Merge pull request #287 from Carreau/misc-c

Misc cleanups
jupyter · Sep 22, 2023 · 05f5461 · 05f5461
2 parents 93fb951 + cf2f9ab
commit 05f5461
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Showing 11 changed files with 162 additions and 238 deletions.
diff --git a/examples/matplotlib.toml b/examples/matplotlib.toml
@@ -98,19 +98,11 @@ VisitSubstitutionDefinitionNotImplementedError = [
     ]
 IncorrectInternalDocsLen = [
     "matplotlib.pyplot:rc",
-    "matplotlib.axes._base:_process_plot_var_args",
     "matplotlib.dates:ConciseDateFormatter",
     "matplotlib.font_manager:win32FontDirectory",
-    "matplotlib.transforms:Affine2D.__init__",
-    "matplotlib.transforms:Affine2D.get_matrix",
-    "matplotlib.transforms:Affine2D.set_matrix",
-    "matplotlib.figure:FigureBase._process_projection_requirements",
     "matplotlib.transforms:Transform.__sub__",
     "matplotlib.patches:ConnectionStyle._Base",
-    "matplotlib.tri.triinterpolate:_safe_inv22_vectorized",
-    "matplotlib.transforms:Affine2D.from_values",
     "matplotlib.ticker:LogLocator.__init__",
-    "matplotlib.backend_bases:FigureCanvasBase._switch_canvas_and_return_print_method",
     ]
 ValueError = [
     "matplotlib.image:thumbnail",
@@ -123,12 +115,6 @@ ValueError = [
     "matplotlib.spines:Spine.set_bounds",
     "matplotlib.patches:FancyArrowPatch.set_connectionstyle",
     ]
-SpaceAfterBlockDirectiveError = [
-    "matplotlib.figure.FigureBase.subplot_mosaic",
-    "matplotlib.image:imsave",
-    "matplotlib.pyplot:imsave",
-    "matplotlib.ft2font:FT2Font"
-    ]
 [global.implied_imports]
 _api = 'matplotlib._api'
 
diff --git a/examples/networkx.toml b/examples/networkx.toml
@@ -36,7 +36,3 @@ ValueError = [ "networkx.generators.geometric:geographical_threshold_graph",
     "networkx.generators.geometric:waxman_graph",
     "networkx.algorithms.cycles:_johnson_cycle_search",
 ]
-AssertionError = [ "networkx.algorithms.minors.contraction:quotient_graph",
-    "networkx.algorithms.smallworld:random_reference",
-    "networkx.generators.joint_degree_seq:_directed_neighbor_switch",
-]
diff --git a/examples/pandas.toml b/examples/pandas.toml
@@ -4,95 +4,10 @@ logo = 'logo_pandas.png'
 exec_failure = "fallback"
 submodules = []
 exclude = [
-    # "AssertionError"
-        "pandas._libs.properties.CachedProperty",
-        "pandas._config.config.CallableDynamicDoc",
-        "pandas._libs.index.BaseMultiIndexCodesEngine",
-        "pandas._libs.properties.AxisProperty",
-    # "ErrorHelper1-<class 'papyri.errors.SpaceAfterBlockDirectiveError'>
-        "pandas.core.algorithms.factorize",
-        "pandas.core.base.IndexOpsMixin.factorize",
-    # "ErrorNoExec-<class 'AssertionError'>
-        "pandas._libs.index.BaseMultiIndexCodesEngine",
-    # "ErrorNoExec-<class 'ValueError'>
-        "pandas.core.accessor.register_dataframe_accessor",
-        "pandas.core.accessor.register_index_accessor",
-        "pandas.core.accessor.register_series_accessor",
-        "pandas.core.accessor._register_accessor",
-        "pandas.core.arrays.base.ExtensionArray.take",
-    # "ErrorNoExec-<class 'papyri.errors.VisitTargetNotImplementedError'>
-        "pandas.plotting._core.PlotAccessor.kde",
-    # "ExecError-<class 'AssertionError'>
-        "pandas._libs.index.BaseMultiIndexCodesEngine",
-    # "ExecError-<class 'ValueError'>
-        "pandas.core.accessor.register_dataframe_accessor",
-        "pandas.core.accessor.register_index_accessor",
-        "pandas.core.accessor.register_series_accessor",
-        "pandas.core.accessor._register_accessor",
-        "pandas.core.arrays.base.ExtensionArray.take",
-    # "ExecError-<class 'papyri.errors.VisitTargetNotImplementedError'>
-        "pandas.plotting._core.PlotAccessor.kde",
-    # "NumpydocError-<class 'AssertionError'>
-        "pandas._libs.properties.CachedProperty",
-        "pandas._config.config.CallableDynamicDoc",
-        "pandas._libs.properties.AxisProperty",
-    # "NumpydocError-<class 'ValueError'>
-        "pandas.io.pytables.Table",
-    # "NumpydocError-<class 'numpydoc.docscrape.ParseError'>
-        "pandas.core.arraylike.array_ufunc",
-        "pandas.io.formats.info.BaseInfo.render",
-        "pandas.core.generic.NDFrame.set_axis",
-        "pandas.core.generic.NDFrame.replace",
-        "pandas.core.generic.NDFrame.isna",
-        "pandas.core.generic.NDFrame.isnull",
-        "pandas.core.generic.NDFrame.notna",
-        "pandas.core.generic.NDFrame.notnull",
-    # "ParseDesc-<class 'IndexError'>
-        "pandas._libs.algos.is_monotonic",
-        "pandas._libs.interval.intervals_to_interval_bounds",
-        "pandas.core.algorithms.duplicated",
-        "pandas._libs.tslibs.offsets.shift_month",
-        "pandas.core.dtypes.cast.astype_array_safe",
-        "pandas.core.window.expanding.Expanding.apply",
-        "pandas.core.window.expanding.Expanding.apply",
-        "pandas.core.window.expanding.Expanding.sum",
-        "pandas.core.window.expanding.Expanding.max",
-        "pandas.core.window.expanding.Expanding.min",
-        "pandas.core.window.expanding.Expanding.mean",
-        "pandas.core.window.expanding.Expanding.median",
-        "pandas.core.window.ewm.ExponentialMovingWindow.mean",
-        "pandas.core.window.rolling.Rolling.apply",
-        "pandas.core.window.rolling.Rolling.apply",
-        "pandas.core.window.rolling.Rolling.sum",
-        "pandas.core.window.rolling.Rolling.max",
-        "pandas.core.window.rolling.Rolling.min",
-        "pandas.core.window.rolling.Rolling.mean",
-        "pandas.core.window.rolling.Rolling.median",
-        "pandas.core.groupby.generic.DataFrameGroupBy.aggregate",
-        "pandas.core.groupby.generic.DataFrameGroupBy.transform",
-        "pandas.core.groupby.generic.SeriesGroupBy.aggregate",
-        "pandas.core.groupby.generic.SeriesGroupBy.transform",
-        "pandas.core.groupby.grouper.Grouping",
-        "pandas.core.internals.blocks.Block.astype",
-        "pandas.core.internals.blocks.Block.where",
-        "pandas.io.parsers.base_parser._get_na_values",
-        "pandas.core.reshape.melt.lreshape",
-    # "VisitTargetNotImplementedError
-        "pandas.plotting._core.PlotAccessor.kde",
-        "pandas.io.gbq.read_gbq",
-        "pandas.core.frame.DataFrame.to_gbq",
-        "pandas.core.indexes.base.Index.drop_duplicates",
-        "pandas.plotting._core.hist_frame",
-    # "ExecError-<class 'ValueError'>": [
-        "pandas._testing._io.network",
-    # "np.bool_" is seen as a reference
-        "pandas._libs.lib.is_bool_list",
-    # Imbalanced backticks
-    "pandas.core.common.pipe"
 ]
 [pandas.expected_errors]
 ValueError = [
- "pandas.io.gbq:read_gbq",                                                                                                                            gen.py:2041
+ "pandas.io.gbq:read_gbq",
  "pandas.io.pickle:to_pickle",
  "pandas.core.frame:DataFrame.to_gbq",
  "pandas.core.generic:NDFrame.to_pickle",

diff --git a/examples/scipy.toml b/examples/scipy.toml
@@ -4,28 +4,26 @@ logo = "../scipy_logo.png"
 exec = true
 submodules = [ "signal","misc"]
 exclude = [
-    # https://github.com/stsewd/tree-sitter-rst/issues/31
-    "scipy.interpolate._fitpack_py.splprep",
-    "scipy.sparse._construct._compressed_sparse_stack",
-    "scipy.sparse._construct._stack_along_minor_axis",
     # OTHER.
-    "scipy.interpolate._fitpack_impl.spalde",
+    "scipy.interpolate._fitpack_impl:spalde",
 
-    "scipy.sparse.csgraph._traversal.breadth_first_tree",
-    "scipy.sparse.csgraph._traversal.depth_first_tree",
+    "scipy.sparse.csgraph._traversal:breadth_first_tree",
+    "scipy.sparse.csgraph._traversal:depth_first_tree",
 
     # Example is incorrect https://github.com/scipy/scipy/issues/15595
-    "scipy.signal._peak_finding._identify_ridge_lines",
-    "scipy.stats._continuous_distns.crystalball_gen._pdf",
-    "scipy.stats._ksstats._kolmogn_PelzGood",
-    "scipy.stats._discrete_distns.betabinom_gen",
-    "scipy.sparse.csgraph._min_spanning_tree.minimum_spanning_tree",
-    "scipy.stats._morestats.wilcoxon",
-    "scipy.stats._distn_infrastructure.rv_continuous",
-    "scipy.stats._stats_py.moment",
-    "scipy.stats._mannwhitneyu.mannwhitneyu",
-    "scipy.stats._resampling.bootstrap",
-    "scipy.sparse.linalg._expm_multiply.expm_multiply",
+    "scipy.signal._peak_finding:_identify_ridge_lines",
+    "scipy.stats._continuous_distns:crystalball_gen._pdf",
+    "scipy.stats._ksstats:_kolmogn_PelzGood",
+    "scipy.stats._discrete_distns:betabinom_gen",
+    "scipy.stats._morestats:wilcoxon",
+    "scipy.stats._distn_infrastructure:rv_continuous",
+    "scipy.stats._stats_py:moment",
+    "scipy.stats._mannwhitneyu:mannwhitneyu",
+    "scipy.stats._resampling:bootstrap",
+    "scipy.sparse.linalg._expm_multiply:expm_multiply",
+
+    # contain ascii diagram
+    "scipy.stats._continuous_distns:crystalball_gen._pdf"
             ]
 exclude_jedi = [
     "scipy.linalg._sketches.clarkson_woodruff_transform",
@@ -40,20 +38,20 @@ exclude_jedi = [
     ]
 
 execute_exclude_patterns = [
-    'scipy._lib._uarray._backend.determine_backend_multi',
-    'scipy.integrate._quadrature._qmc_quad',
-    'scipy.interpolate._bspl.evaluate_all_bspl',
-    'scipy.optimize._root.root',
-    'scipy.signal._filter_design.normalize',
-    'scipy.signal._signaltools.filtfilt',
-    'scipy.stats._axis_nan_policy._broadcast_array_shapes_remove_axis',
-    'scipy.stats._multivariate.multivariate_normal_frozen.__init__',
-    'scipy.stats._multivariate.multivariate_t_frozen.__init__',
-    'scipy.stats._stats_py._ttest_nans',
-    'scipy.io.matlab._mio5.varmats_from_mat',
-    'scipy.io.matlab._byteordercodes.to_numpy_code',
-    'scipy._lib._uarray._backend.determine_backend',
-    'scipy._lib._uarray._backend.all_of_type',
+    'scipy._lib._uarray._backend:determine_backend_multi',
+    'scipy.integrate._quadrature:_qmc_quad',
+    'scipy.interpolate._bspl:evaluate_all_bspl',
+    'scipy.optimize._root:root',
+    'scipy.signal._filter_design:normalize',
+    'scipy.signal._signaltools:filtfilt',
+    'scipy.stats._axis_nan_policy:_broadcast_array_shapes_remove_axis',
+    'scipy.stats._multivariate:multivariate_normal_frozen.__init__',
+    'scipy.stats._multivariate:multivariate_t_frozen.__init__',
+    'scipy.stats._stats_py:_ttest_nans',
+    'scipy.io.matlab._mio5:varmats_from_mat',
+    'scipy.io.matlab._byteordercodes:to_numpy_code',
+    'scipy._lib._uarray._backend:determine_backend',
+    'scipy._lib._uarray._backend:all_of_type',
     'scipy._lib._util._nan_allsame',
     ]
 exec_failure = "fallback"
@@ -71,76 +69,84 @@ ua = 'scipy._lib.uarray'
 array = 'numpy:array'
 arange = 'numpy:arange'
 [global.expected_errors]
-IncorrectInternalDocsLen = [
-    "scipy.interpolate._fitpack_impl.bisplev",
-    "scipy.interpolate._fitpack_impl.spalde",
-    "scipy.interpolate._fitpack_py.spalde",
-    "scipy.linalg._decomp.cdf2rdf",
-    "scipy.linalg._special_matrices.fiedler",
-    "scipy.optimize._lsq.common.regularized_lsq_operator",
-    "scipy.optimize._trustregion_constr.tr_interior_point.BarrierSubproblem.gradient_and_jacobian",
-    "scipy.optimize._trustregion_constr.tr_interior_point.tr_interior_point",
-    "scipy.signal._filter_design._ellipdeg",
-    "scipy.signal._spline.symiirorder1",
-    "scipy.signal._spline.symiirorder2",
-    "scipy.sparse._bsr.bsr_matrix.check_format",
-    ]
 VisitCitationReferenceNotImplementedError = [
-    "scipy.optimize._nonlin.anderson",
-    "scipy.optimize._zeros_py.brenth",
-    "scipy.optimize._zeros_py.brentq",
-    "scipy.optimize._lsq.least_squares.least_squares",
-    "scipy.optimize._lsq.lsq_linear.lsq_linear",
-    "scipy.optimize._zeros_py.ridder",
-    "scipy.special._orthogonal",
-    "scipy.special._orthogonal.roots_chebyc",
-    "scipy.special._orthogonal.roots_gegenbauer",
-    "scipy.special._orthogonal.roots_hermite",
-    "scipy.special._orthogonal.roots_hermitenorm",
-    "scipy.special._orthogonal.roots_jacobi",
-    "scipy.special._orthogonal.roots_sh_jacobi",
-    "scipy.special._orthogonal.roots_laguerre",
-    "scipy.special._orthogonal.roots_genlaguerre",
-    "scipy.special._orthogonal.roots_legendre",
-    "scipy.special._basic.polygamma",
-    "scipy.special._orthogonal.roots_sh_legendre",
-    "scipy.special._orthogonal.roots_chebys",
-    "scipy.special._orthogonal.roots_chebyt",
-    "scipy.special._orthogonal.roots_chebyu",
-    "scipy.special._orthogonal.roots_sh_chebyt",
-    "scipy.special._orthogonal.roots_sh_chebyu",
-    "scipy.special._basic.zeta",
-    "scipy.interpolate.interpnd.CloughTocher2DInterpolator",
-    "scipy.optimize._lsq.dogbox",
-    "scipy.optimize._lsq.trf",
-    "scipy.optimize._nonlin.Anderson",
-    "scipy.special._orthogonal._pbcf",
-    "scipy.spatial._spherical_voronoi.SphericalVoronoi",
-    "scipy.spatial._spherical_voronoi.calculate_solid_angles",
-    "scipy.integrate._ode.ode",
-    ]
+    "scipy.constants",
+    "scipy.integrate._ode:ode",
+    "scipy.interpolate.interpnd:CloughTocher2DInterpolator",
+    "scipy.optimize._nonlin:anderson",
+    "scipy.optimize._zeros_py:brenth",
+    "scipy.optimize._zeros_py:brentq",
+    "scipy.optimize._lsq.least_squares:least_squares",
+    "scipy.optimize._lsq.lsq_linear:lsq_linear",
+    "scipy.optimize._zeros_py:ridder",
+    "scipy.spatial._spherical_voronoi:SphericalVoronoi",
+    "scipy.special._orthogonal:roots_chebyc",
+    "scipy.special._orthogonal:roots_gegenbauer",
+    "scipy.special._orthogonal:roots_hermite",
+    "scipy.special._orthogonal:roots_hermitenorm",
+    "scipy.special._orthogonal:roots_jacobi",
+    "scipy.special._orthogonal:roots_sh_jacobi",
+    "scipy.special._orthogonal:roots_laguerre",
+    "scipy.special._orthogonal:roots_genlaguerre",
+    "scipy.special._orthogonal:roots_legendre",
+    "scipy.special._basic:polygamma",
+    "scipy.special._orthogonal:roots_sh_legendre",
+    "scipy.special._orthogonal:roots_chebys",
+    "scipy.special._orthogonal:roots_chebyt",
+    "scipy.special._orthogonal:roots_chebyu",
+    "scipy.special._orthogonal:roots_sh_chebyt",
+    "scipy.special._orthogonal:roots_sh_chebyu",
+    "scipy.special._basic:zeta",
+    "scipy.optimize._nonlin:Anderson",
+    "scipy.spatial._spherical_voronoi:calculate_solid_angles",
+    "scipy.special._orthogonal:_pbcf",
+]
+IncorrectInternalDocsLen = [
+    "scipy.signal._spline:symiirorder1",
+    "scipy.signal._spline:symiirorder2",
+    "scipy.interpolate._fitpack_impl:bisplev",
+    "scipy.interpolate._fitpack_py:spalde",
+    "scipy.linalg._decomp:cdf2rdf",
+    "scipy.linalg._special_matrices:fiedler",
+    "scipy.signal._filter_design:_ellipdeg",
+    "scipy.stats._ksstats:_kolmogn_PelzGood",
+    "scipy.optimize._lsq.common:regularized_lsq_operator",
+    "scipy.optimize._trustregion_constr.tr_interior_point:tr_interior_point",
+    "scipy.sparse._bsr:_bsr_base.check_format",
+    "scipy.optimize._trustregion_constr.tr_interior_point:BarrierSubproblem.gradient_and_jacobian",
+]
 AssertionError = [
-    "scipy.optimize._linprog_ip._ip_hsd",
-    "scipy.special._orthogonal._compute_tauk",
-    ]
+    "scipy.stats._resampling:bootstrap",
+    "scipy.stats._distn_infrastructure:rv_continuous",
+    "scipy.io.matlab._mio5",
+    "scipy.optimize._linprog_ip:_ip_hsd",
+    "scipy.special._orthogonal:_compute_tauk",
+]
+ValueError = [
+    "scipy.stats._stats_py:iqr",
+    "scipy.stats._mannwhitneyu:mannwhitneyu",
+    "scipy.stats._stats_py:moment",
+    "scipy.stats._morestats:wilcoxon",
+    "scipy.stats._continuous_distns:crystalball_gen._pdf",
+]
 NumpydocParseError = [
-    "scipy.optimize._linprog_doc._linprog_highs_doc",
-    "scipy.optimize._linprog_doc._linprog_highs_ds_doc",
-    "scipy.optimize._linprog_doc._linprog_highs_ipm_doc",
-    "scipy.optimize._linprog_doc._linprog_ip_doc",
-    "scipy.optimize._linprog_doc._linprog_rs_doc",
-    "scipy.optimize._linprog_doc._linprog_simplex_doc",
-    "scipy.optimize._linprog_highs._linprog_highs",
-    "scipy.optimize._linprog_ip._linprog_ip",
-    "scipy.optimize._linprog_rs._linprog_rs",
-    "scipy.optimize._linprog_simplex._linprog_simplex",
-    "scipy.optimize._optimize._minimize_powell",
-    "scipy.optimize._qap._quadratic_assignment_2opt",
-    "scipy.optimize._qap._quadratic_assignment_faq",
-    "scipy.stats._discrete_distns.geom_gen",
-    "scipy.stats._discrete_distns.planck_gen",
-    ]
-SpaceAfterBlockDirectiveError = [
-    "scipy.optimize._tnc._minimize_tnc",
-    ]
-
+    "scipy.optimize._linprog_highs:_linprog_highs",
+    "scipy.optimize._linprog_doc:_linprog_highs_doc",
+    "scipy.optimize._linprog_doc:_linprog_highs_ds_doc",
+    "scipy.optimize._linprog_doc:_linprog_highs_ipm_doc",
+    "scipy.optimize._linprog_ip:_linprog_ip",
+    "scipy.optimize._linprog_doc:_linprog_ip_doc",
+    "scipy.optimize._linprog_rs:_linprog_rs",
+    "scipy.optimize._linprog_doc:_linprog_rs_doc",
+    "scipy.optimize._linprog_simplex:_linprog_simplex",
+    "scipy.optimize._linprog_doc:_linprog_simplex_doc",
+    "scipy.optimize._optimize:_minimize_powell",
+    "scipy.optimize._qap:_quadratic_assignment_2opt",
+    "scipy.optimize._qap:_quadratic_assignment_faq",
+    "scipy.stats._discrete_distns:betabinom_gen",
+    "scipy.stats._discrete_distns:geom_gen",
+    "scipy.stats._discrete_distns:planck_gen",
+]
+ExampleError1 = [
+    "scipy.stats._qmc:PoissonDisk",
+]