Fails to parse some f90 source about ford HOT 22 CLOSED

diff --git a/.gitignore b/.gitignore
index 0ab917d..17f45be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,7 +3,9 @@ structure.ods
 *~
 doc/
 src/
-README.rst
+#README.rst
 FORD.egg-info/
 dist/
 wiki/
+*.mod
+*.o
\ No newline at end of file
diff --git a/ford/fortran_project.py b/ford/fortran_project.py
index bfe1878..5ce9f6f 100644
--- a/ford/fortran_project.py
+++ b/ford/fortran_project.py
@@ -23,7 +23,6 @@
 #  

 #FIXME: Need to add .lower() to all equality tests between strings
-#TODO: Set up a list of the packages that this depends on--in particular, toposort

 from __future__ import print_function

@@ -62,12 +61,13 @@ class Project(object):
                 if item.split('.')[-1] in self.extensions and not item in exclude:
                     # Get contents of the file
                     print("Reading file {}".format(os.path.join(curdir,item)))
-                    try:
-                        self.files.append(ford.sourceform.FortranSourceFile(os.path.join(curdir,item)))
-                    except Exception as e:
-                        print("Warning: Error parsing {}.\n\t{}".format(os.path.join(curdir,item),e.args[0]))
-                        continue
-                        
+                    self.files.append(ford.sourceform.FortranSourceFile(os.path.join(curdir,item)))
+                    #~ try:
+                        #~ self.files.append(ford.sourceform.FortranSourceFile(os.path.join(curdir,item)))
+                    #~ except Exception as e:
+                        #~ print("Warning: Error parsing {}.\n\t{}".format(os.path.join(curdir,item),e.args[0]))
+                        #~ continue
+                    
                     for module in self.files[-1].modules:
                         self.modules.append(module)
                         for function in module.functions:
@@ -119,10 +119,15 @@ class Project(object):
         # Get the order to process other correlations with
         deplist = {}
         for mod in self.modules:
-            deplist[mod] = set(mod.uses)
+            uselist = mod.uses
+            for proc in mod.subroutines:
+                uselist.extend(proc.uses)
+            for proc in mod.functions:
+                uselist.extend(proc.uses)
+            deplist[mod] = set(uselist)
         ranklist = toposort.toposort_flatten(deplist)
         for proc in self.procedures:
-            if proc.parobj == 'sourcefile': ranklist.append(proc[1])
+            if proc.parobj == 'sourcefile': ranklist.append(proc)
         ranklist.extend(self.programs)

         # Perform remaining correlations for the project
diff --git a/ford/sourceform.py b/ford/sourceform.py
index 08f706f..fcc3ec9 100644
--- a/ford/sourceform.py
+++ b/ford/sourceform.py
@@ -194,7 +194,8 @@ class FortranContainer(FortranBase):
     SUBROUTINE_RE = re.compile("^\s*(?:(.+?)\s+)?subroutine\s+(\w+)\s*(\([^()]*\))?(\s*bind\s*\(\s*c.*\))?$",re.IGNORECASE)
     FUNCTION_RE = re.compile("^(?:(.+?)\s+)?function\s+(\w+)\s*(\([^()]*\))?(?:\s*result\s*\(\s*(\w+)\s*\))?(\s*bind\s*\(\s*c.*\))?$",re.IGNORECASE)
     TYPE_RE = re.compile("^type(?:\s+|\s*(,.*)?::\s*)((?!(?:is))\w+)\s*(\([^()]*\))?\s*$",re.IGNORECASE)
-    INTERFACE_RE = re.compile("^(abstract\s+)?interface(?:\s+(\S.+))?$",re.IGNORECASE)
+    INTERFACE_RE = re.compile("^interface(?:\s+(\S.+))?$",re.IGNORECASE)
+    ABS_INTERFACE_RE = re.compile("^abstract\s+interface(?:\s+(\S.+))?$",re.IGNORECASE)
     BOUNDPROC_RE = re.compile("^(generic|procedure)\s*(\([^()]*\))?\s*(.*)\s*::\s*(\w.*)",re.IGNORECASE)
     FINAL_RE = re.compile("^final\s*::\s*(\w.*)",re.IGNORECASE)
     VARIABLE_RE = re.compile("^(integer|real|double\s*precision|character|complex|logical|type(?!\s+is)|class(?!\s+is)|procedure)\s*((?:\(|\s\w|[:,*]).*)$",re.IGNORECASE)
@@ -321,6 +322,13 @@ class FortranContainer(FortranBase):
                                            permission))
                 else:
                     raise Exception("Found INTERFACE in {}".format(type(self).__name__[7:].upper()))
+            elif self.ABS_INTERFACE_RE.match(line):
+                if hasattr(self,'absinterfaces'):
+                    self.absinterfaces.extend(FortranAbstractBlock(source,
+                                           self.INTERFACE_RE.match(line),self,
+                                           permission).absinterfaces)
+                else:
+                    raise Exception("Found INTERFACE in {}".format(type(self).__name__[7:].upper()))
             elif self.BOUNDPROC_RE.match(line) and incontains:
                 if hasattr(self,'boundprocs'):
                     self.boundprocs.append(FortranBoundProcedure(source,
@@ -368,12 +376,12 @@ class FortranCodeUnit(FortranContainer):
     def correlate(self,project):
         # Add procedures, interfaces and types from parent to our lists
         if hasattr(self.parent,'pub_procs'): self.pub_procs.extend(self.parent.pub_procs)
-        if hasattr(self.parent,'procs'): self.procs.extend(self.parent.procs)
+        if hasattr(self.parent,'all_procs'): self.all_procs.extend(self.parent.all_procs)
         #FIXME: It would be better to make the all_interfaces list contain only abstract interfaces, and to start building it during cleanup, as was done for procs
         if hasattr(self.parent,'interfaces'):
-            self.all_interfaces = self.interfaces + self.parent.interfaces
+            self.all_absinterfaces = self.absinterfaces + self.parent.absinterfaces
         else:
-            self.all_interfaces = self.interfaces + []
+            self.all_absinterfaces = self.absinterfaces + []
         if hasattr(self.parent,'all_types'):
             self.all_types = self.types + self.parent.all_types
         else:
@@ -383,14 +391,14 @@ class FortranCodeUnit(FortranContainer):
         for mod in self.uses:
             if type(mod) == str: continue
             self.pub_procs.extend(mod.pub_procs)
-            self.procs.extend(mod.pub_procs)
-            self.all_interfaces.extend(mod.all_interfaces)
+            self.all_procs.extend(mod.pub_procs)
+            self.all_absinterfaces.extend(mod.all_absinterfaces)
             self.all_types.extend(mod.all_types) 

         # Match up called procedures
         if hasattr(self,'calls'):
             for i in range(len(self.calls)):
-                for proc in self.procs:
+                for proc in self.all_procs:
                     if self.calls[i] == proc.name:
                         self.calls[i] = proc
                         break
@@ -471,27 +479,28 @@ class FortranModule(FortranCodeUnit):
         self.functions = []
         self.interfaces = []
         self.types = []
+        self.absinterfaces = []

     def _cleanup(self):
         # Create list of all local procedures. Ones coming from other modules
         # will be added later, during correlation.
-        self.procs = self.functions + self.subroutines
+        self.all_procs = self.functions + self.subroutines
         self.pub_procs = []
         for interface in self.interfaces:
             if interface.name:
-                self.procs.append(interface)
-            elif not interface.abstract:
-                self.procs.extend(interface.functions)
-                self.procs.extend(interface.subroutines)
+                self.all_procs.append(interface)
+            else:
+                self.all_procs.extend(interface.functions)
+                self.all_procs.extend(interface.subroutines)

         for name in self.public_list:
-            for var in self.variables + self.procs + self.types + self.interfaces:
+            for var in self.variables + self.all_procs + self.types + self.interfaces + self.absinterfaces:
                 if (var.name != None):    #JW
                     if name.lower() == var.name.lower():
                         var.permission = "public"

         for name in self.private_list:
-            for var in self.variables + self.procs + self.types + self.interfaces:
+            for var in self.variables + self.all_procs + self.types + self.interfaces + self.absinterfaces:
                 if name.lower() == var.name.lower():
                     var.permission = "private"
         for varname in self.protected_list:
@@ -499,7 +508,7 @@ class FortranModule(FortranCodeUnit):
                 if varname.lower() == var.name.lower():
                     var.permission = "protected"

-        for proc in self.procs:
+        for proc in self.all_procs:
             if proc.permission == "public": self.pub_procs.append(proc)

         del self.public_list
@@ -544,17 +553,18 @@ class FortranSubroutine(FortranCodeUnit):
         self.subroutines = []
         self.functions = []
         self.interfaces = []
+        self.absinterfaces = []
         self.types = []

     def _cleanup(self):
-        self.procs = self.functions + self.subroutines
+        self.all_procs = self.functions + self.subroutines
         self.pub_procs = []
         for interface in self.interfaces:
             if interface.name:
-                self.procs.append(interface)
-            elif not interface.abstract:
-                self.procs.extend(interface.functions)
-                self.procs.extend(interface.subroutines)
+                self.all_procs.append(interface)
+            else:
+                self.all_procs.extend(interface.functions)
+                self.all_procs.extend(interface.subroutines)

         for varname in self.optional_list:
             for var in self.variables:
@@ -626,15 +636,16 @@ class FortranFunction(FortranCodeUnit):
         self.subroutines = []
         self.functions = []
         self.interfaces = []
+        self.absinterfaces = []
         self.types = []

     def _cleanup(self):
-        self.procs = self.functions + self.subroutines
+        self.all_procs = self.functions + self.subroutines
         self.pub_procs = []
         for interface in self.interfaces:
             if interface.name:
                 procs.append(interface)
-            elif not interface.abstract:
+            else:
                 procs.extend(interface.functions)
                 procs.extend(interface.subroutines)

@@ -685,14 +696,15 @@ class FortranProgram(FortranCodeUnit):
         self.types = []
         self.uses = []
         self.calls = []
+        self.absinterfaces = []

     def _cleanup(self):
-        self.procs = self.functions + self.subroutines
+        self.all_procs = self.functions + self.subroutines
         self.pub_procs = []
         for interface in self.interfaces:
             if interface.name:
                 procs.append(interface)
-            elif not interface.abstract:
+            else:
                 procs.extend(interface.functions)
                 procs.extend(interface.subroutines)

@@ -743,9 +755,9 @@ class FortranType(FortranContainer):


     def correlate(self,project):
-        self.all_interfaces = self.parent.all_interfaces
+        self.all_absinterfaces = self.parent.all_absinterfaces
         self.all_types = self.parent.all_types
-        self.procs = self.parent.procs
+        self.all_procs = self.parent.all_procs
         # Get type of extension
         if self.extends:
             for dtype in self.all_types:
@@ -766,12 +778,12 @@ class FortranType(FortranContainer):
                 self.boundprocs.remove(proc)
         # Match finalprocs
         for i in range(len(self.finalprocs)):
-            for proc in self.procs:
+            for proc in self.all_procs:
                 if proc.name.lower() == self.finalprocs[i].lower():
                     self.finalprocs[i] = proc
                     break
         # Find a constructor, if one exists
-        for proc in self.procs:
+        for proc in self.all_procs:
             if proc.name.lower() == self.name.lower():
                 self.constructor = proc
                 break
@@ -788,43 +800,71 @@ class FortranInterface(FortranContainer):
     """
     def _initialize(self,line):
         self.proctype = 'Interface'
-        self.abstract = bool(line.group(1))
-        self.name = line.group(2)
+        self.name = line.group(1)
         self.hasname = bool(self.name)
         self.subroutines = []
         self.functions = []
         self.modprocs = []

     def _cleanup(self):
-        if not self.hasname:
+        if not self.hasname: # FIXME: Not sure if I need this
             contents = self.subroutines + self.functions
             self.name = contents[0].name

     def correlate(self,project):
-        if self.abstract: return
-        self.all_interfaces = self.parent.all_interfaces
+        self.all_absinterfaces = self.parent.all_absinterfaces
         self.all_types = self.parent.all_types
-        self.procs = self.parent.procs
+        self.all_procs = self.parent.all_procs
         for modproc in self.modprocs:
-            for proc in self.procs:
+            for proc in self.all_procs:
                 if modproc.name.lower() == proc.name.lower():
                     modproc.procedure = proc
                     break
         for subrtn in self.subroutines:
             subrtn.correlate(project)
-            #~ for proc in self.parent.procs:
+            #~ for proc in self.parent.all_procs:
                 #~ if subrtn.name.lower() == proc.name.lower():
                     #~ subrtn.procedure = proc
                     #~ break
         for func in self.functions:
             func.correlate(project)
-            #~ for proc in self.parent.procs:
+            #~ for proc in self.parent.all_procs:
                 #~ if func.name.lower() == proc.name.lower():
                     #~ func.procedure = proc
                     #~ break
-                    
+
+class FortranAbstractBlock(FortranContainer):
+    def _initialize(self,line):
+        self.subroutines = []
+        self.functions = []
+        
+    def _cleanup(self):
+        self.absinterfaces = []
+        for proc in (self.subroutines + self.functions):
+            self.absinterfaces.append(FortranAbsInterface(proc,self))


+class FortranAbsInterface(FortranBase):
+    """
+    An object representing a Fortran abstract interface.
+    """
+    def __init__(self,proc,parent):
+        self.name = proc.name
+        self.permission = proc.permission
+        self.parent = parent
+        if self.parent:
+            self.parobj = self.parent.obj
+        self.obj = 'absinterface'
+        self.doc = parent.doc
+
+        self.hierarchy = []
+        cur = self.parent
+        while cur:
+            self.hierarchy.append(cur)
+            cur = cur.parent
+        self.hierarchy.reverse()
+
+    
 class FortranVariable(FortranBase):
     """
     An object representing a variable within Fortran.
@@ -865,19 +905,19 @@ class FortranVariable(FortranBase):


     def correlate(self,project):
-        if self.proto and self.proto[0] == '*': self.proto[0] = '*'
+        if self.proto and self.proto[0] == '*': self.proto[0] = '*' #FIXME: Is this line necessary?
         if (self.vartype == "type" or self.vartype == "class") and self.proto and self.proto[0] != '*':
             for dtype in self.parent.all_types:
                 if dtype.name.lower() == self.proto[0].lower(): 
                     self.proto[0] = dtype
                     break
         elif self.vartype == "procedure" and self.proto:
-            for proc in self.parent.procs:
+            for proc in self.parent.all_procs + self.parent.all_absinterfaces:
                 if proc.name.lower() == str(self.proto).lower():     #JW
                     self.proto = proc
                     break
             if type(self.proto) == str:
-                for interface in self.parent.all_interfaces:
+                for interface in self.parent.all_absinterfaces:
                     if interface.abstract:
                         for proc in interface.subroutines + interface.functions:
                             if proc.name.lower() == self.proto.lower():
@@ -917,9 +957,9 @@ class FortranBoundProcedure(FortranBase):
             self.prototype = None

     def correlate(self,project):
-        self.procs = self.parent.procs
+        self.all_procs = self.parent.all_procs
         for i in range(len(self.bindings)):
-            for proc in self.procs:
+            for proc in self.all_procs:
                 if proc.name.lower() == self.bindings[i].lower():
                     self.bindings[i] = proc
                     break
diff --git a/ford/tipuesearch/img/search.png b/ford/tipuesearch/img/search.png
old mode 100755
new mode 100644
diff --git a/ford/tipuesearch/tipuesearch.css b/ford/tipuesearch/tipuesearch.css
old mode 100755
new mode 100644

$ git apply --check --ignore-space-change --ignore-whitespace  ../ford.patch
error: patch failed: ford/fortran_project.py:119
error: ford/fortran_project.py: patch does not apply
error: patch failed: ford/sourceform.py:383
error: ford/sourceform.py: patch does not apply

-            self.procs.extend(mod.pub_procs)
-            self.all_interfaces.extend(mod.all_interfaces)
+            self.all_procs.extend(mod.pub_procs)
+            self.all_absinterfaces.extend(mod.all_absinterfaces)

            self.procs.extend(mod.pub_procs)
            self.all_interfaces.extend(mod.all_interfaces)

$ patch -p1 <../ford.patch
patching file .gitignore
patching file ford/fortran_project.py
Hunk #3 succeeded at 119 with fuzz 2.
patching file ford/sourceform.py
Hunk #4 FAILED at 391.
Hunk #5 FAILED at 479.
Hunk #9 FAILED at 695.
Hunk #10 succeeded at 753 with fuzz 2.
Hunk #12 FAILED at 798.
4 out of 14 hunks FAILED -- saving rejects to file ford/sourceform.py.rej
patching file ford/tipuesearch/img/search.png
patching file ford/tipuesearch/tipuesearch.css

dan@stanley:/tmp/git$ ford testbed.md
Reading file ./testbed/ruritania.f90

Correlating information from different parts of your project...

Traceback (most recent call last):
  File "/usr/local/bin/ford", line 9, in <module>
    load_entry_point('FORD==1.1.0', 'console_scripts', 'ford')()
  File "/usr/local/lib/python2.7/dist-packages/ford/__init__.py", line 152, in main
    project.correlate()
  File "/usr/local/lib/python2.7/dist-packages/ford/fortran_project.py", line 129, in correlate
    container.correlate(self)
  File "/usr/local/lib/python2.7/dist-packages/ford/sourceform.py", line 396, in correlate
    func.correlate(project)
  File "/usr/local/lib/python2.7/dist-packages/ford/sourceform.py", line 407, in correlate
    arg.correlate(project)
AttributeError: 'str' object has no attribute 'correlate'

 git apply --reject --whitespace=fix /tmp/git/ford.patch

t$ /tmp/git2/ford/ford.py  testbed.md
Reading file ./testbed/ruritania.f90

Correlating information from different parts of your project...

Traceback (most recent call last):
  File "/tmp/git2/ford/ford.py", line 7, in <module>
    main()
  File "/tmp/git2/ford/ford/__init__.py", line 158, in main
    project.correlate()
  File "/tmp/git2/ford/ford/fortran_project.py", line 136, in correlate
    container.correlate(self)
  File "/tmp/git2/ford/ford/sourceform.py", line 408, in correlate
    func.correlate(project)
  File "/tmp/git2/ford/ford/sourceform.py", line 419, in correlate
    arg.correlate(project)
AttributeError: 'str' object has no attribute 'correlate'

$ ford -e F90 f90 ford_master.md
usage: ford [-h] [-d [PROJECT_DIR [PROJECT_DIR ...]]] [-o OUTPUT_DIR] [-s CSS]
            [--exclude EXCLUDE] [-e [EXTENSIONS [EXTENSIONS ...]]] [-w]
            [--no-warn] [-V]
            project_file
ford: error: too few arguments