Sourcery Starbot ⭐ refactored leshaker/python_integration #1

SourceryAI · 2022-08-21T18:59:10Z

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SourceryAI · 2022-08-21T18:59:12Z

cvode_with_sympy.py

-def parseSym(model_dict):   
+def parseSym(model_dict):


Function parseSym refactored with the following changes:

Replace identity comprehension with call to collection constructor [×2] (identity-comprehension)

SourceryAI · 2022-08-21T18:59:12Z

cvode_with_sympy.py

-	fname_def = model_name+'_define.c'
-	fid = open('./includes/'+fname_def, 'w')
-	define_str = "#define NPARS %d\t\t/* number of parameters */\n" % (len(ps))
-	define_str = define_str+"#define NEQ %d\t\t/* number of equations */\n" % len(fs)
-	fid.write(define_str)
-	fid.close()
-
-	fname_init = model_name+'_initialize.c'
-	fid = open('./includes/'+fname_init, 'w')
-	if (type(atol)!=list):
-		atol = [atol for x in range(len(fs))]
-
-	init_str = "hmin = RCONST(%e);\t\t/* minimal stepsize */\n" % hmin
-	init_str = init_str + "hmax = RCONST(%e);\t\t/* maximal stepsize */\n" % hmax
-	init_str = init_str + "mxsteps = RCONST(%e);\t\t/* maximal number of steps */\n" % mxsteps
-	init_str = init_str + "reltol = RCONST(%e);\t\t/* scalar relative tolerance */\n" % rtol
-	for i in range(len(fs)):
-		init_str = init_str + "Ith(abstol,%d) = RCONST(%e);\t\t/* vector absolute tolerance components */\n" % (i+1, atol[i])
-	fid.write(init_str)
-	fid.close()
-
+	fname_def = f'{model_name}_define.c'
+	with open(f'./includes/{fname_def}', 'w') as fid:
+		define_str = "#define NPARS %d\t\t/* number of parameters */\n" % (len(ps))
+		define_str = define_str+"#define NEQ %d\t\t/* number of equations */\n" % len(fs)
+		fid.write(define_str)
+	fname_init = f'{model_name}_initialize.c'
+	with open(f'./includes/{fname_init}', 'w') as fid:
+		if (type(atol)!=list):
+			atol = [atol for _ in range(len(fs))]
+
+		init_str = "hmin = RCONST(%e);\t\t/* minimal stepsize */\n" % hmin
+		init_str = init_str + "hmax = RCONST(%e);\t\t/* maximal stepsize */\n" % hmax
+		init_str = init_str + "mxsteps = RCONST(%e);\t\t/* maximal number of steps */\n" % mxsteps
+		init_str = init_str + "reltol = RCONST(%e);\t\t/* scalar relative tolerance */\n" % rtol
+		for i in range(len(fs)):
+			init_str = init_str + "Ith(abstol,%d) = RCONST(%e);\t\t/* vector absolute tolerance components */\n" % (i+1, atol[i])
+		fid.write(init_str)


Function writeInitSundials refactored with the following changes:

Use f-string instead of string concatenation [×4] (use-fstring-for-concatenation)

Use with when opening file to ensure closure [×2] (ensure-file-closed)

Replace unused for index with underscore (for-index-underscore)

SourceryAI · 2022-08-21T18:59:12Z

cvode_with_sympy.py

-	if checknegative:
-		checknegative_c = "TRUE"
-	else:
-		checknegative_c = "FALSE"
+	checknegative_c = "TRUE" if checknegative else "FALSE"


Function writeOdeSundials refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

Use f-string instead of string concatenation [×2] (use-fstring-for-concatenation)

Use with when opening file to ensure closure (ensure-file-closed)

Replace assignment and augmented assignment with single assignment [×2] (merge-assign-and-aug-assign)

Replace assignment with augmented assignment [×7] (aug-assign)

Simplify logical expression using De Morgan identities (de-morgan)

Replace multiple comparisons of same variable with in operator (merge-comparisons)

This removes the following comments ( why? ):

# write parameter definitions # write header

SourceryAI · 2022-08-21T18:59:12Z

cvode_with_sympy.py

-
-	# write parameter definitions
-	par_def = "\t/* Extract needed constants from data */\n"
-	par_def = par_def+"\tdata = (UserData) user_data;\n"
-	par_def = par_def+"\tdouble p[NPARS];\n"
-	par_def = par_def+"\tfor (i=0; i<NPARS; i++) p[i] = data->p[i];\n\n"
-	fid.write(par_def)
-
-	# write parameter definitions
-	for i, p in enumerate(ps):
-		tmp_str = '\trealtype %s =  p[%d];\n' % (p, i)
-		fid.write(tmp_str)
-		fid.write('\n')   
-
-	#write variables definitions
-	for i, x in enumerate(xs):
-		tmp_str = '\trealtype %s =  Ith(x,%d);\n' % (x, i+1)
-		fid.write(tmp_str)
-		fid.write('\n')
+	fname_jac = f'{model_name}_ode_jac.c'
+	with open(f'./includes/{fname_jac}', 'w') as fid:
+		header = (
+			"static int Jac(long int N, realtype t, N_Vector x, N_Vector fx, DlsMat J, void *user_data,\nN_Vector tmp1, N_Vector tmp2, N_Vector tmp3)\n"
+			+ "{\n\n"
+		)
+
+		header += "\tint i, j;\n"
+		header += "\tUserData data;\n"
+		fid.write(header)
+
+		par_def = (
+			"\t/* Extract needed constants from data */\n"
+			+ "\tdata = (UserData) user_data;\n"
+		)
+
+		par_def += "\tdouble p[NPARS];\n"
+		par_def += "\tfor (i=0; i<NPARS; i++) p[i] = data->p[i];\n\n"
+		fid.write(par_def)
+
+		# write parameter definitions
+		for i, p in enumerate(ps):
+			tmp_str = '\trealtype %s =  p[%d];\n' % (p, i)
+			fid.write(tmp_str)
+			fid.write('\n')   

-	#write alg eqs
-	for alg in alg_dict:
-		tmp_str = '\t%s =  %s;\n' % (alg,alg_dict[alg])
-		fid.write(tmp_str)
-		fid.write('\n')
-
-	# write jacobian
-	for i in range(dfdx.shape[0]):
-		for j in range(dfdx.shape[1]):
-			if not dfdx[i,j]==0:
-				# convert formula to c-style
-				dfdx_c = convToCstr([dfdx[i,j]])
-				tmp_str = '\tIJth(J,%d,%d) = %s;\n' % (i+1,j+1, dfdx_c[0])
-				fid.write(tmp_str)
-				fid.write('\n')
+		#write variables definitions
+		for i, x in enumerate(xs):
+			tmp_str = '\trealtype %s =  Ith(x,%d);\n' % (x, i+1)
+			fid.write(tmp_str)
+			fid.write('\n')

-	# write variables definitions
-	for i, x in enumerate(xs):
-		if x in xs_alg: 
-			tmp_str = '\tIth(x,%d) = %s;\n' % (i+1, x)
+		#write alg eqs
+		for alg in alg_dict:
+			tmp_str = '\t%s =  %s;\n' % (alg,alg_dict[alg])
 			fid.write(tmp_str)
 			fid.write('\n')

-	# write footer  
-	footer = '\treturn(0);\n}\n'
-	fid.write(footer)
-	fid.close()
+			# write jacobian
+		for i in range(dfdx.shape[0]):
+			for j in range(dfdx.shape[1]):
+				if dfdx[i, j] != 0:
+					# convert formula to c-style
+					dfdx_c = convToCstr([dfdx[i,j]])
+					tmp_str = '\tIJth(J,%d,%d) = %s;\n' % (i+1,j+1, dfdx_c[0])
+					fid.write(tmp_str)
+					fid.write('\n')
+
+		# write variables definitions
+		for i, x in enumerate(xs):
+			if x in xs_alg: 
+				tmp_str = '\tIth(x,%d) = %s;\n' % (i+1, x)
+				fid.write(tmp_str)
+				fid.write('\n')

+		# write footer  
+		footer = '\treturn(0);\n}\n'
+		fid.write(footer)


Function writeJacSundials refactored with the following changes:

Use f-string instead of string concatenation [×2] (use-fstring-for-concatenation)

Use with when opening file to ensure closure (ensure-file-closed)

Replace assignment and augmented assignment with single assignment [×2] (merge-assign-and-aug-assign)

Replace assignment with augmented assignment [×6] (aug-assign)

Simplify logical expression using De Morgan identities (de-morgan)

This removes the following comments ( why? ):

# write parameter definitions # write header

SourceryAI · 2022-08-21T18:59:12Z

cvode_with_sympy.py

-			rm_cmd = "rm -rf %s" % os.path.join('./bin/',bin)
+			rm_cmd = f"rm -rf {os.path.join('./bin/', bin)}"


Function writeModelFiles refactored with the following changes:

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

SourceryAI · 2022-08-21T18:59:13Z

helper_funs.py

-	model_dict = {}
-	model_dict['name'] = model_name
-	model_dict['odes'] = dict(zip(x_names,dxdt))
-	model_dict['vars'] = x_names
-	model_dict['pars'] = p_names
-
-	if x0 == []:
-		model_dict['initvars'] = dict(zip(x_names, 0.1*np.ones([len(x_names)])))
-	else:
-		model_dict['initvars'] = dict(zip(x_names, x0))
+	model_dict = {
+		'name': model_name,
+		'odes': dict(zip(x_names, dxdt)),
+		'vars': x_names,
+		'pars': p_names,
+		'initvars': dict(zip(x_names, 0.1 * np.ones([len(x_names)])))
+		if x0 == []
+		else dict(zip(x_names, x0)),
+	}


Function convToDict refactored with the following changes:

Merge dictionary assignment with declaration [×5] (merge-dict-assign)

Replace if statement with if expression (assign-if-exp)

SourceryAI · 2022-08-21T18:59:13Z

model_def.py

-	dxdt = []
+	dxdt = [
+		'- kon * Epo * EpoR + koff * EpoEpoR + kex * EpoEpoRi',
+		'- kon * Epo * EpoR + koff * EpoEpoR + kt * EpoR0 - kt * EpoR + kex * EpoEpoRi',
+		'kon * Epo * EpoR - koff * EpoEpoR - ke * EpoEpoR',
+		'ke * EpoEpoR - kex * EpoEpoRi - kdi * EpoEpoRi - kde * EpoEpoRi',
+		'kdi * EpoEpoRi',
+		'kde * EpoEpoRi',
+	]

-	dxdt.append('- kon * Epo * EpoR + koff * EpoEpoR + kex * EpoEpoRi')
-	dxdt.append('- kon * Epo * EpoR + koff * EpoEpoR + kt * EpoR0 - kt * EpoR + kex * EpoEpoRi')
-	dxdt.append('kon * Epo * EpoR - koff * EpoEpoR - ke * EpoEpoR')
-	dxdt.append('ke * EpoEpoR - kex * EpoEpoRi - kdi * EpoEpoRi - kde * EpoEpoRi')
-	dxdt.append('kdi * EpoEpoRi')
-	dxdt.append('kde * EpoEpoRi')


Function EpoEpoR refactored with the following changes:

Merge append into list declaration [×6] (merge-list-append)

SourceryAI · 2022-08-21T18:59:13Z

model_def.py

-	dxdt = []
+	dxdt = [
+		'- k1 * A + k2 * B - k3 * A * B + k4 * C',
+		'+ k1 * A - k2 * B - k3 * A * B + k4 * C',
+		'+ k3 * A * B - k4 * C',
+	]

-	dxdt.append('- k1 * A + k2 * B - k3 * A * B + k4 * C')
-	dxdt.append('+ k1 * A - k2 * B - k3 * A * B + k4 * C')
-	dxdt.append('+ k3 * A * B - k4 * C')


Function ToyModel refactored with the following changes:

Merge append into list declaration [×3] (merge-list-append)

SourceryAI · 2022-08-21T18:59:13Z

model_def.py

-	dxdt = []
+	dxdt = [
+		'- k1 * log ( A ) + k2 * B ** k3 * log ( A * B ) + C**k4',
+		'+ k1 * A - k2 * B - k3 * A * B + k4 * C',
+		'+ k3 * A * B - k4 * C',
+	]

-	dxdt.append('- k1 * log ( A ) + k2 * B ** k3 * log ( A * B ) + C**k4')
-	dxdt.append('+ k1 * A - k2 * B - k3 * A * B + k4 * C')
-	dxdt.append('+ k3 * A * B - k4 * C')


Function ToyModel2 refactored with the following changes:

Merge append into list declaration [×3] (merge-list-append)

SourceryAI · 2022-08-21T18:59:13Z

model_def.py

-	dxdt = [v[2]+"-"+v[1], 						# MKKK
-			v[1]+"-"+v[2], 						# MKKKp
-			v[6]+"-"+v[3],						# MKK
-			v[3]+"+"+v[5]+"-"+v[4]+"-"+v[6],	# MKKp
-			v[4]+"-"+v[5],						# MKKpp
-			v[10]+"-"+v[7],						# MAPK
-			v[7]+"+"+v[9]+"-"+v[8]+"-"+v[10],	# MAPKp
-			v[8]+"-"+v[9]]						# MAPKpp
+	dxdt = [
+		f"{v[2]}-{v[1]}",
+		f"{v[1]}-{v[2]}",
+		f"{v[6]}-{v[3]}",
+		f"{v[3]}+{v[5]}-{v[4]}-{v[6]}",
+		f"{v[4]}-{v[5]}",
+		f"{v[10]}-{v[7]}",
+		f"{v[7]}+{v[9]}-{v[8]}-{v[10]}",
+		f"{v[8]}-{v[9]}",
+	]
+


Function MAPK refactored with the following changes:

Use f-string instead of string concatenation [×24] (use-fstring-for-concatenation)

This removes the following comments ( why? ):

# MAPKp # MKKK # MAPKpp # MKKpp # MKKKp # MAPK # MKK # MKKp

'Refactored by Sourcery'

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SourceryAI commented Aug 21, 2022

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Sourcery Starbot ⭐ refactored leshaker/python_integration #1

Sourcery Starbot ⭐ refactored leshaker/python_integration #1

SourceryAI commented Aug 21, 2022

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		rm_cmd = "rm -rf %s" % os.path.join('./bin/',bin)
		rm_cmd = f"rm -rf {os.path.join('./bin/', bin)}"

		def parseSym(model_dict):
		def parseSym(model_dict):

Sourcery Starbot ⭐ refactored leshaker/python_integration #1

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Sourcery Starbot ⭐ refactored leshaker/python_integration #1

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SourceryAI commented Aug 21, 2022

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