "PLC0414",
+  "PLE0303",
+  "PLE0304",
+  "PLE0305",
+  "PLE0307",
+  "PLE0308",
+  "PLE0309",
+  "PLE0604",
+  "PLE0605",
+  "PLE1132",
 ]
-ignore = [
-    "E741",
-    "COM812",  # ruff format compat
-    "ANN",  # TODO
+
+[tool.ruff.lint.flake8-import-conventions]
+banned-from = [
+  "numpy",
+  "numpy.dtypes",
+  "numpy.exceptions",
+  "numpy.emath",
+  "numpy.fft",
+  "numpy.linalg",
+  "numpy.ma",
+  "numpy.polynomial",
+  "numpy.random",
+  "numpy.rec",
+  "numpy.typing",
+  "numpy.strings",
+  "optype",
+  "optype.numpy",
+  "optype.typing",
 ]
+[tool.ruff.lint.flake8-import-conventions.extend-aliases]
+"numpy" = "np"
+"numpy.polynomial" = "npp"
+"numpy.typing" = "npt"
+"optype" = "op"
+"optype.numpy" = "onpt"
+"scipy" = "sp"
+"scipy._typing" = "spt"
 
 [tool.ruff.lint.isort]
 combine-as-imports = true
-known-local-folder = ["scipy"]
+known-first-party = ["scipy"]
+no-lines-before = ["typing", "first-party", "local-folder"]
+section-order = [
+  "standard-library",
+  "typing",
+  "third-party",
+  "first-party",
+  "local-folder",
+]
 split-on-trailing-comma = true
 
+[tool.ruff.lint.isort.sections]
+typing = ["collections.abc", "types", "typing", "typing_extensions"]
+
 [tool.ruff.lint.flake8-annotations]
 allow-star-arg-any = true
 mypy-init-return = true