add __init__.py

Empty merge done with "-s ours". To avoid
branch renames to propagate to master source code.

.gitignore

@@ -7,7 +7,7 @@ __pycache__/
 test/*/CMakeLists.txt
 test/*/build*/
 test/*/cmake/update.py
-test/*/cmake/lib/
+test/*/cmake/autocmake/
 test/*/cmake/downloaded/
 test/*/setup
 

.travis.yml

@@ -5,8 +5,9 @@ matrix:
   include:
 
     - os: linux
+      python: 2.7
       compiler: gcc
-      env: SOURCES=ubuntu-toolchain-r-test
+      env: SOURCES=ubuntu-toolchain-r-test TEST_SCRIPT=test.py
       addons:
         apt:
           sources:
@@ -28,6 +29,46 @@ matrix:
               # boost
             - libboost-all-dev
 
+    - os: linux
+      python: 3.5
+      compiler: gcc
+      env: SOURCES=ubuntu-toolchain-r-test TEST_SCRIPT=test.py
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+             # compilers
+            - g++
+            - gfortran
+              # math libraries
+            - libblas-dev
+            - liblapack-dev
+            - libatlas-base-dev
+              # mpi
+            - openmpi-bin
+            - libopenmpi-dev
+              # python library, development version
+            - libpython2.7
+              # boost
+            - libboost-all-dev
+
+    - os: linux
+      python: 3.5
+      compiler: gcc
+      env: SOURCES=ubuntu-toolchain-r-test TEST_SCRIPT=test_openblas.py
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+             # compilers
+            - g++
+            - gfortran
+            - cmake
+            - libblas-dev
+            - libopenblas-dev
+
     - os: osx
       osx_image: xcode6.4
       compiler: gcc
@@ -40,20 +81,21 @@ install:
         pip install virtualenv
     elif [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
         pip install --user virtualenv
+        curl https://cmake.org/files/v3.5/cmake-3.5.2-Linux-x86_64.tar.gz | tar xvz
+        export PATH=~/cmake-3.5.2-Linux-x86_64/bin:$PATH
+        export LD_LIBARY_PATH=~/cmake-3.5.2-Linux-x86_64/lib:$LD_LIBRARY_PATH
     fi
   - virtualenv venv
   - source venv/bin/activate
-  - pip install pep8 pytest
+  - pip install -r requirements.txt
 
 script:
     # pep8 tests
-  - pep8 --ignore=E501 update.py
-  - pep8 --ignore=E501 test/test.py
-  - pep8 --ignore=E501 lib/config.py
+  - pep8 --ignore E501 update.py
+  - pep8 --ignore E501,E265 autocmake
     # unit tests
-  - py.test -vv update.py
-  - py.test -vv test/test.py
-  - py.test -vv lib/config.py
+  - py.test -vv autocmake/*
+  - py.test -vv test/$TEST_SCRIPT
 
 notifications:
   email: false

AUTHORS.md

@@ -7,7 +7,8 @@
 
 - Miroslav Ilias (Windows, portability, earliest adopter testing and feedback, math library testing)
 - Ivan Hrasko (Windows, Appveyor testing)
-- Dan Jonsson (idea for configuration file approach)
+- Dan Jonsson (idea for configuration file approach which preceded YAML solution)
 - Roberto Di Remigio (design ideas and testing, OS X testing, Boost)
 
-For a list of all the contributions see https://github.com/coderefinery/autocmake/contributors.
+For a list of all the contributions,
+see https://github.com/coderefinery/autocmake/contributors.

README.md

@@ -1,16 +1,21 @@
-[![Build Status](https://travis-ci.org/coderefinery/autocmake.svg?branch=stable-0.x)](https://travis-ci.org/coderefinery/autocmake/builds)
-[![Documentation Status](https://readthedocs.org/projects/autocmake/badge/?version=stable-0.x)](http://autocmake.readthedocs.org)
-[![License](https://img.shields.io/badge/license-%20BSD--3-blue.svg)](../stable-0.x/LICENSE)
+[![Build Status](https://travis-ci.org/coderefinery/autocmake.svg?branch=master)](https://travis-ci.org/coderefinery/autocmake/builds)
+[![Documentation Status](https://readthedocs.org/projects/autocmake/badge/?version=latest)](http://autocmake.readthedocs.org)
+[![License](https://img.shields.io/badge/license-%20BSD--3-blue.svg)](../master/LICENSE)
 
-
-# Autocmake
+![alt text](https://github.com/coderefinery/autocmake/raw/master/img/autocmake.png "Autocmake")
 
 A CMake plugin composer.
-Licensed under [BSD-3](../stable-0.x/LICENSE).
+Licensed under [BSD-3](../master/LICENSE).
 See http://autocmake.org.
 
 
-### Projects using Autocmake
+## Documentation
+
+- [Latest stable code](http://autocmake.readthedocs.io/en/stable-0.x/) (stable-0.x branch)
+- [Bleeding edge code](http://autocmake.readthedocs.io/en/latest/) (master branch)
+
+
+## Projects using Autocmake
 
 - [Numgrid](https://github.com/dftlibs/numgrid/)
 - [XCint](https://github.com/dftlibs/xcint/)
@@ -18,5 +23,6 @@ See http://autocmake.org.
 - [mathlib-tester](https://github.com/miroi/mathlibs-tester)
 - [Fortran Input Reader](https://github.com/miroi/fortran_input_reader)
 - [PCMSolver](https://github.com/PCMSolver/pcmsolver)
+- GRASP: General-purpose Relativistic Atomic Structure Program
 
 If you use Autocmake, please link to your project via a pull request.

autocmake/__init__.py

@@ -0,0 +1 @@
+__version__ = '1.0.0-alpha-x'

autocmake/configure.py

@@ -93,16 +93,21 @@ def run_cmake(command, build_path, default_build_path):
     stdout_coded, stderr_coded = p.communicate()
     stdout = stdout_coded.decode('UTF-8')
     stderr = stderr_coded.decode('UTF-8')
+
+    # print cmake output to screen
+    print(stdout)
+
     if stderr:
         sys.stderr.write(stderr)
         sys.exit(1)
-    # print cmake output to screen
-    print(stdout)
+
     # write cmake output to file
     with open('cmake_output', 'w') as f:
         f.write(stdout)
+
     # change directory and return
     os.chdir(topdir)
+
     if 'Configuring incomplete' in stdout:
         # configuration was not successful
         if (build_path == default_build_path):

autocmake/extract.py

@@ -0,0 +1,46 @@
+def extract_list(config, section):
+    from collections import Iterable
+    l = []
+    if 'modules' in config:
+        for module in config['modules']:
+            for k, v in module.items():
+                for x in v:
+                    if section in x:
+                        if isinstance(x[section], Iterable) and not isinstance(x[section], str):
+                            for y in x[section]:
+                                l.append(y)
+                        else:
+                            l.append(x[section])
+    return l
+
+
+def to_d(l):
+    """
+    Converts list of dicts to dict.
+    """
+    _d = {}
+    for x in l:
+        for k, v in x.items():
+            _d[k] = v
+    return _d
+
+
+def test_to_d():
+    l = [{'a': 'b'}, {'c': 'd'}]
+    d = {'a': 'b', 'c': 'd'}
+    assert to_d(l) == d
+
+
+def to_l(x):
+    """
+    Converts list of dicts to dict.
+    """
+    if isinstance(x, str):
+        return [x]
+    else:
+        return x
+
+
+def test_to_l():
+    assert to_l('foo') == ['foo']
+    assert to_l(['foo', 'bar']) == ['foo', 'bar']

autocmake/generate.py

@@ -0,0 +1,176 @@
+def gen_cmake_command(config):
+    """
+    Generate CMake command.
+    """
+    from autocmake.extract import extract_list
+
+    s = []
+    s.append("\n\ndef gen_cmake_command(options, arguments):")
+    s.append('    """')
+    s.append("    Generate CMake command based on options and arguments.")
+    s.append('    """')
+    s.append("    command = []")
+
+    for env in config['export']:
+        s.append('    command.append({0})'.format(env))
+
+    s.append("    command.append(arguments['--cmake-executable'])")
+
+    for definition in config['define']:
+        s.append('    command.append({0})'.format(definition))
+
+    s.append("    command.append('-DCMAKE_BUILD_TYPE={0}'.format(arguments['--type']))")
+    s.append("    command.append('-G \"{0}\"'.format(arguments['--generator']))")
+    s.append("    if arguments['--cmake-options'] != \"''\":")
+    s.append("        command.append(arguments['--cmake-options'])")
+    s.append("    if arguments['--prefix']:")
+    s.append("        command.append('-DCMAKE_INSTALL_PREFIX=\"{0}\"'.format(arguments['--prefix']))")
+
+    s.append("\n    return ' '.join(command)")
+
+    return '\n'.join(s)
+
+
+def autogenerated_notice():
+    from datetime import date
+    from . import __version__
+
+    current_year = date.today().year
+    year_range = '2015-{0}'.format(current_year)
+
+    s = []
+    s.append('# This file is autogenerated by Autocmake v{0} http://autocmake.org'.format(__version__))
+    s.append('# Copyright (c) {0} by Radovan Bast, Jonas Juselius, and contributors.'.format(year_range))
+
+    return '\n'.join(s)
+
+
+def gen_setup(config, relative_path, setup_script_name):
+    """
+    Generate setup script.
+    """
+    from autocmake.extract import extract_list
+
+    s = []
+    s.append('#!/usr/bin/env python')
+    s.append('\n{0}'.format(autogenerated_notice()))
+    s.append('\nimport os')
+    s.append('import sys')
+
+    s.append("\nsys.path.insert(0, '{0}')".format(relative_path))
+
+    s.append('from autocmake import configure')
+    s.append('from autocmake.external import docopt')
+
+    s.append('\n\noptions = """')
+    s.append('Usage:')
+    s.append('  ./{0} [options] [<builddir>]'.format(setup_script_name))
+    s.append('  ./{0} (-h | --help)'.format(setup_script_name))
+    s.append('\nOptions:')
+
+    options = []
+
+    for opt in config['docopt']:
+        first = opt.split()[0].strip()
+        rest = ' '.join(opt.split()[1:]).strip()
+        options.append([first, rest])
+
+    options.append(['--type=<TYPE>', 'Set the CMake build type (debug, release, or relwithdeb) [default: release].'])
+    options.append(['--generator=<STRING>', 'Set the CMake build system generator [default: Unix Makefiles].'])
+    options.append(['--show', 'Show CMake command and exit.'])
+    options.append(['--cmake-executable=<CMAKE_EXECUTABLE>', 'Set the CMake executable [default: cmake].'])
+    options.append(['--cmake-options=<STRING>', "Define options to CMake [default: '']."])
+    options.append(['--prefix=<PATH>', 'Set the install path for make install.'])
+    options.append(['<builddir>', 'Build directory.'])
+    options.append(['-h --help', 'Show this screen.'])
+
+    s.append(align_options(options))
+
+    s.append('"""')
+
+    s.append(gen_cmake_command(config))
+
+    s.append("\n")
+    s.append("# parse command line args")
+    s.append("try:")
+    s.append("    arguments = docopt.docopt(options, argv=None)")
+    s.append("except docopt.DocoptExit:")
+    s.append(r"    sys.stderr.write('ERROR: bad input to {0}\n'.format(sys.argv[0]))")
+    s.append("    sys.stderr.write(options)")
+    s.append("    sys.exit(-1)")
+    s.append("\n")
+    s.append("# use extensions to validate/post-process args")
+    s.append("if configure.module_exists('extensions'):")
+    s.append("    import extensions")
+    s.append("    arguments = extensions.postprocess_args(sys.argv, arguments)")
+    s.append("\n")
+    s.append("root_directory = os.path.dirname(os.path.realpath(__file__))")
+    s.append("\n")
+    s.append("build_path = arguments['<builddir>']")
+    s.append("\n")
+    s.append("# create cmake command")
+    s.append("cmake_command = '{0} {1}'.format(gen_cmake_command(options, arguments), root_directory)")
+    s.append("\n")
+    s.append("# run cmake")
+    s.append("configure.configure(root_directory, build_path, cmake_command, arguments['--show'])")
+
+    return s
+
+
+def gen_cmakelists(project_name, min_cmake_version, relative_path, modules):
+    """
+    Generate CMakeLists.txt.
+    """
+    import os
+
+    s = []
+
+    s.append(autogenerated_notice())
+
+    s.append('\n# set minimum cmake version')
+    s.append('cmake_minimum_required(VERSION {0} FATAL_ERROR)'.format(min_cmake_version))
+
+    s.append('\n# project name')
+    s.append('project({0})'.format(project_name))
+
+    s.append('\n# do not rebuild if rules (compiler flags) change')
+    s.append('set(CMAKE_SKIP_RULE_DEPENDENCY TRUE)')
+
+    s.append('\n# if CMAKE_BUILD_TYPE undefined, we set it to Debug')
+    s.append('if(NOT CMAKE_BUILD_TYPE)')
+    s.append('    set(CMAKE_BUILD_TYPE "Debug")')
+    s.append('endif()')
+
+    if len(modules) > 0:
+        s.append('\n# directories which hold included cmake modules')
+
+    module_paths = [module.path for module in modules]
+    module_paths.append('downloaded')  # this is done to be able to find fetched modules when testing
+    module_paths = list(set(module_paths))
+    module_paths.sort()  # we do this to always get the same order and to minimize diffs
+    for directory in module_paths:
+        rel_cmake_module_path = os.path.join(relative_path, directory)
+        # on windows cmake corrects this so we have to make it wrong again
+        rel_cmake_module_path = rel_cmake_module_path.replace('\\', '/')
+        s.append('set(CMAKE_MODULE_PATH ${{CMAKE_MODULE_PATH}} ${{PROJECT_SOURCE_DIR}}/{0})'.format(rel_cmake_module_path))
+
+    if len(modules) > 0:
+        s.append('\n# included cmake modules')
+    for module in modules:
+        s.append('include({0})'.format(os.path.splitext(module.name)[0]))
+
+    return s
+
+
+def align_options(options):
+    """
+    Indents flags and aligns help texts.
+    """
+    l = 0
+    for opt in options:
+        if len(opt[0]) > l:
+            l = len(opt[0])
+    s = []
+    for opt in options:
+        s.append('  {0}{1}  {2}'.format(opt[0], ' ' * (l - len(opt[0])), opt[1]))
+    return '\n'.join(s)

autocmake/interpolate.py

@@ -0,0 +1,66 @@
+def replace(s, d):
+    from re import findall
+
+    if isinstance(s, str):
+        for var in findall(r"%\(([A-Za-z0-9_]*)\)", s):
+            s = s.replace("%({})".format(var), str(d[var]))
+    return s
+
+
+def test_replace():
+    assert replace('hey %(foo) ho %(bar)',
+                   {'foo': 'hey', 'bar': 'ho'}) == 'hey hey ho ho'
+
+
+def interpolate(d, d_map):
+    from collections import Mapping, Iterable
+    from copy import copy
+
+    for k, v in d.items():
+        if isinstance(v, Mapping):
+            d[k] = interpolate(d[k], d_map)
+        elif isinstance(v, Iterable) and not isinstance(v, str):
+            l = []
+            for x in v:
+                if isinstance(x, Mapping):
+                    l.append(interpolate(x, d_map))
+                else:
+                    l.append(replace(x, d_map))
+            d[k] = copy(l)
+        else:
+            d[k] = replace(d[k], d_map)
+    return d
+
+
+def test_interpolate():
+    d = {'foo': 'hey',
+         'bar': 'ho',
+         'one': 'hey %(foo) ho %(bar)',
+         'two': {'one': 'hey %(foo) ho %(bar)',
+                 'two': 'raboof'}}
+    d_interpolated = {'foo': 'hey',
+                      'bar': 'ho',
+                      'one': 'hey hey ho ho',
+                      'two': {'one': 'hey hey ho ho',
+                              'two': 'raboof'}}
+    assert interpolate(d, d) == d_interpolated
+
+
+def test_interpolate_int():
+    d = {'foo': 1,
+         'bar': 2,
+         'one': 'hey %(foo) ho %(bar)',
+         'two': {'one': 'hey %(foo) ho %(bar)',
+                 'two': 'raboof'}}
+    d_interpolated = {'foo': 1,
+                      'bar': 2,
+                      'one': 'hey 1 ho 2',
+                      'two': {'one': 'hey 1 ho 2',
+                              'two': 'raboof'}}
+    assert interpolate(d, d) == d_interpolated
+
+
+def test_interpolate_nested():
+    d2 = {'modules': [{'fc': [{'source': '%(url_root)fc_optional.cmake'}]}], 'url_root': 'downloaded/downloaded_'}
+    d2_interpolated = {'modules': [{'fc': [{'source': 'downloaded/downloaded_fc_optional.cmake'}]}], 'url_root': 'downloaded/downloaded_'}
+    assert interpolate(d2, d2) == d2_interpolated

autocmake/parse_rst.py

@@ -0,0 +1,132 @@
+def parse_cmake_module(s_in, overrides={}):
+    import sys
+    from collections import Mapping, Iterable, defaultdict
+    from autocmake.parse_yaml import parse_yaml
+
+    # we do not use the nicer sys.version_info.major
+    # for compatibility with Python < 2.7
+    if sys.version_info[0] > 2:
+        from io import StringIO
+    else:
+        from StringIO import StringIO
+
+    parsed_config = defaultdict(lambda: None)
+
+    if 'autocmake.yml configuration::' not in s_in:
+        return parsed_config
+
+    s_out = []
+    is_rst_line = False
+    for line in s_in.split('\n'):
+        if is_rst_line:
+            if len(line) > 0:
+                if line[0] != '#':
+                    is_rst_line = False
+            else:
+                is_rst_line = False
+        if is_rst_line:
+            s_out.append(line[2:])
+        if '#.rst:' in line:
+            is_rst_line = True
+
+    autocmake_entry = '\n'.join(s_out).split('autocmake.yml configuration::')[1]
+    autocmake_entry = autocmake_entry.replace('\n  ', '\n')
+
+    buf = StringIO(autocmake_entry)
+    config = parse_yaml(buf, overrides)
+
+    for k, v in config.items():
+        if isinstance(v, Iterable) and not isinstance(v, str):
+            parsed_config[k] = [x for x in config[k]]
+        else:
+            parsed_config[k] = [config[k]]
+
+    return parsed_config
+
+
+def test_parse_cmake_module():
+
+    s = r'''#.rst:
+#
+# Foo ...
+#
+# autocmake.yml configuration::
+#
+#   docopt:
+#     - "--cxx=<CXX> C++ compiler [default: g++]."
+#     - "--extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: '']."
+#   export: "'CXX={0}'.format(arguments['--cxx'])"
+#   define: "'-DEXTRA_CXXFLAGS=\"{0}\"'.format(arguments['--extra-cxx-flags'])"
+
+enable_language(CXX)
+
+if(NOT DEFINED CMAKE_C_COMPILER_ID)
+    message(FATAL_ERROR "CMAKE_C_COMPILER_ID variable is not defined!")
+endif()'''
+
+    parsed_config = parse_cmake_module(s)
+    assert parsed_config['docopt'] == ["--cxx=<CXX> C++ compiler [default: g++].", "--extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: '']."]
+
+
+def test_parse_cmake_module_no_key():
+
+    s = '''#.rst:
+#
+# Foo ...
+#
+# Bar ...
+
+enable_language(CXX)
+
+if(NOT DEFINED CMAKE_C_COMPILER_ID)
+    message(FATAL_ERROR "CMAKE_C_COMPILER_ID variable is not defined!")
+endif()'''
+
+    parsed_config = parse_cmake_module(s)
+    assert parsed_config['docopt'] is None
+
+
+def test_parse_cmake_module_interpolate():
+
+    s = r'''#.rst:
+#
+# Foo ...
+#
+# autocmake.yml configuration::
+#
+#   major: 1
+#   minor: 2
+#   patch: 3
+#   a: v%(major)
+#   b: v%(minor)
+#   c: v%(patch)
+
+enable_language(CXX)'''
+
+    parsed_config = parse_cmake_module(s)
+    assert parsed_config['a'] == ['v1']
+    assert parsed_config['b'] == ['v2']
+    assert parsed_config['c'] == ['v3']
+
+
+def test_parse_cmake_module_overrides():
+
+    s = r'''#.rst:
+#
+# Foo ...
+#
+# autocmake.yml configuration::
+#
+#   major: 1
+#   minor: 2
+#   patch: 3
+#   a: v%(major)
+#   b: v%(minor)
+#   c: v%(patch)
+
+enable_language(CXX)'''
+
+    parsed_config = parse_cmake_module(s, {'minor': 4})
+    assert parsed_config['a'] == ['v1']
+    assert parsed_config['b'] == ['v4']
+    assert parsed_config['c'] == ['v3']

autocmake/parse_yaml.py

@@ -0,0 +1,30 @@
+def parse_yaml(stream, overrides={}):
+    import yaml
+    import sys
+    from autocmake.interpolate import interpolate
+
+    try:
+        config = yaml.load(stream, yaml.SafeLoader)
+    except yaml.YAMLError as exc:
+        print(exc)
+        sys.exit(-1)
+
+    for k in config:
+        if k in overrides:
+            config[k] = overrides[k]
+
+    config = interpolate(config, config)
+    return config
+
+
+def test_parse_yaml():
+    text = """foo: bar
+this: that
+var: '%(foo)'
+list:
+  - a: '%(foo)'
+  - b: '%(foo)'
+  - c: '%(foo)'"""
+
+    assert parse_yaml(text) == {'foo': 'bar', 'this': 'that', 'var': 'bar',
+                                'list': [{'a': 'bar'}, {'b': 'bar'}, {'c': 'bar'}]}

doc/conf.py

@@ -60,9 +60,9 @@ author = u'Radovan Bast, Jonas Juselius, and contributors'
 # built documents.
 #
 # The short X.Y version.
-version = '0.5'
+version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.5.0'
+release = '1.0.0-alpha-x'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/contributors/doc.rst

@@ -9,12 +9,12 @@ This documentation is refreshed upon each push to the central repository.
 
 The module reference documentation is generated from the module sources using
 ``#.rst:`` tags (compare for instance
-http://autocmake.readthedocs.org/en/latest/module-reference.html#cc-cmake with
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/cc.cmake).
+http://autocmake.readthedocs.io/en/latest/module-reference.html#cc-cmake with
+https://github.com/coderefinery/autocmake/blob/master/modules/cc.cmake).
 
-Please note that the lines following ``# autocmake.cfg configuration::`` are
-understood by the ``update.py`` script to infer autocmake.cfg code from the
+Please note that the lines following ``# autocmake.yml configuration::`` are
+understood by the ``update.py`` script to infer autocmake.yml code from the
 documentation.  As an example consider
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/cc.cmake#L20-L25.
+https://github.com/coderefinery/autocmake/blob/master/modules/cc.cmake#L20-L26.
 Here, ``update.py`` will infer the configurations for ``docopt``, ``export``,
 and ``define``.

doc/contributors/testing.rst

@@ -5,12 +5,16 @@ Testing Autocmake
 
 You will need to install `pytest <http://pytest.org/>`__.
 
-Check also the `Travis  <https://github.com/coderefinery/autocmake/blob/stable-0.x/.travis.yml>`__
+Check also the `Travis  <https://github.com/coderefinery/autocmake/blob/master/.travis.yml>`__
 build and test recipe for other requirements.
 
-Your contributions and changes should preserve the test set. You can run locally all tests with::
+Your contributions and changes should preserve the test set and be PEP8 conform.
+You can run locally all tests with::
 
-  $ py.test test/test.py
+  $ pep8 --ignore E501 update.py
+  $ pep8 --ignore E501,E265 autocmake
+  $ py.test -vv autocmake/*
+  $ py.test -vv test/test.py
 
 You can also select individual tests, for example those with ``fc_blas`` string in the name::
 

doc/developers/bootstrap.rst

@@ -12,48 +12,45 @@ infrastructure files which will be needed to build the project::
 
   $ mkdir cmake  # does not have to be called "cmake" - take the name you prefer
   $ cd cmake
-  $ wget https://github.com/coderefinery/autocmake/raw/stable-0.x/update.py
+  $ wget https://github.com/coderefinery/autocmake/raw/master/update.py
   $ python update.py --self
 
 On the MS Windows system, you can use the PowerShell wget-replacement::
 
-  $ Invoke-WebRequest https://github.com/coderefinery/autocmake/raw/stable-0.x/update.py -OutFile update.py
+  $ Invoke-WebRequest https://github.com/coderefinery/autocmake/raw/master/update.py -OutFile update.py
 
-This creates (or updates) the following files (an existing ``autocmake.cfg`` is
+This creates (or updates) the following files (an existing ``autocmake.yml`` is
 not overwritten by the script)::
 
   cmake/
-      autocmake.cfg      # edit this file
+      autocmake.yml      # edit this file
       update.py          # no need to edit
-      lib/
-          config.py      # no need to edit
-          docopt/
-              docopt.py  # no need to edit
+      autocmake/         # no need to edit
+          ...            # no need to edit
 
-Note that all other listed files are overwritten (use version control).
+Note that ``update.py`` and files under ``autocmake/``
+are overwritten (use version control).
 
 
 Generating the CMake infrastructure
 -----------------------------------
 
-Now customize ``autocmake.cfg`` to your needs
-(see :ref:`autocmake_cfg`)
+Now customize ``autocmake.yml`` to your needs
+(see :ref:`autocmake_yml`)
 and then run the ``update.py`` script which
 creates ``CMakeLists.txt`` and a setup script in the target path::
 
   $ python update.py ..
 
-The script also downloads external CMake modules specified in ``autocmake.cfg`` to a directory
+The script also downloads external CMake modules specified in ``autocmake.yml`` to a directory
 called ``downloaded/``::
 
   cmake/
-      autocmake.cfg      # edit this file
+      autocmake.yml      # edit this file
       update.py          # no need to edit
-      lib/
-          config.py      # no need to edit
-          docopt/
-              docopt.py  # no need to edit
-          downloaded/    # contains CMake modules fetched from the web
+      autocmake/         # no need to edit
+          ...            # no need to edit
+      downloaded/        # contains CMake modules fetched from the web
 
 
 Building the project

doc/developers/configuration.rst

@@ -1,5 +1,5 @@
 
-.. _autocmake_cfg:
+.. _autocmake_yml:
 
 Configuring autocmake.cfg
 =========================
@@ -13,38 +13,38 @@ below::
   min_cmake_version: 2.8
 
   [fc]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/fc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
 
   [cc]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/cc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
 
   [cxx]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/cxx.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/cxx.cmake
 
   [flags]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/compilers/GNU.CXX.cmake
-          https://github.com/coderefinery/autocmake/raw/stable-0.x/compilers/Intel.CXX.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/compilers/GNU.CXX.cmake
+          https://github.com/coderefinery/autocmake/raw/master/compilers/Intel.CXX.cmake
 
   [rpath]
   source: custom/rpath.cmake
 
   [definitions]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/definitions.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/definitions.cmake
 
   [coverage]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/code_coverage.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/code_coverage.cmake
 
   [safeguards]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/safeguards.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/safeguards.cmake
 
   [default_build_paths]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/default_build_paths.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/default_build_paths.cmake
 
   [src]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/src.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
 
   [googletest]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/googletest.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/googletest.cmake
 
   [custom]
   source: custom/api.cmake
@@ -71,13 +71,13 @@ The names of the other sections do not matter to Autocmake. You could name them
   min_cmake_version: 2.8
 
   [one]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/fc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
 
   [two]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/cc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
 
   [whatever]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/cxx.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/cxx.cmake
 
 But it would not make much sense. It is better to choose names that are
 meaningful to you.
@@ -163,7 +163,7 @@ The preferred way to extend ``CMakeLists.txt`` is by editing ``autocmake.cfg``
 and using the ``source`` option::
 
   [fc]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/fc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
 
 This will download ``fc.cmake`` and include it in ``CMakeLists.txt``.
 
@@ -175,8 +175,8 @@ You can also include local CMake modules, e.g.::
 It is also OK to include several modules at once::
 
   [flags]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/compilers/GNU.CXX.cmake
-          https://github.com/coderefinery/autocmake/raw/stable-0.x/compilers/Intel.CXX.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/compilers/GNU.CXX.cmake
+          https://github.com/coderefinery/autocmake/raw/master/compilers/Intel.CXX.cmake
 
 The modules will be included in the same order as they appear in ``autocmake.cfg``.
 
@@ -187,7 +187,7 @@ Fetching files without including them in CMakeLists.txt
 Sometimes you want to fetch a file without including it in ``CMakeLists.txt``.
 This can be done with the ``fetch`` option.  This is for instance done by the
 ``git_info.cmake`` module (see
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/git_info/git_info.cmake#L10-L11).
+https://github.com/coderefinery/autocmake/blob/master/modules/git_info/git_info.cmake#L10-L11).
 
 If ``fetch`` is invoked in ``autocmake.cfg``, then the fetched file is placed
 under ``downloaded/``.  If ``fetch`` is invoked from within a CMake module
@@ -241,7 +241,7 @@ for many core modules which come with own options once you have sourced them.
 The lines following ``# autocmake.cfg configuration::`` are
 understood by the ``update.py`` script to infer ``autocmake.cfg`` code from the
 documentation. As an example consider
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/cc.cmake#L20-L25.
+https://github.com/coderefinery/autocmake/blob/master/modules/cc.cmake#L20-L25.
 Here, ``update.py`` will infer the configurations for ``docopt``, ``export``,
 and ``define``.
 
@@ -251,6 +251,6 @@ Overriding documented configurations
 
 Configurable documented defaults can be achieved using interpolations.  See for
 instance
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/boost/boost.cmake#L33-L36.
+https://github.com/coderefinery/autocmake/blob/master/modules/boost/boost.cmake#L33-L36.
 These can be modified within ``autocmake.cfg`` with a dictionary, e.g.:
-https://github.com/coderefinery/autocmake/blob/stable-0.x/test/boost_libs/cmake/autocmake.cfg#L9
+https://github.com/coderefinery/autocmake/blob/master/test/boost_libs/cmake/autocmake.cfg#L9

doc/developers/customizing-modules.rst

@@ -3,7 +3,7 @@
 Customizing CMake modules
 =========================
 
-The ``update.py`` script assembles modules listed in ``autocmake.cfg`` into
+The ``update.py`` script assembles modules listed in ``autocmake.yml`` into
 ``CMakeLists.txt``. Those that are fetched from the web are placed inside
 ``downloaded/``.  You have several options to customize downloaded CMake
 modules:
@@ -22,7 +22,7 @@ Adapt local copies of CMake modules
 
 A slightly better solution is to download the CMake modules that you wish you customize
 to a separate directory (e.g. ``custom/``) and source the customized CMake
-modules in ``autocmake.cfg``. Alternatively you can serve your custom modules
+modules in ``autocmake.yml``. Alternatively you can serve your custom modules
 from your own http server.
 
 
@@ -34,19 +34,30 @@ the branched customized versions. This will make it easier for you
 to stay up-to-date with upstream development.
 
 
-Overriding defaults
+Overriding settings
 -------------------
 
-Some modules use interpolations to set defaults, see for instance
-https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/boost/boost.cmake#L33-L36.
-These can be modified within ``autocmake.cfg``, e.g.:
-https://github.com/coderefinery/autocmake/blob/stable-0.x/test/boost_libs/cmake/autocmake.cfg#L9
+If you source a module which contains directives such as
+``define``,
+``docopt``,
+``export``, or
+``fetch``, and you wish to modify those,
+then you can override these settings in ``autocmake.yml``.
+Settings in ``autocmake.yml`` take precedence over
+settings imported by a sourced module.
+
+As an example consider the Boost module which defines and uses
+interpolation variables ``major``, ``minor``, and ``patch``, see
+https://github.com/coderefinery/autocmake/blob/master/modules/boost/boost.cmake#L52-L54.
+
+The recommended way to customize these is in ``autocmake.yml``, e.g.:
+https://github.com/coderefinery/autocmake/blob/master/test/boost_libs/cmake/autocmake.yml#L12-L17.
 
 
 Create own CMake modules
 ------------------------
 
-Of course you can also create own modules and source them in ``autocmake.cfg``.
+Of course you can also create own modules and source them in ``autocmake.yml``.
 
 
 Contribute customizations to the "standard library"

doc/developers/example.rst

@@ -4,7 +4,7 @@ Example Hello World project
 ===========================
 
 This is a brief example for the busy and impatient programmer. For a longer
-tour please see :ref:`autocmake_cfg`.
+tour please see :ref:`autocmake_yml`.
 
 We start with a mixed Fortran-C project with the following sources::
 
@@ -25,7 +25,7 @@ Now we create ``cmake/`` and fetch ``update.py``::
 
   $ mkdir cmake
   $ cd cmake/
-  $ wget https://raw.githubusercontent.com/coderefinery/autocmake/stable-0.x/update.py
+  $ wget https://raw.githubusercontent.com/coderefinery/autocmake/master/update.py
   $ python update.py --self
 
 Now from top-level our file tree looks like this::
@@ -50,13 +50,13 @@ Now we edit ``cmake/autocmake.cfg`` to look like this::
   min_cmake_version: 2.8
 
   [fc]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/fc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
 
   [cc]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/cc.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
 
   [src]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/src.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
 
 What we have specified here is the project name and that we wish Fortran and C
 support. The ``src.cmake`` module tells CMake to include a ``src/CMakeLists.txt``.

doc/developers/faq.rst

@@ -107,7 +107,7 @@ overwritten at some point.  A good standard is to organize your sources under
 can include the latter in ``autocmake.cfg`` using::
 
   [src]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/src.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
 
 If you really don't like to do it this way, you can describe your sources and
 targets in a custom module in a local file and include it like this::

doc/developers/updating-modules.rst

@@ -21,7 +21,7 @@ rather fetch an older version, for example with the hash ``abcd123``. To
 achieve this, instead of::
 
   [foo]
-  source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/foo.cmake
+  source: https://github.com/coderefinery/autocmake/raw/master/modules/foo.cmake
 
 pin the version to ``abcd123`` (you do not need to specify the full Git hash, a unique
 beginning will do)::

doc/extract_rst.py

@@ -73,7 +73,7 @@ def main():
             if s_out != '':
                 output.append('\n\n%s' % file_name)
                 output.append('-'*len(file_name))
-                output.append('`[Source code] <https://github.com/coderefinery/autocmake/blob/stable-0.x/modules/%s>`__' % full_file_name)
+                output.append('`[Source code] <https://github.com/coderefinery/autocmake/blob/master/modules/%s>`__' % full_file_name)
                 output.append(s_out)
 
     with open(os.path.join(THIS_DIR, 'module-reference.rst'), 'w') as f:

doc/general/about.rst

@@ -7,9 +7,10 @@ Building libraries and executables from sources can be a complex task. Several
 solutions exist to this problem: GNU Makefiles is the traditional approach.
 Today, CMake is one of the trendier alternatives which can generate Makefiles
 starting from a file called ``CMakeLists.txt``.
+
 Autocmake composes CMake building blocks into a CMake project and generates
 ``CMakeLists.txt`` as well as a setup script, which serves as a front-end to
-``CMakeLists.txt``. All this is done based on a lightweight ``autocmake.cfg``
+``CMakeLists.txt``. All this is done based on a lightweight ``autocmake.yml``
 file::
 
   python update.py --self
@@ -19,14 +20,14 @@ file::
        | and updates the update.py script  |
        |                                   |
        v                           Developer maintaining
-  autocmake.cfg                        Autocmake
+  autocmake.yml                        Autocmake
        |                                   |
        | python update.py ..               |
        |                                   |
        v                                   v
   CMakeLists.txt (and setup front-end)
        |                                   |
-       | python setup                      |
+       | python setup or ./setup           |
        | which invokes CMake               |
        v                             User of the code
   Makefile (or something else)             |
@@ -37,7 +38,7 @@ file::
   Build/install/test targets
 
 Our main motivation to create Autocmake as a CMake framework library and
-CMake module composer was to simplify CMake code transfer between codes. We got
+CMake module composer is to simplify CMake code transfer between codes. We got
 tired of manually diffing and copy-pasting boiler-plate CMake code and watching
 it diverge while maintaining the CMake infrastructure in a growing number of
 scientific projects which typically have very similar requirements:

doc/general/requirements.rst

@@ -3,9 +3,8 @@
 Requirements and dependencies
 =============================
 
-Autocmake update and test scripts require Python 2.7 or higher. We try to also
-support Python 3 (tested with Python 3.4). If the script fails with Python 3,
-consider this a bug and please file an issue.
+Autocmake update and test scripts require Python 2.7 or higher. We also
+support Python 3 (we automatically test with 2.7 and 3.5).
 
 The generated setup script runs with Python >= 2.6 (also tested with Python
-3.4; probably also lower).
+3.5).

doc/index.rst

@@ -1,7 +1,7 @@
 
 
-Autocmake
-=========
+Autocmake (this documentation is outdated, see stable-0.x branch)
+=================================================================
 
 
 General

doc/users/faq.rst

@@ -50,5 +50,8 @@ Like this::
   $ python setup --cmake-options='"-DTHIS_OPTION=ON -DTHAT_OPTION=OFF"'
 
 We use two sets of quotes because the shell swallows one set of them
-before passing the arguments to Python. If you do not use two sets
-of quotes then the setup command may end up incorrectly saved in `build/setup_command`.
+before passing the arguments to Python. Yeah that's not nice, but nothing
+we can do about it on the Python side.
+If you do not use two sets
+of quotes then the setup command may end up
+incorrectly saved in `build/setup_command`.

example/autocmake.cfg

@@ -1,7 +0,0 @@
-# CMakeLists.txt and setup script will be generated from this file
-# see: http://autocmake.readthedocs.org/en/latest/developers/configuration.html
-
-# uncomment the following three lines and set the project name
-# [project]
-# name: myproject
-# min_cmake_version: 2.8

example/autocmake.yml

@@ -0,0 +1,7 @@
+# CMakeLists.txt and setup script will be generated from this file
+# see: http://autocmake.readthedocs.io/en/latest/developers/configuration.html
+# adapt the following lines and expand
+
+name: myproject
+
+min_cmake_version: 2.8

img/autocmake.svg

@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="210mm"
+   height="297mm"
+   viewBox="0 0 744.09448819 1052.3622047"
+   id="svg2"
+   version="1.1"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="autocmake.svg">
+  <defs
+     id="defs4" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
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+         x="192.04724"
+         style="font-style:normal;font-weight:normal;font-size:40px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ffffff;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+         xml:space="preserve"><tspan
+           style="font-style:normal;font-variant:normal;font-weight:500;font-stretch:normal;font-family:'Pet Me 64';-inkscape-font-specification:'Pet Me 64 Medium';fill:#ffffff"
+           y="531.68109"
+           x="192.04724"
+           id="tspan3405"
+           sodipodi:role="line">Autocmake</tspan></text>
+    </g>
+  </g>
+</svg>

modules/boost/boost.cmake

@@ -5,11 +5,14 @@
 # Autocmake update time.
 # Note that the build-up commands are not Windows-compatible!
 #
-# Your autocmake.cfg should look like this::
+# Your autocmake.yml should look like this::
 #
-#   [boost]
-#   override: {'major': 1, 'minor': 59, 'patch': 0, 'components': 'chrono;timer;system'}
-#   source: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost.cmake
+# - boost:
+#   - major: 1
+#   - minor: 59
+#   - patch: 0
+#   - components: "chrono;timer;system"
+#   - source: "https://github.com/coderefinery/autocmake/raw/master/modules/boost/boost.cmake"
 #
 # Cross-dependencies between required components are not checked for.
 # For example, Boost.Timer depends on Boost.Chrono and Boost.System thus you
@@ -43,39 +46,41 @@
 #   MPI_FOUND
 #   BUILD_CUSTOM_BOOST
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   major=1
-#   minor=48
-#   patch=0
-#   components=''
-#   fetch: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_unpack.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_userconfig.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_configure.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_build.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_install.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_headers.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/boost/boost_cleanup.cmake
-#          http://sourceforge.net/projects/boost/files/boost/%(major)s.%(minor)s.%(patch)s/boost_%(major)s_%(minor)s_%(patch)s.zip
-#   docopt: --boost-headers=<BOOST_INCLUDEDIR> Include directories for Boost [default: ''].
-#           --boost-libraries=<BOOST_LIBRARYDIR> Library directories for Boost [default: ''].
-#           --build-boost=<FORCE_CUSTOM_BOOST> Deactivate Boost detection and build on-the-fly <ON/OFF> [default: OFF].
-#   define: '-DBOOST_INCLUDEDIR="{0}"'.format(arguments['--boost-headers'])
-#           '-DBOOST_LIBRARYDIR="{0}"'.format(arguments['--boost-libraries'])
-#           '-DFORCE_CUSTOM_BOOST="{0}"'.format(arguments['--build-boost'])
-#           '-DBOOST_MINIMUM_REQUIRED="%(major)s.%(minor)s.%(patch)s"'
-#           '-DBOOST_COMPONENTS_REQUIRED="%(components)s"'
+#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   major: 1
+#   minor: 48
+#   patch: 0
+#   components: ""
+#   fetch:
+#     - "%(url_root)modules/boost/boost_unpack.cmake"
+#     - "%(url_root)modules/boost/boost_userconfig.cmake"
+#     - "%(url_root)modules/boost/boost_configure.cmake"
+#     - "%(url_root)modules/boost/boost_build.cmake"
+#     - "%(url_root)modules/boost/boost_install.cmake"
+#     - "%(url_root)modules/boost/boost_headers.cmake"
+#     - "%(url_root)modules/boost/boost_cleanup.cmake"
+#     - "http://sourceforge.net/projects/boost/files/boost/%(major).%(minor).%(patch)/boost_%(major)_%(minor)_%(patch).zip"
+#   docopt:
+#     - "--boost-headers=<BOOST_INCLUDEDIR> Include directories for Boost [default: '']."
+#     - "--boost-libraries=<BOOST_LIBRARYDIR> Library directories for Boost [default: '']."
+#     - "--build-boost=<FORCE_CUSTOM_BOOST> Deactivate Boost detection and build on-the-fly <ON/OFF> [default: OFF]."
+#   define:
+#     - "'-DBOOST_INCLUDEDIR=\"{0}\"'.format(arguments['--boost-headers'])"
+#     - "'-DBOOST_LIBRARYDIR=\"{0}\"'.format(arguments['--boost-libraries'])"
+#     - "'-DFORCE_CUSTOM_BOOST={0}'.format(arguments['--build-boost'])"
+#     - "'-DBOOST_MINIMUM_REQUIRED=\"%(major).%(minor).%(patch)\"'"
+#     - "'-DBOOST_COMPONENTS_REQUIRED=\"%(components)\"'"
 
 # FIXME Maintainer should be able to choose between fail (end-user has to satisfy dependency
 #       on its own) and soft-fail (self-build of Boost)
 # Underscore-separated version number
 string(REGEX REPLACE "\\." "_" BOOSTVER ${BOOST_MINIMUM_REQUIRED})
+
 # Where the Boost .zip archive is located
-# CMAKE_CURRENT_LIST_DIR is undefined in CMake 2.8.2
-# see https://public.kitware.com/Bug/print_bug_page.php?bug_id=11675
-# workaround: create CMAKE_CURRENT_LIST_DIR
-get_filename_component(CMAKE_CURRENT_LIST_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
-set(BOOST_ARCHIVE_LOCATION ${CMAKE_CURRENT_LIST_DIR})
+set(BOOST_ARCHIVE_LOCATION ${PROJECT_SOURCE_DIR}/cmake/downloaded)
+
 set(BOOST_ARCHIVE boost_${BOOSTVER}.zip)
 
 # FIXME These are possibly not always good settings

modules/cc.cmake

@@ -17,12 +17,13 @@
 #
 #   CFLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --cc=<CC> C compiler [default: gcc].
-#           --extra-cc-flags=<EXTRA_CFLAGS> Extra C compiler flags [default: ''].
-#   export: 'CC={0}'.format(arguments['--cc'])
-#   define: '-DEXTRA_CFLAGS="{0}"'.format(arguments['--extra-cc-flags'])
+#   docopt:
+#     - "--cc=<CC> C compiler [default: gcc]."
+#     - "--extra-cc-flags=<EXTRA_CFLAGS> Extra C compiler flags [default: '']."
+#   export: "'CC={0}'.format(arguments['--cc'])"
+#   define: "'-DEXTRA_CFLAGS=\"{0}\"'.format(arguments['--extra-cc-flags'])"
 
 enable_language(C)
 

modules/ccache.cmake

@@ -10,10 +10,10 @@
 #
 #   CCACHE_FOUND
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --ccache=<USE_CCACHE> Toggle use of ccache <ON/OFF> [default: ON].
-#   define: '-DUSE_CCACHE="{0}"'.format(arguments['--ccache'])
+#   docopt: "--ccache=<USE_CCACHE> Toggle use of ccache <ON/OFF> [default: ON]."
+#   define: "'-DUSE_CCACHE={0}'.format(arguments['--ccache'])"
 
 if(USE_CCACHE)
     find_program(CCACHE_FOUND ccache)

modules/code_coverage.cmake

@@ -8,10 +8,10 @@
 #   CMAKE_C_FLAGS
 #   CMAKE_CXX_FLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --coverage Enable code coverage [default: False].
-#   define: '-DENABLE_CODE_COVERAGE=%s' % arguments['--coverage']
+#   docopt: "--coverage Enable code coverage [default: False]."
+#   define: "'-DENABLE_CODE_COVERAGE={0}'.format(arguments['--coverage'])"
 
 option(ENABLE_CODE_COVERAGE "Enable code coverage" OFF)
 

modules/cxx.cmake

@@ -17,12 +17,13 @@
 #
 #   CXXFLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --cxx=<CXX> C++ compiler [default: g++].
-#           --extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: ''].
-#   export: 'CXX={0}'.format(arguments['--cxx'])
-#   define: '-DEXTRA_CXXFLAGS="{0}"'.format(arguments['--extra-cxx-flags'])
+#   docopt:
+#     - "--cxx=<CXX> C++ compiler [default: g++]."
+#     - "--extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: '']."
+#   export: "'CXX={0}'.format(arguments['--cxx'])"
+#   define: "'-DEXTRA_CXXFLAGS=\"{0}\"'.format(arguments['--extra-cxx-flags'])"
 
 enable_language(CXX)
 

modules/definitions.cmake

@@ -7,10 +7,10 @@
 #
 #   PREPROCESSOR_DEFINITIONS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --add-definitions=<STRING> Add preprocesor definitions [default: ''].
-#   define: '-DPREPROCESSOR_DEFINITIONS="%s"' % arguments['--add-definitions']
+#   docopt: "--add-definitions=<STRING> Add preprocesor definitions [default: '']."
+#   define: "'-DPREPROCESSOR_DEFINITIONS=\"{0}\"'.format(arguments['--add-definitions'])"
 
 if(NOT "${PREPROCESSOR_DEFINITIONS}" STREQUAL "")
     add_definitions(${PREPROCESSOR_DEFINITIONS})

modules/fc.cmake

@@ -21,12 +21,13 @@
 #
 #   FCFLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --fc=<FC> Fortran compiler [default: gfortran].
-#           --extra-fc-flags=<EXTRA_FCFLAGS> Extra Fortran compiler flags [default: ''].
-#   export: 'FC={0}'.format(arguments['--fc'])
-#   define: '-DEXTRA_FCFLAGS="{0}"'.format(arguments['--extra-fc-flags'])
+#   docopt:
+#     - "--fc=<FC> Fortran compiler [default: gfortran]."
+#     - "--extra-fc-flags=<EXTRA_FCFLAGS> Extra Fortran compiler flags [default: '']."
+#   export: "'FC={0}'.format(arguments['--fc'])"
+#   define: "'-DEXTRA_FCFLAGS=\"{0}\"'.format(arguments['--extra-fc-flags'])"
 
 enable_language(Fortran)
 

modules/fc_optional.cmake

@@ -26,14 +26,16 @@
 #
 #   FCFLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --fc=<FC> Fortran compiler [default: gfortran].
-#           --extra-fc-flags=<EXTRA_FCFLAGS> Extra Fortran compiler flags [default: ''].
-#           --fc-support=<FC_SUPPORT> Toggle Fortran language support (ON/OFF) [default: ON].
-#   export: 'FC={0}'.format(arguments['--fc'])
-#   define: '-DEXTRA_FCFLAGS="{0}"'.format(arguments['--extra-fc-flags'])
-#           '-DENABLE_FC_SUPPORT="{0}"'.format(arguments['--fc-support'])
+#   docopt:
+#     - "--fc=<FC> Fortran compiler [default: gfortran]."
+#     - "--extra-fc-flags=<EXTRA_FCFLAGS> Extra Fortran compiler flags [default: '']."
+#     - "--fc-support=<FC_SUPPORT> Toggle Fortran language support (ON/OFF) [default: ON]."
+#   export: "'FC={0}'.format(arguments['--fc'])"
+#   define:
+#     - "'-DEXTRA_FCFLAGS=\"{0}\"'.format(arguments['--extra-fc-flags'])"
+#     - "'-DENABLE_FC_SUPPORT={0}'.format(arguments['--fc-support'])"
 
 option(ENABLE_FC_SUPPORT "Enable Fortran language support" ON)
 

modules/git_info/git_info.cmake

@@ -5,10 +5,12 @@
 # Git repository version and status information
 # to the program output.
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   fetch: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/git_info/git_info_sub.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/git_info/git_info.h.in
+#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   fetch:
+#     - "%(url_root)modules/git_info/git_info_sub.cmake"
+#     - "%(url_root)modules/git_info/git_info.h.in"
 
 # CMAKE_CURRENT_LIST_DIR is undefined in CMake 2.8.2
 # see https://public.kitware.com/Bug/print_bug_page.php?bug_id=11675

modules/googletest.cmake

@@ -6,9 +6,9 @@
 #
 #   GOOGLETEST_ROOT
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   define: '-DGOOGLETEST_ROOT=external/googletest/googletest'
+#   define: "'-DGOOGLETEST_ROOT=external/googletest/googletest'"
 
 set(GOOGLETEST_ROOT external/googletest/googletest CACHE STRING "Google Test source root")
 

modules/int64.cmake

@@ -6,10 +6,10 @@
 #
 #   CMAKE_Fortran_FLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --int64 Enable 64bit integers [default: False].
-#   define: '-DENABLE_64BIT_INTEGERS=%s' % arguments['--int64']
+#   docopt: "--int64 Enable 64bit integers [default: False]."
+#   define: "'-DENABLE_64BIT_INTEGERS={0}'.format(arguments['--int64'])"
 
 option(ENABLE_64BIT_INTEGERS "Enable 64-bit integers" OFF)
 

modules/math/accelerate.cmake

@@ -8,12 +8,14 @@
 #   ACCELERATE_LIBRARIES - describe me, uncached
 #   ACCELERATE_INCLUDE_DIR - describe me, uncached
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --accelerate Find and link to ACCELERATE [default: False].
-#   define: '-DENABLE_ACCELERATE=%s' % arguments['--accelerate']
-#   fetch: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_libraries.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_include_files.cmake
+#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   docopt: "--accelerate Find and link to ACCELERATE [default: False]."
+#   define: "'-DENABLE_ACCELERATE={0}'.format(arguments['--accelerate'])"
+#   fetch:
+#     - "%(url_root)modules/find/find_libraries.cmake"
+#     - "%(url_root)modules/find/find_include_files.cmake"
 
 option(ENABLE_ACCELERATE "Find and link to ACCELERATE" OFF)
 

modules/math/acml.cmake

@@ -8,10 +8,10 @@
 #   ACML_LIBRARIES
 #   ACML_INCLUDE_DIR
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --acml Find and link to ACML [default: False].
-#   define: '-DENABLE_ACML=%s' % arguments['--acml']
+#   docopt: "--acml Find and link to ACML [default: False]."
+#   define: "'-DENABLE_ACML={0}'.format(arguments['--acml'])"
 
 option(ENABLE_ACML "Find and link to ACML" OFF)
 

modules/math/atlas.cmake

@@ -8,10 +8,10 @@
 #   ATLAS_LIBRARIES
 #   ATLAS_INCLUDE_DIR
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --atlas Find and link to ATLAS [default: False].
-#   define: '-DENABLE_ATLAS=%s' % arguments['--atlas']
+#   docopt: "--atlas Find and link to ATLAS [default: False]."
+#   define: "'-DENABLE_ATLAS={0}'.format(arguments['--atlas'])"
 
 option(ENABLE_ATLAS "Find and link to ATLAS" OFF)
 

modules/math/blas.cmake

@@ -8,10 +8,10 @@
 #   BLAS_LIBRARIES
 #   BLAS_INCLUDE_DIR
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --blas Find and link to BLAS [default: False].
-#   define: '-DENABLE_BLAS=%s' % arguments['--blas']
+#   docopt: "--blas Find and link to BLAS [default: False]."
+#   define: "'-DENABLE_BLAS={0}'.format(arguments['--blas'])"
 
 option(ENABLE_BLAS "Find and link to BLAS" OFF)
 

modules/math/cblas.cmake

@@ -8,12 +8,14 @@
 #   CBLAS_LIBRARIES - describe me, uncached
 #   CBLAS_INCLUDE_DIR - describe me, uncached
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --cblas Find and link to CBLAS [default: False].
-#   define: '-DENABLE_CBLAS=%s' % arguments['--cblas']
-#   fetch: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_libraries.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_include_files.cmake
+#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   docopt: "--cblas Find and link to CBLAS [default: False]."
+#   define: "'-DENABLE_CBLAS={0}'.format(arguments['--cblas'])"
+#   fetch:
+#     - "%(url_root)modules/find/find_libraries.cmake"
+#     - "%(url_root)modules/find/find_include_files.cmake"
 
 option(ENABLE_CBLAS "Find and link to CBLAS" OFF)
 

modules/math/goto.cmake

@@ -8,10 +8,10 @@
 #   GOTO_LIBRARIES
 #   GOTO_INCLUDE_DIR
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --goto Find and link to GOTO [default: False].
-#   define: '-DENABLE_GOTO=%s' % arguments['--goto']
+#   docopt: "--goto Find and link to GOTO [default: False]."
+#   define: "'-DENABLE_GOTO={0}'.format(arguments['--goto'])"
 
 option(ENABLE_GOTO "Find and link to GOTO" OFF)
 

modules/math/lapack.cmake

@@ -8,10 +8,10 @@
 #   LAPACK_LIBRARIES
 #   LAPACK_INCLUDE_DIR
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --lapack Find and link to LAPACK [default: False].
-#   define: '-DENABLE_LAPACK=%s' % arguments['--lapack']
+#   docopt: "--lapack Find and link to LAPACK [default: False]."
+#   define: "'-DENABLE_LAPACK={0}'.format(arguments['--lapack'])"
 
 option(ENABLE_LAPACK "Find and link to LAPACK" OFF)
 

modules/math/lapacke.cmake

@@ -8,12 +8,14 @@
 #   LAPACKE_LIBRARIES - describe me, uncached
 #   LAPACKE_INCLUDE_DIR - describe me, uncached
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --lapacke Find and link to LAPACKE [default: False].
-#   define: '-DENABLE_LAPACKE=%s' % arguments['--lapacke']
-#   fetch: https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_libraries.cmake
-#          https://github.com/coderefinery/autocmake/raw/stable-0.x/modules/find/find_include_files.cmake
+#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   docopt: "--lapacke Find and link to LAPACKE [default: False]."
+#   define: "'-DENABLE_LAPACKE={0}'.format(arguments['--lapacke'])"
+#   fetch:
+#     - "%(url_root)modules/find/find_libraries.cmake"
+#     - "%(url_root)modules/find/find_include_files.cmake"
 
 option(ENABLE_LAPACKE "Find and link to LAPACKE" OFF)
 

modules/math/openblas.cmake

@@ -0,0 +1,124 @@
+# this file is adapted from https://github.com/BVLC/caffe/blob/master/cmake/Modules/FindOpenBLAS.cmake
+# and reused by providing the corresponding copyright notice:
+#
+#
+# COPYRIGHT
+#
+# All contributions by the University of California:
+# Copyright (c) 2014, 2015, The Regents of the University of California (Regents)
+# All rights reserved.
+#
+# All other contributions:
+# Copyright (c) 2014, 2015, the respective contributors
+# All rights reserved.
+#
+# Caffe uses a shared copyright model: each contributor holds copyright over
+# their contributions to Caffe. The project versioning records all such
+# contribution and copyright details. If a contributor wants to further mark
+# their specific copyright on a particular contribution, they should indicate
+# their copyright solely in the commit message of the change when it is
+# committed.
+#
+# LICENSE
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+#
+#.rst:
+#
+# Find and link to OpenBLAS.
+#
+# Variables defined::
+#
+#   OpenBLAS_FOUND
+#   OpenBLAS_LIB
+#   OpenBLAS_INCLUDE_DIR
+#
+# autocmake.yml configuration::
+#
+#   docopt: "--openblas Find and link to OpenBLAS [default: False]."
+#   define: "'-DENABLE_OPENBLAS={0}'.format(arguments['--openblas'])"
+
+option(ENABLE_OPENBLAS "Find and link to OpenBLAS" OFF)
+
+if (ENABLE_OPENBLAS)
+SET(Open_BLAS_INCLUDE_SEARCH_PATHS
+  /usr/include
+  /usr/include/openblas
+  /usr/include/openblas-base
+  /usr/local/include
+  /usr/local/include/openblas
+  /usr/local/include/openblas-base
+  /opt/OpenBLAS/include
+  $ENV{OpenBLAS_HOME}
+  $ENV{OpenBLAS_HOME}/include
+)
+
+SET(Open_BLAS_LIB_SEARCH_PATHS
+        /lib/
+        /lib/openblas-base
+        /lib64/
+        /usr/lib
+        /usr/lib/openblas-base
+        /usr/lib64
+        /usr/local/lib
+        /usr/local/lib64
+        /opt/OpenBLAS/lib
+        $ENV{OpenBLAS}cd
+        $ENV{OpenBLAS}/lib
+        $ENV{OpenBLAS_HOME}
+        $ENV{OpenBLAS_HOME}/lib
+ )
+
+FIND_PATH(OpenBLAS_INCLUDE_DIR NAMES cblas.h PATHS ${Open_BLAS_INCLUDE_SEARCH_PATHS})
+FIND_LIBRARY(OpenBLAS_LIB NAMES openblas PATHS ${Open_BLAS_LIB_SEARCH_PATHS})
+
+SET(OpenBLAS_FOUND ON)
+
+#    Check include files
+IF(NOT OpenBLAS_INCLUDE_DIR)
+    SET(OpenBLAS_FOUND OFF)
+    MESSAGE(STATUS "Could not find OpenBLAS include. Turning OpenBLAS_FOUND off")
+ENDIF()
+
+#    Check libraries
+IF(NOT OpenBLAS_LIB)
+    SET(OpenBLAS_FOUND OFF)
+    MESSAGE(STATUS "Could not find OpenBLAS lib. Turning OpenBLAS_FOUND off")
+ENDIF()
+
+IF (OpenBLAS_FOUND)
+  IF (NOT OpenBLAS_FIND_QUIETLY)
+    MESSAGE(STATUS "Found OpenBLAS libraries: ${OpenBLAS_LIB}")
+    MESSAGE(STATUS "Found OpenBLAS include: ${OpenBLAS_INCLUDE_DIR}")
+  ENDIF (NOT OpenBLAS_FIND_QUIETLY)
+ELSE (OpenBLAS_FOUND)
+  IF (OpenBLAS_FIND_REQUIRED)
+    MESSAGE(FATAL_ERROR "Could not find OpenBLAS")
+  ENDIF (OpenBLAS_FIND_REQUIRED)
+ENDIF (OpenBLAS_FOUND)
+
+MARK_AS_ADVANCED(
+    OpenBLAS_INCLUDE_DIR
+    OpenBLAS_LIB
+    OpenBLAS
+)
+endif()

modules/math_libs.cmake

@@ -37,18 +37,20 @@
 #   MKL_ROOT
 #   MKLROOT
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --blas=<BLAS> Detect and link BLAS library (auto or off) [default: auto].
-#           --lapack=<LAPACK> Detect and link LAPACK library (auto or off) [default: auto].
-#           --mkl=<MKL> Pass MKL flag to the Intel compiler and linker and skip BLAS/LAPACK detection (sequential, parallel, cluster, or off) [default: off].
-#   define: '-DENABLE_BLAS=%s' % arguments['--blas']
-#           '-DENABLE_LAPACK=%s' % arguments['--lapack']
-#           '-DMKL_FLAG=%s' % arguments['--mkl']
-#           '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE"'
-#           '-DBLAS_LANG=Fortran'
-#           '-DLAPACK_LANG=Fortran'
-#   warning: 'This module is deprecated and will be removed in future versions'
+#   docopt:
+#     - "--blas=<BLAS> Detect and link BLAS library (auto or off) [default: auto]."
+#     - "--lapack=<LAPACK> Detect and link LAPACK library (auto or off) [default: auto]."
+#     - "--mkl=<MKL> Pass MKL flag to the Intel compiler and linker and skip BLAS/LAPACK detection (sequential, parallel, cluster, or off) [default: off]."
+#   define:
+#     - "'-DENABLE_BLAS={0}'.format(arguments['--blas'])"
+#     - "'-DENABLE_LAPACK={0}'.format(arguments['--lapack'])"
+#     - "'-DMKL_FLAG={0}'.format(arguments['--mkl'])"
+#     - "'-DMATH_LIB_SEARCH_ORDER=\"MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE\"'"
+#     - "'-DBLAS_LANG=Fortran'"
+#     - "'-DLAPACK_LANG=Fortran'"
+#   warning: "the math_libs.cmake module is deprecated and will be removed in future versions"
 
 #-------------------------------------------------------------------------------
 # ENABLE_STATIC_LINKING

modules/mpi.cmake

@@ -13,10 +13,10 @@
 #   CMAKE_C_FLAGS
 #   CMAKE_CXX_FLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --mpi Enable MPI parallelization [default: False].
-#   define: '-DENABLE_MPI=%s' % arguments['--mpi']
+#   docopt: "--mpi Enable MPI parallelization [default: False]."
+#   define: "'-DENABLE_MPI={0}'.format(arguments['--mpi'])"
 
 option(ENABLE_MPI "Enable MPI parallelization" OFF)
 

modules/omp.cmake

@@ -13,10 +13,10 @@
 #   CMAKE_C_FLAGS
 #   CMAKE_CXX_FLAGS
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --omp Enable OpenMP parallelization [default: False].
-#   define: '-DENABLE_OPENMP=%s' % arguments['--omp']
+#   docopt: "--omp Enable OpenMP parallelization [default: False]."
+#   define: "'-DENABLE_OPENMP={0}'.format(arguments['--omp'])"
 
 option(ENABLE_OPENMP "Enable OpenMP parallelization" OFF)
 

modules/python_interpreter.cmake

@@ -15,10 +15,10 @@
 #   PYTHON_VERSION_MINOR       - Python minor version found e.g. 5
 #   PYTHON_VERSION_PATCH       - Python patch version found e.g. 2
 #
-# autocmake.cfg configuration::
+# autocmake.yml configuration::
 #
-#   docopt: --python=<PYTHON_INTERPRETER> The Python interpreter (development version) to use. [default: ''].
-#   define: '-DPYTHON_INTERPRETER="%s"' % arguments['--python']
+#   docopt: "--python=<PYTHON_INTERPRETER> The Python interpreter (development version) to use. [default: '']."
+#   define: "'-DPYTHON_INTERPRETER=\"{0}\"'.format(arguments['--python'])"
 
 if("${PYTHON_INTERPRETER}" STREQUAL "")
     find_package(PythonInterp REQUIRED)

requirements.txt

@@ -1,2 +1,3 @@
 pep8
 pytest
+pyyaml

test/boost_header_only/cmake/autocmake.cfg

@@ -1,16 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[boost]
-override: {'major': 1, 'minor': 48, 'patch': 0}
-source: ../../../modules/boost/boost.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/boost_header_only/cmake/autocmake.yml

@@ -0,0 +1,14 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- boost:
+  - major: 1
+  - minor: 48
+  - patch: 0
+  - source: ../../../modules/boost/boost.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/boost_libs/cmake/autocmake.cfg

@@ -1,25 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[mpi]
-source: ../../../modules/mpi.cmake
-
-[python_interpreter]
-source: ../../../modules/python_interpreter.cmake
-
-[python_libs]
-source: ../../../modules/python_libs.cmake
-
-[boost]
-override: {'major': 1, 'minor': 59, 'patch': 0, 'components': 'mpi;serialization;python'}
-source: ../../../modules/boost/boost.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/boost_libs/cmake/autocmake.yml

@@ -0,0 +1,21 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- mpi:
+  - source: ../../../modules/mpi.cmake
+- python_interpreter:
+  - source: ../../../modules/python_interpreter.cmake
+- python_libs:
+  - source: ../../../modules/python_libs.cmake
+- boost:
+  - major: 1
+  - minor: 59
+  - patch: 0
+  - components: 'mpi;serialization;python'
+  - source: ../../../modules/boost/boost.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/cxx/cmake/autocmake.cfg

@@ -1,12 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/cxx/cmake/autocmake.yml

@@ -0,0 +1,9 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/cxx_accelerate/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[math]
-source: ../../../modules/math/accelerate.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/cxx_accelerate/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- math:
+  - source: ../../../modules/math/accelerate.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/cxx_cblas/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[math]
-source: ../../../modules/math/cblas.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/cxx_cblas/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- math:
+  - source: ../../../modules/math/cblas.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/extra_cmake_options/cmake/autocmake.cfg

@@ -1,12 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/extra_cmake_options/cmake/autocmake.yml

@@ -0,0 +1,9 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc/cmake/autocmake.cfg

@@ -1,12 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/fc/cmake/autocmake.yml

@@ -0,0 +1,9 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_blas/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[math]
-source: ../../../modules/math/blas.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/fc_blas/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- math:
+  - source: ../../../modules/math/blas.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_git_info/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake
-
-[git_info]
-source: ../../../modules/git_info/git_info.cmake

test/fc_git_info/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake
+- git_info:
+  - source: ../../../modules/git_info/git_info.cmake

test/fc_int64/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[int64]
-source: ../../../modules/int64.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/fc_int64/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- int64:
+  - source: ../../../modules/int64.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_lapack/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[math]
-source: ../../../modules/math/lapack.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/fc_lapack/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- math:
+  - source: ../../../modules/math/lapack.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_omp/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[fc]
-source: ../../../modules/fc.cmake
-
-[omp]
-source: ../../../modules/omp.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/fc_omp/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- omp:
+  - source: ../../../modules/omp.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_openblas/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- fc:
+  - source: ../../../modules/fc.cmake
+- math:
+  - source: ../../../modules/math/openblas.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/fc_openblas/src/CMakeLists.txt

@@ -0,0 +1,6 @@
+if(OpenBLAS_FOUND)
+    add_executable(example example.f90)
+    target_link_libraries(example ${OpenBLAS_LIB})
+else()
+    message(FATAL_ERROR "OpenBLAS library not found")
+endif()

test/fc_openblas/src/example.f90

@@ -0,0 +1,45 @@
+program example
+
+   implicit none
+
+   integer, parameter :: n = 10
+
+   integer :: i, j
+   logical :: test_ok
+
+   real(8), allocatable :: a(:, :)
+   real(8), allocatable :: b(:, :)
+   real(8), allocatable :: c(:, :)
+
+   allocate(a(n, n))
+   allocate(b(n, n))
+   allocate(c(n, n))
+
+   a = 1.0d0
+   b = 2.0d0
+   c = 0.0d0
+
+   call dgemm('n', 'n', n, n, n, 1.0d0, a, n, b, n, 0.0d0, c, n)
+
+   test_ok = .true.
+
+   do i = 1, n
+      do j = 1, n
+         if (dabs(c(i, j) - 20.0d0) > tiny(0.0d0)) then
+            print *, 'ERROR: element', i, j, 'is', c(i, j)
+            test_ok = .false.
+         end if
+      end do
+   end do
+
+   deallocate(a)
+   deallocate(b)
+   deallocate(c)
+
+   if (test_ok) then
+      print *, 'PASSED'
+   else
+      print *, 'FAILED'
+   end if
+
+end program

test/python_interpreter/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[python_interpreter]
-source: ../../../modules/python_interpreter.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/python_interpreter/cmake/autocmake.yml

@@ -0,0 +1,13 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- python_interpreter:
+  - source: ../../../modules/python_interpreter.cmake
+- python_libs:
+  - source: ../../../modules/python_libs.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/python_interpreter_custom/cmake/autocmake.cfg

@@ -1,15 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[python_interpreter]
-source: ../../../modules/python_interpreter.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/python_interpreter_custom/cmake/autocmake.yml

@@ -0,0 +1,11 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- python_interpreter:
+  - source: ../../../modules/python_interpreter.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/python_libs/cmake/autocmake.cfg

@@ -1,18 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[python_interpreter]
-source: ../../../modules/python_interpreter.cmake
-
-[python_libs]
-source: ../../../modules/python_libs.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/python_libs/cmake/autocmake.yml

@@ -0,0 +1,13 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- python_interpreter:
+  - source: ../../../modules/python_interpreter.cmake
+- python_libs:
+  - source: ../../../modules/python_libs.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/python_libs_custom/cmake/autocmake.cfg

@@ -1,18 +0,0 @@
-[project]
-name: example
-min_cmake_version: 2.8
-
-[cxx]
-source: ../../../modules/cxx.cmake
-
-[python_interpreter]
-source: ../../../modules/python_interpreter.cmake
-
-[python_libs]
-source: ../../../modules/python_libs.cmake
-
-[default_build_paths]
-source: ../../../modules/default_build_paths.cmake
-
-[src]
-source: ../../../modules/src.cmake

test/python_libs_custom/cmake/autocmake.yml

@@ -0,0 +1,13 @@
+name: example
+min_cmake_version: 2.8
+modules:
+- cxx:
+  - source: ../../../modules/cxx.cmake
+- python_interpreter:
+  - source: ../../../modules/python_interpreter.cmake
+- python_libs:
+  - source: ../../../modules/python_libs.cmake
+- default_build_paths:
+  - source: ../../../modules/default_build_paths.cmake
+- src:
+  - source: ../../../modules/src.cmake

test/test.py

@@ -15,9 +15,6 @@ skip_on_linux = pytest.mark.skipif('sys.platform == "linux2"', reason="not worki
 skip_always = pytest.mark.skipif('1 == 1', reason="tests are broken")
 
 
-# ------------------------------------------------------------------------------
-
-
 def exe(command):
     """
     Executes command and returns string representations of stdout and stderr captured from the console.
@@ -41,8 +38,6 @@ def exe(command):
 
     return stdout, stderr
 
-# ------------------------------------------------------------------------------
-
 
 def configure_build_and_exe(name, setup_command, launcher=None):
 
@@ -51,15 +46,9 @@ def configure_build_and_exe(name, setup_command, launcher=None):
     os.chdir(os.path.join(HERE, name, 'cmake'))
     shutil.copy(os.path.join('..', '..', '..', 'update.py'), 'update.py')
 
-    dst_dir = 'lib'
-    if not os.path.exists(dst_dir):
-        os.makedirs(dst_dir)
-    shutil.copy(os.path.join('..', '..', '..', dst_dir, 'config.py'), dst_dir)
-
-    dst_dir = os.path.join('lib', 'docopt')
-    if not os.path.exists(dst_dir):
-        os.makedirs(dst_dir)
-    shutil.copy(os.path.join('..', '..', '..', dst_dir, 'docopt.py'), dst_dir)
+    if os.path.exists('autocmake'):
+        shutil.rmtree('autocmake')
+    shutil.copytree(os.path.join('..', '..', '..', 'autocmake'), 'autocmake')
 
     stdout, stderr = exe('python update.py ..')
     os.chdir(os.path.join(HERE, name))
@@ -89,8 +78,6 @@ def configure_build_and_exe(name, setup_command, launcher=None):
 
     assert 'PASSED' in stdout
 
-# ------------------------------------------------------------------------------
-
 
 def test_extra_cmake_options():
     configure_build_and_exe('extra_cmake_options', 'python setup --cxx=g++ --cmake-options="-DENABLE_SOMETHING=OFF -DENABLE_FOO=ON"')

test/test_openblas.py

@@ -0,0 +1,6 @@
+from .test import configure_build_and_exe, skip_on_osx
+
+
+@skip_on_osx
+def test_fc_openblas():
+    configure_build_and_exe('fc_openblas', 'python setup --fc=gfortran --openblas')

update.py

@@ -2,292 +2,75 @@
 
 import os
 import sys
-import datetime
-import ast
-import collections
-
-__version__ = '0.5.0'
-
-# we do not use the nicer sys.version_info.major
-# for compatibility with Python < 2.7
-if sys.version_info[0] > 2:
-    from io import StringIO
-    from configparser import ConfigParser
-    import urllib.request
-
-    class URLopener(urllib.request.FancyURLopener):
-        def http_error_default(self, url, fp, errcode, errmsg, headers):
-            sys.stderr.write("ERROR: could not fetch {0}\n".format(url))
-            sys.exit(-1)
-else:
-    from StringIO import StringIO
-    from ConfigParser import ConfigParser
-    import urllib
-
-    class URLopener(urllib.FancyURLopener):
-        def http_error_default(self, url, fp, errcode, errmsg, headers):
-            sys.stderr.write("ERROR: could not fetch {0}\n".format(url))
-            sys.exit(-1)
 
 
-AUTOCMAKE_GITHUB_URL = 'https://github.com/coderefinery/autocmake'
-
-# ------------------------------------------------------------------------------
+AUTOCMAKE_GITHUB_URL = 'https://github.com/coderefinery/autocmake/raw/master/'
 
 
-def fetch_url(src, dst):
-    """
-    Fetch file from URL src and save it to dst.
-    """
-    dirname = os.path.dirname(dst)
-    if dirname != '':
-        if not os.path.isdir(dirname):
-            os.makedirs(dirname)
-
-    opener = URLopener()
-    opener.retrieve(src, dst)
-
-# ------------------------------------------------------------------------------
+def check_for_yaml():
+    try:
+        import yaml
+    except:
+        sys.stderr.write("ERROR: you need to install the pyyaml package\n")
+        sys.exit(-1)
 
 
 def print_progress_bar(text, done, total, width):
     """
     Print progress bar.
     """
-    n = int(float(width) * float(done) / float(total))
-    sys.stdout.write("\r{0} [{1}{2}] ({3}/{4})".format(text, '#' * n, ' ' * (width - n), done, total))
-    sys.stdout.flush()
-
-# ------------------------------------------------------------------------------
+    if total > 0:
+        n = int(float(width) * float(done) / float(total))
+        sys.stdout.write("\r{0} [{1}{2}] ({3}/{4})".format(text, '#' * n, ' ' * (width - n), done, total))
+        sys.stdout.flush()
 
 
-def align_options(options):
-    """
-    Indents flags and aligns help texts.
-    """
-    l = 0
-    for opt in options:
-        if len(opt[0]) > l:
-            l = len(opt[0])
-    s = []
-    for opt in options:
-        s.append('  {0}{1}  {2}'.format(opt[0], ' ' * (l - len(opt[0])), opt[1]))
-    return '\n'.join(s)
-
-# ------------------------------------------------------------------------------
+def flat_add(l, x):
+    if isinstance(x, int):
+        l.append(x)
+        return l
+    elif isinstance(x, str):
+        l.append(x)
+        return l
+    else:
+        return l + x
 
 
-def gen_cmake_command(config):
-    """
-    Generate CMake command.
-    """
-    s = []
-
-    s.append("\n\ndef gen_cmake_command(options, arguments):")
-    s.append('    """')
-    s.append("    Generate CMake command based on options and arguments.")
-    s.append('    """')
-    s.append("    command = []")
-
-    # take care of environment variables
-    for section in config.sections():
-        if config.has_option(section, 'export'):
-            for env in config.get(section, 'export').split('\n'):
-                s.append('    command.append({0})'.format(env))
-
-    s.append("    command.append(arguments['--cmake-executable'])")
-
-    # take care of cmake definitions
-    for section in config.sections():
-        if config.has_option(section, 'define'):
-            for definition in config.get(section, 'define').split('\n'):
-                s.append('    command.append({0})'.format(definition))
-
-    s.append("    command.append('-DCMAKE_BUILD_TYPE={0}'.format(arguments['--type']))")
-    s.append("    command.append('-G \"{0}\"'.format(arguments['--generator']))")
-    s.append("    if arguments['--cmake-options'] != \"''\":")
-    s.append("        command.append(arguments['--cmake-options'])")
-    s.append("    if arguments['--prefix']:")
-    s.append("        command.append('-DCMAKE_INSTALL_PREFIX=\"{0}\"'.format(arguments['--prefix']))")
-
-    s.append("\n    return ' '.join(command)")
-
-    return '\n'.join(s)
-
-# ------------------------------------------------------------------------------
-
-
-def autogenerated_notice():
-    current_year = datetime.date.today().year
-    year_range = '2015-{0}'.format(current_year)
-    s = []
-    s.append('# This file is autogenerated by Autocmake v{0} http://autocmake.org'.format(__version__))
-    s.append('# Copyright (c) {0} by Radovan Bast, Jonas Juselius, and contributors.'.format(year_range))
-    return '\n'.join(s)
-
-# ------------------------------------------------------------------------------
-
-
-def gen_setup(config, relative_path, setup_script_name):
-    """
-    Generate setup script.
-    """
-    s = []
-    s.append('#!/usr/bin/env python')
-    s.append('\n{0}'.format(autogenerated_notice()))
-    s.append('\nimport os')
-    s.append('import sys')
-
-    s.append("\nsys.path.insert(0, '{0}')".format(relative_path))
-    s.append("sys.path.insert(0, '{0}')".format(os.path.join(relative_path, 'lib')))
-    s.append("sys.path.insert(0, '{0}')".format(os.path.join(relative_path, 'lib', 'docopt')))
-
-    s.append('import config')
-    s.append('import docopt')
-
-    s.append('\n\noptions = """')
-    s.append('Usage:')
-    s.append('  ./{0} [options] [<builddir>]'.format(setup_script_name))
-    s.append('  ./{0} (-h | --help)'.format(setup_script_name))
-    s.append('\nOptions:')
-
-    options = []
-    for section in config.sections():
-        if config.has_option(section, 'docopt'):
-            for opt in config.get(section, 'docopt').split('\n'):
-                first = opt.split()[0].strip()
-                rest = ' '.join(opt.split()[1:]).strip()
-                options.append([first, rest])
-
-    options.append(['--type=<TYPE>', 'Set the CMake build type (debug, release, or relwithdeb) [default: release].'])
-    options.append(['--generator=<STRING>', 'Set the CMake build system generator [default: Unix Makefiles].'])
-    options.append(['--show', 'Show CMake command and exit.'])
-    options.append(['--cmake-executable=<CMAKE_EXECUTABLE>', 'Set the CMake executable [default: cmake].'])
-    options.append(['--cmake-options=<STRING>', "Define options to CMake [default: '']."])
-    options.append(['--prefix=<PATH>', 'Set the install path for make install.'])
-    options.append(['<builddir>', 'Build directory.'])
-    options.append(['-h --help', 'Show this screen.'])
-
-    s.append(align_options(options))
-
-    s.append('"""')
-
-    s.append(gen_cmake_command(config))
-
-    s.append("\n")
-    s.append("# parse command line args")
-    s.append("try:")
-    s.append("    arguments = docopt.docopt(options, argv=None)")
-    s.append("except docopt.DocoptExit:")
-    s.append(r"    sys.stderr.write('ERROR: bad input to {0}\n'.format(sys.argv[0]))")
-    s.append("    sys.stderr.write(options)")
-    s.append("    sys.exit(-1)")
-    s.append("\n")
-    s.append("# use extensions to validate/post-process args")
-    s.append("if config.module_exists('extensions'):")
-    s.append("    import extensions")
-    s.append("    arguments = extensions.postprocess_args(sys.argv, arguments)")
-    s.append("\n")
-    s.append("root_directory = os.path.dirname(os.path.realpath(__file__))")
-    s.append("\n")
-    s.append("build_path = arguments['<builddir>']")
-    s.append("\n")
-    s.append("# create cmake command")
-    s.append("cmake_command = '{0} {1}'.format(gen_cmake_command(options, arguments), root_directory)")
-    s.append("\n")
-    s.append("# run cmake")
-    s.append("config.configure(root_directory, build_path, cmake_command, arguments['--show'])")
-
-    return s
-
-# ------------------------------------------------------------------------------
-
-
-def gen_cmakelists(project_name, min_cmake_version, relative_path, modules):
-    """
-    Generate CMakeLists.txt.
-    """
-    s = []
-
-    s.append(autogenerated_notice())
-
-    s.append('\n# set minimum cmake version')
-    s.append('cmake_minimum_required(VERSION {0} FATAL_ERROR)'.format(min_cmake_version))
-
-    s.append('\n# project name')
-    s.append('project({0})'.format(project_name))
-
-    s.append('\n# do not rebuild if rules (compiler flags) change')
-    s.append('set(CMAKE_SKIP_RULE_DEPENDENCY TRUE)')
-
-    s.append('\n# if CMAKE_BUILD_TYPE undefined, we set it to Debug')
-    s.append('if(NOT CMAKE_BUILD_TYPE)')
-    s.append('    set(CMAKE_BUILD_TYPE "Debug")')
-    s.append('endif()')
-
-    if len(modules) > 0:
-        s.append('\n# directories which hold included cmake modules')
-
-    module_paths = [module.path for module in modules]
-    module_paths.append('downloaded')  # this is done to be able to find fetched modules when testing
-    module_paths = list(set(module_paths))
-    module_paths.sort()  # we do this to always get the same order and to minimize diffs
-    for directory in module_paths:
-        rel_cmake_module_path = os.path.join(relative_path, directory)
-        # on windows cmake corrects this so we have to make it wrong again
-        rel_cmake_module_path = rel_cmake_module_path.replace('\\', '/')
-        s.append('set(CMAKE_MODULE_PATH ${{CMAKE_MODULE_PATH}} ${{PROJECT_SOURCE_DIR}}/{0})'.format(rel_cmake_module_path))
-
-    if len(modules) > 0:
-        s.append('\n# included cmake modules')
-    for module in modules:
-        s.append('include({0})'.format(os.path.splitext(module.name)[0]))
-
-    return s
-
-# ------------------------------------------------------------------------------
-
-
-def prepend_or_set(config, section, option, value, defaults):
-    """
-    If option is already set, then value is prepended.
-    If option is not set, then it is created and set to value.
-    This is used to prepend options with values which come from the module documentation.
-    """
-    if value:
-        if config.has_option(section, option):
-            value += '\n{0}'.format(config.get(section, option, 0, defaults))
-        config.set(section, option, value)
-    return config
-
-# ------------------------------------------------------------------------------
-
-
-def fetch_modules(config, relative_path):
+def fetch_modules(config, relative_path, download_directory):
     """
     Assemble modules which will
     be included in CMakeLists.txt.
     """
+    from collections import Iterable, namedtuple, defaultdict
+    from autocmake.extract import extract_list, to_d, to_l
+    from autocmake.parse_rst import parse_cmake_module
 
-    download_directory = 'downloaded'
-    if not os.path.exists(download_directory):
-        os.makedirs(download_directory)
-
-    l = list(filter(lambda x: config.has_option(x, 'source'),
-                    config.sections()))
-    n = len(l)
+    cleaned_config = defaultdict(lambda: [])
 
     modules = []
-    Module = collections.namedtuple('Module', 'path name')
+    Module = namedtuple('Module', 'path name')
 
-    warnings = []
+    num_sources = len(extract_list(config, 'source'))
 
-    if n > 0:  # otherwise division by zero in print_progress_bar
-        i = 0
-        print_progress_bar(text='- assembling modules:', done=0, total=n, width=30)
-        for section in config.sections():
-            if config.has_option(section, 'source'):
-                for src in config.get(section, 'source').split('\n'):
+    print_progress_bar(text='- assembling modules:',
+                       done=0,
+                       total=num_sources,
+                       width=30)
+
+    i = 0
+    for t in config['modules']:
+        for k, v in t.items():
+
+            d = to_d(v)
+            for _k, _v in to_d(v).items():
+                cleaned_config[_k] = flat_add(cleaned_config[_k], _v)
+
+            # fetch sources and parse them
+            if 'source' in d:
+                for src in to_l(d['source']):
+                    i += 1
+
+                    # we download the file
                     module_name = os.path.basename(src)
                     if 'http' in src:
                         path = download_directory
@@ -306,52 +89,104 @@ def fetch_modules(config, relative_path):
                             sys.stderr.write("ERROR: {0} does not exist\n".format(src))
                             sys.exit(-1)
 
-                    if config.has_option(section, 'override'):
-                        defaults = ast.literal_eval(config.get(section, 'override'))
-                    else:
-                        defaults = {}
-
                     # we infer config from the module documentation
+                    # dictionary d overrides the configuration in the module documentation
+                    # this allows to override interpolation inside the module
                     with open(file_name, 'r') as f:
-                        parsed_config = parse_cmake_module(f.read(), defaults)
-                        if parsed_config['warning']:
-                            warnings.append('WARNING from {0}: {1}'.format(module_name, parsed_config['warning']))
-                        config = prepend_or_set(config, section, 'docopt', parsed_config['docopt'], defaults)
-                        config = prepend_or_set(config, section, 'define', parsed_config['define'], defaults)
-                        config = prepend_or_set(config, section, 'export', parsed_config['export'], defaults)
-                        if parsed_config['fetch']:
-                            for src in parsed_config['fetch'].split('\n'):
-                                dst = os.path.join(fetch_dst_directory, os.path.basename(src))
-                                fetch_url(src, dst)
+                        parsed_config = parse_cmake_module(f.read(), d)
+                        for _k2, _v2 in parsed_config.items():
+                            if _k2 not in to_d(v):
+                                # we add to clean_config only if the entry does not exist
+                                # in parent autocmake.yml already
+                                # this allows to override
+                                cleaned_config[_k2] = flat_add(cleaned_config[_k2], _v2)
 
                     modules.append(Module(path=path, name=name))
-                i += 1
-                print_progress_bar(
-                    text='- assembling modules:',
-                    done=i,
-                    total=n,
-                    width=30
-                )
-            if config.has_option(section, 'fetch'):
-                # when we fetch directly from autocmake.cfg
-                # we download into downloaded/
-                for src in config.get(section, 'fetch').split('\n'):
-                    dst = os.path.join(download_directory, os.path.basename(src))
-                    fetch_url(src, dst)
-        print('')
+                    print_progress_bar(text='- assembling modules:',
+                                       done=i,
+                                       total=num_sources,
+                                       width=30)
 
-    if warnings != []:
-        print('- {0}'.format('\n- '.join(warnings)))
+    print('')
 
-    return modules
+    return modules, cleaned_config
 
-# ------------------------------------------------------------------------------
+
+def process_yaml(argv):
+    from autocmake.parse_yaml import parse_yaml
+    from autocmake.generate import gen_cmakelists, gen_setup
+    from autocmake.extract import extract_list
+
+    project_root = argv[1]
+    if not os.path.isdir(project_root):
+        sys.stderr.write("ERROR: {0} is not a directory\n".format(project_root))
+        sys.exit(-1)
+
+    # read config file
+    print('- parsing autocmake.yml')
+    with open('autocmake.yml', 'r') as stream:
+        config = parse_yaml(stream)
+
+    if 'name' in config:
+        project_name = config['name']
+    else:
+        sys.stderr.write("ERROR: you have to specify the project name in autocmake.yml\n")
+        sys.exit(-1)
+    if ' ' in project_name.rstrip():
+        sys.stderr.write("ERROR: project name contains a space\n")
+        sys.exit(-1)
+
+    if 'min_cmake_version' in config:
+        min_cmake_version = config['min_cmake_version']
+    else:
+        sys.stderr.write("ERROR: you have to specify min_cmake_version in autocmake.yml\n")
+        sys.exit(-1)
+
+    if 'setup_script' in config:
+        setup_script_name = config['setup_script']
+    else:
+        setup_script_name = 'setup'
+
+    # get relative path from setup script to this directory
+    relative_path = os.path.relpath(os.path.abspath('.'), project_root)
+
+    download_directory = 'downloaded'
+    if not os.path.exists(download_directory):
+        os.makedirs(download_directory)
+
+    # fetch modules from the web or from relative paths
+    modules, cleaned_config = fetch_modules(config, relative_path, download_directory)
+
+    # fetch files which are not parsed
+    for src in cleaned_config['fetch']:
+        dst = os.path.join(download_directory, os.path.basename(src))
+        fetch_url(src, dst)
+
+    # print warnings
+    for warning in cleaned_config['warning']:
+        print('- WARNING: {0}'.format(warning))
+
+    # create CMakeLists.txt
+    print('- generating CMakeLists.txt')
+    s = gen_cmakelists(project_name, min_cmake_version, relative_path, modules)
+    with open(os.path.join(project_root, 'CMakeLists.txt'), 'w') as f:
+        f.write('{0}\n'.format('\n'.join(s)))
+
+    # create setup script
+    print('- generating setup script')
+    s = gen_setup(cleaned_config, relative_path, setup_script_name)
+    file_path = os.path.join(project_root, setup_script_name)
+    with open(file_path, 'w') as f:
+        f.write('{0}\n'.format('\n'.join(s)))
+    if sys.platform != 'win32':
+        make_executable(file_path)
 
 
 def main(argv):
     """
     Main function.
     """
+
     if len(argv) != 2:
         sys.stderr.write("\nYou can update a project in two steps.\n\n")
         sys.stderr.write("Step 1: Update or create infrastructure files\n")
@@ -365,183 +200,84 @@ def main(argv):
 
     if argv[1] in ['-h', '--help']:
         print('Usage:')
-        print('  python update.py --self         Update this script and fetch or update infrastructure files under lib/.')
-        print('  python update.py <builddir>     (Re)generate CMakeLists.txt and setup script and fetch or update CMake modules.')
-        print('  python update.py (-h | --help)  Show this help text.')
+        for t, h in [('python update.py --self',
+                      'Update this script and fetch or update infrastructure files under autocmake/.'),
+                     ('python update.py <builddir>',
+                      '(Re)generate CMakeLists.txt and setup script and fetch or update CMake modules.'),
+                     ('python update.py (-h | --help)',
+                      'Show this help text.')]:
+            print('  {0:30} {1}'.format(t, h))
         sys.exit(0)
 
     if argv[1] == '--self':
         # update self
-        if not os.path.isfile('autocmake.cfg'):
-            print('- fetching example autocmake.cfg')
+        if not os.path.isfile('autocmake.yml'):
+            print('- fetching example autocmake.yml')
             fetch_url(
-                src='{0}/raw/stable-0.x/example/autocmake.cfg'.format(AUTOCMAKE_GITHUB_URL),
-                dst='autocmake.cfg'
+                src='{0}example/autocmake.yml'.format(AUTOCMAKE_GITHUB_URL),
+                dst='autocmake.yml'
             )
         if not os.path.isfile('.gitignore'):
             print('- creating .gitignore')
             with open('.gitignore', 'w') as f:
                 f.write('*.pyc\n')
-        print('- fetching lib/config.py')
-        fetch_url(
-            src='{0}/raw/stable-0.x/lib/config.py'.format(AUTOCMAKE_GITHUB_URL),
-            dst='lib/config.py'
-        )
-        print('- fetching lib/docopt/docopt.py')
-        fetch_url(
-            src='{0}/raw/stable-0.x/lib/docopt/docopt.py'.format(AUTOCMAKE_GITHUB_URL),
-            dst='lib/docopt/docopt.py'
-        )
-        print('- fetching update.py')
-        fetch_url(
-            src='{0}/raw/stable-0.x/update.py'.format(AUTOCMAKE_GITHUB_URL),
-            dst='update.py'
-        )
+        for f in ['autocmake/configure.py',
+                  'autocmake/__init__.py',
+                  'autocmake/external/docopt.py',
+                  'autocmake/external/__init__.py',
+                  'autocmake/generate.py',
+                  'autocmake/extract.py',
+                  'autocmake/interpolate.py',
+                  'autocmake/parse_rst.py',
+                  'autocmake/parse_yaml.py',
+                  'update.py']:
+            print('- fetching {0}'.format(f))
+            fetch_url(
+                src='{0}{1}'.format(AUTOCMAKE_GITHUB_URL, f),
+                dst='{0}'.format(f)
+            )
         sys.exit(0)
 
-    project_root = argv[1]
-    if not os.path.isdir(project_root):
-        sys.stderr.write("ERROR: {0} is not a directory\n".format(project_root))
-        sys.exit(-1)
-
-    # read config file
-    print('- parsing autocmake.cfg')
-    config = ConfigParser(dict_type=collections.OrderedDict)
-    config.read('autocmake.cfg')
-
-    if not config.has_option('project', 'name'):
-        sys.stderr.write("ERROR: you have to specify the project name\n")
-        sys.stderr.write("       in autocmake.cfg under [project]\n")
-        sys.exit(-1)
-    project_name = config.get('project', 'name')
-    if ' ' in project_name.rstrip():
-        sys.stderr.write("ERROR: project name contains a space\n")
-        sys.exit(-1)
-
-    if not config.has_option('project', 'min_cmake_version'):
-        sys.stderr.write("ERROR: you have to specify the min_cmake_version for CMake\n")
-        sys.stderr.write("       in autocmake.cfg under [project]\n")
-        sys.exit(-1)
-    min_cmake_version = config.get('project', 'min_cmake_version')
-
-    if config.has_option('project', 'setup_script'):
-        setup_script_name = config.get('project', 'setup_script')
-    else:
-        setup_script_name = 'setup'
-
-    # get relative path from setup script to this directory
-    relative_path = os.path.relpath(os.path.abspath('.'), project_root)
-
-    # fetch modules from the web or from relative paths
-    modules = fetch_modules(config, relative_path)
-
-    # create CMakeLists.txt
-    print('- generating CMakeLists.txt')
-    s = gen_cmakelists(project_name, min_cmake_version, relative_path, modules)
-    with open(os.path.join(project_root, 'CMakeLists.txt'), 'w') as f:
-        f.write('{0}\n'.format('\n'.join(s)))
-
-    # create setup script
-    print('- generating setup script')
-    s = gen_setup(config, relative_path, setup_script_name)
-    file_path = os.path.join(project_root, setup_script_name)
-    with open(file_path, 'w') as f:
-        f.write('{0}\n'.format('\n'.join(s)))
-    if sys.platform != 'win32':
-        make_executable(file_path)
-
-# ------------------------------------------------------------------------------
+    process_yaml(argv)
 
 
-# http://stackoverflow.com/a/30463972
 def make_executable(path):
+    # http://stackoverflow.com/a/30463972
     mode = os.stat(path).st_mode
     mode |= (mode & 0o444) >> 2    # copy R bits to X
     os.chmod(path, mode)
 
-# ------------------------------------------------------------------------------
 
+def fetch_url(src, dst):
+    """
+    Fetch file from URL src and save it to dst.
+    """
+    # we do not use the nicer sys.version_info.major
+    # for compatibility with Python < 2.7
+    if sys.version_info[0] > 2:
+        import urllib.request
 
-def parse_cmake_module(s_in, defaults={}):
+        class URLopener(urllib.request.FancyURLopener):
+            def http_error_default(self, url, fp, errcode, errmsg, headers):
+                sys.stderr.write("ERROR: could not fetch {0}\n".format(url))
+                sys.exit(-1)
+    else:
+        import urllib
 
-    parsed_config = collections.defaultdict(lambda: None)
+        class URLopener(urllib.FancyURLopener):
+            def http_error_default(self, url, fp, errcode, errmsg, headers):
+                sys.stderr.write("ERROR: could not fetch {0}\n".format(url))
+                sys.exit(-1)
 
-    if 'autocmake.cfg configuration::' not in s_in:
-        return parsed_config
+    dirname = os.path.dirname(dst)
+    if dirname != '':
+        if not os.path.isdir(dirname):
+            os.makedirs(dirname)
 
-    s_out = []
-    is_rst_line = False
-    for line in s_in.split('\n'):
-        if is_rst_line:
-            if len(line) > 0:
-                if line[0] != '#':
-                    is_rst_line = False
-            else:
-                is_rst_line = False
-        if is_rst_line:
-            s_out.append(line[2:])
-        if '#.rst:' in line:
-            is_rst_line = True
-
-    autocmake_entry = '\n'.join(s_out).split('autocmake.cfg configuration::')[1]
-    autocmake_entry = autocmake_entry.replace('\n  ', '\n')
-
-    # we prepend a fake section heading so that we can parse it with configparser
-    autocmake_entry = '[foo]\n' + autocmake_entry
-
-    buf = StringIO(autocmake_entry)
-    config = ConfigParser(dict_type=collections.OrderedDict)
-    config.readfp(buf)
-
-    for section in config.sections():
-        for s in ['docopt', 'define', 'export', 'fetch', 'warning']:
-            if config.has_option(section, s):
-                parsed_config[s] = config.get(section, s, 0, defaults)
-
-    return parsed_config
-
-# ------------------------------------------------------------------------------
-
-
-def test_parse_cmake_module():
-
-    s = '''#.rst:
-#
-# Foo ...
-#
-# autocmake.cfg configuration::
-#
-#   docopt: --cxx=<CXX> C++ compiler [default: g++].
-#           --extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: ''].
-#   export: 'CXX={0}'.format(arguments['--cxx'])
-#   define: '-DEXTRA_CXXFLAGS="{0}"'.format(arguments['--extra-cxx-flags'])
-
-enable_language(CXX)
-
-if(NOT DEFINED CMAKE_C_COMPILER_ID)
-    message(FATAL_ERROR "CMAKE_C_COMPILER_ID variable is not defined!")
-endif()'''
-
-    parsed_config = parse_cmake_module(s)
-    assert parsed_config['docopt'] == "--cxx=<CXX> C++ compiler [default: g++].\n--extra-cxx-flags=<EXTRA_CXXFLAGS> Extra C++ compiler flags [default: '']."
-
-    s = '''#.rst:
-#
-# Foo ...
-#
-# Bar ...
-
-enable_language(CXX)
-
-if(NOT DEFINED CMAKE_C_COMPILER_ID)
-    message(FATAL_ERROR "CMAKE_C_COMPILER_ID variable is not defined!")
-endif()'''
-
-    parsed_config = parse_cmake_module(s)
-    assert parsed_config['docopt'] is None
-
-# ------------------------------------------------------------------------------
+    opener = URLopener()
+    opener.retrieve(src, dst)
 
 
 if __name__ == '__main__':
+    check_for_yaml()
     main(sys.argv)