python-libpysal fails to build with Python 3.8.0b3 in Fedora 32. See the build failures at https://koji.fedoraproject.org/koji/search?match=glob&type=package&terms=python-libpysal ====================================================================== ERROR: test_alpha_shapes (libpysal.cg.tests.test_ashapes.Test_Alpha_Shapes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_ashapes.py", line 25, in setUp self.a05 = geopandas.read_file(os.path.join(this_directory, 'data/alpha_05.shp')).geometry.item() File "/usr/lib64/python3.8/site-packages/pandas/core/base.py", line 740, in item return self.values.item() AttributeError: 'GeometryArray' object has no attribute 'item' -------------------- >> begin captured logging << -------------------- fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff531052b0> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff531052b0>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff531052b0> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff531052b0> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff531052b0>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff531052b0>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff53105430> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff53105430> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff53105430> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff53483fd0> --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: test_auto (libpysal.cg.tests.test_ashapes.Test_Alpha_Shapes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_ashapes.py", line 25, in setUp self.a05 = geopandas.read_file(os.path.join(this_directory, 'data/alpha_05.shp')).geometry.item() File "/usr/lib64/python3.8/site-packages/pandas/core/base.py", line 740, in item return self.values.item() AttributeError: 'GeometryArray' object has no attribute 'item' -------------------- >> begin captured logging << -------------------- fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff533b91c0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff53105e50> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff53105e50>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff53105e50> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff533b91c0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff533b91c0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff53105e50> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff53105e50>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff53105e50>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff533b91c0> fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff53105c10> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff53105c10>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff53105c10> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff53105c10> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff53105c10>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff53105c10>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff53483fd0> --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: test_small_n (libpysal.cg.tests.test_ashapes.Test_Alpha_Shapes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_ashapes.py", line 25, in setUp self.a05 = geopandas.read_file(os.path.join(this_directory, 'data/alpha_05.shp')).geometry.item() File "/usr/lib64/python3.8/site-packages/pandas/core/base.py", line 740, in item return self.values.item() AttributeError: 'GeometryArray' object has no attribute 'item' -------------------- >> begin captured logging << -------------------- fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff53105430> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff53105430> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff53105430> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff53105430>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff533dcfa0> fiona.env: DEBUG: Entering env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Starting outermost env fiona.env: DEBUG: No GDAL environment exists fiona.env: DEBUG: New GDAL environment <fiona._env.GDALEnv object at 0x7fff531052e0> created fiona._env: DEBUG: Logging error handler pushed. fiona._env: DEBUG: All drivers registered. fiona._env: DEBUG: GDAL data files are available at built-in paths fiona._env: DEBUG: PROJ data files are available at built-in paths fiona._env: DEBUG: Started GDALEnv <fiona._env.GDALEnv object at 0x7fff531052e0>. fiona.env: DEBUG: Updated existing <fiona._env.GDALEnv object at 0x7fff531052e0> with options {} fiona.env: DEBUG: Entered env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Layer has no coordinate system fiona.ogrext: DEBUG: Projection not found (cogr_crs was NULL) fiona.ogrext: DEBUG: Index: 0 fiona.collection: DEBUG: Flushed buffer fiona.collection: DEBUG: Stopped session fiona.env: DEBUG: Exiting env context: <fiona.env.Env object at 0x7fff53483fd0> fiona.env: DEBUG: Cleared existing <fiona._env.GDALEnv object at 0x7fff531052e0> options fiona._env: DEBUG: Stopping GDALEnv <fiona._env.GDALEnv object at 0x7fff531052e0>. fiona._env: DEBUG: Error handler popped. fiona._env: DEBUG: Stopped GDALEnv <fiona._env.GDALEnv object at 0x7fff531052e0>. fiona.env: DEBUG: Exiting outermost env fiona.env: DEBUG: Exited env context: <fiona.env.Env object at 0x7fff53483fd0> --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: test_rtree (libpysal.cg.tests.test_rtree.Pyrtree_Tester) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_rtree.py", line 27, in test_rtree t.insert(object, self.objects[object]) File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 200, in insert self.cursor.insert(o, orect) File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 417, in insert self._balance() File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 451, in _balance t = time.clock() AttributeError: module 'time' has no attribute 'clock' ====================================================================== ERROR: test_rtree (libpysal.cg.tests.test_rtree.Pyrtree_Tester) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_rtree.py", line 27, in test_rtree t.insert(object, self.objects[object]) File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 200, in insert self.cursor.insert(o, orect) File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 417, in insert self._balance() File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/rtree.py", line 451, in _balance t = time.clock() AttributeError: module 'time' has no attribute 'clock' ====================================================================== ERROR: test_filter (libpysal.weights.tests.test_adjlist.Test_Adjlist) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/weights/tests/test_adjlist.py", line 32, in test_filter alist = grid.to_adjlist(remove_symmetric=True) File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/weights/weights.py", line 263, in to_adjlist return adjtools.filter_adjlist(adjlist) if remove_symmetric else adjlist File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/weights/adjtools.py", line 191, in filter_adjlist to_drop = adjlist.query('focal == {} and neighbor == {}' File "/usr/lib64/python3.8/site-packages/pandas/core/frame.py", line 3184, in query res = self.eval(expr, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/frame.py", line 3300, in eval return _eval(expr, inplace=inplace, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/eval.py", line 322, in eval parsed_expr = Expr(expr, engine=engine, parser=parser, env=env, truediv=truediv) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 827, in __init__ self.terms = self.parse() File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 844, in parse return self._visitor.visit(self.expr) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 441, in visit return visitor(node, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 447, in visit_Module return self.visit(expr, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 441, in visit return visitor(node, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 450, in visit_Expr return self.visit(node.value, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 441, in visit return visitor(node, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 771, in visit_BoolOp return reduce(visitor, operands) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 764, in visitor lhs = self._try_visit_binop(x) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 760, in _try_visit_binop return self.visit(bop) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 441, in visit return visitor(node, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 744, in visit_Compare return self.visit(binop) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 441, in visit return visitor(node, **kwargs) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 563, in visit_BinOp op, op_class, left, right = self._maybe_transform_eq_ne(node) File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 484, in _maybe_transform_eq_ne right = self.visit(node.right, side="right") File "/usr/lib64/python3.8/site-packages/pandas/core/computation/expr.py", line 440, in visit visitor = getattr(self, method) AttributeError: 'PandasExprVisitor' object has no attribute 'visit_Constant' -------------------- >> begin captured logging << -------------------- numexpr.utils: INFO: NumExpr defaulting to 4 threads. --------------------- >> end captured logging << --------------------- ====================================================================== FAIL: test_voronoi (libpysal.cg.tests.test_voronoi.Voronoi) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/libpysal-4.1.0/libpysal/cg/tests/test_voronoi.py", line 20, in test_voronoi self.assertTrue(vertices.tolist() == self.vertices) AssertionError: False is not true ---------------------------------------------------------------------- Ran 490 tests in 57.756s FAILED (failures=1, errors=6, skipped=41) It is not important whether the problem is relevant to Python 3.8, this issue is blocking the Python 3.8 rebuilds. If this package won't build with 3.8, it won't be installable, along with all its dependent packages, in Fedora 32 and further. Furthermore, as it fails to install, its dependent packages will fail to install and/or build as well. Please rebuild the package in Fedora 32 (rawhide). Let us know here if you have any questions. Thank You!
No response upstream so far. Do we keep the package? It fails to install.
Please, respond.
Sorry, I'm focusing on Cartopy at the moment, so I have not looked at what is going on here at all, or whether it's simple to patch or what. I also have no internet right now, so somewhat limited in what I can do in any case.
The idea was to know whether we are keeping the package (and hence we invest the energy into the fix) or not (and possibly orphan it in that case), not to fix it immediately.