- Fix MultiState species reading from BNG
Add unit test to ensure network generation and species readback from BNG works.
- Add multibonds unit test for BNG
alubbock
Showing 2 of 2 files from the diff.
pysb/bng.py
changed.
pysb/tests/test_bng.py
changed.
@@ -807,7 +807,7 @@
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| 807 | 807 | site_name, condition = ss, None |
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| 808 | 808 | site_conditions[site_name].append(condition) |
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| 809 | 809 | ||
| 810 | - | site_conditions = {k: v[0] if len(v) == 1 else tuple(v) |
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| 810 | + | site_conditions = {k: v[0] if len(v) == 1 else pysb.core.MultiState(*v) |
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| 811 | 811 | for k, v in site_conditions.items()} |
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| 812 | 812 | monomer = model.monomers[monomer_name] |
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| 813 | 813 | monomer_compartment = model.compartments.get(monomer_compartment_name) |
@@ -1,5 +1,6 @@
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| 1 | 1 | from pysb.testing import * |
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| 2 | 2 | from pysb import * |
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| 3 | + | from pysb.core import as_complex_pattern |
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| 3 | 4 | from pysb.bng import * |
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| 4 | 5 | import os |
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| 5 | 6 | import unittest |
@@ -218,6 +219,42 @@
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| 218 | 219 | assert num_non_zeros == 0 |
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| 219 | 220 | ||
| 220 | 221 | ||
| 222 | + | @with_model |
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| 223 | + | def test_multistate(): |
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| 224 | + | Monomer('A', ['a', 'a'], {'a': ['u', 'p']}) |
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| 225 | + | Parameter('k1', 100) |
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| 226 | + | Parameter('A_0', 200) |
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| 227 | + | Rule('r1', None >> A(a=MultiState('u', 'p')), k1) |
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| 228 | + | Initial(A(a=MultiState(('u', 1), 'p')) % |
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| 229 | + | A(a=MultiState(('u', 1), 'u')), A_0) |
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| 230 | + | ||
| 231 | + | generate_equations(model) |
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| 232 | + | ||
| 233 | + | assert model.species[0].is_equivalent_to( |
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| 234 | + | A(a=MultiState(('u', 1), 'p')) % A(a=MultiState(('u', 1), 'u'))) |
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| 235 | + | assert model.species[1].is_equivalent_to( |
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| 236 | + | as_complex_pattern(A(a=MultiState('u', 'p')))) |
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| 237 | + | ||
| 238 | + | ||
| 239 | + | @with_model |
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| 240 | + | def test_multibonds(): |
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| 241 | + | Monomer('A', ['a']) |
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| 242 | + | Monomer('B', ['b']) |
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| 243 | + | Parameter('k1', 100) |
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| 244 | + | Parameter('A_0', 200) |
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| 245 | + | Parameter('B_0', 50) |
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| 246 | + | Rule('r1', A(a=None) + A(a=None) + B(b=None) >> |
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| 247 | + | A(a=1) % A(a=[1, 2]) % B(b=2), k1) |
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| 248 | + | Initial(A(a=None), A_0) |
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| 249 | + | Initial(B(b=None), B_0) |
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| 250 | + | ||
| 251 | + | generate_equations(model) |
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| 252 | + | ||
| 253 | + | assert model.species[2].is_equivalent_to( |
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| 254 | + | A(a=1) % A(a=[1, 2]) % B(b=2) |
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| 255 | + | ) |
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| 256 | + | ||
| 257 | + | ||
| 221 | 258 | def _bng_print(expr): |
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| 222 | 259 | return BngPrinter(order='none').doprint(expr) |
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| 223 | 260 |
| Files | Coverage |
|---|---|
| pysb | 79.45% |
| Project Totals (96 files) | 79.45% |
933.3
TRAVIS_PYTHON_VERSION=3.6 TRAVIS_OS_NAME=linux
933.2
TRAVIS_PYTHON_VERSION=3.6 TRAVIS_OS_NAME=linux
933.1
TRAVIS_PYTHON_VERSION=3.6 TRAVIS_OS_NAME=linux
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