fix stubtest __all__ errors

.github/workflows/ci.yml

@@ -52,7 +52,7 @@ jobs:
 
       # TODO: don't continue on error
       - name: basedmypy stubtest
-        run: poetry run stubtest --concise --mypy-config-file=pyproject.toml --allowlist=tests/stubtest/allowlist.txt scipy
+        run: poetry run stubtest --concise --ignore-positional-only --mypy-config-file=pyproject.toml --allowlist=tests/stubtest/allowlist.txt scipy
         continue-on-error: true
 
       # TODO

README.md

@@ -104,7 +104,6 @@ pyright), the "type completeness score" is **42.4%**.
 | `scipy.odr`                       | 1: skeleton     |
 | `scipy.optimize`                  | 2: partial      |
 | `scipy.optimize.cython_optimize`  | 0: missing      |
-| `scipy.optimize.zeros`            | 0: missing      |
 | `scipy.signal`                    | 2: partial      |
 | `scipy.signal.windows`            | 1: skeleton     |
 | `scipy.sparse`                    | 2: partial      |

scipy-stubs/spatial/transform/rotation.pyi

@@ -1,3 +1,3 @@
 from ._rotation import Rotation, Slerp
 
-__all__ = "Rotation", "Slerp"
+__all__ = ["Rotation", "Slerp"]

tests/stubtest/allowlist.txt

@@ -72,35 +72,107 @@ scipy._lib.array_api_compat.dask.*
 scipy._lib.array_api_compat.numpy.*
 scipy._lib.array_api_compat.torch
 scipy._lib.array_api_compat.common._typing.*
-scipy._lib.cobyqa
+scipy._lib.cobyqa.*
 scipy._lib.messagestream
 scipy.fft._pocketfft.pypocketfft.*
 scipy.special.add_newdocs
 scipy.special.libsf_error_state
 scipy.special._precompute.*
 scipy.special._support_alternative_backends.*
 scipy.stats._rcont.rcont
-scipy.stats._rcont.rcont
 scipy.stats._unuran.unuran_wrapper
 
-# deprecated public api
+# deprecated public api (will be removed in scipy 2.0.0)
+scipy.constants.codata
+scipy.constants.constants
+scipy.integrate.lsoda.*
+scipy.integrate.odepack.*
+scipy.integrate.quadpack.*
 scipy.integrate.quadrature
 scipy.integrate.romberg
 scipy.integrate._quadrature.quadrature
 scipy.integrate._quadrature.romberg
+scipy.linalg.basic.*
+scipy.linalg.decomp.*
+scipy.linalg.matfuncs.*
+scipy.linalg.misc.*
+scipy.linalg.special_matrices.*
+scipy.optimize.cobyla.*
+scipy.optimize.lbfgsb.*
+scipy.optimize.linesearch.*
+scipy.optimize.minpack.*
+scipy.optimize.nonlin.*
+scipy.optimize.optimize.*
+scipy.optimize.slsqp.*
+scipy.optimize.tnc.*
+scipy.optimize.zeros.*
 scipy.special.basic
 scipy.special.orthogonal
 scipy.special.sf_error
 scipy.special.specfun
 scipy.special.spfun_stats
 scipy.linalg.basic
-scipy.linalg.decomp*
 scipy.stats.kde.*
 scipy.stats.morestats.*
 scipy.stats.mstats_basic.*
+scipy.stats.mstats_extras.*
 scipy.stats.stats.*
 
 # random mypy hallucinations
 scipy.interpolate.AAA
 scipy.interpolate._aaa
 scipy.interpolate._interpnd_info
+
+# mypy didn't read the typing specs on `__all__` within stubs
+scipy._lib._ccallback.__all__
+scipy._lib.array_api_compat.__all__
+scipy._lib.array_api_compat.common.__all__
+scipy.integrate._ivp.__all__
+scipy.linalg._decomp_lu_cython.__all__
+scipy.linalg._solve_toeplitz.__all__
+scipy.optimize._constraints.__all__
+scipy.optimize._lsap.__all__
+scipy.optimize._remove_redundancy.__all__
+scipy.optimize._trlib._trlib.__all__
+scipy.signal._signaltools.__all__
+scipy.sparse._matrix.__all__
+scipy.sparse.csgraph.__all__
+scipy.sparse.csgraph._flow.__all__
+scipy.sparse.csgraph._laplacian.__all__
+scipy.sparse.csgraph._matching.__all__
+scipy.sparse.csgraph._min_spanning_tree.__all__
+scipy.sparse.csgraph._reordering.__all__
+scipy.sparse.csgraph._shortest_path.__all__
+scipy.sparse.csgraph._tools.__all__
+scipy.sparse.csgraph._traversal.__all__
+scipy.sparse.linalg._dsolve._superlu.__all__
+scipy.spatial.transform._rotation.__all__
+scipy.spatial.transform._rotation_spline.__all__
+scipy.special._add_newdocs.__all__
+scipy.special._ellip_harm.__all__
+scipy.special._lambertw.__all__
+scipy.special._orthogonal.__all__
+scipy.special._sf_error.__all__
+scipy.special._spherical_bessel.__all__
+scipy.special.cython_special.__all__
+scipy.stats._binomtest.__all__
+scipy.stats._bws_test.__all__
+scipy.stats._censored_data.__all__
+scipy.stats._common.__all__
+scipy.stats._distn_infrastructure.__all__
+scipy.stats._distr_params.__all__
+
+# mypy doesn't know how to sort `__all__`
+scipy.constants.__all__
+scipy.integrate.__all__
+scipy.linalg.__all__
+scipy.sparse.linalg._dsolve.__all__
+scipy.spatial.ckdtree.__all__
+scipy.spatial.kdtree.__all__
+scipy.spatial.qhull.__all__
+scipy.special.__all__
+scipy.stats.__all__
+scipy.stats._continuous_distns.__all__
+scipy.stats._discrete_distns.__all__
+scipy.stats.distributions.__all__
+scipy.stats.sampling.__all__