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Merged
ramez17khaled merged 1 commit into from
Feb 26, 2026
Merged

update v0.1.3: add models to manifest #9

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2 changes: 1 addition & 1 deletion damn/_version.py
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@@ -1 +1 @@
__version__ = "0.1.1"
__version__ = "0.1.3"
21 changes: 21 additions & 0 deletions damn/models/ecoli/M28_OD_20.csv
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281 changes: 281 additions & 0 deletions damn/models/ecoli/M28_media.csv
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177,359 changes: 177,359 additions & 0 deletions damn/models/ecoli/iML1515_duplicated.xml
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174,334 changes: 174,334 additions & 0 deletions damn/models/putida/IJN1463EXP_duplicated.xml
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Binary file added damn/models/putida/modul.zip
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21 changes: 21 additions & 0 deletions damn/models/putida/putida_OD_81.csv
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82 changes: 82 additions & 0 deletions damn/models/putida/putida_media_81.csv
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@@ -0,0 +1,82 @@
ID,glc__D_e,xyl__D_e,succ_e,ala__L_e,arg__L_e,asn__L_e,asp__L_e,cys__L_e,glu__L_e,gln__L_e,gly_e,his__L_e,ile__L_e,leu__L_e,lys__L_e,met__L_e,phe__L_e,pro__L_e,ser__L_e,thr__L_e,trp__L_e,tyr__L_e,val__L_e,ade_e,gua_e,csn_e,ura_e,thymd_e
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22 changes: 15 additions & 7 deletions damn/train.py
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@@ -1,14 +1,24 @@
import os
import numpy as np
import tensorflow as tf
from importlib.resources import files
import damn
from damn import model
from damn import plot

os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
DAMN_DIR = os.path.dirname(os.path.abspath(damn.__file__))
PROJECT_ROOT = os.path.dirname(DAMN_DIR)
DOCS_DIR = os.path.join(PROJECT_ROOT, "docs")
#DAMN_DIR = os.path.dirname(os.path.abspath(damn.__file__))
#PROJECT_ROOT = os.path.dirname(DAMN_DIR)
#DOCS_DIR = os.path.join(PROJECT_ROOT, "docs")


def get_default_model(organism):
if organism.lower() == "putida":
return str(files("damn.models.putida").joinpath("IJN1463EXP_duplicated.xml"))
elif organism.lower() == "ecoli":
return str(files("damn.models.ecoli").joinpath("iML1515_duplicated.xml"))
else:
raise ValueError("Custom model must be provided")

def train_damn(
organism="custom",
Expand Down Expand Up @@ -48,8 +58,7 @@ def train_damn(
"file_name": "putida_OD_81",
"od_file": "putida_OD_81.csv",
"media_file": "putida_media_81.csv",
"cobra_model_file": os.path.join(
DOCS_DIR, "putida", "IJN1463EXP_duplicated.xml"),
"cobra_model_file": get_default_model('putida'),
"biomass_rxn_id": "BIOMASS_KT2440_WT3",
"seed": 1,
"num_epochs": 500,
Expand All @@ -62,8 +71,7 @@ def train_damn(
"file_name": "M28_OD_20",
"od_file": "M28_OD_20.csv",
"media_file": "M28_media.csv",
"cobra_model_file": os.path.join(
DOCS_DIR, "putida","iML1515_duplicated.xml"),
"cobra_model_file": get_default_model('ecoli'),
"biomass_rxn_id": "BIOMASS_Ec_iML1515_core_75p37M",
"seed": 30,
"num_epochs": 1000,
Expand Down
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