Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package #29766

dimpase · 2020-05-30T22:21:35Z

Follow-up from the update of numpy to 1.16.6 (#29429):

We update

https://pypi.org/project/numpy/ to 1.19.1 (latest as of 2020-07-21)
https://pypi.org/project/scipy/ to 1.5.2 (latest as of 2020-07-31)
networkx to the latest release, 2.4 (latest as of 2020-07-04)
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]

Depends on #29929

Upstream: Fixed upstream, but not in a stable release.

CC: @antonio-rojas @mkoeppe @kiwifb @isuruf @slel @dcoudert @tscrim @fchapoton @alexjbest

Component: packages: standard

Author: Dima Pasechnik, Matthias Koeppe

Branch: 5d4b013

Reviewer: Travis Scrimshaw, Isuru Fernando, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29766

The text was updated successfully, but these errors were encountered:

dimpase · 2020-06-01T17:52:00Z

Branch: u/dimpase/packages/networkx24

dimpase · 2020-06-01T17:52:00Z

Last 10 new commits:

`fa20111`	`build/pkgs/pybind11: New, dependency of scipy`
`a5c17a8`	`build/pkgs/cython: Update to 0.29.16`
`c7cc999`	`build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern`
`d54b715`	`Update Cython to 0.29.17`
`5958d38`	`build/pkgs/numpy: Update numpy to 1.18.2, back out numpy-1.10.2-no-hardcode-blas.patch (does not apply)`
`0075beb`	`Update numpy to 1.18.4`
`204213d`	`Update scipy to 1.4.1`
`14bcb1f`	`build/pkgs/pybind11: New, dependency of scipy`
`1d5ea9e`	`Merge branch 'u/mkoeppe/local_conda_forge_macos_standard__build_error_with_numpy' of trac.sagemath.org:sage into networkx24`
`2310c79`	`update networkx to version 2.4`

dimpase · 2020-06-01T17:52:00Z

Dependencies: #29425

dimpase · 2020-06-01T17:52:00Z

Commit: 2310c79

dimpase · 2020-06-01T17:52:00Z

Author: Dima Pasechnik

kiwifb · 2020-06-01T21:04:18Z

comment:2

You may get more stuff if you are using scipy 1.4 with that. I patched all the deprecation I could in sage-on-gentoo
https://github.com/cschwan/sage-on-gentoo/blob/master/dev-python/networkx/files/networkx-2.4-scipy-1.4.patch

dimpase · 2020-06-02T09:26:23Z

comment:3

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)

tscrim · 2020-06-03T23:55:14Z

comment:4

Minor (perhaps trivial) point, but pulling it from that link gave a zip file named networkx-networkx-2.4.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 1e-9

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 1e-9

dimpase · 2020-06-04T00:23:04Z

comment:5

Could you post deprecation warnings you get? Cause I thought these were fixed on #29425

tscrim · 2020-06-04T00:25:18Z

comment:6

Both of them are like this:

    doctest:warning
      File "/home/uqtscrim/sage-build/src/bin/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in start
        super(DocTestWorker, self).start()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 112, in start
        self._popen = self._Popen(self)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
        self._launch(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
        code = process_obj._bootstrap()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
        self.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2150, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/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 1e-9
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/graphs/generic_graph.py", line 9877, in pagerank
        dangling=dangling)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/networkx/algorithms/link_analysis/pagerank_alg.py", line 432, in pagerank_scipy
        S = scipy.array(M.sum(axis=1)).flatten()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 19, in call
        stacklevel=stacklevel)
      File "/home/uqtscrim/sage-build/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/sage-build/src/bin/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in start
        super(DocTestWorker, self).start()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 112, in start
        self._popen = self._Popen(self)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
        self._launch(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
        code = process_obj._bootstrap()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
        self.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2150, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/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 1e-9
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/graphs/generic_graph.py", line 9877, in pagerank
        dangling=dangling)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/networkx/algorithms/link_analysis/pagerank_alg.py", line 439, in pagerank_scipy
        x = scipy.repeat(1.0 / N, N)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 19, in call
        stacklevel=stacklevel)
      File "/home/uqtscrim/sage-build/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/sage-build/src/bin/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in start
        super(DocTestWorker, self).start()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 112, in start
        self._popen = self._Popen(self)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
        self._launch(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
        code = process_obj._bootstrap()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
        self.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2150, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/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 1e-9
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/graphs/generic_graph.py", line 9877, in pagerank
        dangling=dangling)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/networkx/algorithms/link_analysis/pagerank_alg.py", line 446, in pagerank_scipy
        p = scipy.repeat(1.0 / N, N)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 19, in call
        stacklevel=stacklevel)
      File "/home/uqtscrim/sage-build/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/sage-build/src/bin/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in start
        super(DocTestWorker, self).start()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 112, in start
        self._popen = self._Popen(self)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
        self._launch(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
        code = process_obj._bootstrap()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
        self.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2150, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/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 1e-9
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/graphs/generic_graph.py", line 9877, in pagerank
        dangling=dangling)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/networkx/algorithms/link_analysis/pagerank_alg.py", line 459, in pagerank_scipy
        is_dangling = scipy.where(S == 0)[0]
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 19, in call
        stacklevel=stacklevel)
      File "/home/uqtscrim/sage-build/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/sage-build/src/bin/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in start
        super(DocTestWorker, self).start()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 112, in start
        self._popen = self._Popen(self)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
        self._launch(process_obj)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
        code = process_obj._bootstrap()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
        self.run()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2150, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/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 1e-9
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/sage/graphs/generic_graph.py", line 9877, in pagerank
        dangling=dangling)
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/networkx/algorithms/link_analysis/pagerank_alg.py", line 467, in pagerank_scipy
        err = scipy.absolute(x - xlast).sum()
      File "/home/uqtscrim/sage-build/local/lib/python3.7/site-packages/scipy/_lib/deprecation.py", line 19, in call
        stacklevel=stacklevel)
      File "/home/uqtscrim/sage-build/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

tscrim · 2020-06-04T00:26:37Z

comment:7

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/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1226, in run
        self.run_doctests()
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 927, in run_doctests
        self.dispatcher.dispatch()
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2011, in dispatch
        self.parallel_dispatch()
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1906, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/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/site-packages/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/site-packages/sage/doctest/forker.py", line 2478, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2527, in _run
        result = runner.run(test)
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 878, in run
        return self._run(test, compileflags, out)
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 680, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/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/site-packages/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/site-packages/decorator.py:decorator-gen-354>", line 2, in minimum_cycle_basis
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/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/site-packages/decorator.py:decorator-gen-353>", line 2, in minimum_cycle_basis
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/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/site-packages/networkx/algorithms/cycles.py", line 525, in minimum_cycle_basis
        nx.connected_component_subgraphs(G)), [])
      File "/home/uqtscrim/sage/local/lib/python3.7/site-packages/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/site-packages/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]]

kiwifb · 2020-06-04T00:30:28Z

comment:8

You shouldn't have this warning with networkx 2.4. It implies you are still using 2.2.

dimpase · 2020-06-04T00:33:08Z

comment:9

I didn't fully merge #29425 into this branch. I can do it (must I?), or leave it to the release manager.

as to the url - I guess it's something to do with GitHub naming of archives.

tscrim · 2020-06-04T00:41:23Z

comment:10

@kiwifb 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.

tscrim · 2020-06-04T00:42:34Z

comment:11

Since the doctests do pass for me with #29425 (and you don't need to merge it in any further I think), positive review.

tscrim · 2020-06-04T00:42:34Z

Reviewer: Travis Scrimshaw

dimpase · 2020-06-04T14:41:04Z

comment:12

Replying to @tscrim:

Minor (perhaps trivial) point, but pulling it from that link gave a zip file named networkx-networkx-2.4.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 --enable-download-from-upstream-url option).

And this automation works for me on Linux. The ULR is copied verbatim from https://github.com/networkx/networkx/releases/tag/networkx-2.4

tscrim · 2020-06-05T00:38:42Z

comment:13

Replying to @dimpase:

Replying to @tscrim:

Minor (perhaps trivial) point, but pulling it from that link gave a zip file named networkx-networkx-2.4.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 --enable-download-from-upstream-url option).

And this automation works for me on Linux. The ULR is copied verbatim from https://github.com/networkx/networkx/releases/tag/networkx-2.4

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.

mkoeppe · 2020-06-06T04:39:40Z

comment:15

From #29425: running the testsuite of networkx requires pytest.

mkoeppe · 2020-07-31T18:47:18Z

comment:115

Replying to @dimpase:

I don't understand that meaning of this poorly half-implemented LISPy thing:
$(PYTHON) decorator | $(PYTHON_TOOLCHAIN) scipy $(and $(filter-out no,$(SAGE_CHECK_networkx)), nose pytest)

It keeps "nose pytest" only when running the networkx test suite is requested.

Because these are testsuite-only dependencies.

dimpase · 2020-07-31T18:49:15Z

comment:116

Replying to @mkoeppe:

Replying to @dimpase:
I don't understand that meaning of this poorly half-implemented LISPy thing:
$(PYTHON) decorator | $(PYTHON_TOOLCHAIN) scipy $(and $(filter-out no,$(SAGE_CHECK_networkx)), nose pytest)
It keeps "nose pytest" only when running the networkx test suite is requested.

Because these are testsuite-only dependencies.

but somehow it does not work in the GH Actions realm (or maybe at all), no?

mkoeppe · 2020-07-31T18:57:12Z

comment:117

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.

mkoeppe · 2020-07-31T18:57:25Z

comment:118

Replying to @dimpase:

anyhow, how about upgrading to scipy 1.5.2 along the way?

Sure, let's do it.

sagetrac-git · 2020-08-01T01:34:37Z

Changed commit from 7fe5985 to 3890e1a

sagetrac-git · 2020-08-01T01:34:37Z

Branch pushed to git repo; I updated commit sha1. New commits:

`5fa0bba`	`build/pkgs/scipy: Update to 1.5.2`
`3890e1a`	`build/make/Makefile.in: Improve handling of SAGE_CHECK_PACKAGES`

mkoeppe · 2020-08-01T01:37:15Z

comment:121

Tests run at https://github.com/mkoeppe/sage/actions/runs/190765555

sagetrac-git · 2020-08-01T23:32:17Z

Changed commit from 3890e1a to 5d4b013

sagetrac-git · 2020-08-01T23:32:17Z

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`

mkoeppe · 2020-08-01T23:45:07Z

comment:125

Replying to @mkoeppe:

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.

That was not quite the right explanation, but now I have fixed it. Subtleties of Makefile variables and who overrides whom.

mkoeppe · 2020-08-01T23:46:01Z

comment:126

Let's please get this in?

dimpase · 2020-08-02T10:20:26Z

comment:127

lgtm

mkoeppe · 2020-08-02T13:36:00Z

comment:128

Thank you!

vbraun · 2020-08-07T19:07:46Z

Changed branch from u/mkoeppe/packages/networkx24 to 5d4b013

jhpalmieri · 2020-08-14T04:03:33Z

comment:130

Why is there no SPKG.rst file for pybind11? Are these suddenly optional?

jhpalmieri · 2020-08-14T04:03:33Z

Changed commit from 5d4b013 to none

mkoeppe · 2020-08-14T16:49:39Z

comment:131

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.

slel · 2020-08-14T18:06:01Z

comment:132

Somehow this broke building documentation on macOS. See #30351.

jhpalmieri · 2020-08-14T23:15:03Z

comment:133

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.

dimpase added this to the sage-9.2 milestone May 30, 2020

dimpase added c: packages: standard labels May 30, 2020

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dimpase changed the title ~~update networkx and fix scipy 1.4 compat warnings~~ update networkx to 2.4 Jun 1, 2020

dimpase added the s: needs review label Jun 1, 2020

tscrim added s: positive review and removed s: needs review labels Jun 4, 2020

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mkoeppe changed the title ~~Upgrade NumPy to 1.19.1, scipy to 1.5.1, networkx to 2.4, add pybind11 package~~ Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package Aug 1, 2020

mkoeppe added s: needs work and removed s: needs review labels Aug 1, 2020

mkoeppe added s: needs review and removed s: needs work labels Aug 1, 2020

dimpase added s: positive review and removed s: needs review labels Aug 2, 2020

vbraun removed the s: positive review label Aug 7, 2020

vbraun closed this as completed in 34e01d1 Aug 7, 2020

embray mentioned this issue Mar 29, 2021

Cygwin: can't build Numpy 1.19.1 with GCC < 8.4 #30392

Closed

Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package #29766

Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package #29766

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