Merge pull request #32 from AgriculturalModelExchangeInitiative/master

update newb

.gitignore

@@ -71,3 +71,6 @@ nosetests.xml
 
 # Jupyter
 .ipynb_checkpoints
+
+# VS Code
+.vscode

conda/meta.yaml

@@ -22,7 +22,7 @@ requirements:
   run:
     - python {{PY_VER}}
     - antlr4-python3-runtime  ==4.8
-    - cython
+    - cython ==0.29.21
     - xmlformatter
     - path
     - numpy ==1.16.6

src/pycropml/cyml.py

@@ -5,6 +5,7 @@
 @author: midingoy
 """
 import os
+from os.path import isdir
 from path import Path
 import pycropml
 from pycropml.transpiler.main import Main
@@ -72,31 +73,31 @@ def transpile_package(package, language):
     dir_doc = Path(os.path.join(pkg, 'doc'))
 
     # Generate packages if the directories does not exists.
-    if not output.isdir():
+    if not isdir(output):
         output.mkdir()
-    if not dir_test.isdir():
+    if not isdir(dir_test):
         dir_test.mkdir()
-    if not dir_doc.isdir():
+    if not isdir(dir_doc):
         dir_doc.mkdir()
 
     dir_images = Path(os.path.join(dir_doc, 'images'))
-    if not dir_images.isdir():
+    if not isdir(dir_images):
         dir_images.mkdir()
 
     m2p = render_cyml.Model2Package(models, dir=output)
     m2p.generate_package()  # generate cyml models in "pyx" directory
     tg_rep1 = Path(os.path.join(output, language))  # target language models  directory in output
     dir_test_lang = Path(os.path.join(dir_test, language))
 
-    if not tg_rep1.isdir():
+    if not isdir(tg_rep1):
         tg_rep1.mkdir()
 
     namep_ = namep.replace("-", "_")    
     tg_rep = Path(os.path.join(tg_rep1, namep_))
-    if not tg_rep.isdir():
+    if not isdir(tg_rep):
         tg_rep.mkdir()
 
-    if not dir_test_lang.isdir():  #Create if it doesn't exist
+    if not isdir(dir_test_lang):  #Create if it doesn't exist
         dir_test_lang.mkdir()
 
     m2p.write_tests()
@@ -154,7 +155,7 @@ def transpile_package(package, language):
 
     # create computing algorithm
     if language == "py":
-        simulation = PythonSimulation(T.model)
+        simulation = PythonSimulation(T.model, package_name=namep)
         simulation.generate()
         code = ''.join(simulation.result)
         filename = Path(os.path.join(tg_rep, "simulation.py"))
@@ -163,10 +164,13 @@ def transpile_package(package, language):
             tg_file.write(code.encode("utf-8"))
         with open(initfile, "wb") as tg_file:
             tg_file.write("".encode("utf-8"))
-        setup = PythonSimulation(T.model)
-        setup.generate_setup()
+
+        setup = PythonSimulation(T.model, package_name=namep)
+        #setup.generate_setup()
+        setup.generate_pyproject()
         code = ''.join(setup.result)
-        setupfile = Path(os.path.join(tg_rep1, "setup.py"))
+        #setupfile = Path(os.path.join(tg_rep1, "setup.py"))
+        setupfile = Path(os.path.join(tg_rep1, "pyproject.toml"))
         with open(setupfile, "wb") as tg_file:
             tg_file.write(code.encode("utf-8"))
 

src/pycropml/render_cyml.py

@@ -5,14 +5,16 @@
 """
 from __future__ import print_function
 from __future__ import absolute_import
-from path import Path
-from datetime import datetime
 import os.path
-from pycropml.modelunit import ModelUnit
+from os.path import isdir
+import sys
+from path import Path
 import six
 import shutil
+from datetime import datetime
+from pycropml.modelunit import ModelUnit
 from . import error
-import sys
+from . import split_function
 
 DATATYPE = {}
 DATATYPE['INT'] = "int"
@@ -63,12 +65,13 @@ def generate_package(self):
         # Create a directory (mymodel)
 
         directory = Path(os.path.join(self.cwd, 'pyx'))
-        if directory.isdir():
+        if isdir(directory):
             self.dir = directory
         else:
             self.dir = directory.mkdir()
 
         files = []
+
         count = 0
         for model in self.models:          
             self.generate_component(model) 
@@ -83,10 +86,13 @@ def generate_package(self):
 
     def generate_component(self, model_unit):
         """Todo"""
+
+        functions = []
         if model_unit.modelid.split(".")[0] != "function":
             func_name = f"model_{signature(model_unit)}"
         else:
             func_name = signature(model_unit)
+
         types = [inp.datatype for inp in model_unit.inputs] + [out.datatype for out in model_unit.outputs]
         self.code = "import numpy\n"
         self.code += "from math import *\n"
@@ -98,19 +104,15 @@ def generate_component(self, model_unit):
 
         self.code += self.generate_function_signature(func_name, model_unit.inputs) + "\n"
         self.code += self.generate_function_doc(model_unit) + "\n"
-        if sys.version_info[0] >= 3:
-            self.code += self.generate_algorithm(model_unit) + "\n"
-        else:
-            self.code += self.generate_algorithm(model_unit).decode("utf-8") + "\n"
-
-        if model_unit.function:
-            for function in model_unit.function:
-                if function.language in ("Cyml", "cyml"):
-                    filefunc = Path(os.path.join(model_unit.path, "crop2ml", function.filename))
-                    with open(filefunc.encode('utf-8'), 'r') as f:
-                        source = f.read()
-                        self.code += source 
-                        self.code += "\n\n\n"
+        self.code += self.generate_algorithm(model_unit) + "\n"
+
+        if model_unit.function: 
+            function_files = [Path(os.path.join(model_unit.path, "crop2ml", function.filename))
+                              for function in model_unit.function if function.language.lower() == "cyml"]
+
+            content = split_function.unique_functions(function_files)
+            self.code += content
+            self.code += "\n"
 
         return self.code
 
@@ -335,7 +337,7 @@ def write_tests(self):
         TODO: Manage several models rather than just one.
         """
         self.rep = Path(os.path.join(self.rep, 'test', 'pyx'))
-        if not self.rep.isdir():
+        if not isdir(self.rep):
             self.rep.mkdir()
         files = []
         count = 0

src/pycropml/render_notebook.py

@@ -7,13 +7,15 @@
 """
 from __future__ import print_function
 from __future__ import absolute_import
+import six
+import os
+from os.path import isdir
 from path import Path
 
 # The package used to generate Notebook
 import nbformat as nbf
 
 from . import render_python as rp
-import six
 
 
 
@@ -48,7 +50,7 @@ def generate_notebook(self):
         # Create a directory (mymodel)
         cwd = Path(self.dir)
         directory=cwd/'python_notebook'
-        if (directory).isdir() :
+        if isdir(directory):
             _dir = directory
         else:
             _dir = directory.mkdir()

src/pycropml/render_notebook_csharp.py

@@ -8,6 +8,8 @@
 """
 from __future__ import print_function
 from __future__ import absolute_import
+import os
+from os.path import isdir
 from path import Path
 
 # The package used to generate Notebook
@@ -51,7 +53,7 @@ def generate_notebook(self):
         # Create a directory (mymodel)
         cwd = Path(self.dir)
         directory=cwd/'csharp_notebook'
-        if (directory).isdir() :
+        if isdir(directory):
             _dir = directory
         else:
             _dir = directory.mkdir()

src/pycropml/render_notebook_java.py

@@ -8,6 +8,8 @@
 """
 from __future__ import print_function
 from __future__ import absolute_import
+import os
+from os.path import isdir
 from path import Path
 
 # The package used to generate Notebook
@@ -48,7 +50,7 @@ def generate_notebook(self):
         # Create a directory (mymodel)
         cwd = Path(self.dir)
         directory=cwd/'java_notebook'
-        if (directory).isdir() :
+        if isdir(directory):
             _dir = directory
         else:
             _dir = directory.mkdir()

src/pycropml/render_python.py

@@ -8,11 +8,12 @@
 """
 from __future__ import print_function
 from __future__ import absolute_import
-from path import Path
-import numpy
-from datetime import datetime
 import os.path
+from os.path import isdir
 import six
+from datetime import datetime
+from path import Path
+import numpy
 
 try:
     from openalea.core import interface as inter
@@ -78,7 +79,7 @@ def generate_package(self):
         # Create a directory (mymodel)
         cwd = Path(self.dir)
         directory=cwd/'python_model'
-        if (directory).isdir() :
+        if isdir(directory):
             self.dir = directory
         else:
             self.dir = directory.mkdir()
@@ -458,7 +459,8 @@ def generate_doc(model):
     Institution: %s
     ExtendedDescription: %s
     ShortDescription: %s
-""" %(desc.Title, "-Version: " + model.version +  "  -Time step: " + model.timestep, desc.Authors, desc.Reference, desc.Institution, desc.ExtendedDescription, desc.ShortDescription)
+""" %(desc.Title, "-Version: " + model.version +  "  -Time step: " + model.timestep, 
+      desc.Authors, desc.Reference, desc.Institution, desc.ExtendedDescription, desc.ShortDescription)
 
     code = '\n'
     code += _doc

src/pycropml/split_function.py

@@ -0,0 +1,73 @@
+""" Merge files into one file with unique functions.
+
+Render a set of pyx files containing the same function several into one file containing one and only one function of each name.
+
+"""
+import re
+
+def function_names(code):
+    # Regular expression pattern to match function names
+    # It assumes functions start with 'def' or 'cpdef'
+    pattern = r'\b(?:def|cpdef)\s+([a-zA-Z_]\w*)\s*\('
+
+    # Find all function names using regex
+    function_names = re.findall(pattern, code)
+
+    # Remove duplicates by converting to a set
+    unique_function_names = list(function_names)
+
+    return unique_function_names
+
+# Define a function to retrieve the code of a specific function
+def get_function_code(content, function_name):
+    # Regex to capture function definition
+    function_pattern = rf'(def|cpdef)\s+{function_name}\s*\((?:[^()]*(?:\([^()]*\))?)*\)\s*:[\s\S]*?'
+
+    # Position of the function
+    match = re.search(function_pattern, content, re.MULTILINE)
+
+    if not match:
+        return ''
+
+    start = match.start()
+    lines = content[start:].splitlines()
+    function_lines = []
+
+    # Iter on the next lines from the function
+    # First line is the function definition
+    count = 0
+    for line in lines:
+        if (line.startswith('def ') or line.startswith('cpdef ')) and count != 0:
+            # Stop after the first line begining with def without indent
+            break  
+        function_lines.append(line)
+        count +=1
+
+    function_lines.append('')
+    return '\n'.join(function_lines)
+
+
+
+def unique_functions(files):
+    unique_functions = []
+
+    codes = []
+    for fn in files:
+        with open(fn.encode('utf-8'), 'r') as file:
+            content = file.read()
+
+        funs = function_names(content)
+        for fun in funs:
+            if fun in unique_functions:
+                print(f'{fun} is duplicated')
+            else:
+                unique_functions.append(fun)
+                function_code = get_function_code(content, fun)
+                #print(function_code)
+                codes.append(function_code)
+
+    content = '\n'.join(codes)
+
+    return content
+
+

src/pycropml/transpiler/antlr_py/bioma/run.py

@@ -2,8 +2,15 @@
 
 from __future__ import absolute_import
 from __future__ import print_function
-from path import Path
 import os
+from os.path import isdir
+from copy import deepcopy
+from typing import *
+from path import Path
+
+import networkx as nx
+import itertools
+
 from pycropml.transpiler.antlr_py.to_CASG import to_dictASG, to_CASG
 from pycropml.transpiler.antlr_py.bioma.biomaExtraction import BiomaExtraction
 from pycropml.transpiler.pseudo_tree import Node
@@ -13,8 +20,6 @@
 from pycropml.transpiler.antlr_py.generateCyml import writeCyml
 from pycropml.transpiler.antlr_py.createXml import Pl2Crop2ml
 from pycropml.transpiler.antlr_py import repowalk
-from copy import deepcopy
-from typing import *
 
 from pycropml.transpiler.antlr_py.csharp.csharp_preprocessing import ExprStatNode, TransformLocal, CheckingInOut, Custom_call, Declarations,Assignment, Member_access, Binary_op, Index, Local
 from pycropml.transpiler.antlr_py.codeExtraction import extraction
@@ -58,19 +63,18 @@
 
 def create_package(output):
     crop2ml_rep = Path(os.path.join(output, 'crop2ml'))
-    if not crop2ml_rep.isdir():
+    if not isdir(crop2ml_rep):
         crop2ml_rep.mkdir()
     algo_rep = Path(os.path.join(crop2ml_rep, 'algo'))
-    if not algo_rep.isdir():
+    if not isdir(algo_rep):
         algo_rep.mkdir()
     cyml_rep = Path(os.path.join(algo_rep, 'pyx'))
-    if not cyml_rep.isdir():
+    if not isdir(cyml_rep):
         cyml_rep.mkdir()
     return crop2ml_rep, cyml_rep    
 
 
-import networkx as nx
-import itertools
+
 
 def function_dependency(st, f):
     r = [f]