Merge branch 'master' of github.com:scemama/irpf90

src/Makefile

@@ -1,7 +1,21 @@
 PYTHON=python
 PYVERSION=$(shell $(PYTHON) -c "import sys; print(sys.version[:3])")
+HAS_CYTHON=$(shell bash -c "which cython &> /dev/null && echo 1 || echo 0")
+ifneq ($(HAS_CYTHON),0)
+
+../bin/irpf90: irpf90.so
+	rm ../bin/irpf90 ; cd ../bin ; ln -s ../src/irpf90_python.exe irpf90
+
+irpf90.so : $(wildcard *.py) irpf90.c
+	./cython_setup.py build_ext --inplace
+
+irpf90.c: irpf90.py
+	cython --embed irpf90.py
+
+else
 ../bin/irpf90: irpf90_python.exe
 	rm ../bin/irpf90 ; cd ../bin ; ln -s ../src/irpf90_python.exe irpf90
+endif
 
 clean:
 	rm -f *.c *.so *.pyc *.pyo 2>/dev/null

src/build_file.py

@@ -42,7 +42,7 @@ def dress(f, in_root=False):
     """ Transfoms the filename into $PWD/IRPF90_temp/f 
 
     Note:
-         In root=True resurn $PWD/f
+	 In root=True resurn $PWD/f
     """
 
     pwd = os.getcwd()
@@ -110,7 +110,7 @@ def create_build_link(t, l_irp_m, l_usr_m, l_ext_m, ninja=True):
     # (Module, List[str], List[str]) -> str
     """ Create the build command who will link the .o file into the target executable
 
-        To link we need the .o file corresponding to the target, and the ar lib.
+	To link we need the .o file corresponding to the target, and the ar lib.
     """
 
     irp_id = irpf90_t.irp_id
@@ -154,8 +154,8 @@ def create_build_compile(t, l_module, l_ext_modfile=[], ninja=True):
  
      - The module can produce a .MOD file
      - The module can Need another .MOD file. 
-        This .MOD file can be produced by:
+	 This .MOD file can be produced by:
-        1) a file generated by IRP_F90 preprocessor.
+	     1) a file generated by IRP_F90 preprocessor.
              2) a file defined by the user but a .irp.f90 file.
              3) a file not handle at all by IRPF90.
 
@@ -215,12 +215,12 @@ def create_build_compile(t, l_module, l_ext_modfile=[], ninja=True):
         list_of_includes = ' '
 
     l_build = [
-        "build {target_o}: compile_fortran_{irp_id} {target_F90} | {list_of_includes}  {list_of_modules} {list_of_modules_irp}",
+        "build {target_o}: compile_fortran_{irp_id} {target_F90} | ../Makefile {list_of_includes}  {list_of_modules} {list_of_modules_irp}",
         "   short_in  = {short_target_F90}", "   short_out = {short_target}", ""
     ]
 
     l_build_make = [
-        "{target_o}: {target_F90} | {list_of_includes}  {list_of_modules} {list_of_modules_irp}",
+        "{target_o}: {target_F90} | ../Makefile {list_of_includes}  {list_of_modules} {list_of_modules_irp}",
         '\t@printf "F: {short_target_F90} -> {short_target}\\n"', "\t@$(FC) $(FCFLAGS) -c $^ -o $@",
         ""
     ]
@@ -297,10 +297,10 @@ def create_make_all_clean(l_main):
     # 
     '''Create the ALL and CLEAN target of Makefile
 
-        Note: Portability doesn't mater. -delete is maybe not posix
+	Note: Portability doesn't mater. -delete is maybe not posix
-              but  -exec rm {} + is far more ugly!
+	      but  -exec rm {} + is far more ugly!
 	
-         '''
+	 '''
 
     l_executable = ' '.join(dress(t.filename, in_root=True) for t in l_main)
 
@@ -371,8 +371,8 @@ def run(d_module, ninja):
     """Wrote the ninja file needed to compile the program
 
     Note:
-        - FC,AR,CC,CXX,LIB, FCFLAGS, CFLAGS, CXXFLAGS are compiler enviroment read
+	- FC,AR,CC,CXX,LIB, FCFLAGS, CFLAGS, CXXFLAGS are compiler enviroment read
-        - SRC,OBJ: Are the not irp.f file defined by the user 
+	- SRC,OBJ: Are the not irp.f file defined by the user 
     """
 
     # Add required flags

src/entity.py

@@ -42,12 +42,12 @@ class Entity(object):
         # (list[str], str, int, Irpy_comm_world)
         '''Instantiate the object. 
 
-        Args:
+	Args:
-                text: List of lines between BEGIN_PROVIDER and END_PROVIDER included
+		text: List of lines between BEGIN_PROVIDER and END_PROVIDER included
-                int:  An unique int id (usefull when profilling)
+		int:  An unique int id (usefull when profilling)
-                name: The name of the provider defined after the chosen BEGIN_PROVIDER statement
+		name: The name of the provider defined after the chosen BEGIN_PROVIDER statement
-                comm_world: A object to communicate we the external world.
+		comm_world: A object to communicate we the external world.
-        '''
+	'''
 
         assert type(text) == list
         assert len(text) > 0
@@ -69,8 +69,8 @@ class Entity(object):
         # () -> Dict[str,Entity]
         '''Create an alias to the global dictionary of Entity.
 
-        Note: Be aware of the possiblity of Cyclic Dependency.
+	Note: Be aware of the possiblity of Cyclic Dependency.
-        '''
+	'''
         return self.comm_world.d_entity
 
     @irpy.lazy_property
@@ -78,9 +78,9 @@ class Entity(object):
         # () -> Tuple[str, Parsed_text]
         '''Create an alias to the global tuple for parsed text
 
-        Note: self.comm_world.t_filename_parsed_text need d_entity. 
+	Note: self.comm_world.t_filename_parsed_text need d_entity. 
-                Be aware of the possibility of Cyclic Dependency
+		Be aware of the possibility of Cyclic Dependency
-        '''
+	'''
         return self.comm_world.t_filename_parsed_text
 
     @irpy.lazy_property
@@ -105,8 +105,8 @@ class Entity(object):
 		BEGIN_PROVIDER [pi, double precision] &
                 BEGIN_PROVIDER [e, double preision]
 	
-                return True for 'pi' and False for 'e'
+		return True for 'pi' and False for 'e'
-        '''
+	'''
         return self.name == self.same_as
 
     @irpy.lazy_property
@@ -114,12 +114,12 @@ class Entity(object):
         # () -> Line
         '''Find the declaration statement associated with the name of the provider
 
-        Exemple:
+	Exemple:
-                BEGIN_PROVIDER [pi, double precision] &
+		BEGIN_PROVIDER [pi, double precision] &
-                BEGIN_PROVIDER [e, double preision]
+		BEGIN_PROVIDER [e, double preision]
 
-                if self.name == e, will return BEGIN_PROVIDER [e, double preision]
+		if self.name == e, will return BEGIN_PROVIDER [e, double preision]
-        '''
+	'''
 
         d = self.d_type_lines
         return next(line for _, line in d[Begin_provider] + d[Cont_provider]
@@ -247,16 +247,16 @@ class Entity(object):
         # () -> List[str]
         '''Extract the dimension of the needed array in a form of list of variable name
 
-        Exemple:
+	Exemple:
-                BEGIN_PROVIDER [real, ao_num ]
+		BEGIN_PROVIDER [real, ao_num ]
-                -> []
+		-> []
 
-                BEGIN_PROVIDER [ real, ao_oneD_p, (ao_num) ]
+		BEGIN_PROVIDER [ real, ao_oneD_p, (ao_num) ]
-                -> ['ao_num']
+		-> ['ao_num']
 
-                BEGIN_PROVIDER [ real, ao_oneD_prim_p, (ao_num,ao_prim_num_max) ]
+		BEGIN_PROVIDER [ real, ao_oneD_prim_p, (ao_num,ao_prim_num_max) ]
-                -> ['ao_num', 'ao_prim_num_max']
+		-> ['ao_num', 'ao_prim_num_max']
-        '''
+	'''
 
         line = self.prototype.text.split('!')[0]
         buffer = line.replace(']', '').split(',', 2)

src/irpf90.py

@@ -169,9 +169,6 @@ def main():
     if not command_line.do_run:
         return
 
-    import irp_stack
-    irp_stack.create()
-
     comm_world.create_buildfile(command_line.do_ninja)
     comm_world.write_modules()
 

src/parsed_text.py

@@ -216,15 +216,15 @@ def move_to_top_list(text, it):
 
     Note:
         - The permutation neeed to be done following `it` order
-        - We can have `nested` subroutine / Function. (Because of interface)
+	- We can have `nested` subroutine / Function. (Because of interface)
-        - This function is called way to much. Is need to be efficient
+	- This function is called way to much. Is need to be efficient
-                      - This function is Impure
+                      - This function is Unpure
-                      - One pass over `text`
+     		      - One pass over `text`
 
 
    NB:
-        - I am not really proud of the Sentinel value for the deleted,
+	- I am not really proud of the Sentinel value for the deleted,
-          but I waste already so much time on more cleaver but not working solution...
+	  but I waste already so much time on more cleaver but not working solution...
    '''
 
     assert set(it).issubset([NoDep, Declaration, Implicit, Use, Cont_provider])
@@ -284,7 +284,7 @@ def move_interface(parsed_text, s_type=(Use, Implicit, Declaration, Subroutine,
     '''Move everything containt into 'interface' below the first instance of s_type who preced it
 
    Note:
-        = This function is impure
+	= This function is unpur
    '''
 
     # Get the born of the interface	
@@ -311,7 +311,7 @@ def build_sub_needs(parsed_text, d_subroutine):
     '''Set the needs, and provides arguements of Routine present in parsed_text
     
     Note:
-        This function is impure
+	This function is unpure	
     '''
 
     l_buffer = []

src/preprocessed_text.py

@@ -204,8 +204,8 @@ def save_and_execute(irpdir, scriptname, code, interpreter):
     ''' Save the script in irpdir/scriptname and Execute it
 
     Note:
-        The script are executed in the orginal directory of the .irp.f (aka '..')
+	The script are executed in the orginal directory of the .irp.f (aka '..')
-        and this directory is added to PYTHONPATH.
+	and this directory is added to PYTHONPATH.
     '''
 
     irpdir_scriptname = os.path.abspath(os.path.join(irpdir, scriptname))
@@ -418,7 +418,7 @@ def remove_comments(text, form):
     '''Remove all comments
 
     Note:
-        This function is impure
+	This function is unpur
     '''
     result = []
 
@@ -800,8 +800,8 @@ def process_old_style_do(text):
 ######################################################################
 def change_single_line_ifs(text):
     # List[Line] -> List[Line]
-    '''Changes: `if (test) result`
+    '''Changes:	`if (test) result`
-        into
+	into
                 `if (test) then
                     result
                  endif`'''

src/util.py

@@ -75,11 +75,11 @@ def parmap(f, it, parallel=False):
     The parallel flag is set to togle the // execusion
 	
     Note:
-        - We try to use the Mulprocesses map is possible else we use our own
+	- We try to use the Mulprocesses map is possible else we use our own
-        - The order of the sequence if concerved
+	- The order of the sequence if concerved
         - Will use all the processesor possible
-        - We return a List
+	- We return a List
-        - The traceback is loose if an error occur but a Exception is raise.
+	- The traceback is loose if an error occur but a Exception is raise.
     '''
 
     if not parallel:
@@ -95,12 +95,12 @@ def parmap(f, it, parallel=False):
     # https://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled
     #from cPickle import PicklingError
     #try:
-    #    p = multiprocessing.Pool(nproc)
+    #	 p = multiprocessing.Pool(nproc)
-    #    l_res = p.map(f, it,nproc)
+    #  	 l_res = p.map(f, it,nproc)
     #except PicklingError:
-    #   pass    
+    #	pass	
     #else:
-    #   return l_res
+    #	return l_res
 
     # ~!~!~!
     # Parallelisation By Us
@@ -129,10 +129,10 @@ def parmap(f, it, parallel=False):
         '''Read a task from q_in, excute it, and store it in q_out
 
        Note:
-          - We use 'F' and not 'f'. 
+	  - We use 'F' and not 'f'. 
-          - The for loop will break when stop_contition occur
+	  - The for loop will break when stop_contition occur
-          - We get, and put an idx to allow the possibility of ordering afterward
+	  - We get, and put an idx to allow the possibility of ordering afterward
-          - We store any exeception, to raise her afterward
+	  - We store any exeception, to raise her afterward
        '''
         for i, x in iter(q_in.get, stop_condition):
 
@@ -192,7 +192,7 @@ def cached_file(filename, text):
     '''Check if file locatte at filename containt the same data as text
 
     Return:
-        True if data is the same, false otherwise
+	True if data is the same, false otherwise
     '''
 
     def digest(data):
@@ -213,7 +213,7 @@ def lazy_write_file(filename, text, conservative=False, touch=False):
     '''Write data lazily in filename location.
 
     Note:
-        If convervative is set, we don't overwrite.
+	If convervative is set, we don't overwrite.
     '''
 
     if not os.path.exists(filename) or not cached_file(filename, text) and not conservative:
@@ -286,7 +286,7 @@ def flatten(l_2d):
     '''Construct a copy of the 2d list collapsed into one dimension.
 
     Note:
-        -  We collapse in a C-style fashion (row_major).
+	-  We collapse in a C-style fashion (row_major).
     '''
 
     return [item for l_1d in l_2d for item in l_1d]
@@ -322,8 +322,8 @@ def build_dim(l_dim, colons=False):
     '''Contruct a valid fortran90 array dimension code from a list dimension
 
     Exemple:
-        [4,8] -> (4,8) if not colons
+	[4,8] -> (4,8) if not colons
-        [4,8] -> (:,:) if colons
+	[4,8] -> (:,:) if colons
 	
     '''
     if not l_dim: