Extend function support in BNGL import and pysb export

[FFroehlich]

This adds support of all BNGL supported functions during import of BNGL models. For export of pysb models to file, all supported functions are always imported from sympy such that model evaluation does not fail in case any of these functions is used in an pysb.Expression.

[codecov-io]

Codecov Report

Merging #518 (2dfc357) into master (cc94061) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #518   +/-   ##
=======================================
  Coverage   80.27%   80.27%           
=======================================
  Files         101      101           
  Lines       10664    10668    +4     
=======================================
+ Hits         8560     8564    +4     
  Misses       2104     2104           

Impacted Files	Coverage Δ
pysb/export/pysb_flat.py	92.68% <100.00%> (+0.57%)	⬆️
pysb/importers/bngl.py	93.01% <100.00%> (+0.02%)	⬆️

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[alubbock]

Is enumerating the functions like this necessary? It seems to work on current master branch already. Here's a test program:

from pysb.importers.bngl import model_from_bngl
import tempfile

bngl_test = """
begin seed species
  A 100
  B 100
end seed species

begin reaction rules
  A() + B() <-> C() 0.01, 1
end reaction rules

# not used in model, only for import tests
begin functions
  f1() = exp(10)
  f2() = atanh(10)
  f3() = sqrt(log2(50))
end functions
"""

with tempfile.NamedTemporaryFile('w', suffix='.bngl', encoding='utf8') as tf:
    tf.write(bngl_test)
    tf.flush()
    model = model_from_bngl(tf.name)

print(model)

for expr in model.expressions:
    print(f'{expr.name}: {expr.expr.evalf()}')

[FFroehlich]

It's been a while since I wrote that code, so I am not sure. I am surprised that log2 actually works, since this definitely used to require the mapping. This might be due to recent changes by @jmuhlich or sympy added log10 and log2 functions function.

[codecov-commenter]

Codecov Report

Merging #518 (1d18513) into master (85b6c8a) will increase coverage by 0.08%.
The diff coverage is 100.00%.

❗ Current head 1d18513 differs from pull request most recent head dd4b5d4. Consider uploading reports for the commit dd4b5d4 to get more accurate results

@@            Coverage Diff             @@
##           master     #518      +/-   ##
==========================================
+ Coverage   80.16%   80.25%   +0.08%     
==========================================
  Files         100      101       +1     
  Lines       10650    10717      +67     
==========================================
+ Hits         8538     8601      +63     
- Misses       2112     2116       +4     

Impacted Files	Coverage Δ
pysb/export/pysb_flat.py	92.10% <100.00%> (+0.92%)	⬆️
pysb/importers/bngl.py	93.01% <100.00%> (+0.05%)	⬆️
pysb/core.py	88.72% <0.00%> (ø)
pysb/export/__init__.py	96.00% <0.00%> (ø)
pysb/tools/render_reactions.py	16.84% <0.00%> (ø)
pysb/export/python.py	93.22% <0.00%> (ø)
pysb/tests/test_exporters.py	94.50% <0.00%> (+0.12%)	⬆️

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