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Piecewise functions #83

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wants to merge 28 commits into from
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Piecewise functions #83

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@tclose tclose commented Jan 27, 2015

This PR addresses issue #74.

In the MathML subset used by SBML you are able to define piecewise functions, which could (probably will) be the long term plan to support this feature. However, in the mean time this PR adds similar functionality to NineML MathInline syntax, copying most of the format from MathML.

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Coverage Status

Coverage increased (+1.05%) to 75.17% when pulling 5b04ba07bb988c2ce1c849d027b8894bc1621024 on tclose:piecewise into 9e5b232 on INCF:master.

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Again, I don't think I can really review this until the refactoring PR is merged.

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tclose commented Feb 3, 2015

No worries, I am testing out the Brunel model now so hopefully I can get
back to you soon.

On 3 February 2015 at 21:32, Andrew Davison [email protected]
wrote:

Again, I don't think I can really review this until the refactoring PR
is merged.

—
Reply to this email directly or view it on GitHub
#83 (comment).

Thomas G. Close, PhD.
Postdoctoral Researcher,
Computational Neuroscience Unit,
Okinawa Institute of Science and Technology
e: [email protected]
w: +81 98 966 8804

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tclose commented Feb 3, 2015

I meant to say that I could rebase them on to the old master if there is a
problem with the refactoring but if there is not a problem it would be
easier to wait until it is merged

On 3 February 2015 at 21:34, Tom Close [email protected] wrote:

No worries, I am testing out the Brunel model now so hopefully I can get
back to you soon.

On 3 February 2015 at 21:32, Andrew Davison [email protected]
wrote:

Again, I don't think I can really review this until the refactoring PR
is merged.

—
Reply to this email directly or view it on GitHub
#83 (comment).

Thomas G. Close, PhD.
Postdoctoral Researcher,
Computational Neuroscience Unit,
Okinawa Institute of Science and Technology
e: [email protected]
w: +81 98 966 8804

Thomas G. Close, PhD.
Postdoctoral Researcher,
Computational Neuroscience Unit,
Okinawa Institute of Science and Technology
e: [email protected]
w: +81 98 966 8804

Tom Close added 26 commits February 6, 2015 10:24
Removed old entries from catalog, which don't match new format
0061f01
added entire old catalog under _archive
bdd03fb
standardized random distribution names
3861fea 
Conflicts:
	catalog/randomdistributions/bernoulli.xml
	catalog/randomdistributions/beta.xml
	catalog/randomdistributions/binomial.xml
	catalog/randomdistributions/cauchy.xml
	catalog/randomdistributions/chi-square.xml
	catalog/randomdistributions/dirichlet.xml
	catalog/randomdistributions/exponential.xml
	catalog/randomdistributions/geometric.xml
	catalog/randomdistributions/hypergeometric.xml
	catalog/randomdistributions/laplace.xml
	catalog/randomdistributions/log-normal.xml
	catalog/randomdistributions/logistic.xml
	catalog/randomdistributions/multinomial.xml
	catalog/randomdistributions/multivariate-normal.xml
	catalog/randomdistributions/multivariate-student-t.xml
	catalog/randomdistributions/negative-binomial.xml
	catalog/randomdistributions/normal-inverse-gamma.xml
	catalog/randomdistributions/normal.xml
	catalog/randomdistributions/pareto.xml
	catalog/randomdistributions/poisson.xml
	catalog/randomdistributions/student-t.xml
	catalog/randomdistributions/uniform.xml
	catalog/randomdistributions/weibull.xml
	catalog/randomdistributions/wishart.xml
renamed _archive to _old_formats to be a little clearer what they are
849301f
moved aliases outside of regime
d380659
updated unit-test to point to new xml path
bd58c6a
edited Izhikevich model in catalog to match NineML paper
98e9d2f
added dimensions and removed unused parameters
f942eaf
removed duplicated units
31c6764
converted Izhikevich model to 2-regime version
7d11603
fixed dimensions in izhikevich model
24720b0
fixed target regime attributes
0b583b3
removed old development version of schema and updated name of EventOut
bf0b845 
to OutputEvent (should have really been part of 'update_schema' PR but
that has been merged now)
copied across the changes made for "constants" and renamed to piecewise
10b2ba0 
(as a shortcut for having to make nearly identical changes for the most
part)
specialising the copied code for piecewise functions
2801972
added piecewise structures to xml reader/writer
240d320
implemented rhs_atoms for piecewise objects
1b4c9e0
added unit testing structure for piecewise tests
38f9222
fixing bugs with constructors, rhs_atoms and unit tests for piecewise
4b34f6a 
functions
updating piecewise test
37833e8
added piecewise xml test
01119d5
debugging piecewise xml roundtrip
0297a28
fixed xml write name for Piece
afa3951
piecewise passes xml roundtrip
1e0e28c
removed mistaken attributes with units addition
03d8c96
debugged various handling of piecewise objects
b857bee
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Coverage Status

Coverage decreased (-0.08%) to 76.19% when pulling 48d92e7 on tclose:piecewise into 86967a9 on INCF:master.

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tclose commented Mar 22, 2015

Will reopen this in the new lib9ML repository

@tclose tclose closed this Mar 22, 2015
@tclose tclose deleted the piecewise branch April 6, 2015 04:45
@tclose tclose mentioned this pull request May 26, 2015
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@tclose @coveralls @apdavison