odesolve(...verbose=True) hangs under python 3 #164
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jmuhlich
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Sep 29, 2015
* Remove all verbose=True args to Solver, as verbose mode hangs the Popen communication with BNG for some reason under py3. Fixes pysb#164. * Eliminate direct comparison of Monomer objects in core by comparing their ids instead. * Properly import scipy.integrate in integrate.py rather than rely on an unrelated scipy.weave import just coincidentally making it work. Since weave doesn't exist under py3, the whole thing fell apart. This change necessitated a little refactoring around checking that the user-requested integrator module exists. Fixes pysb#163.
jmuhlich
added a commit
to jmuhlich/pysb
that referenced
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Sep 29, 2015
* Remove all verbose=True args to Solver, as verbose mode hangs the Popen communication with BNG for some reason under py3. Fixes pysb#164. * Eliminate direct comparison of Monomer objects in core by comparing their ids instead. * Properly import scipy.integrate in integrate.py rather than rely on an unrelated scipy.weave import just coincidentally making it work. Since weave doesn't exist under py3, the whole thing fell apart. This change necessitated a little refactoring around checking that the user-requested integrator module exists. Fixes pysb#163.
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Oops, #167 shouldn't close this. Try to remember to reopen after the PR merge auto-closes it. :) |
alubbock
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Oct 1, 2015
* Remove all verbose=True args to Solver, as verbose mode hangs the Popen communication with BNG for some reason under py3. Fixes pysb#164. * Eliminate direct comparison of Monomer objects in core by comparing their ids instead. * Properly import scipy.integrate in integrate.py rather than rely on an unrelated scipy.weave import just coincidentally making it work. Since weave doesn't exist under py3, the whole thing fell apart. This change necessitated a little refactoring around checking that the user-requested integrator module exists. Fixes pysb#163.
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Has this been resolved? Works for me on Python 3.5.2 macOS/homebrew. |
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The full test suite seems to run fine on Python 3.6.4 on macOS for me. There have been a lot of changes to the simulation engine since this issue was filed in September 2015, so I'll presume this has been fixed somewhere along the line. Please reopen if you're still experiencing issues. Thanks. |
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test_integrate.py's test_integrate_with_expression calls
odesolvewith verbose=True, and it seems like the communication with BNG hangs when waiting for the end of the output. This happens on python 3.4.3 on homebrew on the mac I'm using right now, not sure about other platforms yet. There shouldn't be any verbose=True integrator calls in the test suite, so that's the quick fix to make the tests run to completion, but we do need to figure out what's wrong with the verbose=True code in bng.py under python 3 for general usage.The text was updated successfully, but these errors were encountered: