SciPy

Signature file

The syntax specification for signature files (.pyf files) is borrowed from the Fortran 90/95 language specification. Almost all Fortran 90/95 standard constructs are understood, both in free and fixed format (recall that Fortran 77 is a subset of Fortran 90/95). F2PY introduces also some extensions to Fortran 90/95 language specification that help designing Fortran to Python interface, make it more “Pythonic”.

Signature files may contain arbitrary Fortran code (so that Fortran codes can be considered as signature files). F2PY silently ignores Fortran constructs that are irrelevant for creating the interface. However, this includes also syntax errors. So, be careful not making ones;-).

In general, the contents of signature files is case-sensitive. When scanning Fortran codes and writing a signature file, F2PY lowers all cases automatically except in multiline blocks or when --no-lower option is used.

The syntax of signature files is overvied below.

Python module block

A signature file may contain one (recommended) or more python module blocks. python module block describes the contents of a Python/C extension module <modulename>module.c that F2PY generates.

Exception: if <modulename> contains a substring __user__, then the corresponding python module block describes the signatures of so-called call-back functions (see Call-back arguments).

A python module block has the following structure:

python module <modulename>
  [<usercode statement>]...
  [
  interface
    <usercode statement>
    <Fortran block data signatures>
    <Fortran/C routine signatures>
  end [interface]
  ]...
  [
  interface
    module <F90 modulename>
      [<F90 module data type declarations>]
      [<F90 module routine signatures>]
    end [module [<F90 modulename>]]
  end [interface]
  ]...
end [python module [<modulename>]]

Here brackets [] indicate a optional part, dots ... indicate one or more of a previous part. So, []... reads zero or more of a previous part.

Fortran/C routine signatures

The signature of a Fortran routine has the following structure:

[<typespec>] function | subroutine <routine name> \
              [ ( [<arguments>] ) ] [ result ( <entityname> ) ]
  [<argument/variable type declarations>]
  [<argument/variable attribute statements>]
  [<use statements>]
  [<common block statements>]
  [<other statements>]
end [ function | subroutine [<routine name>] ]

From a Fortran routine signature F2PY generates a Python/C extension function that has the following signature:

def <routine name>(<required arguments>[,<optional arguments>]):
     ...
     return <return variables>

The signature of a Fortran block data has the following structure:

block data [ <block data name> ]
  [<variable type declarations>]
  [<variable attribute statements>]
  [<use statements>]
  [<common block statements>]
  [<include statements>]
end [ block data [<block data name>] ]

Type declarations

The definition of the <argument/variable type declaration> part is

<typespec> [ [<attrspec>] :: ] <entitydecl>

where

<typespec> := byte | character [<charselector>]
           | complex [<kindselector>] | real [<kindselector>]
           | double complex | double precision
           | integer [<kindselector>] | logical [<kindselector>]

<charselector> := * <charlen>
               | ( [len=] <len> [ , [kind=] <kind>] )
               | ( kind= <kind> [ , len= <len> ] )
<kindselector> := * <intlen> | ( [kind=] <kind> )

<entitydecl> := <name> [ [ * <charlen> ] [ ( <arrayspec> ) ]
                      | [ ( <arrayspec> ) ] * <charlen> ]
                     | [ / <init_expr> / | = <init_expr> ] \
                       [ , <entitydecl> ]

and

  • <attrspec> is a comma separated list of attributes;
  • <arrayspec> is a comma separated list of dimension bounds;
  • <init_expr> is a C expression.
  • <intlen> may be negative integer for integer type specifications. In such cases integer*<negintlen> represents unsigned C integers.

If an argument has no <argument type declaration>, its type is determined by applying implicit rules to its name.

Statements

Attribute statements:
The <argument/variable attribute statement> is <argument/variable type declaration> without <typespec>. In addition, in an attribute statement one cannot use other attributes, also <entitydecl> can be only a list of names.
Use statements:

The definition of the <use statement> part is

use <modulename> [ , <rename_list> | , ONLY : <only_list> ]

where

<rename_list> := <local_name> => <use_name> [ , <rename_list> ]

Currently F2PY uses use statement only for linking call-back modules and external arguments (call-back functions), see Call-back arguments.

Common block statements:

The definition of the <common block statement> part is

common / <common name> / <shortentitydecl>

where

<shortentitydecl> := <name> [ ( <arrayspec> ) ] [ , <shortentitydecl> ]

One python module block should not contain two or more common blocks with the same name. Otherwise, the latter ones are ignored. The types of variables in <shortentitydecl> are defined using <argument type declarations>. Note that the corresponding <argument type declarations> may contain array specifications; then you don’t need to specify these in <shortentitydecl>.

Other statements:

The <other statement> part refers to any other Fortran language constructs that are not described above. F2PY ignores most of them except

  • call statements and function calls of external arguments (more details?);

  • include statements
    include '<filename>'
    include "<filename>"

    If a file <filename> does not exist, the include statement is ignored. Otherwise, the file <filename> is included to a signature file. include statements can be used in any part of a signature file, also outside the Fortran/C routine signature blocks.

  • implicit statements
    implicit none
    implicit <list of implicit maps>

    where

    <implicit map> := <typespec> ( <list of letters or range of letters> )

    Implicit rules are used to determine the type specification of a variable (from the first-letter of its name) if the variable is not defined using <variable type declaration>. Default implicit rule is given by

    implicit real (a-h,o-z,$_), integer (i-m)
  • entry statements
    entry <entry name> [([<arguments>])]

    F2PY generates wrappers to all entry names using the signature of the routine block.

    Tip: entry statement can be used to describe the signature of an arbitrary routine allowing F2PY to generate a number of wrappers from only one routine block signature. There are few restrictions while doing this: fortranname cannot be used, callstatement and callprotoargument can be used only if they are valid for all entry routines, etc.

In addition, F2PY introduces the following statements:

  • threadsafe

    Use Py_BEGIN_ALLOW_THREADS .. Py_END_ALLOW_THREADS block around the call to Fortran/C function.

  • callstatement <C-expr|multi-line block>

    Replace F2PY generated call statement to Fortran/C function with <C-expr|multi-line block>. The wrapped Fortran/C function is available as (*f2py_func). To raise an exception, set f2py_success = 0 in <C-expr|multi-line block>.

  • callprotoargument <C-typespecs>

    When callstatement statement is used then F2PY may not generate proper prototypes for Fortran/C functions (because <C-expr> may contain any function calls and F2PY has no way to determine what should be the proper prototype). With this statement you can explicitly specify the arguments of the corresponding prototype:

    extern <return type> FUNC_F(<routine name>,<ROUTINE NAME>)(<callprotoargument>);
  • fortranname [<actual Fortran/C routine name>]

    You can use arbitrary <routine name> for a given Fortran/C function. Then you have to specify <actual Fortran/C routine name> with this statement.

    If fortranname statement is used without <actual Fortran/C routine name> then a dummy wrapper is generated.

  • usercode <multi-line block>

    When used inside python module block, then given C code will be inserted to generated C/API source just before wrapper function definitions. Here you can define arbitrary C functions to be used in initialization of optional arguments, for example. If usercode is used twice inside python module block then the second multiline block is inserted after the definition of external routines.

    When used inside <routine singature>, then given C code will be inserted to the corresponding wrapper function just after declaring variables but before any C statements. So, usercode follow-up can contain both declarations and C statements.

    When used inside the first interface block, then given C code will be inserted at the end of the initialization function of the extension module. Here you can modify extension modules dictionary. For example, for defining additional variables etc.

  • pymethoddef <multiline block>

    Multiline block will be inserted to the definition of module methods PyMethodDef-array. It must be a comma-separated list of C arrays (see Extending and Embedding Python documentation for details). pymethoddef statement can be used only inside python module block.

Attributes

The following attributes are used by F2PY:

optional

The corresponding argument is moved to the end of <optional arguments> list. A default value for an optional argument can be specified <init_expr>, see entitydecl definition. Note that the default value must be given as a valid C expression.

Note that whenever <init_expr> is used, optional attribute is set automatically by F2PY.

For an optional array argument, all its dimensions must be bounded.

required

The corresponding argument is considered as a required one. This is default. You need to specify required only if there is a need to disable automatic optional setting when <init_expr> is used.

If Python None object is used as an required argument, the argument is treated as optional. That is, in the case of array argument, the memory is allocated. And if <init_expr> is given, the corresponding initialization is carried out.

dimension(<arrayspec>)
The corresponding variable is considered as an array with given dimensions in <arrayspec>.
intent(<intentspec>)

This specifies the “intention” of the corresponding argument. <intentspec> is a comma separated list of the following keys:

  • in

    The argument is considered as an input-only argument. It means that the value of the argument is passed to Fortran/C function and that function is expected not to change the value of an argument.

  • inout

    The argument is considered as an input/output or in situ output argument. intent(inout) arguments can be only “contiguous” Numpy arrays with proper type and size. Here “contiguous” can be either in Fortran or C sense. The latter one coincides with the contiguous concept used in Numpy and is effective only if intent(c) is used. Fortran contiguity is assumed by default.

    Using intent(inout) is generally not recommended, use intent(in,out) instead. See also intent(inplace) attribute.

  • inplace

    The argument is considered as an input/output or in situ output argument. intent(inplace) arguments must be Numpy arrays with proper size. If the type of an array is not “proper” or the array is non-contiguous then the array will be changed in-place to fix the type and make it contiguous.

    Using intent(inplace) is generally not recommended either. For example, when slices have been taken from an intent(inplace) argument then after in-place changes, slices data pointers may point to unallocated memory area.

  • out

    The argument is considered as an return variable. It is appended to the <returned variables> list. Using intent(out) sets intent(hide) automatically, unless also intent(in) or intent(inout) were used.

    By default, returned multidimensional arrays are Fortran-contiguous. If intent(c) is used, then returned multidimensional arrays are C-contiguous.

  • hide

    The argument is removed from the list of required or optional arguments. Typically intent(hide) is used with intent(out) or when <init_expr> completely determines the value of the argument like in the following example:

    integer intent(hide),depend(a) :: n = len(a)
    real intent(in),dimension(n) :: a
  • c

    The argument is treated as a C scalar or C array argument. In the case of a scalar argument, its value is passed to C function as a C scalar argument (recall that Fortran scalar arguments are actually C pointer arguments). In the case of an array argument, the wrapper function is assumed to treat multidimensional arrays as C-contiguous arrays.

    There is no need to use intent(c) for one-dimensional arrays, no matter if the wrapped function is either a Fortran or a C function. This is because the concepts of Fortran- and C contiguity overlap in one-dimensional cases.

    If intent(c) is used as an statement but without entity declaration list, then F2PY adds intent(c) attibute to all arguments.

    Also, when wrapping C functions, one must use intent(c) attribute for <routine name> in order to disable Fortran specific F_FUNC(..,..) macros.

  • cache

    The argument is treated as a junk of memory. No Fortran nor C contiguity checks are carried out. Using intent(cache) makes sense only for array arguments, also in connection with intent(hide) or optional attributes.

  • copy

    Ensure that the original contents of intent(in) argument is preserved. Typically used in connection with intent(in,out) attribute. F2PY creates an optional argument overwrite_<argument name> with the default value 0.

  • overwrite

    The original contents of the intent(in) argument may be altered by the Fortran/C function. F2PY creates an optional argument overwrite_<argument name> with the default value 1.

  • out=<new name>

    Replace the return name with <new name> in the __doc__ string of a wrapper function.

  • callback

    Construct an external function suitable for calling Python function from Fortran. intent(callback) must be specified before the corresponding external statement. If ‘argument’ is not in argument list then it will be added to Python wrapper but only initializing external function.

    Use intent(callback) in situations where a Fortran/C code assumes that a user implements a function with given prototype and links it to an executable. Don’t use intent(callback) if function appears in the argument list of a Fortran routine.

    With intent(hide) or optional attributes specified and using a wrapper function without specifying the callback argument in argument list then call-back function is looked in the namespace of F2PY generated extension module where it can be set as a module attribute by a user.

  • aux

    Define auxiliary C variable in F2PY generated wrapper function. Useful to save parameter values so that they can be accessed in initialization expression of other variables. Note that intent(aux) silently implies intent(c).

The following rules apply:

  • If no intent(in | inout | out | hide) is specified, intent(in) is assumed.
  • intent(in,inout) is intent(in).
  • intent(in,hide) or intent(inout,hide) is intent(hide).
  • intent(out) is intent(out,hide) unless intent(in) or intent(inout) is specified.
  • If intent(copy) or intent(overwrite) is used, then an additional optional argument is introduced with a name overwrite_<argument name> and a default value 0 or 1, respectively.
  • intent(inout,inplace) is intent(inplace).
  • intent(in,inplace) is intent(inplace).
  • intent(hide) disables optional and required.
check([<C-booleanexpr>])

Perform consistency check of arguments by evaluating <C-booleanexpr>; if <C-booleanexpr> returns 0, an exception is raised.

If check(..) is not used then F2PY generates few standard checks (e.g. in a case of an array argument, check for the proper shape and size) automatically. Use check() to disable checks generated by F2PY.

depend([<names>])

This declares that the corresponding argument depends on the values of variables in the list <names>. For example, <init_expr> may use the values of other arguments. Using information given by depend(..) attributes, F2PY ensures that arguments are initialized in a proper order. If depend(..) attribute is not used then F2PY determines dependence relations automatically. Use depend() to disable dependence relations generated by F2PY.

When you edit dependence relations that were initially generated by F2PY, be careful not to break the dependence relations of other relevant variables. Another thing to watch out is cyclic dependencies. F2PY is able to detect cyclic dependencies when constructing wrappers and it complains if any are found.

allocatable
The corresponding variable is Fortran 90 allocatable array defined as Fortran 90 module data.
external

The corresponding argument is a function provided by user. The signature of this so-called call-back function can be defined

  • in __user__ module block,
  • or by demonstrative (or real, if the signature file is a real Fortran code) call in the <other statements> block.

For example, F2PY generates from

external cb_sub, cb_fun
integer n
real a(n),r
call cb_sub(a,n)
r = cb_fun(4)

the following call-back signatures:

subroutine cb_sub(a,n)
    real dimension(n) :: a
    integer optional,check(len(a)>=n),depend(a) :: n=len(a)
end subroutine cb_sub
function cb_fun(e_4_e) result (r)
    integer :: e_4_e
    real :: r
end function cb_fun

The corresponding user-provided Python function are then:

def cb_sub(a,[n]):
    ...
    return
def cb_fun(e_4_e):
    ...
    return r

See also intent(callback) attribute.

parameter
The corresponding variable is a parameter and it must have a fixed value. F2PY replaces all parameter occurrences by their corresponding values.

Extensions

F2PY directives

The so-called F2PY directives allow using F2PY signature file constructs also in Fortran 77/90 source codes. With this feature you can skip (almost) completely intermediate signature file generations and apply F2PY directly to Fortran source codes.

F2PY directive has the following form:

<comment char>f2py ...

where allowed comment characters for fixed and free format Fortran codes are cC*!# and !, respectively. Everything that follows <comment char>f2py is ignored by a compiler but read by F2PY as a normal Fortran, non-comment line:

When F2PY finds a line with F2PY directive, the directive is first replaced by 5 spaces and then the line is reread.

For fixed format Fortran codes, <comment char> must be at the first column of a file, of course. For free format Fortran codes, F2PY directives can appear anywhere in a file.

C expressions

C expressions are used in the following parts of signature files:

  • <init_expr> of variable initialization;
  • <C-booleanexpr> of the check attribute;
  • <arrayspec> of the ``dimension attribute;
  • callstatement statement, here also a C multiline block can be used.

A C expression may contain:

  • standard C constructs;

  • functions from math.h and Python.h;

  • variables from the argument list, presumably initialized before according to given dependence relations;

  • the following CPP macros:

    rank(<name>)

    Returns the rank of an array <name>.

    shape(<name>,<n>)

    Returns the <n>-th dimension of an array <name>.

    len(<name>)

    Returns the lenght of an array <name>.

    size(<name>)

    Returns the size of an array <name>.

    slen(<name>)

    Returns the length of a string <name>.

For initializing an array <array name>, F2PY generates a loop over all indices and dimensions that executes the following pseudo-statement:

<array name>(_i[0],_i[1],...) = <init_expr>;

where _i[<i>] refers to the <i>-th index value and that runs from 0 to shape(<array name>,<i>)-1.

For example, a function myrange(n) generated from the following signature

subroutine myrange(a,n)
  fortranname        ! myrange is a dummy wrapper
  integer intent(in) :: n
  real*8 intent(c,out),dimension(n),depend(n) :: a = _i[0]
end subroutine myrange

is equivalent to numpy.arange(n,dtype=float).

Warning

F2PY may lower cases also in C expressions when scanning Fortran codes (see --[no]-lower option).

Multiline blocks

A multiline block starts with ''' (triple single-quotes) and ends with ''' in some strictly subsequent line. Multiline blocks can be used only within .pyf files. The contents of a multiline block can be arbitrary (except that it cannot contain ''') and no transformations (e.g. lowering cases) are applied to it.

Currently, multiline blocks can be used in the following constructs:

  • as a C expression of the callstatement statement;
  • as a C type specification of the callprotoargument statement;
  • as a C code block of the usercode statement;
  • as a list of C arrays of the pymethoddef statement;
  • as documentation string.