phraSED-ML Activity
Paraphrased Human-Readable Adaptation of SED-ML
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luciansmith
Activity for phraSED-ML
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Lucian Smith created ticket #26
Move to github
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Update python setup so that the wheel file it creates will be platform-specific.
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Deepa posted a comment on ticket #25
Hi Matthias, Sorry for the delay in updating here. I was able to use the virtualenv and get it running.
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Update canonical output files to SED-ML v3, instead of v2 (using latest libsedml). Also update one error message because the default number writing algorithm in C++ seems to have changed back to using only two digits for exponents instead of always three (i.e. '1e-10' vs. '1e-010').
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Matthias König posted a comment on ticket #25
Hi Deepa, unfortunately the complete tellurium/roadrunner stack is not running on python 3.7 yet. To track the progress see https://sourceforge.net/p/phrasedml/tickets/25/ https://sourceforge.net/p/antimony/bug-reports/49/ https://github.com/sys-bio/roadrunner/issues/505 https://github.com/sys-bio/tellurium/issues/417 This affects many downstream projects, e.g., https://github.com/matthiaskoenig/sbmlutils/issues/113 In my opinion this is a major issue and should be solved asap. Basically anaconda...
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Hi, Is this issue resolved now? I get the same error that is reported above while trying to install phrasedml on python 3.7.
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Kyle Medley committed [r105]
disable swigdoc
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use namespaces for libsbml and libsedml
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Support for python 3.7 (pip packages)
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bump ver to 1.0.10
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Squashed commit of the following:
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Squashed commit of the following:
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Squashed commit of the following:
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Squashed commit of the following:
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I just made a commit to this repo that should fix this. The fix is available in PhraSEDML 1.0.8, just uploaded to PyPI for win/mac/lin 64-bit.
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bump ver to 1.0.8
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fix https://sourceforge.net/p/phrasedml/tickets/24/
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Phrasedml with URNs broken
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lsoda is 88
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bump ver to 1.0.7
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add initialConcentration selector
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add lsoda phrasedml name
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add lsoda to phrasedml algo names
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add else block
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fix xml extension not being applied in some cases
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fix for jws quirks
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bump ver to 1.0.6
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Add functional range support for pulse experiment
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add .gitignore
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I fixed this in phrasedml 1.0.5 via a string substitution hack. There doesn't seem...
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add hack to fix min/max symbol encodings. see h...
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bump ver to 1.0.5
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allow making model changes via xpath
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Matthias, are you able to read SED-ML with the special csymbol definitions using...
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fix version
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add linux/osx shared libs to python package
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remove v from __version__ and add myself to aut...
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bump version to 1.0.4
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use relative imports (should work for py2/3)
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use correct flags for linux
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dyn binding on osx/linux
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add my name to authors since I am creating the ...
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The problem is that it is written in the specs ;) Just make a bad hack without thinking...
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Phew, that's a problem. The encoding of min and max is very low level, and uses libsbml's...
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Hi Lucian, this is a really critical issue. If you fix anything than please this....
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phraSED-ML released /1.0/phrasedml_python_setup_1.0.3.zip
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Kiri Choi committed [r74]
Update setup.py
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Added example files
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Get rid of .pth file
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Closing this as 'wontfix', since we're encouraging people to use alternate methods...
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Support XMLChanges
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That certainly works for me! A further argument in favor of not trying to support...
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Perfect. So in my opinion we should drop XMLChange support in tellurium/phrasedml...
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add conda files
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As you suspected, the issue is with the asterisk, which means 'Use this model as...
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Perfect. This works great and solves lots of issues in tellurium & with round trips....
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Version number not consistent between pip and python
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I am handling the max in the current form. But the current encoding could be the...
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Hi Lucian, this works great for the given example. I tried a bit more complex case...
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As a workaround, I would suggest doing this with modular Antimony: model one() const...
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SEDML encoding bugs: Max/min function encoding & id on curves
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The curves (and surfaces) now have useless ID's ;-) The max/min thing is going to...
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XPath expressions very unspecific
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I went ahead and looked into making this more specific, and discovered that in most...
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Write out more explicit XPaths, so that people ...
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SEDML encoding bugs: Max/min function encoding & id on curves
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Support XMLChanges
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This can be changed to won't fix. I can handle this via tellurium. Unfortunately,...
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Everything working. Finally no more timestamps ;) This can be closed.
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Thanks! Tested on Mac and works.
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This was caused by a mismatch in function names between the header file and the .cpp...
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Undefined functions break Python API
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This was caused by a mismatch between the function name in the header file vs. the...
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Fixed the name of the function in the header fi...
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Undefined functions break Python API
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comment undefined function setPhrasedWriteSBMLT...
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Hi Lucian, builds, but when trying to import the python bindings I get undefined...
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Now that libSBML allows this (and, via it, libSEDML), SVN now will not write out...
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No timestamp when creating SEDML
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Increase release number to 1.0.3; allow non-tim...
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XPath expressions very unspecific
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Don't think this is a good idea. There should be much more math allowed on calculating...
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Can be closed. Is an SBML issue.
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Added documentation about the change, as well. New version is 1.0.2
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.xml extension missing if model source is SBML file
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Update documentation.
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Updated docs to mention new API function; updat...
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Iterating multiple tasks over local variable creates invalid SEDML
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Great--thanks for testing!
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Moving on to https://groups.google.com/forum/#!topic/libsbml-development/Yy78LSw...
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perfect. Works like a charm. sedmlStr = phrasedml.convertString(phrasedmlStr) # necessary...
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Solved. Build works and problem solved. thanks. Can be closed.
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Not sure if this is a C++11 incompatibility or not, but at any rate, just checked...
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Apparently 'erase' behaves differently on some ...
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.xml extension missing if model source is SBML file
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OK, this is in! You'll need to do something like the following to get it to work...
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New API function for Mattias: a way to add '.x...
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`stiff` is not a supported keyword for AlgorithmParameter
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Great! Let me know if you run into more issues.
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