def test_Text(self):
t=Text(remove_indentation("""\
---
title: Model $title
author: $entryAuthor
---
"""), title="Model title", entryAuthor="Veronika")
target_string = remove_indentation("""\
---
title: Model Model title
author: Veronika
---
""")
self.assertEqual(t.pandoc_markdown(), target_string)
desc = "Reference to $F_NSC$, not to $F_{x}$"
t = Text("$d", d=desc)
target_string = "Reference to $F_{NSC}$, not to $F_{x}$"
self.assertEqual(t.pandoc_markdown(), target_string)
def test_Meta(self):
d=OrderedDict()
d["name"]="Hilbert 1991"
d["version"]="2"
res=Meta(d).pandoc_markdown()
ref=remove_indentation("""\
---
name: Hilbert 1991
version: 2
---
"""
)
self.assertEqual(res,ref)
def test_as_str(self):
doi = "10.1556/Select.2.2001.1-2.14"
bibtex_entry = self.entry_dict[doi]
# check plain style
result = bibtex_entry.as_str("plain")
target_string = """\
@article{Meszena2002Selection,
author = {Meszéna, G. and Kisdi, É. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journal = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {Evolutionary Optimisation Models and Matrix Games in the Unified Perspective of Adaptive Dynamics},
volume = {2},
year = {2002}
}
"""
self.assertEqual(remove_indentation(result), remove_indentation(target_string))
# check BibTeX style
result = bibtex_entry.as_str("BibTeX")
target_string = r"""@article{Meszena2002Selection,
author = {Mesz{\'e}na, G. and Kisdi, {\'E}. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journal = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {{E}volutionary {O}ptimisation {M}odels and {M}atrix {G}ames in the {U}nified {P}erspective of {A}daptive {D}ynamics},
volume = {2},
year = {2002}
}
"""
self.assertEqual(remove_indentation(result), remove_indentation(target_string))
# check BibLaTeX style
result = bibtex_entry.as_str("BibLaTeX")
target_string = """\
@article{Meszena2002Selection,
author = {Meszéna, G. and Kisdi, É. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journaltitle = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {{E}volutionary {O}ptimisation {M}odels and {M}atrix {G}ames in the {U}nified {P}erspective of {A}daptive {D}ynamics},
volume = {2},
year = {2002}
}
"""
self.assertEqual(remove_indentation(result), remove_indentation(target_string))
def test_edited(self):
#yaml_str =remove_indentation("""\
# edits:
# - {time: !!timestamp '2001-12-15 02:59:43', user: mm}
#""")
yaml_str = """\
citationKey: Arora2005GCB
name: CTEM
version: 1
entryAuthor: "Verónika Ceballos-Núñez"
entryAuthorOrcid: 0000-0002-0046-1160
entryCreationDate: 21/1/2016 # changeset 3032
entryCreationDate: _ecd_
lastModification: _lm_
modApproach: process based
partitioningScheme: dynamic #if L and W change with time
# Dynamically performs allocation on the basis of the light, water and phenological status pf the canopy.
spaceScale: global
# unit: "1°"
timeResolution: monthly
doi: 10.1111/j.1365-2486.2004.00890.x
model:
- state_variables:
# Live vegetation pools:
- C_L:
desc: Amount of carbon for the leaf
key: "foliage"
unit: "kgC*m^{-2}"
- C_S:
desc: Amount of carbon for the stem
key: "wood"
unit: "kgC*m^{-2}"
- C_R:
desc: Amount of carbon for the root
key: "fine_roots"
unit: "kgC*m^{-2}"
# Dead carbon pools:
- C_D:
desc: Amount of carbon for the litter (debris)
unit: "kgC*m^{-2}"
- C_H:
desc: Amount of soil carbon (humus)
unit: "kgC*m^{-2}"
- respiration_fluxes:
- R_gL:
desc: Growth respiration flux for the leaves
type: parameter
- R_mL:
desc: Maintenance respiration flux for the leaves
type: parameter
- R_gS:
desc: Growth respiration flux for the stem
type: parameter
- R_mS:
desc: Maintenance respiration flux for the stem
type: parameter
- R_gR:
desc: Growth respiration flux for the root
type: parameter
- R_mR:
desc: Maintenance respiration flux for the root
type: parameter
- R_hD:
desc: Heterotrophic respiration from litter (debris)
type: parameter
- R_hH:
desc: Heterotrophic respiration from soil carbon (humus)
type: parameter
- photosynthetic_parameters:
- G:
desc: Carbon gain via photosynthesis (Gross Primary Productivity, GPP)
type: variable
key: GPP
- N:
desc: Net primary Productivity (NPP)
type: variable
key: NPP
exprs: "N=G-(R_gL+R_gS+R_gR)-(R_mL+R_mS+R_mR)"
- LAI:
desc: Leaf Area Index
type: parameter
- k_n:
desc: PFT-dependent light extinction coefficient
type: parameter
- L:
desc: Light availability (scalar index between 0 and 1)
type: variable
#exprs: "L=(Piecewise(((exp(-k_n*LAI)),FOR TREES AND CROPS),((Max(0,1-(LAI/4.5))),FOR GRASSES)))"
exprs: "L=(exp(-k_n*LAI))"
- water_availability:
# Measured by a linear scalar index (varies from 0 to 1)
- theta_i:
desc: Volumetric soil moisture content
type: variable
- theta_field:
desc: Field capacity
type: parameter
- theta_wilt:
desc: Wilting point
type: parameter
- W_i:
desc: Availability of water in soil layer i. Weighted by the fraction of roots present in each soil layer
type: variable
exprs: "W_i=(Max(0,(Min(1,((theta_i-theta_wilt)/(theta_field-theta_wilt))))))"
- W:
desc: Averaged soil water availability index
type: variable
- allocation_fractions:
- epsilon_L:
desc: PFT-dependent parameter for leaf
type: parameter
- epsilon_S:
desc: PFT-dependent parameter for stem
type: parameter
- epsilon_R:
desc: PFT-dependent parameter for root
type: parameter
exprs: "epsilon_R=1-epsilon_L-epsilon_S"
- omega:
desc: PFT-dependent parameter
type: parameter
- a_S:
desc: Stem allocation fraction
type: variable
# vary between 0 and 1
exprs: "a_S=((epsilon_S+(omega*(1-L)))/(1+(omega*(2-L-W))))"
- a_R:
desc: Root allocation fration
type: variable
# vary between 0 and 1
exprs: "a_R=((epsilon_R+(omega*(1-W)))/(1+(omega*(2-L-W))))"
#exprs: "a_R=((epsilon_R+(omega*(1-W)))/(1+(omega*(1-L-W))))" # For grasses
- a_L:
desc: Leaf allocation fraction
type: variable
key: "part_foliage"
#exprs: "a_L=(epsilon_L/(1+(omega*(2-L-W))))"
exprs: "a_L=1-a_S-a_R"
#exprs: "a_L=((epsilon_L+(omega*L))/(1+(omega*(1-L-W))))" # For grasses
- allocation_coefficients:
- A_S:
desc: Amount of carbon allocated to the stem
type: variable
key: "part_wood"
exprs: "A_S=(Piecewise((a_S*G,N<0),(a_S*N+R_gS+R_mS,N>0)))"
- A_R:
desc: Amount of carbon allocated to the root
type: variable
key: "part_roots"
exprs: "A_R=(Piecewise((a_R*G,N<0),(a_R*N+R_gR+R_mR,N>=0)))"
- temperature:
- T_air:
desc: Temperature of the air
type: variable
key: "air_temperature"
unit: "°C"
- T_cold:
desc: Cold temperature threshold for a PFT below which leaf loss begins to occur
type: parameter
unit: "°C"
- b_T:
desc: "Parameter that describes sensitivity of leaf loss to temp. below the T$_{cold}$"
type: parameter
- beta_T:
desc: Temperature measure (varies between 0 and 1)
type: variable
exprs: "beta_T=(Piecewise((1,T_air>= T_cold),(Piecewise((((T_air-T_cold-5)/5),T_air>(T_cold-5)),(0,T_air<=(T_cold-5))),T_cold>T_air)))"
- cycling_rates_:
- gamma_N:
desc: Loss rate (normal turnover)
type: parameter
unit: day^{-1}
- gamma_W:
desc: Loss rate under drought stress
type: parameter
unit: day^{-1}
- gamma_Tmax:
desc: Maximum loss rate of specified PFT
type: parameter
- gamma_T:
desc: Loss rate under cold stress
type: variable
unit: day^{-1}
exprs: "gamma_T=gamma_Tmax*(1-beta_T)**b_T"
- gamma_S:
desc: Stem turnover rate
type: parameter
key: "cyc_wood"
unit: years
- gamma_R:
desc: Root turnover rate
type: parameter
key: "cyc_roots"
unit: years
- litter_fluxes:
- D_L:
desc: Litter loss from the leaves
type: variable
exprs: "D_L=(gamma_N+gamma_W+gamma_T)*C_L"
- D_S:
desc: Litter loss from the stem
type: variable
- D_R:
desc: Litter loss from the root
type: variable
- C_D_H:
desc: Transfer of humidified litter to the soil carbon pool. Symbolized as C$_D->H$ in the original publication. #I had to change it since this formulation has a conflict when trying to evaluate.
type: variable
- components:
- f_v:
exprs: "fv = Matrix(5,1,[G-A_R-A_S-R_gL-R_mL-D_L, A_S-R_gS-R_mS-D_S, A_R-R_gR-R_mR-D_R, D_L+D_S+D_R-R_hD-C_D_H, C_D_H-R_hH])"
desc: the righthandside of the ode
- parameter_sets:
- "{k_n: 0.5,omega: 0.8,epsilon_L: 0.35,epsilon_S: 0.1,epsilon_R: 0.55}":
desc: Eastern US and Germany, cold broadleaf deciduous
edits:
- time: 2001-12-15 02:59:43
user: mm
"""
fn = "test.yaml"
p = Path(fn)
with p.open("w") as f:
f.write(yaml_str)
#simulate opening with vim
test_time = datetime.datetime(2001, 12, 15, 13, 45)
add_edit_date(p, test_time)
#assertions
with p.open("r") as f:
yaml_str_after = f.read()
print(yaml_str_after)
#yaml_str_ref = remove_indentation("""\
# edits:
# - {time: !!timestamp '2001-12-15 02:59:43', user: mm}
# - {time: !!timestamp '2001-12-15 13:45:00', user: mm}
#""")
yaml_str_ref = remove_indentation("""\
edits:
- time: 2001-12-15 02:59:43
user: mm
- time: 2001-12-15 13:45:00
user: mm
""")
def test_entry_list_to_file(self):
bibtex_entry_list = []
bibtex_entry_list.append(bibtexc.BibtexEntry.from_doi(doi="10.1556/Select.2.2001.1-2.14"))
bibtex_entry_list.append(bibtexc.BibtexEntry.from_doi(doi="10.1139/x91-151"))
# check plain style
test_file = "plain.bib"
bibtexc.entry_list_to_file(test_file, bibtex_entry_list, "plain")
with open(test_file, "r") as f:
result = f.read()
target_string = """\
@article{Meszena2002Selection,
author = {Meszéna, G. and Kisdi, É. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journal = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {Evolutionary Optimisation Models and Matrix Games in the Unified Perspective of Adaptive Dynamics},
volume = {2},
year = {2002}
}
@article{Korol1991CanadianJournalofForestResearch,
author = {Korol, R. L. and Running, S. W. and Milner, K. S. and Hunt Jr., E. R.},
doi = {10.1139/x91-151},
journal = {Canadian Journal of Forest Research},
link = {http://dx.doi.org/10.1139/x91-151},
number = {7},
pages = {1098-1105},
title = {Testing a mechanistic carbon balance model against observed tree growth},
volume = {21},
year = {1991}
}
"""
self.maxDiff = None
self.assertEqual(remove_indentation(result), remove_indentation(target_string))
# check BibTeX style
test_file = "BibTeX.bib"
bibtexc.entry_list_to_file(test_file, bibtex_entry_list, "BibTeX")
with open(test_file, "r") as f:
result = f.read()
target_string = r"""@article{Meszena2002Selection,
author = {Mesz{\'e}na, G. and Kisdi, {\'E}. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journal = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {{E}volutionary {O}ptimisation {M}odels and {M}atrix {G}ames in the {U}nified {P}erspective of {A}daptive {D}ynamics},
volume = {2},
year = {2002}
}
@article{Korol1991CanadianJournalofForestResearch,
author = {Korol, R. L. and Running, S. W. and Milner, K. S. and Hunt Jr., E. R.},
doi = {10.1139/x91-151},
journal = {Canadian Journal of Forest Research},
link = {http://dx.doi.org/10.1139/x91-151},
number = {7},
pages = {1098-1105},
title = {{T}esting a mechanistic carbon balance model against observed tree growth},
volume = {21},
year = {1991}
}
"""
self.assertEqual(remove_indentation(result), remove_indentation(target_string))
# check BibLaTeX style
test_file = "BibLaTeX.bib"
bibtexc.entry_list_to_file(test_file, bibtex_entry_list, "BibLaTeX")
with open(test_file, "r") as f:
result = f.read()
target_string = """\
@article{Meszena2002Selection,
author = {Meszéna, G. and Kisdi, É. and Dieckmann, U. and Geritz, S. a. H. and Metz, J. a. J.},
doi = {10.1556/Select.2.2001.1-2.14},
journaltitle = {Selection},
link = {http://dx.doi.org/10.1556/Select.2.2001.1-2.14},
number = {1-2},
pages = {193-220},
title = {{E}volutionary {O}ptimisation {M}odels and {M}atrix {G}ames in the {U}nified {P}erspective of {A}daptive {D}ynamics},
volume = {2},
year = {2002}
}
@article{Korol1991CanadianJournalofForestResearch,
author = {Korol, R. L. and Running, S. W. and Milner, K. S. and Hunt Jr., E. R.},
doi = {10.1139/x91-151},
journaltitle = {Canadian Journal of Forest Research},
link = {http://dx.doi.org/10.1139/x91-151},
number = {7},
pages = {1098-1105},
title = {{T}esting a mechanistic carbon balance model against observed tree growth},
volume = {21},
year = {1991}
}
"""
self.assertEqual(remove_indentation(result), remove_indentation(target_string))