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Python wrapper for XML output generator for Open Fortran Parser

Project description

Extension of Java-based Open Fortran Parser and a Python wrapper enabling Fortran parsing from Python.

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Implementation has 2 parts: the XML generator written in Java, and Python wrapper for the generator.

The implementation is tested on Linux, OS X and Windows.

In this file, first the AST specification is described, then the Java implementation, and then the Python wrapper.

AST specification

For any Fortran file, the resulting XML file has the following structure:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<ofp version="0.8.5-1"> <!-- version of the Open Fortran Parser used -->
  <file path="/path/to/parsed/file.f90">
    <!-- Fortran syntax goes here -->
  </file>
</ofp>

Root node is <ofp>, it has one subnode <file>.

Inside the <file>, there might be one or many of the following nodes:

  • <program>
  • <subroutine>
  • <function>
  • <module>
  • <interface>

Additionally, every XML node that was built using tokens from the source code (which means almost any XML node) has its source code location described in the following way:

<node col_begin="..." col_end="..." line_begin="..." line_end="..." />

For simplicity, the above XML file boilerplate as well as locations are stripped from the examples that follow.

For each presented construct, Fortran code snippet and corresponding XML AST is given.

Comments and directives

Comment:

! my comment
!$omp parallel do
<comment text="! my comment"/>
<comment text="!$omp parallel do"/>

Directive:

#define NDIMS 3
<directive text="#define NDIMS 3"/>

Nodes <comment> and <directive> exist to carry comments and preprocessor directives, respectively. These nodes might be in principle inserted before, after or within any of other nodes, however, in practice they are either surrounding the top-level nodes (e.g. program or subroutine) or are placed in-between non-compound declarations and/or statements within them.

Note: compiler directives are comments in Fortran.

Program

program empty
  ...
end program empty
<program name="empty">
  <body>
    ...
  </body>
</program>

In the body, Declarations followed by any number of statements can be found.

And each of the statements listed after the declarations, can be one of Simple statements or Compound statements.

Declarations

A special node <specification> wraps all declarations:

<specification declarations="0" implicits="0" imports="0" uses="0">
  ...
</specification>

It provides counts for each of the declaration type and contains a collection of declarations, which can any of the following:

  • <use>
  • <declaraion>

The <declaraion> node is special in a sense that it has type attribute that specifies what kind of declaration it is.

Implicit declaration

implicit none
implicit real (A-H,O-Z)
<declaration subtype="none" type="implicit" />
<declaration subtype="some" type="implicit">
  <type name="real" type="intrinsic" />
  <letter-ranges>
    <letter-range begin="A" end="H" />
    <letter-range begin="O" end="Z" />
  </letter-ranges>
</declaration>

Variable declaration

integer i, j
<declaration type="variable">
  <type name="integer" type="intrinsic"/>
  <variables count="2">
    <variable name="i"/>
    <variable name="j"/>
  </variables>
</declaration>

External declaration

external omp_get_num_procs

Save declaration

save n

Use

use mpi
use my_interface, only: subroutine1, subroutine2
use, non_intrinsic :: my_module
use, intrinsic :: iso_c_binding, only: c_int, c_float
<use name="mpi" />
<use name="my_interface">
  <only>
    <name id="subroutine1" />
    <name id="subroutine2" />
  </only>
</use>
<use name="my_module">
  <nature name="non_intrinsic" />
</use>
<use name="iso_c_binding">
  <nature name="intrinsic" />
  <only>
    <name id="c_int" />
    <name id="c_float" />
  </only>
</use>

Compound statements

Compound statements, e.g.:

  • <if>
  • <loop>
  • <select>

each have <header> and <body>.

If

In the header of <if>, an expression is present.

See Expressions for a definition.

Loop

In the header of the <loop>, at least one <index-variable> is present. It has <lower-bound>, <upper-bound> and <step>.

Select

In the body of <select> there multiple <case> nodes. These are also compound (i.e. each of them has <header> and <body>), however they exist only within the body of select statement.

Simple statements

<statement>
  ...
</statement>

All simple statements are using <statement> node, which wraps around nodes like:

  • <assignment>
  • <pointer-assignment>
  • <call>
  • <open>
  • <close>
  • <write>
  • <format>
  • <print>
  • <allocate>
  • <deallocate>
  • <return>
  • <stop>
  • <continue>
  • <cycle>
  • <arithmetic-if>

Assignment

x = 1
<assignment>
  <target>
    <name id="i" />
  </target>
  <value>
    <literal type="int" value="1" />
  </value>
</assignment>

Call

call configure
call initialize()
call calculate(1, 2)
call something(thing=my_value)
<call>
  <name hasSubscripts="false" id="configure" type="procedure" />
</call>
<call>
  <name hasSubscripts="true" id="initialize" type="procedure">
    <subscripts count="0" />
  </name>
</call>
<call>
  <name hasSubscripts="true" id="calculate" type="procedure">
    <subscripts count="2">
      <subscript type="simple">
        <literal  type="int" value="1" />
      </subscript>
      <subscript type="simple">
        <literal type="int" value="2" />
      </subscript>
    </subscripts>
  </name>
</call>
<call >
  <name hasSubscripts="true" id="something" type="procedure">
    <subscripts count="1">
      <argument name="thing">
        <name id="my_value" />
      </argument>
    </subscripts>
  </name>
</call>

Expressions

Expression might be a single node like:

  • <name>
  • <literal>

More complex expressions are built from the <operation> nodes, each of which contains a collection of <operand> and <operator> nodes. Each operand contains an expression.

Unary operation

.not. flag
<operation type="unary">
  <operator operator=".not." />
  <operand>
    <name id="flag" />
  </operand>
</operation>

Multiary operation

'Hello' // ' world'
5 + x
<operation type="multiary">
  <operand >
    <literal type="char" value="'Hello'" />
  </operand>
  <operator operator="//" />
  <operand>
    <literal type="char" value="' world'" />
  </operand>
</operation>
<operation type="multiary">
  <operand>
    <literal type="int" value="5" />
  </operand>
  <operator operator="+" />
  <operand>
    <name id="x" />
  </operand>
</operation>

Subroutine

Many complex nodes contain <header> and <body>.

The contents of the header depend on the type of the node. For example, in case of subroutines, it contains list of parameters.

Function

function foo
  ...
end function foo
<function name="foo">
  <header>
    ...
  </header>
  <body>
    ...
  </body>
</function>

Module

module abc
  integer i
  ...
contains
  subroutine sub()
    ...
  end subroutine sub
  ...
end module abc
<module name="abc">
  <body>
    <specification declarations="1" implicits="0" imports="0" uses="0">
      <declaration type="variable">
        <type name="integer" type="intrinsic"/>
        <variables count="1">
          <variable name="i"/>
        </variables>
      </declaration>
    </specification>
    ...
  </body>
  <members>
    <subroutine name="sub">
      <header/>
      <body>
        ...
      </body>
    </subroutine>
    ...
  </members>
</module>

Work in progress

Remaining details of AST are not decided yet. For the time being, to see implementation details, please take a look into src/fortran/ofp/XMLPrinter.java.

Unhandled corner cases

in certain corner cases, the parse tree might deviate from the above description.

This might be due to two main reasons:

  1. Some feature is not yet implemented in this XML output generator
  2. The events provided by OFP are not sufficient to generate a correct tree.

In case 1, all contributions to this project are very welcome. The implementation of any one of the missing features might not be very troublesome. The main reason why many of those features are not implemented yet is because the Fortran codes the current contributors work with do not use them.

In case 2, there is a need to dynamically reorder/modify/delete nodes, or otherwise manipulate existing parse tree while adding new nodes. Contributions are also very welcome, but implementation might be much more challenging in this case.

Java XML generator for OFP

latest GitHub release

This is an extension of Open Fortran Parser (OFP), which outputs abstract syntaxt tree (AST) of parsed Fortran file in XML format - to a file or to System.out.

dependencies

how to build

Get dependencies, either manually, or using the provided script:

pip3 install -U -r requirements.txt
python3 -m open_fortran_parser --deps
export CLASSPATH="${CLASSPATH}:$(pwd)/lib/*"

Build:

ant
export CLASSPATH="${CLASSPATH}:$(pwd)/dist/*"

This will create a .jar file in dist directory, and add it to the Java classpath.

If you use a different python executable to install requirements, please provide it to ant too:

ant -Dpython=/custom/python

Because the build script by default relies on “python3” executable.

how to run

java fortran.ofp.FrontEnd --class fortran.ofp.XMLPrinter \
  --output output.xml --verbosity 0~100 input.f

where:

  • The --verbosity flag controls verbosity of the parse tree. Defaluts to 100 when omitted.
    • Maximum, 100, means that all details picked up by Open Fortran Parser will be preserved.
    • Minimum, 0, means that tree will contain only what is needed to reconstruct the program without changing it’s meaning.
  • The --output flag controls where the XML should be written. Defaults to standard output when omitted.

and remaining command-line options are exactly as defined in OFP 0.8.5.

To parse some_fortran_file.f and save XML output in tree.xml with minimum verbosity:

java fortran.ofp.FrontEnd --class fortran.ofp.XMLPrinter \
  --output tree.xml --verbosity 0 some_fortran_file.f

And to dump XML with maximum verbosity to console:

java fortran.ofp.FrontEnd --class fortran.ofp.XMLPrinter \
  --verbosity 100 some_fortran_file.f

Python wrapper for the generator

package version from PyPI

Using the wrapper should not require any special knowledge about the generator itself, other than knowing the abstract syntax tree (AST) specification.

dependencies

Java XML generator for OFP and all of its dependencies.

Python version 3.5 or later.

Python libraries as specified in requirements.txt.

Building and running tests additionally requires packages listed in test_requirements.txt.

how to build

pip3 install -U -r test_requirements.txt
python3 setup.py sdist --formats=gztar,zip
python3 setup.py bdist_wheel

how to install

You can simply install from PyPI:

pip3 install open-fortran-parser

Or using any of below commands, when installing from source:

pip3 install .
pip3 install dist/<filename>.whl
pip3 install dist/<filename>.tar.gz
pip3 install dist/<filename>.zip

how to run

The wrapper can be used as a script, or as a library.

When running any installed version, even if installed from source, dependencies are automatically installed together with the wrapper.

Before running from source (without installation), however, please follow “how to build” section for Java implementation above. You can make sure that dependencies are configured correctly by running:

python3 -m open_fortran_parser --check-deps

If the depenencies changed since you first ran the wrapper from the source tree, you can cleanup outdated dependencies by executing:

python3 -m open_fortran_parser --cleanup-deps

as script

$ python3 -m open_fortran_parser -h
usage: open_fortran_parser [-h] [--version] [-v VERBOSITY]
                           [--check-dependencies]
                           [input] [output]

Python wrapper around XML generator for Open Fortran Parser

positional arguments:
  input                 path to Fortran source code file (default: None)
  output                writable path for where to store resulting XML,
                        defaults to stdout if no path provided (default: None)

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v VERBOSITY, --verbosity VERBOSITY
                        level of verbosity, from 0 to 100 (default: 100)
  --check-dependencies, --check-deps
                        check if all required dependencies are present and
                        exit (default: False)

Copyright 2017-2019 by the contributors, Apache License 2.0,
https://github.com/mbdevpl/open-fortran-parser-xml

as library

from open_fortran_parser import parse

xml = parse('my_legacy_code.f', verbosity=0)

More examples available in examples.ipynb.

testing

Run basic tests:

python3 -m unittest -v
TEST_LONG=1 python3 -m unittest -v  # this might take a long time...

code coverage

Getting code coverage results for Java requires JaCoCo agent, and JaCoCo CLI, and both are dowonloaded automatically along with other development dependencies.

Currently, test setup relies on JaCoCo 0.8.3:

  • JaCoCo agent 0.8.3 (runtime)
  • JaCoCo CLI 0.8.3 (nodeps)

Run all test and gather code coverage:

TEST_LONG=1 TEST_COVERAGE=1 python3 -m coverage run --branch --source . -m unittest -v

This will take a long while.

Then, generate results for Python code:

python3 -m coverage report --show-missing
python3 -m coverage html

Finally, generate results for Java code:

java -jar "lib/org.jacoco.cli-0.8.3-nodeps.jar" report "jacoco.exec" --classfiles "bin/" --sourcefiles "src/" --html jacoco

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