Commit d2bf1f24 authored by eladnoor's avatar eladnoor

fixing dependencies

parent 580a3135
Pipeline #46745743 passed with stage
in 18 minutes and 33 seconds
......@@ -5,7 +5,7 @@ stages:
- deploy
before_script:
- pip install --upgrade pip setuptools wheel tox quilt
- pip install --upgrade pip setuptools wheel tox
test36:
stage: test
......
......@@ -106,7 +106,7 @@ Then inside the python3 shell:
from equilibrator_api import Pathway
pp = Pathway.from_sbtab('example.tsv')
mdf_res = pp.calc_mdf()
print('MDF = %.2f RT' % mdf_res.mdf)
print('MDF = %s' % mdf_res.mdf)
mdf_res.reaction_plot.show()
mdf_res.compound_plot.show()
```
......
......@@ -33,8 +33,8 @@ install_requires =
pyparsing>=2.2.0
sbtab>=0.9.49
matplotlib>=3.0.0
equilibrator-cache>=0.1.6
component-contribution>=0.1.3
equilibrator-cache>=0.1.7
component-contribution>=0.1.4
python_requires = >=3.6
tests_require =
tox
......
......@@ -62,8 +62,7 @@ class ComponentContribution(object):
def standard_dg_prime_multi(
self,
reactions: List[PhasedReaction],
raise_exception: bool = False
reactions: List[PhasedReaction]
) -> Tuple[np.array, np.array]:
"""Calculate the transformed reaction energies of a list of reactions.
......@@ -79,14 +78,12 @@ class ComponentContribution(object):
reactions,
p_h=self.p_h,
ionic_strength=self.ionic_strength,
temperature=self.temperature,
raise_exception=raise_exception
temperature=self.temperature
)
def standard_dg_prime(
self,
reaction: PhasedReaction,
raise_exception: bool = False
reaction: PhasedReaction
) -> Tuple[float, float]:
"""Calculate the transformed reaction energies of a reaction.
......@@ -99,15 +96,13 @@ class ComponentContribution(object):
reaction,
p_h=self.p_h,
ionic_strength=self.ionic_strength,
temperature=self.temperature,
raise_exception=raise_exception
temperature=self.temperature
)
def dg_prime(
self,
reaction: PhasedReaction,
compound_to_conc: Dict[Compound, float],
raise_exception: bool = False
compound_to_conc: Dict[Compound, float]
) -> Tuple[float, float]:
"""
Calculate the dG'0 of a single reaction
......@@ -124,8 +119,7 @@ class ComponentContribution(object):
"""
dg_prime, dg_uncertainty = self.standard_dg_prime(
reaction,
raise_exception=raise_exception
reaction
)
dg_prime += self.RT * reaction.dg_correction(compound_to_conc)
return dg_prime, dg_uncertainty
......@@ -188,9 +182,7 @@ class ComponentContribution(object):
return E0_prime, E0_uncertainty
def dG0_analysis(self, reaction: PhasedReaction) -> List[Dict[str, object]]:
return self.predictor.get_dg_analysis(reaction,
raise_exception=False)
return self.predictor.get_dg_analysis(reaction)
def IsUsingGroupContributions(self, reaction: PhasedReaction) -> bool:
return self.predictor.is_using_group_contribution(reaction,
raise_exception=False)
return self.predictor.is_using_group_contribution(reaction)
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