Metadata-Version: 2.1
Name: f90wrap
Version: 0.2.4
Summary: Fortran to Python interface generator with derived type support
Home-page: https://github.com/jameskermode/f90wrap
Author: James Kermode
Author-email: james.kermode@gmail.com
License: UNKNOWN
Download-URL: https://github.com/jameskermode/f90wrap/archive/refs/tags/v0.2.4.tar.gz
Description: f90wrap: Fortran to Python interface generator with derived type support
        ========================================================================
        
        [![Build Status](https://travis-ci.com/jameskermode/f90wrap.svg?branch=master)](https://travis-ci.com/jameskermode/f90wrap)
        
        f90wrap is a tool to automatically generate Python extension modules
        which interface to Fortran code that makes use of derived types. It
        builds on the capabilities of the popular
        [f2py](https://sysbio.ioc.ee/projects/f2py2e/) utility by generating a
        simpler Fortran 90 interface to the original Fortran code which is then
        suitable for wrapping with f2py, together with a higher-level Pythonic
        wrapper that makes the existance of an additional layer transparent to
        the final user.
        
        Copyright (C) James Kermode 2011-2021. Released under the GNU Lesser General
        Public License, version 3. Parts originally based on f90doc - automatic
        documentation generator for Fortran 90. Copyright (C) 2004 Ian Rutt.
        
        If you would like to license the source code under different terms,
        please contact James Kermode <james.kermode@gmail.com>
        
        Dependencies
        ------------
        
         1.  [Python](http://www.python.org) 3.6+ (Python 2.7 no longer supported)
         2.  Recent version of [numpy](http://www.numpy.org) which includes `f2py`
         3.  Fortran compiler - tested with `gfortran` 4.6+ and recent `ifort` 12+
        
        Installation
        ------------
        
        For the latest stable release, install with either `pip`:
        
        ```
        pip install f90wrap
        ```
        
        For the development version, installation is as follows:
        
        ```
        pip install git+https://github.com/jameskermode/f90wrap
        ```
        
        Note that if your Fortran 90 compiler has a non-standard name
        (e.g. gfortran-9) then you need to set the `F90` environment variable
        prior to installing f90wrap to ensure it uses the correct one, e.g.
        
        ```
        F90=gfortran-9 pip install f90wrap
        ```
        
        Examples and Testing
        --------------------
        
        To test the installation, run `make test` from the `examples/`
        directory. You may find the code in the various examples useful.
        
        Citing f90wrap
        --------------
        
        If you find `f90wrap` useful in academic work, please cite the following
        (open access) publication:
        
        > J. R. Kermode, f90wrap: an automated tool for constructing 
        > deep Python interfaces to modern Fortran codes. 
        > J. Phys. Condens. Matter (2020) 
        >[doi:10.1088/1361-648X/ab82d2](https://dx.doi.org/10.1088/1361-648X/ab82d2)
        
        BibTeX entry:
        
        ```bibtex
        
        @ARTICLE{Kermode2020-f90wrap,
          title    = "f90wrap: an automated tool for constructing deep Python
                      interfaces to modern Fortran codes",
          author   = "Kermode, James R",
          journal  = "J. Phys. Condens. Matter",
          month    =  mar,
          year     =  2020,
          keywords = "Fortran; Interfacing; Interoperability; Python; Wrapping codes;
                      f2py",
          language = "en",
          issn     = "0953-8984, 1361-648X",
          pmid     = "32209737",
          doi      = "10.1088/1361-648X/ab82d2"
        }
        
        ```
        
        Case studies
        ------------
        
        f90wrap has been used to wrap the following large-scale scientific
        applications:
        
         - [QUIP](http://libatoms.github.io/QUIP/) - molecular dynamics code
         - [CASTEP](http://www.castep.org) - electronic structure code
        
        See this [Jupyter notebook](https://github.com/jameskermode/f90wrap/blob/master/docs/tutorials/f90wrap-demo-feb-2020.ipynb) 
        from a recent seminar for more details.
        
        Usage
        -----
        
        To use `f90wrap` to wrap a set of Fortran 90 source files and produce
        wrappers suitable for input to f2py use:
        
            f90wrap -m MODULE F90_FILES
        
        where `MODULE` is the name of the Python module you want to produce (e.g.
        the name of the Fortran code you are wrapping) and `F90_FILES` is a list
        of Fortran 90 source files containing the modules, types and subroutines
        you would like to expose via Python.
        
        This will produce two types of output: Fortran 90 wrapper files suitable
        for input to `f2py` to produce a low-level Python extension module, and a
        high-level Python module desinged to be used together with the
        f2py-generated module to give a more Pythonic interface.
        
        One Fortran 90 wrapper file is written for each source file, named
        `f90wrap_F90_FILE.f90`, plus possibly an extra file named
        `f90wrap_toplevel.f90` if there are any subroutines or functions defined
        outside of modules in `F90_FILES`.
        
        To use f2py to compile these wrappers into an extension module, use:
        
            f2py -c -m _MODULE OBJ_FILES f90wrap_*.f90 *.o
        
        where `_MODULE` is the name of the low-level extension module.
        
        Optionally, you can replace `f2py` with `f2py-f90wrap`, which is a
        slightly modified version of `f2py` included in this distribution
        that introduces the following features:
        
        1.  Allow the Fortran `present()` intrinsic function to work correctly with
            optional arguments. If an argument to an f2py wrapped function is
            optional and is not given, replace it with `NULL`.
        2.  Allow Fortran routines to raise a RuntimeError exception with a
            message by calling an external function `f90wrap_abort`().
            This is implemented using a `setjmp()/longjmp()` trap.
        3.  Allow Fortran routines to be interrupted with `Ctrl+C` by installing
            a custom interrupt handler before the call into Fortran is made.
            After the Fortran routine returns, the previous interrupt handler
            is restored.
        
        Notes
        -----
        
        - Unlike standard `f2py`, `f90wrap` converts all `intent(out)` arrays to
        `intent(in, out)`. This was a deliberate design decision to allow allocatable and automatic arrays of unknown output size to be used. It is hard in general to work out what size array needs to be allocated, so relying on the the user to pre-allocate from Python is the safest solution.
        - Scalar arguments without `intent` are treated as `intent(in)` by `f2py`. To have `inout` scalars, you need to call `f90wrap` with the `--default-to-inout` flag and declare the python variables as 1-length numpy arrays (`numpy.zeros(1)` for example).
        - Pointer arguments are not supported.
        - Arrays of derived types are currently not fully supported: a workaround is provided for 1D-fixed-length arrays, i.e. `type(a), dimension(b) :: c`. In this case, the super-type `Type_a_Xb_Array` will be created, and the array of types can be accessed through `c.items`. Note that dimension b can not be `:`, but can be a parameter.
        
        
        How f90wrap works
        -----------------
        
        There are five steps in the process of wrapping a Fortran 90 routine to
        allow it to be called from Python.
        
        1.  The Fortran source files are scanned, building up an
            abstract symbol tree (AST) which describes all the modules, types,
            subroutines and functions found.
        2.  The AST is transformed to remove nodes which
            should not be wrapped (e.g. private symbols in modules, routines
            with arguments of a derived type not defined in the project, etc.)
        3.  The `f90wrap.f90wrapgen.F90WrapperGenerator` class is used to write
            a simplified Fortran 90 prototype for each routine, with derived
            type arguments replaced by integer arrays containing a
            representation of a pointer to the derived type, in the manner
            described in
            [Pletzer2008](https://doi.org/10.1109/MCSE.2008.94).
            This allows opaque references to the
            true Fortran derived type data structures to be passed back and
            forth between Python and Fortran.
        4.  f2py is used to combine the F90 wrappers and the original compiled
            functions into a Python extension module (optionally, f2py can be
            replaced by f2py-f90wrap, a slightly modified version which adds
            support for exception handling and interruption during exceution of
            Fortran code).
        5.  The `f90wrap.pywrapgen.PythonWrapperGenerator` class is used to
            write a thin object-oriented layer on top of the f2py generated
            wrapper functions which handles conversion between Python object
            instances and Fortran derived-type variables, converting arguments
            back and forth automatically.
        
        Advanced Features
        -----------------
        
        Additional command line arguments can be passed to f90wrap to customize
        how the wrappers are generated. See the `examples/` directory to see how
        some of the options are used:
        
              -h, --help            show this help message and exit
              -v, --verbose         set verbosity level [default: None]
              -V, --version         show program's version number and exit
              -p PREFIX, --prefix PREFIX
                                    Prefix to prepend to arguments and subroutines.
              -c [CALLBACK [CALLBACK ...]], --callback [CALLBACK [CALLBACK ...]]
                                    Names of permitted callback routines.
              -C [CONSTRUCTORS [CONSTRUCTORS ...]], --constructors [CONSTRUCTORS [CONSTRUCTORS ...]]
                                    Names of constructor routines.
              -D [DESTRUCTORS [DESTRUCTORS ...]], --destructors [DESTRUCTORS [DESTRUCTORS ...]]
                                    Names of destructor routines.
              -k KIND_MAP, --kind-map KIND_MAP
                                    File containting Python dictionary in f2py_f2cmap
                                    format
              -s STRING_LENGTHS, --string-lengths STRING_LENGTHS
                                    "File containing Python dictionary mapping string
                                    length names to values
              -S DEFAULT_STRING_LENGTH, --default-string-length DEFAULT_STRING_LENGTH
                                    Default length of character strings
              -i INIT_LINES, --init-lines INIT_LINES
                                    File containing Python dictionary mapping type names
                                    to necessary initialisation code
              -I INIT_FILE, --init-file INIT_FILE
                                    Python source file containing code to be added to
                                    autogenerated __init__.py
              -A ARGUMENT_NAME_MAP, --argument-name-map ARGUMENT_NAME_MAP
                                    File containing Python dictionary to rename Fortran
                                    arguments
              --short-names SHORT_NAMES
                                    File containing Python dictionary mapping full type
                                    names to abbreviations
              --py-mod-names PY_MOD_NAMES
                                    File containing Python dictionary mapping Fortran
                                    module names to Python ones
              --class-names CLASS_NAMES
                                    File containing Python dictionary mapping Fortran type
                                    names to Python classes
              --joint-modules JOINT_MODULES
                                    File containing Python dictionary mapping modules
                                    defining times to list of additional modules defining
                                    methods
              -m MOD_NAME, --mod-name MOD_NAME
                                    Name of output extension module (without .so
                                    extension).
              -M, --move-methods    Convert routines with derived type instance as first
                                    agument into class methods
              --shorten-routine-names
                                    Remove type name prefix from routine names, e.g.
                                    cell_symmetrise() -> symmetrise()
              -P, --package         Generate a Python package instead of a single module
              -a ABORT_FUNC, --abort-func ABORT_FUNC
                                    Name of Fortran subroutine to invoke if a fatal error
                                    occurs
              --only [ONLY [ONLY ...]]
                                    Subroutines to include in wrapper
              --skip [SKIP [SKIP ...]]
                                    Subroutines to exclude modules and subroutines from
                                    wrapper
              --skip-types [SKIP_TYPES [SKIP_TYPES ...]]
                                    Subroutines to exclude types from wrapper
              --force-public [FORCE_PUBLIC [FORCE_PUBLIC ...]]
                                    Names which are forced to be make public
              --default-to-inout    Sets all arguments without intent to intent(inout)
              --conf-file CONF_FILE
                                    Use Python configuration script to set options
              --documentation-plugin DOCUMENTATION_PLUGIN
                                    Use Python script for expanding the documentation of
                                    functions and subroutines. All lines of the given tree
                                    object are passed to it with a reference to its
                                    documentation
              --py-max-line-length PY_MAX_LINE_LENGTH
                                    Maximum length of lines in python files written.
                                    Default: 80
              --f90-max-line-length F90_MAX_LINE_LENGTH
                                    Maximum length of lines in fortan files written.
                                    Default: 120
                 
        
        Author
        ------
        
        James Kermode [jameskermode](https://github.com/jameskermode)
        
        Contributors
        ------------
        
        - Tamas Stenczel [stenczelt](https://github.com/stenczelt)
        - Steven Murray [steven-murray](https://github.com/steven-murray)
        - Greg Corbett  [gregcorbett](https://github.com/gregcorbett)
        - Bob Fischer [citibob](https://github.com/citibob)
        - David Verelst [davidovitch](https://github.com/davidovitch)
        - James Orr [jamesorr](https://github.com/jamesorr)
        - [yvesch](https://github.com/yvesch)
        - [Matthias Cuntz](https://github.com/mcuntz)
        - Balthasar Reuter [reuterbal](https://github.com/reuterbal)
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
