Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#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: sage-9.2
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:

Status badges

Description (last modified by mkoeppe)

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

We update

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 dimpase

  • Authors set to Dima Pasechnik
  • 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

Last 10 new commits:

fa20111build/pkgs/pybind11: New, dependency of scipy
a5c17a8build/pkgs/cython: Update to 0.29.16
c7cc999build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern
d54b715Update Cython to 0.29.17
5958d38build/pkgs/numpy: Update numpy to 1.18.2, back out numpy-1.10.2-no-hardcode-blas.patch (does not apply)
0075bebUpdate numpy to 1.18.4
204213dUpdate scipy to 1.4.1
14bcb1fbuild/pkgs/pybind11: New, dependency of scipy
1d5ea9eMerge branch 'u/mkoeppe/local_conda_forge_macos_standard__build_error_with_numpy' of trac.sagemath.org:sage into networkx24
2310c79update networkx to version 2.4

comment:2 Changed 2 years ago by fbissey

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

comment:3 Changed 2 years ago by dimpase

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 follow-up: Changed 2 years ago by 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.

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

comment:5 Changed 2 years ago by dimpase

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

comment:6 Changed 2 years ago by tscrim

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

comment:7 Changed 2 years ago by tscrim

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]]

comment:8 Changed 2 years ago by fbissey

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 dimpase

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.

Last edited 2 years ago by dimpase (previous) (diff)

comment:10 Changed 2 years ago by tscrim

@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 tscrim

  • 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 ; follow-up: Changed 2 years ago by 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

comment:13 in reply to: ↑ 12 Changed 2 years ago by tscrim

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.

comment:14 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:15 follow-up: Changed 2 years ago by mkoeppe

  • 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 mkoeppe

Replying to mkoeppe:

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

I'll add pytest in #29813.

comment:17 Changed 2 years ago by mkoeppe

  • Dependencies changed from #29425 to #29425, #29813
  • Description modified (diff)

comment:18 Changed 2 years ago by mkoeppe

  • Branch changed from u/dimpase/packages/networkx24 to u/mkoeppe/packages/networkx24

comment:19 Changed 2 years ago by git

  • Commit changed from 2310c79596838489831ffd1eb55b8ada4ac6784d to e592bdc05120fdb91069cfc61c3ce2f82d45ace2

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

9a3617dbuild/pkgs/cython: Update to 0.29.16
4a606b6build/pkgs/cython/checksums.ini: Use predictable URL for upstream_url pattern
e9a7cb0Update Cython to 0.29.17
15911cbbuild/pkgs/numpy: Update numpy to 1.18.2, back out numpy-1.10.2-no-hardcode-blas.patch (does not apply)
96e7a41Update numpy to 1.18.4
78b4907Update scipy to 1.4.1
54595b0build/pkgs/pybind11: New, dependency of scipy
c005562suppress scipy deprecation warnings
56a6fe1build/pkgs/numpy: Update to 1.18.5
e592bdcMerge 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 mkoeppe

Merged in updated #29425 and #29813.

comment:22 Changed 2 years ago by mkoeppe

  • Status changed from needs_work to needs_review

comment:23 Changed 2 years ago by mkoeppe

  • Authors changed from Dima Pasechnik to Dima Pasechnik, Matthias Koeppe

comment:24 Changed 2 years ago by mkoeppe

  • Status changed from needs_review to needs_work

#29813 needs to be fixed.

comment:25 Changed 2 years ago by mkoeppe

  • 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 mkoeppe

Merged ticket #29425 into this ticket because #29245 could not be separately tested because of networkx 2.2 testsuite errors triggered by updates.

Last edited 2 years ago by mkoeppe (previous) (diff)

comment:27 Changed 2 years ago by git

  • Commit changed from e592bdc05120fdb91069cfc61c3ce2f82d45ace2 to 11bf67f601c626d62aa8896a3a20342e7b2d4318

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

bedc7aebuild/make/Makefile.in: Allow pip packages as dependencies
11bf67fMerge branch 't/29813/add_pytest_as_a_type_optional__source_pip_package' into t/29766/packages/networkx24

comment:28 Changed 2 years ago by mkoeppe

  • Status changed from needs_work to needs_review

comment:29 Changed 2 years ago by mkoeppe

Tests at https://github.com/mkoeppe/sage/actions/runs/128112212:

On ubuntu-eoan-standard (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 mkoeppe

Failure on cygwin-standard (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 mkoeppe

The int64_t issue is fixed in https://github.com/scipy/scipy/pull/11320 for the upcoming 1.5.0, marked "backport-candidate", but so far no 1.4.x with the fix has been released...

comment:32 Changed 2 years ago by git

  • Commit changed from 11bf67f601c626d62aa8896a3a20342e7b2d4318 to db0fa417db01ade8efb1b7c616ec53c7269d94d8

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

db0fa41build/pkgs/scipy: Add patch for scipy pr 11320

comment:33 Changed 2 years ago by mkoeppe

  • Cc dcoudert added

comment:34 Changed 2 years ago by mkoeppe

  • Cc tscrim chapoton added

comment:35 Changed 2 years ago by tscrim

Everything builds and works for me on Ubuntu.

comment:36 Changed 2 years ago by dimpase

  • Status changed from needs_review to positive_review

lgtm

comment:37 Changed 2 years ago by mkoeppe

Comment 29 is unresolved

comment:38 Changed 2 years ago by dimpase

a package fails its own testsuite. it's not the 1st one (happens on Gentoo as well)

comment:39 Changed 2 years ago by mkoeppe

OK, good to know. No objection then

comment:40 Changed 2 years ago by slelievre

  • Description modified (diff)

comment:41 Changed 2 years ago by vbraun

  • 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/sage-runtests", line 178, in <module>
        err = DC.run()
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1231, in run
        self.run_doctests()
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 931, in run_doctests
        self.dispatcher.dispatch()
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2045, in dispatch
        self.parallel_dispatch()
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1940, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/release/Sage/local/lib/python3.7/site-packages/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/site-packages/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/site-packages/sage/doctest/forker.py", line 2513, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2562, in _run
        result = runner.run(test)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 912, in run
        return self._run(test, compileflags, out)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 707, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/release/Sage/local/lib/python3.7/site-packages/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/site-packages/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 --warn-long 37.2 src/sage/modular/modform_hecketriangle/abstract_space.py  # 2 doctests failed
----------------------------------------------------------------------

comment:42 Changed 2 years ago by fbissey

This looks strange. I have done a test run of sage 9.2.beta2 with numpy-1.19/scipy-1.5/networkx-2.4 in sage-on-gentoo and I have seen no such things [in fact the number of doctest failures in sage-on-gentoo 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 arojas

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 dimpase

oh dear. ok, we can suppress these, too

comment:45 follow-up: Changed 2 years ago by slelievre

From the SciPy 1.5.1 Release Notes:

SciPy 1.5.1 is a bug-fix 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 mkoeppe

  • Description modified (diff)

comment:47 Changed 2 years ago by git

  • Commit changed from db0fa417db01ade8efb1b7c616ec53c7269d94d8 to a2e19785a2c670ba165905c78498a841e2b1ded4

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

2efe841Merge tag '9.2.beta3' into t/29766/packages/networkx24
634ce73build/pkgs: Update numpy to 1.19, scipy to 1.5.1
a2e1978build/pkgs/scipy/patches/pr-11320.patch: Remove

comment:49 Changed 2 years ago by mkoeppe

  • 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 follow-up: Changed 2 years ago by mkoeppe

The warnings.filterwarnings issue needs to be addressed

comment:51 Changed 2 years ago by dimpase

  • Description modified (diff)

comment:52 Changed 2 years ago by dimpase

  • Description modified (diff)

comment:53 in reply to: ↑ 45 Changed 2 years ago by dimpase

Replying to slelievre:

From the SciPy 1.5.1 Release Notes:

SciPy 1.5.1 is a bug-fix 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 dimpase

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 dimpase

Currently it is

  • build/pkgs/numpy/checksums.ini

    a b  
    11tarball=numpy-VERSION.tar.gz
    2 sha1=0b1792c8a828d6a9fb148fb33dfa11549391d858
    3 md5=3f5ce88a859302f0a1aceb5f75b563fc
    4 cksum=1603544858
     2sha1=a6c099c0929e0b437a72fd60aad76d23061087c6
     3md5=e3baa59da67348c2d6596803514129db
     4cksum=1607167529
    55upstream_url=https://github.com/numpy/numpy/releases/download/vVERSION/numpy-VERSION.tar.gz

but of course it's not really stable...

comment:56 Changed 2 years ago by dimpase

And now md5 as advertised on Numpy pages:

  • build/pkgs/numpy/checksums.ini

    a b  
    11tarball=numpy-VERSION.tar.gz
    2 sha1=0b1792c8a828d6a9fb148fb33dfa11549391d858
    3 md5=3f5ce88a859302f0a1aceb5f75b563fc
    4 cksum=1603544858
     2sha1=ba35592527bd01f53244ae1bb55c896101bbf0f3
     3md5=d59aadf47354bd10c7b9996032ba4da0
     4cksum=3500020755

Sucks.

comment:57 Changed 2 years ago by git

  • Commit changed from a2e19785a2c670ba165905c78498a841e2b1ded4 to 0879c3b5f25ac5eb68e6a4317433f8ff670934d7

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

0879c3bbuild/pkgs/{numpy,scipy}/checksums.ini: Set upstream_url to pypi.io

comment:58 Changed 2 years ago by mkoeppe

Hopefully the sources packages on PyPI are more stable.

comment:59 Changed 2 years ago by mkoeppe

  • Priority changed from major to critical

comment:60 in reply to: ↑ 50 ; follow-up: Changed 2 years ago by dimpase

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, 
    8787# Ignore all deprecations from IPython etc.
    8888warnings.filterwarnings('ignore', category=DeprecationWarning,
    8989    module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic|jedi)')
     90warnings.filterwarnings('ignore', category=DeprecationWarning,
     91    module='.*(scipy|networkx)')
    9092# Ignore collections.abc warnings, there are a lot of them but they are
    9193# harmless.
    9294warnings.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): 
    881881        #             and will be removed in SciPy 2.0.0, use numpy.array instead
    882882        # This affects networkx 2.2 up and including 2.4
    883883        # We filter them out here:
    884         warnings.filterwarnings('ignore', '.*Deprec.*scipy.*instead',) # cf trac #29425
     884 #       warnings.filterwarnings('ignore', '.*Deprec.*scipy.*instead',) # cf trac #29425
    885885
    886886        warnings.showwarning = showwarning_with_traceback
    887887        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 ; follow-up: Changed 2 years ago by arojas

Basically, we already did suppression of deprecation warnings from other packages right, now the same has to be done for scipy and networkx

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 dimpase

Replying to arojas:

Basically, we already did suppression of deprecation warnings from other packages right, now the same has to be done for scipy and networkx

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='.*(scipy|networkx)' 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 dimpase

needless to say, each upgrade to scipy|networkx will need to re-evaluate these.

We should add something to the Developer manual on this.

comment:64 Changed 2 years ago by dimpase

  • 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:

8a70eberight place for warnings.filterwarnings() for networkx & scipy

comment:65 Changed 2 years ago by mkoeppe

  • Dependencies changed from #29480, #29813 to #29480, #29813, #30118

comment:66 Changed 2 years ago by mkoeppe

  • Branch changed from u/dimpase/packages/networkx24 to u/mkoeppe/packages/networkx24

comment:67 Changed 2 years ago by mkoeppe

  • Commit changed from 8a70ebedcf063d0a77564c01537a9600dd2accda to 0356be918ab0c9ed20347360db5eed7b94ab697b
  • Dependencies changed from #29480, #29813, #30118 to #29480, #29813, #29929, #30118

Last 10 new commits:

b7bf43bbuild/bin/write-dockerfile.sh: ADD src/bin for bootstrapping, needed by src/doc/bootstrap after #29884
365ce61Merge branch 'u/mkoeppe/fix_tox_docker_builds_broken_by__29884' of git://trac.sagemath.org/sage into HEAD
fb61a31Merge 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+ci-fixes
bfb2fb4tox.ini: Add environment local-homebrew-usrlocal
aded967Merge commit '8195cb821e01e0cb627240d7135d5634c265cab0' of git://trac.sagemath.org/sage into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
07d657dMerge tag '9.2.beta4' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
bd15fb9build/bin/write-dockerfile.sh, tox.ini: Do not run testsuites that need pip (ssl)
25393b0Handle SAGE_CHECK_PACKAGES in build/make/Makefile.in, not sage-spkg
5aca238Merge 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
0356be9Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24

comment:68 Changed 2 years ago by mkoeppe

  • 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:70 Changed 2 years ago by git

  • Commit changed from 0356be918ab0c9ed20347360db5eed7b94ab697b to 6954debc04519488cc4b8f299166797fe95eb204

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

6954debbuild/pkgs/networkx/dependencies: Conditionalize on SAGE_CHECK_networkx

comment:71 Changed 2 years ago by mkoeppe

Tests as part of Meta-ticket #29456 (Support gcc/gfortran 10) at https://github.com/mkoeppe/sage/actions/runs/167913617

On debian-jessie-standard (https://github.com/mkoeppe/sage/runs/866989168) and debian-jessie-minimal:

gcc: build/src.linux-x86_64-3.7/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’ [-Wimplicit-function-declaration]
     __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’ [-Wimplicit-function-declaration]
     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 mkoeppe

debian-jessie uses gcc version 4.9.2 (Debian 4.9.2-10+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:74 Changed 2 years ago by mkoeppe

  • Report Upstream changed from N/A to Reported upstream. No feedback yet.

comment:75 Changed 2 years ago by mkoeppe

Let's go back to 1.18.5 (released Jun 3, 2020).

comment:76 Changed 2 years ago by git

  • Commit changed from 6954debc04519488cc4b8f299166797fe95eb204 to d39817fe52d756382d33e21da4866939fbfff571

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

d39817fbuild/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie

comment:77 Changed 2 years ago by mkoeppe

  • 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:80 Changed 2 years ago by mkoeppe

In these tests, fedora-32-standard uses gcc/gfortran 10 from the system, fedora-32-minimal uses gcc 10 from the system and gfortran from spkg, and the various homebrew-macos 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 mkoeppe

On local-conda-forge-macos-maximal (https://github.com/mkoeppe/sage/runs/867731009), numpy 1.18.5 builds but building sagelib fails as follows:

  [sagelib-9.2.beta5] error installing, exit status 1. End of log file:
  [sagelib-9.2.beta5]       from . import core
  [sagelib-9.2.beta5]     File "/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-maximal/local/lib/python3.7/site-packages/numpy/core/__init__.py", line 50, in <module>
  [sagelib-9.2.beta5]       raise ImportError(msg)
  [sagelib-9.2.beta5]   ImportError: 
  [sagelib-9.2.beta5]   
  [sagelib-9.2.beta5]   IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
  [sagelib-9.2.beta5]   
  [sagelib-9.2.beta5]   Importing the numpy C-extensions failed. This error can happen for
  [sagelib-9.2.beta5]   many reasons, often due to issues with your setup or how NumPy was
  [sagelib-9.2.beta5]   installed.
...
  [sagelib-9.2.beta5]   Original error was: dlopen(/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-maximal/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Symbol not found: _aheapsort_bool
  [sagelib-9.2.beta5]     Referenced from: /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-maximal/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
  [sagelib-9.2.beta5]     Expected in: flat namespace
  [sagelib-9.2.beta5]    in /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-maximal/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so

Also building matplotlib fails with a similar error.

Last edited 2 years ago by mkoeppe (previous) (diff)

comment:82 Changed 2 years ago by mkoeppe

  • Report Upstream changed from Reported upstream. No feedback yet. to Reported upstream. Developers acknowledge bug.

comment:83 Changed 2 years ago by mkoeppe

numpy 1.19 had worked OK on local-conda-forge-macos when that was tested (https://github.com/mkoeppe/sage/runs/858960241).

comment:85 Changed 2 years ago by git

  • Commit changed from d39817fe52d756382d33e21da4866939fbfff571 to 355873714763fe9df4955af6d31e5725e4f64c0d

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

fcddf69Revert "build/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie"
3558737build/pkgs/numpy/patches/16871.patch: New

comment:87 Changed 2 years ago by mkoeppe

Unfortunately the patch does not apply by itself

comment:88 Changed 2 years ago by mkoeppe

Running tests with numpy master + pr-16871 at https://github.com/mkoeppe/sage/actions/runs/169620460

comment:89 Changed 2 years ago by mkoeppe

  • 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 mkoeppe

https://github.com/numpy/numpy/pull/16871 has been merged in numpy master. Hoping for a backport

comment:91 Changed 2 years ago by alexjbest

  • Cc alexjbest added

comment:92 Changed 2 years ago by dimpase

there are more deprecation warnings to suppress, e.g.

2020-07-15T10:18:00.4452989Z File "src/sage/calculus/interpolators.pyx", line 48, in sage.calculus.interpolators.polygon_spline
2020-07-15T10:18:00.4453182Z Failed example:
2020-07-15T10:18:00.4453370Z     ps = polygon_spline(pts)
2020-07-15T10:18:00.4453562Z Expected nothing
2020-07-15T10:18:00.4453746Z Got:
2020-07-15T10:18:00.4453928Z     doctest:warning
2020-07-15T10:18:00.4454284Z       File "/sage/src/bin/sage-runtests", line 177, in <module>
2020-07-15T10:18:00.4454494Z         err = DC.run()
2020-07-15T10:18:00.4454877Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1207, in run
2020-07-15T10:18:00.4455104Z         self.run_doctests()
2020-07-15T10:18:00.4455498Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 908, in run_doctests
2020-07-15T10:18:00.4455721Z         self.dispatcher.dispatch()
2020-07-15T10:18:00.4456125Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2039, in dispatch
2020-07-15T10:18:00.4456344Z         self.parallel_dispatch()
2020-07-15T10:18:00.4456736Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1934, in parallel_dispatch
2020-07-15T10:18:00.4456963Z         w.start()  # This might take some time
2020-07-15T10:18:00.4457348Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2206, in start
2020-07-15T10:18:00.4457571Z         super(DocTestWorker, self).start()
2020-07-15T10:18:00.4457778Z       File "/sage/local/lib/python3.7/multiprocessing/process.py", line 112, in start
2020-07-15T10:18:00.4457985Z         self._popen = self._Popen(self)
2020-07-15T10:18:00.4458194Z       File "/sage/local/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
2020-07-15T10:18:00.4458409Z         return _default_context.get_context().Process._Popen(process_obj)
2020-07-15T10:18:00.4458621Z       File "/sage/local/lib/python3.7/multiprocessing/context.py", line 277, in _Popen
2020-07-15T10:18:00.4458822Z         return Popen(process_obj)
2020-07-15T10:18:00.4459027Z       File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
2020-07-15T10:18:00.4459245Z         self._launch(process_obj)
2020-07-15T10:18:00.4459447Z       File "/sage/local/lib/python3.7/multiprocessing/popen_fork.py", line 74, in _launch
2020-07-15T10:18:00.4459645Z         code = process_obj._bootstrap()
2020-07-15T10:18:00.4459852Z       File "/sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
2020-07-15T10:18:00.4460066Z         self.run()
2020-07-15T10:18:00.4460446Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2178, in run
2020-07-15T10:18:00.4461480Z         task(self.options, self.outtmpfile, msgpipe, self.result_queue)
2020-07-15T10:18:00.4462380Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2507, in __call__
2020-07-15T10:18:00.4462669Z         doctests, extras = self._run(runner, options, results)
2020-07-15T10:18:00.4463154Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2553, in _run
2020-07-15T10:18:00.4463441Z         result = runner.run(test)
2020-07-15T10:18:00.4463902Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 906, in run
2020-07-15T10:18:00.4464158Z         return self._run(test, compileflags, out)
2020-07-15T10:18:00.4464793Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 707, in _run
2020-07-15T10:18:00.4465103Z         self.compile_and_execute(example, compiler, test.globs)
2020-07-15T10:18:00.4465621Z       File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1132, in compile_and_execute
2020-07-15T10:18:00.4465963Z         exec(compiled, globs)
2020-07-15T10:18:00.4466212Z       File "<doctest sage.calculus.interpolators.polygon_spline[1]>", line 1, in <module>
2020-07-15T10:18:00.4466479Z         ps = polygon_spline(pts)
2020-07-15T10:18:00.4466937Z       File "/sage/local/lib/python3.7/site-packages/numpy/__init__.py", line 237, in __getattr__
2020-07-15T10:18:00.4467232Z         warnings.warn(msg, DeprecationWarning, stacklevel=2)
2020-07-15T10:18:00.4467504Z       File "/sage/local/lib/python3.7/warnings.py", line 110, in _showwarnmsg
2020-07-15T10:18:00.4467750Z         msg.file, msg.line)
2020-07-15T10:18:00.4468009Z     :
2020-07-15T10:18:01.5210352Z     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 mkoeppe

these deprecation warnings are coming from numpy master, they will not hit us now, only later

comment:94 Changed 2 years ago by mkoeppe

numpy 1.19.1 is out but unfortunately does not have a backport of ​https://github.com/numpy/numpy/pull/16871

Last edited 2 years ago by mkoeppe (previous) (diff)

comment:95 Changed 2 years ago by mkoeppe

However, thanks to other backported fixes, the pull request is now easier to apply.

comment:96 Changed 2 years ago by mkoeppe

  • Dependencies changed from #29480, #29813, #29929, #30118 to #29480, #29813, #29929, #30118, #29861

numpy 1.19.1 needs newest Cython (#29861)

Last edited 2 years ago by mkoeppe (previous) (diff)

comment:97 Changed 2 years ago by git

  • Commit changed from 355873714763fe9df4955af6d31e5725e4f64c0d to 061e975e3116d390b6faf6ca37f942512964dab5

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

1bf6249Update numpy to 1.19.1, add patches
c24d109build/pkgs/cython: Updatt to 0.29.21
061e975Merge branch 'u/mkoeppe/upgrade_cython_to_0_29_20' of git://trac.sagemath.org/sage into t/29766/packages/networkx24

comment:98 Changed 2 years ago by mkoeppe

  • 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:100 follow-up: Changed 2 years ago by mkoeppe

I see a number of doctest failures related to printing of deprecation warnings. Did something on this ticket cause this? For example (on ubuntu-trusty-standard, 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/sage-runtests", line 177, in <module>
        err = DC.run()
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1207, in run
        self.run_doctests()
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 908, in run_doctests
        self.dispatcher.dispatch()
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2045, in dispatch
        self.parallel_dispatch()
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1940, in parallel_dispatch
        w.start()  # This might take some time
      File "/sage/local/lib/python3.7/site-packages/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/site-packages/sage/doctest/forker.py", line 2184, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2513, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2559, in _run
        result = runner.run(test)
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 912, in run
        return self._run(test, compileflags, out)
      File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 707, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/sage/local/lib/python3.7/site-packages/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/site-packages/sage/structure/unique_representation.py", line 1008, in __classcall__
        instance = typecall(cls, *args, **options)
      File "/sage/local/lib/python3.7/site-packages/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/site-packages/sage/misc/superseded.py", line 181, in experimental_warning
        warning(trac_number, message, FutureWarning, stacklevel)
      File "/sage/local/lib/python3.7/site-packages/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 git

  • Commit changed from 061e975e3116d390b6faf6ca37f942512964dab5 to fc7592cdafb6ed3b1d947faeeb67841c3491e843

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

d1a2cbfMerge branch 't/30088/fix__make_sdist___add_test_run_to_github_actions' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
b62f775Merge tag '9.2.beta6' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
fc7592cMerge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24

comment:102 Changed 2 years ago by mkoeppe

  • 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 dimpase

Replying to mkoeppe:

I see a number of doctest failures related to printing of deprecation warnings. Did something on this ticket cause this?

https://git.sagemath.org/sage.git/diff/src/sage/doctest/forker.py?id=fc7592cdafb6ed3b1d947faeeb67841c3491e843&id2=ddaba54f6d69276ed1b9c60193ace839542eb5a9

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:105 Changed 2 years ago by git

  • Commit changed from fc7592cdafb6ed3b1d947faeeb67841c3491e843 to 7fe59852445ff75037fcdc3dd0ae42070fe0c5ed

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

7fe5985right place for warnings.filterwarnings() for networkx & scipy

comment:107 Changed 2 years ago by vdelecroix

  • Description modified (diff)

scipy 1.5.2 is now available.

comment:108 Changed 2 years ago by vdelecroix

I report that compilation succeeded with gcc 10.1.0 and this ticket merged.

comment:109 Changed 2 years ago by mkoeppe

I think this is good to go. Reviewers?

comment:110 Changed 2 years ago by vdelecroix

Don't you want to make the upgrade scipy 1.5.1 -> 1.5.2?

comment:111 follow-up: Changed 2 years ago by dimpase

self-tests of networkx need pytest, but logs show that pytest might bot be installed. I don't understand the meaning of this poorly half-implemented LISPy thing:

$(PYTHON) decorator | $(PYTHON_TOOLCHAIN) scipy $(and $(filter-out no,$(SAGE_CHECK_networkx)), nose pytest)

Last edited 2 years ago by dimpase (previous) (diff)

comment:112 follow-up: Changed 2 years ago by mkoeppe

which log? link please

comment:113 in reply to: ↑ 112 Changed 2 years ago by dimpase

comment:114 follow-up: Changed 2 years ago by dimpase

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

comment:115 in reply to: ↑ 111 ; follow-up: Changed 2 years ago by 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.

comment:116 in reply to: ↑ 115 Changed 2 years ago by dimpase

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?

comment:117 follow-up: Changed 2 years ago by mkoeppe

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 mkoeppe

Replying to dimpase:

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

Sure, let's do it.

comment:119 Changed 2 years ago by mkoeppe

  • 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 git

  • Commit changed from 7fe59852445ff75037fcdc3dd0ae42070fe0c5ed to 3890e1a1540abeecc2d9e8898e8463dea42c9547

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

5fa0bbabuild/pkgs/scipy: Update to 1.5.2
3890e1abuild/make/Makefile.in: Improve handling of SAGE_CHECK_PACKAGES

comment:122 Changed 2 years ago by mkoeppe

  • Status changed from needs_review to needs_work

comment:123 Changed 2 years ago by git

  • Commit changed from 3890e1a1540abeecc2d9e8898e8463dea42c9547 to 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b

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

5d4b013build/make/Makefile.in: Handle the case in which SAGE_CHECK_PACKAGES is set using a command argument

comment:124 Changed 2 years ago by mkoeppe

  • Status changed from needs_work to needs_review

comment:125 in reply to: ↑ 117 Changed 2 years ago by mkoeppe

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.

comment:126 Changed 2 years ago by mkoeppe

Let's please get this in?

comment:127 Changed 2 years ago by dimpase

  • Status changed from needs_review to positive_review

lgtm

comment:128 Changed 2 years ago by mkoeppe

Thank you!

comment:129 Changed 2 years ago by vbraun

  • Branch changed from u/mkoeppe/packages/networkx24 to 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:130 follow-up: Changed 2 years ago by jhpalmieri

  • Commit 5d4b013d64a18a7b8eb5d4aa91c26cf01828cb6b deleted

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

Last edited 2 years ago by jhpalmieri (previous) (diff)

comment:131 in reply to: ↑ 130 Changed 2 years ago by mkoeppe

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 slelievre

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

comment:133 Changed 2 years ago by jhpalmieri

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.

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