#29766 closed defect (fixed)
Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package
Reported by:  dimpase  Owned by:  

Priority:  blocker  Milestone:  sage9.2 
Component:  packages: standard  Keywords:  
Cc:  arojas, mkoeppe, fbissey, isuruf, slelievre, dcoudert, tscrim, chapoton, alexjbest  Merged in:  
Authors:  Dima Pasechnik, Matthias Koeppe  Reviewers:  Travis Scrimshaw, Isuru Fernando, Dima Pasechnik 
Report Upstream:  Fixed upstream, but not in a stable release.  Work issues:  
Branch:  5d4b013 (Commits, GitHub, GitLab)  Commit:  
Dependencies:  #29929  Stopgaps: 
Description (last modified by )
Followup from the update of numpy to 1.16.6 (#29429):
We update
 https://pypi.org/project/numpy/ to 1.19.1 (latest as of 20200721)
 https://pypi.org/project/scipy/ to 1.5.2 (latest as of 20200731)
 networkx to the latest release, 2.4 (latest as of 20200704)
All of the above versions support Python >= 3.6.
One deprecation warning is removed here, another suppressed (from #29425), the rest it trivial.
Tarballs: see checksums.ini [upstream_url]
Change History (133)
comment:1 Changed 2 years ago by
 Branch set to u/dimpase/packages/networkx24
 Cc arojas mkoeppe fbissey isuruf added
 Commit set to 2310c79596838489831ffd1eb55b8ada4ac6784d
 Dependencies set to #29425
 Description modified (diff)
 Status changed from new to needs_review
 Summary changed from update networkx and fix scipy 1.4 compat warnings to update networkx to 2.4
comment:2 Changed 2 years ago by
You may get more stuff if you are using scipy 1.4 with that. I patched all the deprecation I could in sageongentoo https://github.com/cschwan/sageongentoo/blob/master/devpython/networkx/files/networkx2.4scipy1.4.patch
comment:3 Changed 2 years ago by
for scipy 1.4 (cf #29425  which is a dependency of this ticket!) I chose to suppress these warnings in a Pythonic way, rather than doing patching already done by upstream (just not yet released)
comment:4 followup: ↓ 12 Changed 2 years ago by
Minor (perhaps trivial) point, but pulling it from that link gave a zip file named networkxnetworkx2.4.zip
, which caused it to fail without manually downloading and naming the tarball correctly.
With this ticket, I get two deprecation warnings in generic_graph.py
on these two tests:
File "src/sage/graphs/generic_graph.py", line 9786, in sage.graphs.generic_graph.GenericGraph.? Failed example: G.pagerank(algorithm="Scipy") # abs tol 1e9 File "src/sage/graphs/generic_graph.py", line 9793, in sage.graphs.generic_graph.GenericGraph.? Failed example: G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9
comment:5 Changed 2 years ago by
Could you post deprecation warnings you get? Cause I thought these were fixed on #29425
comment:6 Changed 2 years ago by
Both of them are like this:
doctest:warning File "/home/uqtscrim/sagebuild/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.?[8]>", line 1, in <module> G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9 File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 9877, in pagerank dangling=dangling) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/networkx/algorithms/link_analysis/pagerank_alg.py", line 432, in pagerank_scipy S = scipy.array(M.sum(axis=1)).flatten() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/scipy/_lib/deprecation.py", line 19, in call stacklevel=stacklevel) File "/home/uqtscrim/sagebuild/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: scipy.array is deprecated and will be removed in SciPy 2.0.0, use numpy.array instead doctest:warning File "/home/uqtscrim/sagebuild/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.?[8]>", line 1, in <module> G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9 File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 9877, in pagerank dangling=dangling) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/networkx/algorithms/link_analysis/pagerank_alg.py", line 439, in pagerank_scipy x = scipy.repeat(1.0 / N, N) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/scipy/_lib/deprecation.py", line 19, in call stacklevel=stacklevel) File "/home/uqtscrim/sagebuild/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: scipy.repeat is deprecated and will be removed in SciPy 2.0.0, use numpy.repeat instead doctest:warning File "/home/uqtscrim/sagebuild/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.?[8]>", line 1, in <module> G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9 File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 9877, in pagerank dangling=dangling) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/networkx/algorithms/link_analysis/pagerank_alg.py", line 446, in pagerank_scipy p = scipy.repeat(1.0 / N, N) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/scipy/_lib/deprecation.py", line 19, in call stacklevel=stacklevel) File "/home/uqtscrim/sagebuild/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: scipy.repeat is deprecated and will be removed in SciPy 2.0.0, use numpy.repeat instead doctest:warning File "/home/uqtscrim/sagebuild/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.?[8]>", line 1, in <module> G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9 File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 9877, in pagerank dangling=dangling) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/networkx/algorithms/link_analysis/pagerank_alg.py", line 459, in pagerank_scipy is_dangling = scipy.where(S == 0)[0] File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/scipy/_lib/deprecation.py", line 19, in call stacklevel=stacklevel) File "/home/uqtscrim/sagebuild/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: scipy.where is deprecated and will be removed in SciPy 2.0.0, use numpy.where instead doctest:warning File "/home/uqtscrim/sagebuild/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sagebuild/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.?[8]>", line 1, in <module> G.pagerank(algorithm="Scipy", by_weight=True) # abs tol 1e9 File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 9877, in pagerank dangling=dangling) File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/networkx/algorithms/link_analysis/pagerank_alg.py", line 467, in pagerank_scipy err = scipy.absolute(x  xlast).sum() File "/home/uqtscrim/sagebuild/local/lib/python3.7/sitepackages/scipy/_lib/deprecation.py", line 19, in call stacklevel=stacklevel) File "/home/uqtscrim/sagebuild/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: scipy.absolute is deprecated and will be removed in SciPy 2.0.0, use numpy.absolute instead
comment:7 Changed 2 years ago by
When I run the file as a standalone, I get
File "src/sage/graphs/generic_graph.py", line 4762, in sage.graphs.generic_graph.GenericGraph.minimum_cycle_basis Failed example: sorted(g.minimum_cycle_basis(by_weight=True, algorithm='NetworkX')) Expected: [[1, 2, 3], [1, 2, 3, 4], [5, 6, 7]] Got: doctest:warning File "/home/uqtscrim/sage/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1226, in run self.run_doctests() File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 927, in run_doctests self.dispatcher.dispatch() File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2011, in dispatch self.parallel_dispatch() File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1906, in parallel_dispatch w.start() # This might take some time File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in start super(DocTestWorker, self).start() File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/uqtscrim/sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2150, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2478, in __call__ doctests, extras = self._run(runner, options, results) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2527, in _run result = runner.run(test) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 878, in run return self._run(test, compileflags, out) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 680, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1104, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.minimum_cycle_basis[3]>", line 1, in <module> sorted(g.minimum_cycle_basis(by_weight=True, algorithm='NetworkX')) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/sage/graphs/generic_graph.py", line 4805, in minimum_cycle_basis return networkx.minimum_cycle_basis(G, weight='weight') File "</home/uqtscrim/sage/local/lib/python3.7/sitepackages/decorator.py:decoratorgen354>", line 2, in minimum_cycle_basis File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/networkx/utils/decorators.py", line 82, in _not_implemented_for return not_implement_for_func(*args, **kwargs) File "</home/uqtscrim/sage/local/lib/python3.7/sitepackages/decorator.py:decoratorgen353>", line 2, in minimum_cycle_basis File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/networkx/utils/decorators.py", line 82, in _not_implemented_for return not_implement_for_func(*args, **kwargs) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/networkx/algorithms/cycles.py", line 525, in minimum_cycle_basis nx.connected_component_subgraphs(G)), []) File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/networkx/algorithms/cycles.py", line 524, in <genexpr> return sum((_min_cycle_basis(c, weight) for c in File "/home/uqtscrim/sage/local/lib/python3.7/sitepackages/networkx/algorithms/components/connected.py", line 86, in connected_component_subgraphs _warnings.warn(msg, DeprecationWarning) File "/home/uqtscrim/sage/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : DeprecationWarning: connected_component_subgraphs is deprecated and will be removedin 2.2. Use (G.subgraph(c).copy() for c in connected_components(G)) [[1, 2, 3], [1, 2, 3, 4], [5, 6, 7]]
comment:8 Changed 2 years ago by
You shouldn't have this warning with networkx 2.4. It implies you are still using 2.2.
comment:9 Changed 2 years ago by
comment:10 Changed 2 years ago by
@fbissey I am using 2.4 as far as Sage knows:
./sage installed ... networkx................................2.4 (2.4)
@dimpase I didn't realize the entire branch of #29425 had not been merged in. It looked like it had from a quick glance. Once I did that then indeed I do not get the deprecation warnings.
comment:11 Changed 2 years ago by
 Reviewers set to Travis Scrimshaw
 Status changed from needs_review to positive_review
Since the doctests do pass for me with #29425 (and you don't need to merge it in any further I think), positive review.
comment:12 in reply to: ↑ 4 ; followup: ↓ 13 Changed 2 years ago by
Replying to tscrim:
Minor (perhaps trivial) point, but pulling it from that link gave a zip file named
networkxnetworkx2.4.zip
, which caused it to fail without manually downloading and naming the tarball correctly.
I don't quite understand what "pulling it from that link" means. The idea of
upstream_url
in checksum.ini
is to allow automatic download of the package archive from that URL. (which can either be enabled with o
, as follows, ./sage i o networkx
of if one runs ./configure
with enabledownloadfromupstreamurl
option).
And this automation works for me on Linux. The ULR is copied verbatim from https://github.com/networkx/networkx/releases/tag/networkx2.4
comment:13 in reply to: ↑ 12 Changed 2 years ago by
Replying to dimpase:
Replying to tscrim:
Minor (perhaps trivial) point, but pulling it from that link gave a zip file named
networkxnetworkx2.4.zip
, which caused it to fail without manually downloading and naming the tarball correctly.I don't quite understand what "pulling it from that link" means. The idea of
upstream_url
inchecksum.ini
is to allow automatic download of the package archive from that URL. (which can either be enabled witho
, as follows,./sage i o networkx
of if one runs./configure
withenabledownloadfromupstreamurl
option).And this automation works for me on Linux. The ULR is copied verbatim from https://github.com/networkx/networkx/releases/tag/networkx2.4
Okay, I tried with just make
instead of directly with sage i
(which worked by itself when I did this on another spkg previously), so maybe that is why it didn't work. I was just thinking it came from the zip file having an unexpected name.
comment:14 Changed 2 years ago by
 Description modified (diff)
comment:15 followup: ↓ 16 Changed 2 years ago by
 Status changed from positive_review to needs_work
From #29425: running the testsuite of networkx requires pytest.
comment:16 in reply to: ↑ 15 Changed 2 years ago by
comment:17 Changed 2 years ago by
 Dependencies changed from #29425 to #29425, #29813
 Description modified (diff)
comment:18 Changed 2 years ago by
 Branch changed from u/dimpase/packages/networkx24 to u/mkoeppe/packages/networkx24
comment:19 Changed 2 years ago by
 Commit changed from 2310c79596838489831ffd1eb55b8ada4ac6784d to e592bdc05120fdb91069cfc61c3ce2f82d45ace2
Branch pushed to git repo; I updated commit sha1. New commits:
9a3617d  build/pkgs/cython: Update to 0.29.16

4a606b6  build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern

e9a7cb0  Update Cython to 0.29.17

15911cb  build/pkgs/numpy: Update numpy to 1.18.2, back out numpy1.10.2nohardcodeblas.patch (does not apply)

96e7a41  Update numpy to 1.18.4

78b4907  Update scipy to 1.4.1

54595b0  build/pkgs/pybind11: New, dependency of scipy

c005562  suppress scipy deprecation warnings

56a6fe1  build/pkgs/numpy: Update to 1.18.5

e592bdc  Merge branch 't/29425/trac/local_conda_forge_macos_standard__build_error_with_numpy' into t/29766/packages/networkx24

comment:20 Changed 2 years ago by
comment:21 Changed 2 years ago by
comment:22 Changed 2 years ago by
 Status changed from needs_work to needs_review
comment:23 Changed 2 years ago by
comment:24 Changed 2 years ago by
 Status changed from needs_review to needs_work
#29813 needs to be fixed.
comment:25 Changed 2 years ago by
 Cc slelievre added
 Dependencies changed from #29425, #29813 to #29480, #29813
 Description modified (diff)
 Reviewers changed from Travis Scrimshaw to Travis Scrimshaw, Isuru Fernando, Dima Pasechnik
 Summary changed from update networkx to 2.4 to Upgrade NumPy to 1.18.5, scipy to 1.4.1, networkx to 2.4, add pybind11 package
comment:26 Changed 2 years ago by
comment:27 Changed 2 years ago by
 Commit changed from e592bdc05120fdb91069cfc61c3ce2f82d45ace2 to 11bf67f601c626d62aa8896a3a20342e7b2d4318
comment:28 Changed 2 years ago by
 Status changed from needs_work to needs_review
comment:29 Changed 2 years ago by
Tests at https://github.com/mkoeppe/sage/actions/runs/128112212:
On ubuntueoanstandard
(https://github.com/mkoeppe/sage/runs/748390625), LOTS of failures in the networkx testsuite:
Ran 3618 tests in 386.630s FAILED (errors=808)
Is this expected?
comment:30 Changed 2 years ago by
Failure on cygwinstandard (https://github.com/mkoeppe/sage/runs/748608397):
g++: scipy/optimize/rectangular_lsap/rectangular_lsap.cpp scipy/optimize/rectangular_lsap/rectangular_lsap.cpp:117:43: error: ‘int64_t’ has not been declared 117  solve(int nr, int nc, double* input_cost, int64_t* output_col4row)  ^~~~~~~ scipy/optimize/rectangular_lsap/rectangular_lsap.cpp:186:41: error: ‘int64_t’ has not been declared 186  int64_t* col4row)  ^~~~~~~
comment:31 Changed 2 years ago by
The int64_t
issue is fixed in https://github.com/scipy/scipy/pull/11320
for the upcoming 1.5.0, marked "backportcandidate", but so far no 1.4.x with the fix has been released...
comment:32 Changed 2 years ago by
 Commit changed from 11bf67f601c626d62aa8896a3a20342e7b2d4318 to db0fa417db01ade8efb1b7c616ec53c7269d94d8
Branch pushed to git repo; I updated commit sha1. New commits:
db0fa41  build/pkgs/scipy: Add patch for scipy pr 11320

comment:33 Changed 2 years ago by
 Cc dcoudert added
comment:34 Changed 2 years ago by
 Cc tscrim chapoton added
comment:35 Changed 2 years ago by
Everything builds and works for me on Ubuntu.
comment:37 Changed 2 years ago by
Comment 29 is unresolved
comment:38 Changed 2 years ago by
a package fails its own testsuite. it's not the 1st one (happens on Gentoo as well)
comment:39 Changed 2 years ago by
OK, good to know. No objection then
comment:40 Changed 2 years ago by
 Description modified (diff)
comment:41 Changed 2 years ago by
 Status changed from positive_review to needs_work
Lots of failures of the form
********************************************************************** File "src/sage/modular/modform_hecketriangle/abstract_space.py", line 2235, in sage.modular.modform_hecketriangle.abstract_space.FormsSpace_abstract.ZZ Failed example: qexp_int = WF.rationalize_series(qexp) Expected nothing Got: doctest:warning File "/home/release/Sage/src/bin/sageruntests", line 178, in <module> err = DC.run() File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1231, in run self.run_doctests() File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 931, in run_doctests self.dispatcher.dispatch() File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2045, in dispatch self.parallel_dispatch() File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1940, in parallel_dispatch w.start() # This might take some time File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2212, in start super(DocTestWorker, self).start() File "/home/release/Sage/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/home/release/Sage/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/home/release/Sage/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/release/Sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/home/release/Sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/home/release/Sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2184, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2513, in __call__ doctests, extras = self._run(runner, options, results) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2562, in _run result = runner.run(test) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 912, in run return self._run(test, compileflags, out) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 707, in _run self.compile_and_execute(example, compiler, test.globs) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1138, in compile_and_execute exec(compiled, globs) File "<doctest sage.modular.modform_hecketriangle.abstract_space.FormsSpace_abstract.ZZ[4]>", line 1, in <module> qexp_int = WF.rationalize_series(qexp) File "/home/release/Sage/local/lib/python3.7/sitepackages/sage/modular/modform_hecketriangle/abstract_space.py", line 2309, in rationalize_series warn("Using an experimental rationalization of coefficients, please check the result for correctness!") File "/home/release/Sage/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : UserWarning: Using an experimental rationalization of coefficients, please check the result for correctness! ********************************************************************** 2 items had failures: 1 of 29 in sage.modular.modform_hecketriangle.abstract_space.FormsSpace_abstract.ZZ 1 of 41 in sage.modular.modform_hecketriangle.abstract_space.FormsSpace_abstract.construct_quasi_form [566 tests, 2 failures, 7.37 s]  sage t long warnlong 37.2 src/sage/modular/modform_hecketriangle/abstract_space.py # 2 doctests failed 
comment:42 Changed 2 years ago by
This looks strange. I have done a test run of sage 9.2.beta2 with numpy1.19/scipy1.5/networkx2.4 in sageongentoo and I have seen no such things [in fact the number of doctest failures in sageongentoo is at its lowest in years  3 doctests across 2 files].
I would think another ticket would be the cause of this, although I am at a loss as to which one when inspecting your last commits. Running my own tests on your branch ASAP.
comment:43 Changed 2 years ago by
This is caused by the
warnings.filterwarnings('ignore', '.*Deprec.*scipy.*instead',)
line. This is run on every examples block, and resets the registry of already displayed warnings  so warnings which are not affected by a filter, which by default are only displayed the first time they are hit, are shown again.
comment:44 Changed 2 years ago by
oh dear. ok, we can suppress these, too
comment:45 followup: ↓ 53 Changed 2 years ago by
From the SciPy 1.5.1 Release Notes:
SciPy 1.5.1 is a bugfix release with no new features compared to 1.5.0. In particular, an issue where DLL loading can fail for SciPy wheels on Windows with Python 3.6 has been fixed.
comment:46 Changed 2 years ago by
 Description modified (diff)
comment:47 Changed 2 years ago by
 Commit changed from db0fa417db01ade8efb1b7c616ec53c7269d94d8 to a2e19785a2c670ba165905c78498a841e2b1ded4
comment:48 Changed 2 years ago by
comment:49 Changed 2 years ago by
 Description modified (diff)
 Summary changed from Upgrade NumPy to 1.18.5, scipy to 1.4.1, networkx to 2.4, add pybind11 package to Upgrade NumPy to 1.19.0, scipy to 1.5.1, networkx to 2.4, add pybind11 package
comment:50 followup: ↓ 60 Changed 2 years ago by
The warnings.filterwarnings
issue needs to be addressed
comment:51 Changed 2 years ago by
 Description modified (diff)
comment:52 Changed 2 years ago by
 Description modified (diff)
comment:53 in reply to: ↑ 45 Changed 2 years ago by
Replying to slelievre:
From the SciPy 1.5.1 Release Notes:
SciPy 1.5.1 is a bugfix release with no new features compared to 1.5.0. In particular, an issue where DLL loading can fail for SciPy wheels on Windows with Python 3.6 has been fixed.
no worries, the ticket description was not updated, that's all.
comment:54 Changed 2 years ago by
wrong tarball hash for numpy. See https://github.com/numpy/numpy/issues/16754
 the usual GH crappy tarballs stuff I guess.
comment:55 Changed 2 years ago by
Currently it is

build/pkgs/numpy/checksums.ini
a b 1 1 tarball=numpyVERSION.tar.gz 2 sha1= 0b1792c8a828d6a9fb148fb33dfa11549391d8583 md5= 3f5ce88a859302f0a1aceb5f75b563fc4 cksum=160 35448582 sha1=a6c099c0929e0b437a72fd60aad76d23061087c6 3 md5=e3baa59da67348c2d6596803514129db 4 cksum=1607167529 5 5 upstream_url=https://github.com/numpy/numpy/releases/download/vVERSION/numpyVERSION.tar.gz
but of course it's not really stable...
comment:56 Changed 2 years ago by
And now md5 as advertised on Numpy pages:

build/pkgs/numpy/checksums.ini
a b 1 1 tarball=numpyVERSION.tar.gz 2 sha1= 0b1792c8a828d6a9fb148fb33dfa11549391d8583 md5= 3f5ce88a859302f0a1aceb5f75b563fc4 cksum= 16035448582 sha1=ba35592527bd01f53244ae1bb55c896101bbf0f3 3 md5=d59aadf47354bd10c7b9996032ba4da0 4 cksum=3500020755
Sucks.
comment:57 Changed 2 years ago by
 Commit changed from a2e19785a2c670ba165905c78498a841e2b1ded4 to 0879c3b5f25ac5eb68e6a4317433f8ff670934d7
Branch pushed to git repo; I updated commit sha1. New commits:
0879c3b  build/pkgs/{numpy,scipy}/checksums.ini: Set upstream_url to pypi.io

comment:58 Changed 2 years ago by
Hopefully the sources packages on PyPI are more stable.
comment:59 Changed 2 years ago by
 Priority changed from major to critical
comment:60 in reply to: ↑ 50 ; followup: ↓ 61 Changed 2 years ago by
Replying to mkoeppe:
The
warnings.filterwarnings
issue needs to be addressed
It appears I figured out this issue; doing

src/sage/all.py
a b warnings.filterwarnings('ignore', category=RuntimeWarning, 87 87 # Ignore all deprecations from IPython etc. 88 88 warnings.filterwarnings('ignore', category=DeprecationWarning, 89 89 module='.*(IPythonipykerneljupyter_clientjupyter_corenbformatnotebookipywidgetsstoremagicjedi)') 90 warnings.filterwarnings('ignore', category=DeprecationWarning, 91 module='.*(scipynetworkx)') 90 92 # Ignore collections.abc warnings, there are a lot of them but they are 91 93 # harmless. 92 94 warnings.filterwarnings('ignore', category=DeprecationWarning, 
src/sage/doctest/forker.py
diff git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py index 9646ddee18..bd7e1a5a97 100644
a b class SageDocTestRunner(doctest.DocTestRunner, object): 881 881 # and will be removed in SciPy 2.0.0, use numpy.array instead 882 882 # This affects networkx 2.2 up and including 2.4 883 883 # We filter them out here: 884 warnings.filterwarnings('ignore', '.*Deprec.*scipy.*instead',) # cf trac #29425884 # warnings.filterwarnings('ignore', '.*Deprec.*scipy.*instead',) # cf trac #29425 885 885 886 886 warnings.showwarning = showwarning_with_traceback 887 887 self.running_doctest_digest = hashlib.md5()
appears to fix it  still testing, but expect a success.
Basically, we already did suppression of deprecation warnings
from other packages right, now the same has to be done for scipy
and networkx
comment:61 in reply to: ↑ 60 ; followup: ↓ 62 Changed 2 years ago by
Basically, we already did suppression of deprecation warnings from other packages right, now the same has to be done for
scipy
andnetworkx
Doesn't that also hide deprecation warnings coming from sage code, and thus would prevent detecting such deprecated code use with future scipy/networkx updates? That sort of defeats the point of the previous
deprecationWarning = ('ignore', None, DeprecationWarning, None, 0) if deprecationWarning in warnings.filters: warnings.filters.remove(deprecationWarning)
comment:62 in reply to: ↑ 61 Changed 2 years ago by
Replying to arojas:
Basically, we already did suppression of deprecation warnings from other packages right, now the same has to be done for
scipy
andnetworkx
Doesn't that also hide deprecation warnings coming from sage code, and thus would prevent detecting such deprecated code use with future scipy/networkx updates? That sort of defeats the point of the previous
deprecationWarning = ('ignore', None, DeprecationWarning, None, 0) if deprecationWarning in warnings.filters: warnings.filters.remove(deprecationWarning)
module='.*(scipynetworkx)'
suppresses deprecation warnings emitted by code in scipy
or in networkx
. It does not do anything to these warnings from Sage code itself.
Indeed, the tests in src/sage/tests/deprecation_test.py
still pass.
comment:63 Changed 2 years ago by
needless to say, each upgrade to scipynetworkx will need to reevaluate these.
We should add something to the Developer manual on this.
comment:64 Changed 2 years ago by
 Branch changed from u/mkoeppe/packages/networkx24 to u/dimpase/packages/networkx24
 Commit changed from 0879c3b5f25ac5eb68e6a4317433f8ff670934d7 to 8a70ebedcf063d0a77564c01537a9600dd2accda
 Status changed from needs_work to needs_review
correct suppression of warnings
New commits:
8a70ebe  right place for warnings.filterwarnings() for networkx & scipy

comment:65 Changed 2 years ago by
 Dependencies changed from #29480, #29813 to #29480, #29813, #30118
comment:66 Changed 2 years ago by
 Branch changed from u/dimpase/packages/networkx24 to u/mkoeppe/packages/networkx24
comment:67 Changed 2 years ago by
 Commit changed from 8a70ebedcf063d0a77564c01537a9600dd2accda to 0356be918ab0c9ed20347360db5eed7b94ab697b
 Dependencies changed from #29480, #29813, #30118 to #29480, #29813, #29929, #30118
Last 10 new commits:
b7bf43b  build/bin/writedockerfile.sh: ADD src/bin for bootstrapping, needed by src/doc/bootstrap after #29884

365ce61  Merge branch 'u/mkoeppe/fix_tox_docker_builds_broken_by__29884' of git://trac.sagemath.org/sage into HEAD

fb61a31  Merge branch 'u/mkoeppe/tox_ini__debian_bullseye___sid_have_python3_8_instead_of_3_7' of git://trac.sagemath.org/sage into 9.2.beta3+cifixes

bfb2fb4  tox.ini: Add environment localhomebrewusrlocal

aded967  Merge commit '8195cb821e01e0cb627240d7135d5634c265cab0' of git://trac.sagemath.org/sage into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda

07d657d  Merge tag '9.2.beta4' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda

bd15fb9  build/bin/writedockerfile.sh, tox.ini: Do not run testsuites that need pip (ssl)

25393b0  Handle SAGE_CHECK_PACKAGES in build/make/Makefile.in, not sagespkg

5aca238  Merge branch 't/30118/handle_sage_check_packages_in_build_make_makefile_in__not_sage_spkg' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda

0356be9  Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24

comment:68 Changed 2 years ago by
 Priority changed from critical to blocker
Elevating this upgrade ticket to "blocker" because homebrew builds are currently broken because they now ship gfortran 10.
comment:69 Changed 2 years ago by
(see for example https://github.com/sagemath/sage/runs/862451287)
comment:70 Changed 2 years ago by
 Commit changed from 0356be918ab0c9ed20347360db5eed7b94ab697b to 6954debc04519488cc4b8f299166797fe95eb204
Branch pushed to git repo; I updated commit sha1. New commits:
6954deb  build/pkgs/networkx/dependencies: Conditionalize on SAGE_CHECK_networkx

comment:71 Changed 2 years ago by
Tests as part of Metaticket #29456 (Support gcc/gfortran 10) at https://github.com/mkoeppe/sage/actions/runs/167913617
On debianjessiestandard
(https://github.com/mkoeppe/sage/runs/866989168) and debianjessieminimal
:
gcc: build/src.linuxx86_643.7/numpy/core/src/umath/loops.c In file included from numpy/core/src/umath/loops.c.src:50:0: numpy/core/src/umath/simd.inc.src: In function ‘avx512_conjugate_ps’: numpy/core/src/umath/simd.inc.src:1843:5: warning: implicit declaration of function ‘_mm512_castps_si512’ [Wimplicitfunctiondeclaration] __m512i cast_x = _mm512_cast@vsub@_si512(x); ^ numpy/core/src/umath/simd.inc.src:1843:22: error: incompatible types when initializing type ‘__vector(8) long long int’ using type ‘int’ __m512i cast_x = _mm512_cast@vsub@_si512(x); ^ numpy/core/src/umath/simd.inc.src:1846:5: warning: implicit declaration of function ‘_mm512_castsi512_ps’ [Wimplicitfunctiondeclaration] return _mm512_castsi512_@vsub@(res); ^ numpy/core/src/umath/simd.inc.src:1846:5: error: incompatible types when returning type ‘int’ but ‘__vector(16) float’ was expected
comment:72 Changed 2 years ago by
debianjessie
uses gcc version 4.9.2 (Debian 4.9.210+deb8u2), and a fix for something that looks related is in gcc 4.9.3  https://gcc.gnu.org/bugzilla/show_bug.cgi?id=61878
comment:73 Changed 2 years ago by
This was added to numpy in https://github.com/numpy/numpy/commit/5562a8c93fe18f0a51d9051f0c25c7cf525312fe (new in 1.19.0) (https://github.com/numpy/numpy/pull/15408)
comment:74 Changed 2 years ago by
 Report Upstream changed from N/A to Reported upstream. No feedback yet.
comment:75 Changed 2 years ago by
Let's go back to 1.18.5 (released Jun 3, 2020).
comment:76 Changed 2 years ago by
 Commit changed from 6954debc04519488cc4b8f299166797fe95eb204 to d39817fe52d756382d33e21da4866939fbfff571
Branch pushed to git repo; I updated commit sha1. New commits:
d39817f  build/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debianjessie

comment:77 Changed 2 years ago by
 Description modified (diff)
 Summary changed from Upgrade NumPy to 1.19.0, scipy to 1.5.1, networkx to 2.4, add pybind11 package to Upgrade NumPy to 1.18.5, scipy to 1.5.1, networkx to 2.4, add pybind11 package
comment:78 Changed 2 years ago by
comment:79 Changed 2 years ago by
comment:80 Changed 2 years ago by
In these tests, fedora32standard
uses gcc/gfortran 10 from the system, fedora32minimal
uses gcc 10 from the system and gfortran from spkg, and the various homebrewmacos
tests use gcc = apple clang, gfortran 10 from homebrew.
They all succeed. Still waiting for other tests to finish.
comment:81 Changed 2 years ago by
On localcondaforgemacosmaximal
(https://github.com/mkoeppe/sage/runs/867731009), numpy
1.18.5 builds but building sagelib fails as follows:
[sagelib9.2.beta5] error installing, exit status 1. End of log file: [sagelib9.2.beta5] from . import core [sagelib9.2.beta5] File "/Users/runner/work/sage/sage/.tox/localcondaforgemacosmaximal/local/lib/python3.7/sitepackages/numpy/core/__init__.py", line 50, in <module> [sagelib9.2.beta5] raise ImportError(msg) [sagelib9.2.beta5] ImportError: [sagelib9.2.beta5] [sagelib9.2.beta5] IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! [sagelib9.2.beta5] [sagelib9.2.beta5] Importing the numpy Cextensions failed. This error can happen for [sagelib9.2.beta5] many reasons, often due to issues with your setup or how NumPy was [sagelib9.2.beta5] installed. ... [sagelib9.2.beta5] Original error was: dlopen(/Users/runner/work/sage/sage/.tox/localcondaforgemacosmaximal/local/lib/python3.7/sitepackages/numpy/core/_multiarray_umath.cpython37mdarwin.so, 2): Symbol not found: _aheapsort_bool [sagelib9.2.beta5] Referenced from: /Users/runner/work/sage/sage/.tox/localcondaforgemacosmaximal/local/lib/python3.7/sitepackages/numpy/core/_multiarray_umath.cpython37mdarwin.so [sagelib9.2.beta5] Expected in: flat namespace [sagelib9.2.beta5] in /Users/runner/work/sage/sage/.tox/localcondaforgemacosmaximal/local/lib/python3.7/sitepackages/numpy/core/_multiarray_umath.cpython37mdarwin.so
Also building matplotlib
fails with a similar error.
comment:82 Changed 2 years ago by
 Report Upstream changed from Reported upstream. No feedback yet. to Reported upstream. Developers acknowledge bug.
comment:83 Changed 2 years ago by
numpy 1.19 had worked OK on localcondaforgemacos
when that was tested (https://github.com/mkoeppe/sage/runs/858960241).
comment:84 Changed 2 years ago by
Trying next with https://github.com/numpy/numpy/pull/16871
comment:85 Changed 2 years ago by
 Commit changed from d39817fe52d756382d33e21da4866939fbfff571 to 355873714763fe9df4955af6d31e5725e4f64c0d
comment:86 Changed 2 years ago by
comment:87 Changed 2 years ago by
Unfortunately the patch does not apply by itself
comment:88 Changed 2 years ago by
Running tests with numpy master + pr16871 at https://github.com/mkoeppe/sage/actions/runs/169620460
comment:89 Changed 2 years ago by
 Report Upstream changed from Reported upstream. Developers acknowledge bug. to Fixed upstream, but not in a stable release.
comment:90 Changed 2 years ago by
https://github.com/numpy/numpy/pull/16871 has been merged in numpy master. Hoping for a backport
comment:91 Changed 2 years ago by
 Cc alexjbest added
comment:92 Changed 2 years ago by
there are more deprecation warnings to suppress, e.g.
20200715T10:18:00.4452989Z File "src/sage/calculus/interpolators.pyx", line 48, in sage.calculus.interpolators.polygon_spline 20200715T10:18:00.4453182Z Failed example: 20200715T10:18:00.4453370Z ps = polygon_spline(pts) 20200715T10:18:00.4453562Z Expected nothing 20200715T10:18:00.4453746Z Got: 20200715T10:18:00.4453928Z doctest:warning 20200715T10:18:00.4454284Z File "/sage/src/bin/sageruntests", line 177, in <module> 20200715T10:18:00.4454494Z err = DC.run() 20200715T10:18:00.4454877Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1207, in run 20200715T10:18:00.4455104Z self.run_doctests() 20200715T10:18:00.4455498Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 908, in run_doctests 20200715T10:18:00.4455721Z self.dispatcher.dispatch() 20200715T10:18:00.4456125Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2039, in dispatch 20200715T10:18:00.4456344Z self.parallel_dispatch() 20200715T10:18:00.4456736Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1934, in parallel_dispatch 20200715T10:18:00.4456963Z w.start() # This might take some time 20200715T10:18:00.4457348Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2206, in start 20200715T10:18:00.4457571Z super(DocTestWorker, self).start() 20200715T10:18:00.4457778Z File "/sage/local/lib/python3.7/multiprocessing/process.py", line 112, in start 20200715T10:18:00.4457985Z self._popen = self._Popen(self) 20200715T10:18:00.4458194Z File "/sage/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen 20200715T10:18:00.4458409Z return _default_context.get_context().Process._Popen(process_obj) 20200715T10:18:00.4458621Z File "/sage/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen 20200715T10:18:00.4458822Z return Popen(process_obj) 20200715T10:18:00.4459027Z File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ 20200715T10:18:00.4459245Z self._launch(process_obj) 20200715T10:18:00.4459447Z File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch 20200715T10:18:00.4459645Z code = process_obj._bootstrap() 20200715T10:18:00.4459852Z File "/sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap 20200715T10:18:00.4460066Z self.run() 20200715T10:18:00.4460446Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2178, in run 20200715T10:18:00.4461480Z task(self.options, self.outtmpfile, msgpipe, self.result_queue) 20200715T10:18:00.4462380Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2507, in __call__ 20200715T10:18:00.4462669Z doctests, extras = self._run(runner, options, results) 20200715T10:18:00.4463154Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2553, in _run 20200715T10:18:00.4463441Z result = runner.run(test) 20200715T10:18:00.4463902Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 906, in run 20200715T10:18:00.4464158Z return self._run(test, compileflags, out) 20200715T10:18:00.4464793Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 707, in _run 20200715T10:18:00.4465103Z self.compile_and_execute(example, compiler, test.globs) 20200715T10:18:00.4465621Z File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1132, in compile_and_execute 20200715T10:18:00.4465963Z exec(compiled, globs) 20200715T10:18:00.4466212Z File "<doctest sage.calculus.interpolators.polygon_spline[1]>", line 1, in <module> 20200715T10:18:00.4466479Z ps = polygon_spline(pts) 20200715T10:18:00.4466937Z File "/sage/local/lib/python3.7/sitepackages/numpy/__init__.py", line 237, in __getattr__ 20200715T10:18:00.4467232Z warnings.warn(msg, DeprecationWarning, stacklevel=2) 20200715T10:18:00.4467504Z File "/sage/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg 20200715T10:18:00.4467750Z msg.file, msg.line) 20200715T10:18:00.4468009Z : 20200715T10:18:01.5210352Z DeprecationWarning: `np.complex` is a deprecated alias for the builtin `complex`. Use `complex` by itself, which is identical in behavior, to silence this warning. If you specifically wanted the numpy scalar type, use `np.complex_` here.
comment:93 Changed 2 years ago by
these deprecation warnings are coming from numpy master, they will not hit us now, only later
comment:94 Changed 2 years ago by
numpy 1.19.1 is out but unfortunately does not have a backport of https://github.com/numpy/numpy/pull/16871
comment:95 Changed 2 years ago by
However, thanks to other backported fixes, the pull request is now easier to apply.
comment:96 Changed 2 years ago by
 Dependencies changed from #29480, #29813, #29929, #30118 to #29480, #29813, #29929, #30118, #29861
numpy 1.19.1 needs newest Cython (#29861)
comment:97 Changed 2 years ago by
 Commit changed from 355873714763fe9df4955af6d31e5725e4f64c0d to 061e975e3116d390b6faf6ca37f942512964dab5
comment:98 Changed 2 years ago by
 Description modified (diff)
 Summary changed from Upgrade NumPy to 1.18.5, scipy to 1.5.1, networkx to 2.4, add pybind11 package to Upgrade NumPy to 1.19.1, scipy to 1.5.1, networkx to 2.4, add pybind11 package
comment:99 Changed 2 years ago by
comment:100 followup: ↓ 103 Changed 2 years ago by
I see a number of doctest failures related to printing of deprecation warnings. Did something on this ticket cause this? For example (on ubuntutrustystandard
, https://github.com/mkoeppe/sage/runs/896153611):
sage t src/sage/algebras/lie_algebras/free_lie_algebra.py ********************************************************************** File "src/sage/algebras/lie_algebras/free_lie_algebra.py", line 194, in sage.algebras.lie_algebras.free_lie_algebra.FreeLieBasis_abstract.basis Failed example: L.Hall().basis() Expected: Disjoint union of Lazy family (graded basis(i))_{i in Positive integers} Got: doctest:warning File "/sage/src/bin/sageruntests", line 177, in <module> err = DC.run() File "/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 1207, in run self.run_doctests() File "/sage/local/lib/python3.7/sitepackages/sage/doctest/control.py", line 908, in run_doctests self.dispatcher.dispatch() File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2045, in dispatch self.parallel_dispatch() File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1940, in parallel_dispatch w.start() # This might take some time File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2212, in start super(DocTestWorker, self).start() File "/sage/local/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/sage/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/sage/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch code = process_obj._bootstrap() File "/sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2184, in run task(self.options, self.outtmpfile, msgpipe, self.result_queue) File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2513, in __call__ doctests, extras = self._run(runner, options, results) File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 2559, in _run result = runner.run(test) File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 912, in run return self._run(test, compileflags, out) File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 707, in _run self.compile_and_execute(example, compiler, test.globs) File "/sage/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1138, compile_and_execute exec(compiled, globs) File "<doctest sage.algebras.lie_algebras.free_lie_algebra.FreeLieBasis_abstract.basis[1]>", line 1, in <module> L.Hall().basis() File "/sage/local/lib/python3.7/sitepackages/sage/structure/unique_representation.py", line 1008, in __classcall__ instance = typecall(cls, *args, **options) File "/sage/local/lib/python3.7/sitepackages/sage/algebras/lie_algebras/free_lie_algebra.py", line 445, in __init__ experimental_warning(16823, "The Hall basis has not been fully proven correct," File "/sage/local/lib/python3.7/sitepackages/sage/misc/superseded.py", line 181, in experimental_warning warning(trac_number, message, FutureWarning, stacklevel) File "/sage/local/lib/python3.7/sitepackages/sage/misc/superseded.py", line 146, in warning warn(message, warning_class, stacklevel) File "/sage/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg msg.file, msg.line) : FutureWarning: The Hall basis has not been fully proven correct, but currently no bugs are known See http://trac.sagemath.org/16823 for details. Disjoint union of Lazy family (graded basis(i))_{i in Positive integers} **********************************************************************
comment:101 Changed 2 years ago by
 Commit changed from 061e975e3116d390b6faf6ca37f942512964dab5 to fc7592cdafb6ed3b1d947faeeb67841c3491e843
Branch pushed to git repo; I updated commit sha1. New commits:
d1a2cbf  Merge branch 't/30088/fix__make_sdist___add_test_run_to_github_actions' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda

b62f775  Merge tag '9.2.beta6' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda

fc7592c  Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24

comment:102 Changed 2 years ago by
 Dependencies changed from #29480, #29813, #29929, #30118, #29861 to #29929
Merged 9.2.beta6
comment:103 in reply to: ↑ 100 Changed 2 years ago by
Replying to mkoeppe:
I see a number of doctest failures related to printing of deprecation warnings. Did something on this ticket cause this?
this  which is actually a wrong place to deal with this stuff. This branch seems to be obsolete at this place  there is a better place to handle these warnings, and I think I've put it on this ticket some time back  but then it did not stick for some reason.
comment:104 Changed 2 years ago by
namely, you need https://git.sagemath.org/sage.git/commit?id=8a70ebedcf063d0a77564c01537a9600dd2accda
(cf. comment:64)
comment:105 Changed 2 years ago by
 Commit changed from fc7592cdafb6ed3b1d947faeeb67841c3491e843 to 7fe59852445ff75037fcdc3dd0ae42070fe0c5ed
Branch pushed to git repo; I updated commit sha1. New commits:
7fe5985  right place for warnings.filterwarnings() for networkx & scipy

comment:106 Changed 2 years ago by
comment:108 Changed 2 years ago by
I report that compilation succeeded with gcc 10.1.0 and this ticket merged.
comment:109 Changed 2 years ago by
I think this is good to go. Reviewers?
comment:110 Changed 2 years ago by
Don't you want to make the upgrade scipy 1.5.1 > 1.5.2?
comment:111 followup: ↓ 115 Changed 2 years ago by
selftests of networkx need pytest, but logs show that pytest might bot be installed. I don't understand the meaning of this poorly halfimplemented LISPy thing:
$(PYTHON) decorator  $(PYTHON_TOOLCHAIN) scipy $(and $(filterout no,$(SAGE_CHECK_networkx)), nose pytest)
comment:112 followup: ↓ 113 Changed 2 years ago by
which log? link please
comment:113 in reply to: ↑ 112 Changed 2 years ago by
Replying to mkoeppe:
which log? link please
https://github.com/mkoeppe/sage/runs/912558796?check_suite_focus=true
comment:114 followup: ↓ 118 Changed 2 years ago by
anyhow, how about upgrading to scipy 1.5.2 along the way?
comment:115 in reply to: ↑ 111 ; followup: ↓ 116 Changed 2 years ago by
Replying to dimpase:
I don't understand that meaning of this poorly halfimplemented LISPy thing:
$(PYTHON) decorator  $(PYTHON_TOOLCHAIN) scipy $(and $(filterout no,$(SAGE_CHECK_networkx)), nose pytest)
It keeps "nose pytest" only when running the networkx
test suite is requested.
Because these are testsuiteonly dependencies.
comment:116 in reply to: ↑ 115 Changed 2 years ago by
Replying to mkoeppe:
Replying to dimpase:
I don't understand that meaning of this poorly halfimplemented LISPy thing:
$(PYTHON) decorator  $(PYTHON_TOOLCHAIN) scipy $(and $(filterout no,$(SAGE_CHECK_networkx)), nose pytest)It keeps "nose pytest" only when running the
networkx
test suite is requested.Because these are testsuiteonly dependencies.
but somehow it does not work in the GH Actions realm (or maybe at all), no?
comment:117 followup: ↓ 125 Changed 2 years ago by
Yes, there is a problem  thanks for catching it.
I am running GH Actions build with SAGE_CHECK=warn
, and the code added in #30118 does not handle the exclusions given in SAGE_CHECK_PACKAGES in that case.
Let's change that.
comment:118 in reply to: ↑ 114 Changed 2 years ago by
comment:119 Changed 2 years ago by
 Description modified (diff)
 Summary changed from Upgrade NumPy to 1.19.1, scipy to 1.5.1, networkx to 2.4, add pybind11 package to Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package
comment:120 Changed 2 years ago by
 Commit changed from 7fe59852445ff75037fcdc3dd0ae42070fe0c5ed to 3890e1a1540abeecc2d9e8898e8463dea42c9547
comment:121 Changed 2 years ago by
comment:122 Changed 2 years ago by
 Status changed from needs_review to needs_work
comment:123 Changed 2 years ago by
 Commit changed from 3890e1a1540abeecc2d9e8898e8463dea42c9547 to 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b
Branch pushed to git repo; I updated commit sha1. New commits:
5d4b013  build/make/Makefile.in: Handle the case in which SAGE_CHECK_PACKAGES is set using a command argument

comment:124 Changed 2 years ago by
 Status changed from needs_work to needs_review
comment:125 in reply to: ↑ 117 Changed 2 years ago by
comment:126 Changed 2 years ago by
Let's please get this in?
comment:128 Changed 2 years ago by
Thank you!
comment:129 Changed 2 years ago by
 Branch changed from u/mkoeppe/packages/networkx24 to 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b
 Resolution set to fixed
 Status changed from positive_review to closed
comment:130 followup: ↓ 131 Changed 2 years ago by
 Commit 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b deleted
Why is there no SPKG.rst file for pybind11? Are these suddenly optional?
comment:131 in reply to: ↑ 130 Changed 2 years ago by
Replying to jhpalmieri:
Why is there no SPKG.rst file for pybind11? Are these suddenly optional?
A simple mistake. There's actually nothing in our scripts that checks the presence of these files (see e.g. #29334). Let's fix it in #30357.
comment:132 Changed 2 years ago by
Somehow this broke building documentation on macOS. See #30351.
comment:133 Changed 2 years ago by
I have no idea why this would broke docbuilding, but that's what it looks like. Does anyone have ideas how to debug it? Please discuss at #30351.
Last 10 new commits:
build/pkgs/pybind11: New, dependency of scipy
build/pkgs/cython: Update to 0.29.16
build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern
Update Cython to 0.29.17
build/pkgs/numpy: Update numpy to 1.18.2, back out numpy1.10.2nohardcodeblas.patch (does not apply)
Update numpy to 1.18.4
Update scipy to 1.4.1
build/pkgs/pybind11: New, dependency of scipy
Merge branch 'u/mkoeppe/local_conda_forge_macos_standard__build_error_with_numpy' of trac.sagemath.org:sage into networkx24
update networkx to version 2.4