💥 Removed pipfile

preserve quotes in setup_command; closes #169

.default.nix

@@ -0,0 +1,32 @@
+let
+  hostPkgs = import <nixpkgs> {};
+  nixpkgs = (hostPkgs.fetchFromGitHub {
+    owner = "NixOS";
+    repo = "nixpkgs-channels";
+    rev = "nixos-unstable";
+    sha256 = "1rc1pjnvfi194gka45zc1nivzsncc819kvxlfv277l2c8ryhgbpc";
+  });
+in
+  with import nixpkgs {};
+  stdenv.mkDerivation {
+    name = "Autocmake";
+    buildInputs = [
+      ccache
+      cmake
+      doxygen
+      gcc
+      gfortran
+      liblapack
+      openmpi
+      pipenv
+      python3Packages.pep8
+      python3Packages.pytest
+      python3Packages.pyyaml
+      zlib
+    ];
+    src = null;
+    shellHook = ''
+    export NINJA_STATUS="[Built edge %f of %t in %e sec]"
+    SOURCE_DATE_EPOCH=$(date +%s)
+    '';
+  }

.envrc

@@ -0,0 +1 @@
+use nix .default.nix

.gitignore

@@ -10,6 +10,10 @@ test/*/cmake/update.py
 test/*/cmake/autocmake/
 test/*/cmake/downloaded/
 test/*/setup
+test/*/cmake_output
 
 # generated by doc/extract_rst.py
 doc/module-reference.rst
+.idea/
+/tmp/
+_build

.travis.yml

@@ -16,7 +16,6 @@ matrix:
              # compilers
             - g++
             - gfortran
-            - cmake
               # math libraries
             - libblas-dev
             - liblapack-dev
@@ -26,8 +25,6 @@ matrix:
             - libopenmpi-dev
               # python library, development version
             - libpython2.7
-              # boost
-            - libboost-all-dev
 
     - os: linux
       python: 3.5
@@ -50,33 +47,33 @@ matrix:
             - libopenmpi-dev
               # python library, development version
             - libpython2.7
-              # boost
-            - libboost-all-dev
 
     - os: osx
-      osx_image: xcode6.4
+      osx_image: xcode11
       compiler: gcc
-      env: SOURCES=homebrew
+      env:
+        - SOURCES=homebrew
 
 install:
   - |
     if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-        brew install cmake boost python gcc open-mpi
+        brew update &> /dev/null
         pip install virtualenv
     elif [[ "${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
+        mkdir -p $HOME/dependencies/cmake
+        curl -Ls https://cmake.org/files/v3.8/cmake-3.8.0-Linux-x86_64.tar.gz | tar -xz -C $HOME/dependencies/cmake --strip-components=1
+        export PATH=$HOME/dependencies/cmake/bin${PATH:+:$PATH}
     fi
+  - cmake --version
   - virtualenv venv
   - source venv/bin/activate
   - pip install -r requirements.txt
 
 script:
-    # pep8 tests
-  - pep8 --ignore E501 update.py
-  - pep8 --ignore E501,E265 autocmake
+    # pycodestyle tests
+  - pycodestyle --ignore E501 update.py
+  - pycodestyle --ignore E501,E265,E741 autocmake --exclude autocmake/external/docopt.py
     # unit tests
   - py.test -vv autocmake/*
   - py.test -vv test/test.py

AUTHORS.md

@@ -1,14 +1,14 @@
 # Authors
 
-- Jonas Juselius
 - Radovan Bast
+- Roberto Di Remigio
+- Jonas Juselius
 
 # Contributors
 
 - Miroslav Ilias (Windows, portability, earliest adopter testing and feedback, math library testing)
 - Ivan Hrasko (Windows, Appveyor testing)
 - 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.
+see https://github.com/dev-cafe/autocmake/contributors.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2016 by Radovan Bast, Jonas Juselius, and contributors.
+Copyright (c) 2015-2017 by Radovan Bast, Roberto Di Remigio, Jonas Juselius, and contributors.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,11 +1,12 @@
-[![Build Status](https://travis-ci.org/coderefinery/autocmake.svg?branch=master)](https://travis-ci.org/coderefinery/autocmake/builds)
+[![Build Status](https://travis-ci.org/dev-cafe/autocmake.svg?branch=master)](https://travis-ci.org/dev-cafe/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)
+[![License](https://img.shields.io/badge/license-%20BSD--3-blue.svg)](LICENSE)
+[![DOI](https://zenodo.org/badge/36069881.svg)](https://zenodo.org/badge/latestdoi/36069881)
 
-![alt text](https://github.com/coderefinery/autocmake/raw/master/img/autocmake.png "Autocmake")
+![alt text](https://github.com/dev-cafe/autocmake/raw/master/img/autocmake.png "Autocmake")
 
 A CMake plugin composer.
-Licensed under [BSD-3](../master/LICENSE).
+Licensed under [BSD-3](LICENSE).
 See http://autocmake.org.
 
 
@@ -17,12 +18,17 @@ See http://autocmake.org.
 
 ## Projects using Autocmake
 
-- [Numgrid](https://github.com/dftlibs/numgrid/)
-- [XCint](https://github.com/dftlibs/xcint/)
+- [Numgrid](https://github.com/dftlibs/numgrid)
+- [XCint](https://github.com/dftlibs/xcint)
 - [DIRAC](http://diracprogram.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
+- [MRChem](https://github.com/MRChemSoft/mrchem)
+- [ReSpect](http://rel-qchem.sav.sk)
+- [Flanders](https://github.com/bast/flanders)
+- [Polygons](https://github.com/bast/polygons)
+- [GIMIC](https://github.com/qmcurrents/gimic)
 
 If you use Autocmake, please link to your project via a pull request.

autocmake/__init__.py

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

autocmake/configure.py

@@ -18,10 +18,11 @@ def check_cmake_exists(cmake_command):
     """
     from subprocess import Popen, PIPE
 
-    p = Popen('{0} --version'.format(cmake_command),
-              shell=True,
-              stdin=PIPE,
-              stdout=PIPE)
+    p = Popen(
+        '{0} --version'.format(cmake_command),
+        shell=True,
+        stdin=PIPE,
+        stdout=PIPE)
     if not ('cmake version' in p.communicate()[0].decode('UTF-8')):
         sys.stderr.write('   This code is built using CMake\n\n')
         sys.stderr.write('   CMake is not found\n')
@@ -41,55 +42,46 @@ def setup_build_path(build_path):
         fname = os.path.join(build_path, 'CMakeCache.txt')
         if os.path.exists(fname):
             sys.stderr.write('aborting setup\n')
-            sys.stderr.write('build directory {0} which contains CMakeCache.txt already exists\n'.format(build_path))
-            sys.stderr.write('remove the build directory and then rerun setup\n')
+            sys.stderr.write(
+                'build directory {0} which contains CMakeCache.txt already exists\n'.
+                format(build_path))
+            sys.stderr.write(
+                'remove the build directory and then rerun setup\n')
             sys.exit(1)
     else:
         os.makedirs(build_path, 0o755)
 
 
-def test_adapt_cmake_command_to_platform():
-
-    cmake_command = "FC=foo CC=bar CXX=RABOOF cmake -DTHIS -DTHAT='this and that cmake' .."
-    res = adapt_cmake_command_to_platform(cmake_command, 'linux')
-    assert res == cmake_command
-    res = adapt_cmake_command_to_platform(cmake_command, 'win32')
-    assert res == "set FC=foo && set CC=bar && set CXX=RABOOF && cmake -DTHIS -DTHAT='this and that cmake' .."
-
-    cmake_command = "cmake -DTHIS -DTHAT='this and that cmake' .."
-    res = adapt_cmake_command_to_platform(cmake_command, 'linux')
-    assert res == cmake_command
-    res = adapt_cmake_command_to_platform(cmake_command, 'win32')
-    assert res == cmake_command
-
-
-def adapt_cmake_command_to_platform(cmake_command, platform):
+def add_quotes_to_argv(argv, arguments):
     """
-    Adapt CMake command to MS Windows platform.
+    This function tries to solve this problem:
+    https://stackoverflow.com/questions/19120247/python-sys-argv-to-preserve-or
+
+    The problem is that sys.argv has been stripped of quotes by the shell but
+    docopt's arguments contains quotes.
+
+    So what we do is cycle through all docopt arguments: if they are also
+    present in sys.argv and contain spaces, we add quotes.
     """
-    if platform == 'win32':
-        pos = cmake_command.find('cmake')
-        s = ['set {0} &&'.format(e) for e in cmake_command[:pos].split()]
-        s.append(cmake_command[pos:])
-        return ' '.join(s)
-    else:
-        return cmake_command
+    setup_command = ' '.join(argv[:])
+
+    for k, v in arguments.items():
+        if isinstance(v, str):
+            if ' ' in v:
+                if v in setup_command:
+                    setup_command = setup_command.replace(v, '"{}"'.format(v))
+
+    return setup_command
 
 
-def run_cmake(command, build_path, default_build_path):
+def run_cmake(command, build_path, default_build_path, arguments):
     """
     Execute CMake command.
     """
     from subprocess import Popen, PIPE
-    from shutil import rmtree
 
     topdir = os.getcwd()
-    os.chdir(build_path)
-    p = Popen(command,
-              shell=True,
-              stdin=PIPE,
-              stdout=PIPE,
-              stderr=PIPE)
+    p = Popen(command, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
     stdout_coded, stderr_coded = p.communicate()
     stdout = stdout_coded.decode('UTF-8')
     stderr = stderr_coded.decode('UTF-8')
@@ -98,25 +90,28 @@ def run_cmake(command, build_path, default_build_path):
     print(stdout)
 
     if stderr:
+        # we write out stderr but we do not stop yet
+        # this is because CMake warnings are sent to stderr
+        # and they might be benign
         sys.stderr.write(stderr)
-        sys.exit(1)
 
     # write cmake output to file
-    with open('cmake_output', 'w') as f:
+    with open(os.path.join(build_path, '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):
-            # remove build_path iff not set by the user
-            # otherwise removal can be dangerous
-            rmtree(default_build_path)
-    else:
-        # configuration was successful
-        save_setup_command(sys.argv, build_path)
+    # to figure out whether configuration was a success
+    # we check for 3 sentences that should be part of stdout
+    configuring_done = '-- Configuring done' in stdout
+    generating_done = '-- Generating done' in stdout
+    build_files_written = '-- Build files have been written to' in stdout
+    configuration_successful = configuring_done and generating_done and build_files_written
+
+    if configuration_successful:
+        setup_command = add_quotes_to_argv(sys.argv, arguments)
+        save_setup_command(setup_command, build_path)
         print_build_help(build_path, default_build_path)
 
 
@@ -133,16 +128,16 @@ def print_build_help(build_path, default_build_path):
     print('   $ make')
 
 
-def save_setup_command(argv, build_path):
+def save_setup_command(setup_command, build_path):
     """
     Save setup command to a file.
     """
     file_name = os.path.join(build_path, 'setup_command')
     with open(file_name, 'w') as f:
-        f.write(' '.join(argv[:]) + '\n')
+        f.write(setup_command + '\n')
 
 
-def configure(root_directory, build_path, cmake_command, only_show):
+def configure(root_directory, build_path, cmake_command, arguments):
     """
     Main configure function.
     """
@@ -154,13 +149,12 @@ def configure(root_directory, build_path, cmake_command, only_show):
     # deal with build path
     if build_path is None:
         build_path = default_build_path
-    if not only_show:
+    if not arguments['--show']:
         setup_build_path(build_path)
 
-    cmake_command = adapt_cmake_command_to_platform(cmake_command, sys.platform)
-
+    cmake_command += ' -B' + build_path
     print('{0}\n'.format(cmake_command))
-    if only_show:
+    if arguments['--show']:
         sys.exit(0)
 
-    run_cmake(cmake_command, build_path, default_build_path)
+    run_cmake(cmake_command, build_path, default_build_path, arguments)

autocmake/external/__init__.py

@@ -0,0 +1 @@
+# empty - this line is here to avoid problem when fetching empty files from web

autocmake/extract.py

@@ -1,5 +1,5 @@
 def extract_list(config, section):
-    from collections import Iterable
+    from collections.abc import Iterable
     l = []
     if 'modules' in config:
         for module in config['modules']:

autocmake/generate.py

@@ -20,7 +20,7 @@ def gen_cmake_command(config):
         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("    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']:")
@@ -40,12 +40,49 @@ def autogenerated_notice():
 
     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))
+    s.append('# Copyright (c) {0} by Radovan Bast, Roberto Di Remigio, Jonas Juselius, and contributors.'.format(year_range))
 
     return '\n'.join(s)
 
 
-def gen_setup(config, relative_path, setup_script_name):
+def gen_cmake_options_wrappers():
+    s = """\n# Options handling utilities
+include(CMakeDependentOption)
+# Macro for printing an option in a consistent manner
+# Written by Lori A. Burns (@loriab) and Ryan M. Richard (@ryanmrichard)
+# Syntax: print_option(<option to print> <was specified>)
+macro(print_option variable default)
+  if(NOT DEFINED ${variable} OR "${${variable}}" STREQUAL "")
+    message(STATUS "Setting (unspecified) option ${variable}: ${default}")
+  else()
+    message(STATUS "Setting option ${variable}: ${${variable}}")
+  endif()
+endmacro()
+
+# Wraps an option with default ON/OFF. Adds nice messaging to option()
+# Written by Lori A. Burns (@loriab) and Ryan M. Richard (@ryanmrichard)
+# Syntax: option_with_print(<option name> <description> <default value>)
+macro(option_with_print variable msge default)
+  print_option(${variable} ${default})
+  option(${variable} ${msge} ${default})
+endmacro()
+
+# Wraps an option with a default other than ON/OFF and prints it
+# Written by Lori A. Burns (@loriab) and Ryan M. Richard (@ryanmrichard)
+# NOTE: Can't combine with above b/c CMake handles ON/OFF options specially
+# NOTE2: CMake variables are always defined so need to further check for if
+#       they are the NULL string. This is also why we need the force
+# Syntax: option_with_default(<option name> <description> <default value>)
+macro(option_with_default variable msge default)
+  print_option(${variable} "${default}")
+  if(NOT DEFINED ${variable} OR "${${variable}}" STREQUAL "")
+    set(${variable} "${default}" CACHE STRING ${msge} FORCE)
+  endif()
+endmacro()"""
+    return s
+
+
+def gen_setup(config, default_build_type, relative_path, setup_script_name):
     """
     Generate setup script.
     """
@@ -56,6 +93,7 @@ def gen_setup(config, relative_path, setup_script_name):
     s.append('\n{0}'.format(autogenerated_notice()))
     s.append('\nimport os')
     s.append('import sys')
+    s.append('assert sys.version_info >= (2, 6), \'Python >= 2.6 is required\'')
 
     s.append("\nsys.path.insert(0, '{0}')".format(relative_path))
 
@@ -75,7 +113,7 @@ def gen_setup(config, relative_path, setup_script_name):
         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(['--type=<TYPE>', 'Set the CMake build type (debug, release, relwithdebinfo, minsizerel) [default: {0}].'.format(default_build_type)])
     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].'])
@@ -109,15 +147,15 @@ def gen_setup(config, relative_path, setup_script_name):
     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("cmake_command = '{0} -H{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'])")
+    s.append("configure.configure(root_directory, build_path, cmake_command, arguments)")
 
     return s
 
 
-def gen_cmakelists(project_name, min_cmake_version, relative_path, modules):
+def gen_cmakelists(project_name, project_language, min_cmake_version, default_build_type, relative_path, modules):
     """
     Generate CMakeLists.txt.
     """
@@ -131,33 +169,31 @@ def gen_cmakelists(project_name, min_cmake_version, relative_path, modules):
     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('project({0} LANGUAGES {1})'.format(project_name, project_language))
 
     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')
+    build_type_capitalized = {'debug': 'Debug',
+                              'release': 'Release',
+                              'relwithdebinfo': 'RelWithDebInfo',
+                              'minsizerel': 'MinSizeRel'}
+
+    _build_type = build_type_capitalized[default_build_type]
+    s.append('\n# if CMAKE_BUILD_TYPE undefined, we set it to {0}'.format(_build_type))
     s.append('if(NOT CMAKE_BUILD_TYPE)')
-    s.append('    set(CMAKE_BUILD_TYPE "Debug")')
+    s.append('    set(CMAKE_BUILD_TYPE "{0}")'.format(_build_type))
     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))
+    s.append(gen_cmake_options_wrappers())
 
     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]))
+        s.append('include({0})'.format(os.path.join('${PROJECT_SOURCE_DIR}',
+                                                    relative_path,
+                                                    module.path,
+                                                    module.name)))
 
     return s
 

autocmake/interpolate.py

@@ -3,7 +3,7 @@ def replace(s, d):
 
     if isinstance(s, str):
         for var in findall(r"%\(([A-Za-z0-9_]*)\)", s):
-            s = s.replace("%({})".format(var), str(d[var]))
+            s = s.replace("%({0})".format(var), str(d[var]))
     return s
 
 
@@ -13,7 +13,7 @@ def test_replace():
 
 
 def interpolate(d, d_map):
-    from collections import Mapping, Iterable
+    from collections.abc import Mapping, Iterable
     from copy import copy
 
     for k, v in d.items():

autocmake/parse_rst.py

@@ -1,14 +1,9 @@
 def parse_cmake_module(s_in, overrides={}):
     import sys
-    from collections import Mapping, Iterable, defaultdict
+    from collections.abc import Mapping, Iterable
+    from collections import 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
+    from io import StringIO
 
     parsed_config = defaultdict(lambda: None)
 

compilers/Clang.C.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{CFLAGS})
     if(CMAKE_C_COMPILER_ID MATCHES Clang)
-        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wextra")
         set(CMAKE_C_FLAGS_RELEASE "-O3")
         set(CMAKE_C_FLAGS_DEBUG "-O0 -g")
     endif()

compilers/Clang.CXX.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{CXXFLAGS})
     if(CMAKE_CXX_COMPILER_ID MATCHES Clang)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
         set(CMAKE_CXX_FLAGS_RELEASE "-Ofast")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
     endif()

compilers/GNU.C.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{CFLAGS})
     if(CMAKE_C_COMPILER_ID MATCHES GNU)
-        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wextra")
         set(CMAKE_C_FLAGS_RELEASE "-O3")
         set(CMAKE_C_FLAGS_DEBUG "-O0 -g")
     endif()

compilers/GNU.CXX.cmake

@@ -1,7 +1,7 @@
 if(NOT DEFINED ENV{CXXFLAGS})
     if(CMAKE_CXX_COMPILER_ID MATCHES GNU)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-        set(CMAKE_CXX_FLAGS_RELEASE "-Ofast")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
+        set(CMAKE_CXX_FLAGS_RELEASE "-O3")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
     endif()
 endif()

compilers/GNU.Fortran.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{FCFLAGS})
     if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
-        set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
+        set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Wall -Wextra")
         set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -funroll-all-loops")
         set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -fbacktrace")
     endif()

compilers/Intel.C.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{CFLAGS})
     if(CMAKE_C_COMPILER_ID MATCHES Intel)
-        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall")
         set(CMAKE_C_FLAGS_RELEASE "-O3")
         set(CMAKE_C_FLAGS_DEBUG "-O0 -g")
     endif()

compilers/Intel.CXX.cmake

@@ -1,6 +1,6 @@
 if(NOT DEFINED ENV{CXXFLAGS})
     if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall")
         set(CMAKE_CXX_FLAGS_RELEASE "-O3")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
     endif()

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

@@ -1,289 +1,48 @@
-# -*- coding: utf-8 -*-
+# Configuration file for the Sphinx documentation builder.
 #
-# Autocmake documentation build configuration file, created by
-# sphinx-quickstart on Mon Jun  1 16:41:30 2015.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import sys
 import os
-import shlex
+import time
 
-sys.path.append(os.path.relpath(os.path.abspath('.')))
+sys.path.insert(0, os.path.abspath("."))
 import extract_rst
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath(".."))
+from autocmake import __version__ as _version
 
-# -- General configuration ------------------------------------------------
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+project = "Autocmake"
+copyright = f'2015-{time.strftime("%Y")}, Radovan Bast, Roberto Di Remigio, Jonas Juselius, and contributors'
+author = "Radovan Bast, Roberto Di Remigio, Jonas Juselius, and contributors"
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.todo',
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'Autocmake'
-copyright = u'2015-2016, Radovan Bast, Jonas Juselius, and contributors'
-author = u'Radovan Bast, Jonas Juselius, and contributors'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0-alpha-x'
+release = _version
+# The short X.Y version.
+version = ".".join(release.split(".")[0:2])
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
+extensions = [
+    "sphinx.ext.todo",
+]
 todo_include_todos = True
 
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-# -- Options for HTML output ----------------------------------------------
+root_doc = "index"
+pygments_style = "sphinx"
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = 'default'
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-#html_logo = None
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
-
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
-
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'Autocmakedoc'
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  (master_doc, 'Autocmake.tex', u'Autocmake Documentation',
-   u'Radovan Bast and Jonas Juselius', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'autocmake', u'Autocmake Documentation',
-     [author], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  (master_doc, 'Autocmake', u'Autocmake Documentation',
-   author, 'Autocmake', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+html_theme = "classic"
+html_theme_options = {"body_max_width": "none", "sidebarwidth": "16%"}
+html_static_path = ["_static"]
+html_sidebars = {"**": ["globaltoc.html", "sourcelink.html", "searchbox.html"]}

doc/contributors/doc.rst

@@ -10,11 +10,11 @@ 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.io/en/latest/module-reference.html#cc-cmake with
-https://github.com/coderefinery/autocmake/blob/master/modules/cc.cmake).
+https://github.com/dev-cafe/autocmake/blob/master/modules/cc.cmake).
 
 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/master/modules/cc.cmake#L20-L26.
+https://github.com/dev-cafe/autocmake/blob/master/modules/cc.cmake#L20-L26.
 Here, ``update.py`` will infer the configurations for ``docopt``, ``export``,
 and ``define``.

doc/contributors/testing.rst

@@ -5,14 +5,14 @@ Testing Autocmake
 
 You will need to install `pytest <http://pytest.org/>`__.
 
-Check also the `Travis  <https://github.com/coderefinery/autocmake/blob/master/.travis.yml>`__
+Check also the `Travis  <https://github.com/dev-cafe/autocmake/blob/master/.travis.yml>`__
 build and test recipe for other requirements.
 
 Your contributions and changes should preserve the test set and be PEP8 conform.
 You can run locally all tests with::
 
-  $ pep8 --ignore E501 update.py
-  $ pep8 --ignore E501,E265 autocmake
+  $ pycodestyle --ignore E501 update.py
+  $ pycodestyle --ignore E501,E265 autocmake
   $ py.test -vv autocmake/*
   $ py.test -vv test/test.py
 
@@ -23,5 +23,5 @@ You can also select individual tests, for example those with ``fc_blas`` string
 For more options, see the ``py.test`` flags.
 
 This test set is run upon each push to the central repository.
-See also the `Travis <https://travis-ci.org/coderefinery/autocmake/builds>`__
+See also the `Travis <https://travis-ci.org/dev-cafe/autocmake/builds>`__
 build and test history.

doc/developers/bootstrap.rst

@@ -12,12 +12,15 @@ 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/master/update.py
+  $ wget https://github.com/dev-cafe/autocmake/raw/master/update.py
+  $ virtualenv venv
+  $ source venv/bin/activate
+  $ pip install pyyaml
   $ python update.py --self
 
 On the MS Windows system, you can use the PowerShell wget-replacement::
 
-  $ Invoke-WebRequest https://github.com/coderefinery/autocmake/raw/master/update.py -OutFile update.py
+  $ Invoke-WebRequest https://github.com/dev-cafe/autocmake/raw/master/update.py -OutFile update.py
 
 This creates (or updates) the following files (an existing ``autocmake.yml`` is
 not overwritten by the script)::

doc/developers/configuration.rst

@@ -1,99 +1,86 @@
 
 .. _autocmake_yml:
 
-Configuring autocmake.cfg
+Configuring autocmake.yml
 =========================
 
-The script ``autocmake.cfg`` is the high level place where you configure
+The script ``autocmake.yml`` is the high level place where you configure
 your project. Here is an example. We will discuss it in detail further
 below::
 
-  [project]
   name: numgrid
-  min_cmake_version: 2.8
 
-  [fc]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
+  min_cmake_version: 3.1
 
-  [cc]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
+  default_build_type: release
 
-  [cxx]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/cxx.cmake
+  language:
+    - Fortran
+    - C
+    - CXX
 
-  [flags]
-  source: https://github.com/coderefinery/autocmake/raw/master/compilers/GNU.CXX.cmake
-          https://github.com/coderefinery/autocmake/raw/master/compilers/Intel.CXX.cmake
+  url_root: https://github.com/dev-cafe/autocmake/raw/master/
 
-  [rpath]
-  source: custom/rpath.cmake
-
-  [definitions]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/definitions.cmake
-
-  [coverage]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/code_coverage.cmake
-
-  [safeguards]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/safeguards.cmake
-
-  [default_build_paths]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/default_build_paths.cmake
-
-  [src]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
-
-  [googletest]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/googletest.cmake
-
-  [custom]
-  source: custom/api.cmake
-          custom/test.cmake
+  modules:
+  - compilers:
+    - source:
+      - '%(url_root)modules/fc.cmake'
+      - '%(url_root)modules/cc.cmake'
+      - '%(url_root)modules/cxx.cmake'
+  - flags:
+    - source:
+      - '%(url_root)compilers/GNU.CXX.cmake'
+      - '%(url_root)compilers/Intel.CXX.cmake'
+      - 'compilers/Clang.CXX.cmake'
+  - plugins:
+    - source:
+      - '%(url_root)modules/ccache.cmake'
+      - 'custom/rpath.cmake'
+      - '%(url_root)modules/definitions.cmake'
+      - '%(url_root)modules/code_coverage.cmake'
+      - '%(url_root)modules/safeguards.cmake'
+      - '%(url_root)modules/default_build_paths.cmake'
+      - '%(url_root)modules/src.cmake'
+      - '%(url_root)modules/googletest.cmake'
+      - 'custom/api.cmake'
+      - 'custom/test.cmake'
 
 
 Name and order of sections
 --------------------------
 
-We see that the configuration file has sections.
-The only section where the name matters is ``[project]``::
+First we define the project name (here "numgrid"). This section has to be there
+and it has to be called "project" (but it does not have to be on top).
 
-  [project]
-  name: numgrid
-  min_cmake_version: 2.8
+We also have to define ``min_cmake_version`` as well as set the supported language(s).
 
-This is where we define the project name (here "numgrid"). This section has to
-be there and it has to be called "project" (but it does not have to be on top).
+The definition ``url_root`` is an interpolation (see :ref:`interpolation`) and
+we use it to avoid retyping the same line over and over and to be able to
+change it in one place.  The explicit name "url_root" has no special meaning to
+Autocmake and we could have chosen a different name.
 
-The names of the other sections do not matter to Autocmake. You could name them like this::
+The section ``modules`` is a list of CMake plugins.  The names of the list
+elements (here "compilers", "flags", and "plugins") does not matter to
+Autocmake. We could have called them "one", "two", and "whatever", but it would
+not make much sense. It is better to choose names that are meaningful to you
+and readers of your code.
 
-  [project]
-  name: numgrid
-  min_cmake_version: 2.8
-
-  [one]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
-
-  [two]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
-
-  [whatever]
-  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.
-
-The order of the sections does matter and the sections will be processed in the
-exact order as you specify them in ``autocmake.cfg``.
+The order of the elements under ``modules`` does matter and the list will be
+processed in the exact order as you specify them in ``autocmake.yml``.
 
 
 Minimal example
 ---------------
 
-As a minimal example we take an ``autocmake.cfg`` which only contains::
+As a minimal example we take an ``autocmake.yml`` which only contains::
 
-  [project]
   name: minime
-  min_cmake_version: 2.8
+  min_cmake_version: 3.1
+  language: C
+
+If you don't have the ``update.py`` script yet, you need to fetch it from the web::
+
+  $ wget https://github.com/dev-cafe/autocmake/raw/master/update.py
 
 First we make sure that the ``update.py`` script is up-to-date and that it has access
 to all libraries it needs::
@@ -101,15 +88,22 @@ to all libraries it needs::
   $ python update.py --self
 
   - creating .gitignore
-  - fetching lib/config.py
-  - fetching lib/docopt/docopt.py
+  - fetching autocmake/configure.py
+  - fetching autocmake/__init__.py
+  - fetching autocmake/external/docopt.py
+  - fetching autocmake/external/__init__.py
+  - fetching autocmake/generate.py
+  - fetching autocmake/extract.py
+  - fetching autocmake/interpolate.py
+  - fetching autocmake/parse_rst.py
+  - fetching autocmake/parse_yaml.py
   - fetching update.py
 
 Good. Now we can generate ``CMakeLists.txt`` and the setup script::
 
-  $ python update ..
+  $ python update.py ..
 
-  - parsing autocmake.cfg
+  - parsing autocmake.yml
   - generating CMakeLists.txt
   - generating setup script
 
@@ -119,7 +113,7 @@ Excellent. Here is the generated ``CMakeLists.txt``::
   cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
 
   # project name
-  project(minime)
+  project(minime C)
 
   # do not rebuild if rules (compiler flags) change
   set(CMAKE_SKIP_RULE_DEPENDENCY TRUE)
@@ -129,8 +123,6 @@ Excellent. Here is the generated ``CMakeLists.txt``::
       set(CMAKE_BUILD_TYPE "Debug")
   endif()
 
-  set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake/downloaded)
-
 This is the very bare minimum. Every Autocmake project will have at least these
 settings.
 
@@ -147,38 +139,38 @@ the following default options::
     --show                                 Show CMake command and exit.
     --cmake-executable=<CMAKE_EXECUTABLE>  Set the CMake executable [default: cmake].
     --cmake-options=<STRING>               Define options to CMake [default: ''].
+    --prefix=<PATH>                        Set the install path for make install.
     <builddir>                             Build directory.
     -h --help                              Show this screen.
 
 That's not too bad although currently we cannot do much with this since there
 are no sources listed, no targets, hence nothing to build. We need to flesh out
-``CMakeLists.txt`` by extending ``autocmake.cfg``
-and this is what we will do in the next section.
+``CMakeLists.txt`` by extending ``autocmake.yml`` and this is what we will do
+in the next section.
 
 
 Assembling CMake plugins
 ------------------------
 
-The preferred way to extend ``CMakeLists.txt`` is by editing ``autocmake.cfg``
+The preferred way to extend ``CMakeLists.txt`` is by editing ``autocmake.yml``
 and using the ``source`` option::
 
-  [fc]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
+  - compilers:
+    - source:
+      - '%(url_root)modules/fc.cmake'
+      - '%(url_root)modules/cc.cmake'
+      - '%(url_root)modules/cxx.cmake'
 
-This will download ``fc.cmake`` and include it in ``CMakeLists.txt``.
+This will download ``fc.cmake``, ``cc.cmake``, and ``cxx.cmake``, and include
+them in ``CMakeLists.txt``, in this order.
 
 You can also include local CMake modules, e.g.::
 
-  [rpath]
-  source: custom/rpath.cmake
+  - source:
+    - 'custom/rpath.cmake'
 
-It is also OK to include several modules at once::
-
-  [flags]
-  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``.
+It is also OK to include several modules at once as we have seen above.  The
+modules will be included in the same order as they appear in ``autocmake.yml``.
 
 
 Fetching files without including them in CMakeLists.txt
@@ -187,9 +179,9 @@ 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/master/modules/git_info/git_info.cmake#L10-L11).
+https://github.com/dev-cafe/autocmake/blob/master/modules/git_info/git_info.cmake#L10-L13).
 
-If ``fetch`` is invoked in ``autocmake.cfg``, then the fetched file is placed
+If ``fetch`` is invoked in ``autocmake.yml``, then the fetched file is placed
 under ``downloaded/``.  If ``fetch`` is invoked from within a CMake module
 documentation (see below), then the fetched file is placed into the same
 directory as the CMake module file which fetches it.
@@ -199,11 +191,11 @@ Generating setup options
 ------------------------
 
 Options for the setup script can be generated with the ``docopt``
-option. As an example, the following ``autocmake.cfg`` snippet will add a
+option. As an example, the following ``autocmake.yml`` snippet will add a
 ``--something`` flag::
 
-  [my_section]
-  docopt: --something Enable something [default: False].
+  - my_section:
+    - docopt: "--something Enable something [default: False]."
 
 
 Setting CMake options
@@ -213,9 +205,9 @@ Configure-time CMake options can be generated with the ``define`` option.
 Consider the following example which toggles the CMake variable
 ``ENABLE_SOMETHING``::
 
-  [my_section]
-  docopt: --something Enable something [default: False].
-  define: '-DENABLE_SOMETHING={0}'.format(arguments['--something'])
+  - my_section:
+    - docopt: "--something Enable something [default: False]."
+    - define: "'-DENABLE_SOMETHING={0}'.format(arguments['--enable-something'])"
 
 
 Setting environment variables
@@ -224,33 +216,23 @@ Setting environment variables
 You can export environment variables at configure-time using the ``export``
 option. Consider the following example::
 
-  [cc]
-  docopt: --cc=<CC> C compiler [default: gcc].
-          --extra-cc-flags=<EXTRA_CFLAGS> Extra C compiler flags [default: ''].
-  export: 'CC=%s' % arguments['--cc']
-  define: '-DEXTRA_CFLAGS="%s"' % 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'])"
 
 
 Auto-generating configurations from the documentation
 -----------------------------------------------------
 
-To avoid a boring re-typing of boilerplate ``autocmake.cfg`` code it is possible
+To avoid a boring re-typing of boilerplate ``autocmake.yml`` code it is possible
 to auto-generate configurations from the documentation. This is the case
 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
+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/master/modules/cc.cmake#L20-L25.
+https://github.com/dev-cafe/autocmake/blob/master/modules/cc.cmake#L20-L26.
 Here, ``update.py`` will infer the configurations for ``docopt``, ``export``,
 and ``define``.
-
-
-Overriding documented configurations
-------------------------------------
-
-Configurable documented defaults can be achieved using interpolations.  See for
-instance
-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/master/test/boost_libs/cmake/autocmake.cfg#L9

doc/developers/customizing-modules.rst

@@ -47,11 +47,11 @@ 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.
+interpolation variables ``major``, ``minor``, ``patch``, and ``components``, see
+https://github.com/dev-cafe/autocmake/blob/master/modules/boost/boost.cmake#L52-L55.
 
 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.
+https://github.com/dev-cafe/autocmake/blob/master/test/boost_libs/cmake/autocmake.yml#L12-L17.
 
 
 Create own CMake modules
@@ -65,5 +65,5 @@ Contribute customizations to the "standard library"
 
 If you think that your customization will be useful for other users as well,
 you may consider contributing the changes directly to
-https://github.com/coderefinery/autocmake/. We very much encourage such
+https://github.com/dev-cafe/autocmake/. We very much encourage such
 contributions. But we also strive for generality and portability.

doc/developers/example.rst

@@ -1,6 +1,6 @@
 
 
-Example Hello World project
+Example hello world project
 ===========================
 
 This is a brief example for the busy and impatient programmer. For a longer
@@ -23,40 +23,53 @@ there. This is not necessary for Autocmake but it is a generally good practice::
 
 Now we create ``cmake/`` and fetch ``update.py``::
 
-  $ mkdir cmake
-  $ cd cmake/
-  $ wget https://raw.githubusercontent.com/coderefinery/autocmake/master/update.py
+  $ mkdir cmake  # does not have to be called "cmake" - take the name you prefer
+  $ cd cmake
+  $ wget https://github.com/dev-cafe/autocmake/raw/master/update.py
   $ python update.py --self
 
 Now from top-level our file tree looks like this::
 
   .
   |-- cmake
-  |   |-- autocmake.cfg
-  |   |-- lib
-  |   |   |-- config.py
-  |   |   `-- docopt
-  |   |       `-- docopt.py
+  |   |-- autocmake
+  |   |   |-- __init__.py
+  |   |   |-- configure.py
+  |   |   |-- external
+  |   |   |   |-- __init__.py
+  |   |   |   `-- docopt.py
+  |   |   |-- extract.py
+  |   |   |-- generate.py
+  |   |   |-- interpolate.py
+  |   |   |-- parse_rst.py
+  |   |   `-- parse_yaml.py
+  |   |-- autocmake.yml
   |   `-- update.py
   `-- src
       |-- feature1.F90
       |-- feature2.c
       `-- main.F90
 
-Now we edit ``cmake/autocmake.cfg`` to look like this::
+Now we edit ``cmake/autocmake.yml`` to look like this::
 
-  [project]
   name: hello
-  min_cmake_version: 2.8
 
-  [fc]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/fc.cmake
+  min_cmake_version: 3.1
 
-  [cc]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/cc.cmake
+  language:
+    - Fortran
+    - C
 
-  [src]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
+  url_root: https://github.com/dev-cafe/autocmake/raw/master/
+
+  modules:
+  - compilers:
+    - source:
+      - '%(url_root)modules/fc.cmake'
+      - '%(url_root)modules/cc.cmake'
+  - src_support:
+    - source:
+      - '%(url_root)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``.
@@ -76,20 +89,32 @@ Now we have everything to generate ``CMakeLists.txt`` and a setup script::
   $ cd cmake
   $ python update ..
 
+  - parsing autocmake.yml
+  - assembling modules: [##############################] (3/3)
+  - generating CMakeLists.txt
+  - generating setup script
+
 And this is what we got::
 
   .
   |-- CMakeLists.txt
   |-- cmake
-  |   |-- autocmake.cfg
+  |   |-- autocmake
+  |   |   |-- __init__.py
+  |   |   |-- configure.py
+  |   |   |-- external
+  |   |   |   |-- __init__.py
+  |   |   |   `-- docopt.py
+  |   |   |-- extract.py
+  |   |   |-- generate.py
+  |   |   |-- interpolate.py
+  |   |   |-- parse_rst.py
+  |   |   `-- parse_yaml.py
+  |   |-- autocmake.yml
   |   |-- downloaded
   |   |   |-- autocmake_cc.cmake
   |   |   |-- autocmake_fc.cmake
   |   |   `-- autocmake_src.cmake
-  |   |-- lib
-  |   |   |-- config.py
-  |   |   `-- docopt
-  |   |       `-- docopt.py
   |   `-- update.py
   |-- setup
   `-- src
@@ -100,12 +125,12 @@ And this is what we got::
 
 Now we are ready to build::
 
-  $ python setup --fc=gfortran --cc=gcc
+  $ ./setup --fc=gfortran --cc=gcc
 
-  FC=gfortran CC=gcc cmake -DEXTRA_FCFLAGS="''" -DENABLE_FC_SUPPORT="ON" -DEXTRA_CFLAGS="''" -DCMAKE_BUILD_TYPE=release -G "Unix Makefiles" None /home/user/example
+  FC=gfortran CC=gcc cmake -DEXTRA_FCFLAGS="''" -DEXTRA_CFLAGS="''" -DCMAKE_BUILD_TYPE=release -G "Unix Makefiles" /home/user/hello
 
-  -- The C compiler identification is GNU 4.9.2
-  -- The CXX compiler identification is GNU 4.9.2
+  -- The C compiler identification is GNU 6.1.1
+  -- The CXX compiler identification is GNU 6.1.1
   -- Check for working C compiler: /usr/bin/gcc
   -- Check for working C compiler: /usr/bin/gcc -- works
   -- Detecting C compiler ABI info
@@ -118,7 +143,7 @@ Now we are ready to build::
   -- Detecting CXX compiler ABI info - done
   -- Detecting CXX compile features
   -- Detecting CXX compile features - done
-  -- The Fortran compiler identification is GNU 4.9.2
+  -- The Fortran compiler identification is GNU 6.1.1
   -- Check for working Fortran compiler: /usr/bin/gfortran
   -- Check for working Fortran compiler: /usr/bin/gfortran  -- works
   -- Detecting Fortran compiler ABI info
@@ -127,14 +152,14 @@ Now we are ready to build::
   -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
   -- Configuring done
   -- Generating done
-  -- Build files have been written to: /home/user/example/build
+  -- Build files have been written to: /home/user/hello/build
 
      configure step is done
      now you need to compile the sources:
      $ cd build
      $ make
 
-  $ cd build/
+  $ cd build
   $ make
 
   Scanning dependencies of target hello.x

doc/developers/faq.rst

@@ -4,6 +4,18 @@ FAQ for developers
 ==================
 
 
+Which files do I need to edit?
+------------------------------
+
+Let us start with files which you normally never edit: ``CMakeLists.txt`` and
+``setup`` - these are generated based on ``autocmake.yml``. Have a look in
+``autocmake.yml`` and you will see all CMake files which are assembled into
+``CMakeLists.txt``.  You can edit those files. If you change the order of files
+listed in ``autocmake.yml`` or if you add or remove CMake modules, then you
+need to rerun the ``update.py`` script to refresh ``CMakeLists.txt`` and
+``setup``.
+
+
 Autocmake does not do feature X - I really need feature X and a setup flag --X
 ------------------------------------------------------------------------------
 
@@ -19,18 +31,22 @@ naming)::
 
   cmake/custom/my_feature.cmake
 
-And include this feature to the main ``CMakeLists.txt`` in ``autocmake.cfg``::
+And include this feature to the main ``CMakeLists.txt`` in ``autocmake.yml``
+under the ``modules`` section::
 
-  [my_feature]
-  source: custom/my_feature.cmake
+  modules:
+  - my_feature:
+    - source:
+      - custom/my_feature.cmake
 
 Now your code is included in the main ``CMakeLists.txt``. Perhaps you also
 want a setup script flag to toggle the feature::
 
-  [my_feature]
-  source: custom/my_feature.cmake
-  docopt: --my-feature Enable my feature [default: False].
-  define: '-DENABLE_MY_FEATURE={0}'.format(arguments['--my-feature'])
+  - my_feature:
+    - docopt: "--enable-my-feature Enable my feature [default: False]."
+    - define: "'-DENABLE_MY_FEATURE={0}'.format(arguments['--enable-my-feature'])"
+    - source:
+      - custom/my_feature.cmake
 
 Implement your ideas, test them, and share them.  If your module is portable,
 good code quality, and of general interest, you can suggest it to be part of
@@ -43,20 +59,33 @@ How can I get a setup flag --X that toggles a CMake variable?
 The following will add a ``--something`` flag which toggles the CMake variable
 ``ENABLE_SOMETHING``::
 
-  [my_section]
-  docopt: --something Enable something [default: False].
-  define: '-DENABLE_SOMETHING={0}'.format(arguments['--something'])
+  - my_section:
+    - docopt: "--something Enable something [default: False]."
+    - define: "'-DENABLE_SOMETHING={0}'.format(arguments['--enable-something'])"
 
 
 Can I change the name of the setup script?
 ------------------------------------------
 
-Yes you can do that in ``autocmake.cfg``. Here we for instance change the name to "configure"::
+Yes you can do that in ``autocmake.yml``. Here we for instance change the name to "configure":
+
+.. code-block:: yaml
+  :emphasize-lines: 4
 
-  [project]
   name: myproject
-  min_cmake_version: 2.8
+  min_cmake_version: 3.1
+  default_build_type: release
   setup_script: configure
+  language:
+    - Fortran
+    - C
+    - CXX
+
+
+Can I prevent Autocmake from creating any front-end setup script?
+-----------------------------------------------------------------
+
+Yes, with ``setup_script: None``.
 
 
 In CMake I can do feature X - can I do that also with Autocmake?
@@ -70,12 +99,13 @@ realized in Autocmake.
 Should I include and track also files generated by Autocmake in my repository?
 ------------------------------------------------------------------------------
 
-Yes, you probably want to do that. Autocmake generates a number of files which
-in principle could be generated at configure- or build-time.  However, you
-probably do not want the users of your code to run any Autocmake scripts like
-``update.py`` to generate the files they need to build the project. The users
-of your code will run ``setup`` directly and expect everything to just work
-(TM).
+Yes, you probably want to do that. Autocmake downloads and generates a number
+of files which in principle could be generated at configure- or build-time.
+However, you probably do not want the users of your code to run any Autocmake
+scripts like ``update.py`` to generate the files they need to build the
+project. The users of your code will run ``setup`` directly and typically expect
+everything to just work (TM). Note also that the users of your code will
+not need to install the pyyaml package.
 
 
 The update.py script is overwriting my CMakeLists.txt and setup, isn't this bad?
@@ -93,7 +123,7 @@ But I need to manually edit and customize CMakeLists.txt and setup every time I
 -----------------------------------------------------------------------------------------------
 
 You typically never need to manually edit and customize ``CMakeLists.txt`` and
-``setup`` directly. You can introduce customizations in ``autocmake.cfg``
+``setup`` directly. You can introduce customizations in ``autocmake.yml``
 which get assembled into the front-end scripts.
 
 
@@ -101,19 +131,21 @@ Where is a good place to list my sources and targets?
 -----------------------------------------------------
 
 As mentioned above ``CMakeLists.txt`` is not a good place because this file is
-generated from ``autocmake.cfg`` and your modifications would become
+generated from ``autocmake.yml`` and your modifications would become
 overwritten at some point.  A good standard is to organize your sources under
 ``src/`` and to list your sources and targets in ``src/CMakeLists.txt``.  You
-can include the latter in ``autocmake.cfg`` using::
+can include the latter in ``autocmake.yml`` using::
 
-  [src]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/src.cmake
+  - my_sources:
+    - source:
+      - https://github.com/dev-cafe/autocmake/raw/master/modules/src.cmake
 
-If you really don't like to do it this way, you can describe your sources and
+If you really do not 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::
 
-  [my_sources]
-  source: custom/my_sources.cmake
+  - my_sources:
+    - source:
+      - custom/my_sources.cmake
 
 
 How can I do some more sophisticated validation of setup flags?
@@ -121,7 +153,7 @@ How can I do some more sophisticated validation of setup flags?
 
 Sometimes you need to do more sophisticated validation and post-processing
 of setup flags. This can be done by placing a module called ``extensions.py``
-under ``cmake/`` (or wherever you have ``autocmake.cfg``).
+under ``cmake/`` (or wherever you have ``autocmake.yml``).
 This file should implement a function with the following signature:
 
 .. code-block:: python
@@ -135,5 +167,37 @@ This file should implement a function with the following signature:
       return arguments
 
 In this function you can do any validation and post-processing you like.
-This function is run after the flags are parsed and before the ``CMake`` command
+This function is run after the flags are parsed and before the CMake command
 is run.
+
+Example for a validation of MPI flags to the setup script:
+
+.. code-block:: python
+
+  import sys
+
+  def contains_flag(sys_argv, flag):
+      return (any(x for x in sys_argv if x.startswith('--{0}='.format(flag))))
+
+  def postprocess_args(sys_argv, arguments):
+
+      # if --mpi is selected and compilers are not selected
+      # then compilers default to mpif90, mpicc, and mpicxx
+      if arguments['--mpi']:
+          if not contains_flag(sys_argv, 'fc') and not contains_flag(sys_argv, 'cc') and not contains_flag(sys_argv, 'cxx'):
+             arguments['--fc'] = 'mpif90'
+             arguments['--cc'] = 'mpicc'
+             arguments['--cxx'] = 'mpicxx'
+
+      # if one of the compilers contains "mpi" and --mpi is not selected, it is probably a user error
+      # in this case stop the configuration
+      asking_for_mpi_compiler = False
+      for flag in ['fc', 'cc', 'cxx']:
+          if contains_flag(sys_argv, 'fc'):
+              if 'mpi' in arguments['--fc']:
+                  asking_for_mpi_compiler = True
+      if asking_for_mpi_compiler and not arguments['--mpi']:
+          sys.stderr.write('ERROR: you ask for an MPI compiler but have not specified --mpi\n')
+          sys.exit(1)
+
+      return arguments

doc/developers/interpolation.rst

@@ -0,0 +1,34 @@
+
+.. _interpolation:
+
+Interpolation
+=============
+
+In a custom extension to the YAML specification you can define and reuse
+variables like this (observe how we interpolate ``url_root``, ``major``,
+``minor``, ``patch``, and ``components`` in this example)::
+
+  url_root: https://github.com/dev-cafe/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)\"'"

doc/developers/updating-modules.rst

@@ -20,11 +20,11 @@ Sometimes you may want to avoid using the latest version of a CMake module and
 rather fetch an older version, for example with the hash ``abcd123``. To
 achieve this, instead of::
 
-  [foo]
-  source: https://github.com/coderefinery/autocmake/raw/master/modules/foo.cmake
+  - my_feature:
+    - source: https://github.com/dev-cafe/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)::
 
-  [foo]
-  source: https://github.com/coderefinery/autocmake/raw/abcd123/modules/foo.cmake
+  - my_feature:
+    - source: https://github.com/dev-cafe/autocmake/raw/abcd123/modules/foo.cmake

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/master/modules/%s>`__' % full_file_name)
+                output.append('`[Source code] <https://github.com/dev-cafe/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

@@ -38,7 +38,7 @@ file::
   Build/install/test targets
 
 Our main motivation to create Autocmake as a CMake framework library and
-CMake module composer is to simplify CMake code transfer between codes. We got
+CMake module composer is to simplify CMake code transfer between programs. 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

@@ -8,3 +8,6 @@ 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
 3.5).
+
+To generate ``CMakeLists.txt`` and the ``setup`` script, Autocmake
+requires the pyyaml package.

doc/index.rst

@@ -1,25 +1,21 @@
 
 
-Autocmake (this documentation is outdated, see stable-0.x branch)
-=================================================================
+Autocmake
+=========
 
 
-General
--------
-
 .. toctree::
    :maxdepth: 2
+   :caption: General
 
    general/about.rst
    general/requirements.rst
    general/help.rst
 
 
-For developers who use Autocmake
---------------------------------
-
 .. toctree::
    :maxdepth: 2
+   :caption: For developers who use Autocmake
 
    developers/faq.rst
    developers/bootstrap.rst
@@ -27,32 +23,27 @@ For developers who use Autocmake
    developers/example.rst
    developers/customizing-modules.rst
    developers/updating-modules.rst
+   developers/interpolation.rst
 
 
-For users of projects which use Autocmake
------------------------------------------
-
 .. toctree::
    :maxdepth: 2
+   :caption: For users of projects which use Autocmake
 
    users/faq.rst
 
 
-For developers/contributors to Autocmake
-----------------------------------------
-
 .. toctree::
    :maxdepth: 2
+   :caption: For developers/contributors to Autocmake
 
    contributors/guidelines.rst
    contributors/testing.rst
    contributors/doc.rst
 
 
-Reference
----------
-
 .. toctree::
    :maxdepth: 2
+   :caption: Reference
 
    module-reference.rst

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/users/faq.rst

@@ -49,9 +49,7 @@ 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. 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`.
+We use two sets of quotes because the shell swallows one set of them 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.yml

@@ -4,4 +4,4 @@
 
 name: myproject
 
-min_cmake_version: 2.8
+min_cmake_version: 3.1

modules/attach-license-header.py

@@ -0,0 +1,13 @@
+import glob
+
+license_text = '''# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
+'''
+
+for filename in glob.iglob('**/*.cmake', recursive=True):
+    with open(filename, 'r') as old:
+        text = old.read()
+    with open(filename, 'w') as new:
+        new.write(license_text)
+        new.write(text)

modules/boost/boost.cmake

@@ -1,189 +0,0 @@
-#.rst:
-#
-# Detect, build, and link Boost libraries.
-# This modules downloads the .zip archive from SourceForge at
-# Autocmake update time.
-# Note that the build-up commands are not Windows-compatible!
-#
-# Your autocmake.yml should look like this::
-#
-# - 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
-# should ask explicitly for all three.
-# If the self-build of Boost components is triggered the `BUILD_CUSTOM_BOOST` variable is set
-# to `TRUE`. The CMake target `custom_boost` is also added.
-# You should use these two to ensure the right dependencies between your targets
-# and the Boost headers/libraries, in case the self-build is triggered.
-# For example::
-#
-#   if(BUILD_CUSTOM_BOOST)
-#     add_dependencies(your_target custom_boost)
-#   endif()
-#
-# will ensure that `your_target` is built after `custom_boost` if and only if the self-build
-# of Boost took place. This is an important step to avoid race conditions when building
-# on multiple processes.
-#
-# Dependencies::
-#
-#   mpi                        - Only if the Boost.MPI library is a needed component
-#   python_libs                - Only if the Boost.Python library is a needed component
-#
-# Variables used::
-#
-#   BOOST_MINIMUM_REQUIRED     - Minimum required version of Boost
-#   BOOST_COMPONENTS_REQUIRED  - Components (compiled Boost libraries) required
-#   PROJECT_SOURCE_DIR
-#   PROJECT_BINARY_DIR
-#   CMAKE_BUILD_TYPE
-#   MPI_FOUND
-#   BUILD_CUSTOM_BOOST
-#
-# autocmake.yml configuration::
-#
-#   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
-set(BOOST_ARCHIVE_LOCATION ${PROJECT_SOURCE_DIR}/cmake/downloaded)
-
-set(BOOST_ARCHIVE boost_${BOOSTVER}.zip)
-
-# FIXME These are possibly not always good settings
-set(Boost_USE_STATIC_LIBS    ON)
-set(Boost_USE_MULTITHREADED  ON)
-set(Boost_USE_STATIC_RUNTIME OFF)
-set(Boost_DEBUG OFF)
-set(Boost_DETAILED_FAILURE_MESSAGE OFF)
-
-set(BUILD_CUSTOM_BOOST FALSE)
-if(FORCE_CUSTOM_BOOST)
-    set(BUILD_CUSTOM_BOOST TRUE)
-    message(STATUS "Force automatic build of Boost")
-    # Just to avoid unused variable warning from CMake
-    set(BOOST_INCLUDEDIR "")
-    set(BOOST_LIBRARYDIR "")
-else()
-    # Read from cache, needed for rebuilds
-    set(BOOST_INCLUDEDIR ${Boost_INCLUDE_DIR})
-    set(BOOST_LIBRARYDIR ${Boost_LIBRARY_DIR})
-    find_package(Boost ${BOOST_MINIMUM_REQUIRED} COMPONENTS "${BOOST_COMPONENTS_REQUIRED}")
-    if(NOT Boost_FOUND)
-        set(BUILD_CUSTOM_BOOST TRUE)
-    endif()
-endif()
-
-if(BUILD_CUSTOM_BOOST)
-    ## Preliminary work
-    # 0. Root directory for the custom build
-    set(CUSTOM_BOOST_LOCATION ${PROJECT_BINARY_DIR}/boost)
-    file(MAKE_DIRECTORY ${CUSTOM_BOOST_LOCATION})
-    # 1. Where Boost will be built
-    set(BOOST_BUILD_DIR ${CUSTOM_BOOST_LOCATION}/boost_${BOOSTVER})
-    # 2. Select toolset according to compilers specified by the user
-    set(toolset   "")
-    if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
-        set(toolset "intel-linux")
-    elseif(CMAKE_CXX_COMPILER_ID MATCHES Clang)
-        set(toolset "clang")
-    else()
-        if(CMAKE_SYSTEM_NAME MATCHES Darwin)
-            set(toolset "darwin")
-        else()
-            set(toolset "gcc")
-        endif()
-    endif()
-    string(TOLOWER ${CMAKE_BUILD_TYPE} type)
-
-   # 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 ${CMAKE_CURRENT_LIST_FILE} PATH)
-    include(${CMAKE_CURRENT_LIST_DIR}/boost_unpack.cmake)
-    include(${CMAKE_CURRENT_LIST_DIR}/boost_userconfig.cmake)
-
-    if(NOT "${BOOST_COMPONENTS_REQUIRED}" STREQUAL "")
-        # Non-empty list. Compiled libraries needed
-        # Transform the ;-separated list to a ,-separated list (digested by the Boost build toolchain!)
-        string(REPLACE ";" "," b2_needed_components "${BOOST_COMPONENTS_REQUIRED}")
-        # Replace unit_test_framework (used by CMake's find_package) with test (understood by Boost build toolchain)
-        string(REPLACE "unit_test_framework" "test" b2_needed_components "${b2_needed_components}")
-        set(select_libraries "--with-libraries=${b2_needed_components}")
-        string(REPLACE ";" ", " printout "${BOOST_COMPONENTS_REQUIRED}")
-        message(STATUS "  Libraries to be built: ${printout}")
-        message(STATUS "  Toolset to be used: ${toolset}")
-        include(${CMAKE_CURRENT_LIST_DIR}/boost_configure.cmake)
-        include(${CMAKE_CURRENT_LIST_DIR}/boost_build.cmake)
-        include(${CMAKE_CURRENT_LIST_DIR}/boost_install.cmake)
-    else()
-        # Empty list. Header-only libraries needed
-        # Just unpack to known location
-        message(STATUS "  No libraries required, installing headers")
-        include(${CMAKE_CURRENT_LIST_DIR}/boost_headers.cmake)
-    endif()
-
-    include(${CMAKE_CURRENT_LIST_DIR}/boost_cleanup.cmake)
-    add_custom_target(custom_boost DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.cleanedup)
-    # 4. Set all variables related to Boost that find_package would have set
-    set(Boost_FOUND TRUE)
-    string(REGEX REPLACE "\\." "0" Boost_VERSION ${BOOST_MINIMUM_REQUIRED})
-    math(EXPR Boost_MAJOR_VERSION "${Boost_VERSION} / 100000")
-    math(EXPR Boost_MINOR_VERSION "${Boost_VERSION} / 100 % 1000")
-    math(EXPR Boost_SUBMINOR_VERSION "${Boost_VERSION} % 100")
-    set(Boost_LIB_VERSION ${Boost_MAJOR_VERSION}_${Boost_MINOR_VERSION})
-    set(Boost_INCLUDE_DIR ${CUSTOM_BOOST_LOCATION}/include CACHE PATH "Boost include directory" FORCE)
-    set(Boost_LIBRARY_DIR ${CUSTOM_BOOST_LOCATION}/lib CACHE PATH "Boost library directory" FORCE)
-
-    foreach(_component ${BOOST_COMPONENTS_REQUIRED})
-        string(TOUPPER ${_component} _COMP)
-        set(Boost_${_COMP}_FOUND TRUE)
-        set(Boost_${_COMP}_LIBRARY libboost_${_component}.a)
-        set(Boost_${_COMP}_LIBRARY_DEBUG ${Boost_LIBRARY_DIR}/${Boost_${_COMP}_LIBRARY} CACHE FILEPATH "Boost ${_component} library (debug)" FORCE)
-        set(Boost_${_COMP}_LIBRARY_RELEASE ${Boost_LIBRARY_DIR}/${Boost_${_COMP}_LIBRARY} CACHE FILEPATH "Boost ${_component} library (release)" FORCE)
-        list(APPEND Boost_LIBRARIES ${Boost_${_COMP}_LIBRARY})
-    endforeach()
-
-    set(Boost_INCLUDE_DIRS ${Boost_INCLUDE_DIR})
-    set(Boost_LIBRARY_DIRS ${Boost_LIBRARY_DIR})
-    if(CMAKE_SYSTEM_NAME MATCHES Linux)
-        list(APPEND Boost_LIBRARIES rt)
-    endif()
-endif()
-
-include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
-
-link_directories(${Boost_LIBRARY_DIRS})

modules/boost/boost_build.cmake

@@ -1,10 +0,0 @@
-# Build Boost
-# This is not Windows-friendly!
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.built
-    COMMAND ./b2 toolset=${toolset} variant=${type} link=static cxxflags=-fPIC
-    threading=multi --user-config=user-config.jam 1> ${CUSTOM_BOOST_LOCATION}/boost.built.log 2> ${CUSTOM_BOOST_LOCATION}/boost.built.err
-    COMMAND ${CMAKE_COMMAND} -E touch ${CUSTOM_BOOST_LOCATION}/boost.built
-    WORKING_DIRECTORY ${BOOST_BUILD_DIR}
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.configured
-    COMMENT "Building Boost")

modules/boost/boost_cleanup.cmake

@@ -1,8 +0,0 @@
-# Clean-up
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.cleanedup
-    COMMAND ${CMAKE_COMMAND} -E remove_directory ${BOOST_BUILD_DIR}
-    COMMAND ${CMAKE_COMMAND} -E touch ${CUSTOM_BOOST_LOCATION}/boost.cleanedup
-    WORKING_DIRECTORY ${CUSTOM_BOOST_LOCATION}
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.installed
-    COMMENT "Clean-up Boost")

modules/boost/boost_configure.cmake

@@ -1,12 +0,0 @@
-# Run bootstrap.sh to configure the build. We will install in ${PROJECT_BINARY_DIR}/boost
-# This is not Windows-friendly!
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.configured
-    COMMAND ./bootstrap.sh --with-toolset=${toolset}
-            ${select_libraries}
-	    --with-python=${PYTHON_EXECUTABLE}
-        --prefix=${CUSTOM_BOOST_LOCATION} 1> ${CUSTOM_BOOST_LOCATION}/boost.configured.log 2> ${CUSTOM_BOOST_LOCATION}/boost.configured.err
-    COMMAND ${CMAKE_COMMAND} -E touch ${CUSTOM_BOOST_LOCATION}/boost.configured
-    WORKING_DIRECTORY ${BOOST_BUILD_DIR}
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.user-config
-    COMMENT "Configuring Boost")

modules/boost/boost_headers.cmake

@@ -1,8 +0,0 @@
-# Install Boost
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.installed
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${BOOST_BUILD_DIR}/boost ${CUSTOM_BOOST_LOCATION}/include/boost
-    COMMAND ${CMAKE_COMMAND} -E touch ${CUSTOM_BOOST_LOCATION}/boost.installed
-    WORKING_DIRECTORY ${BOOST_BUILD_DIR}
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.user-config
-    COMMENT "Installing Boost headers")

modules/boost/boost_install.cmake

@@ -1,10 +0,0 @@
-# Install Boost
-# This is not Windows-friendly!
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.installed
-    COMMAND ./b2 install toolset=${toolset} variant=${type} link=static
-    threading=multi --user-config=user-config.jam 1> ${CUSTOM_BOOST_LOCATION}/boost.installed.log 2> ${CUSTOM_BOOST_LOCATION}/boost.installed.err
-    COMMAND ${CMAKE_COMMAND} -E touch ${CUSTOM_BOOST_LOCATION}/boost.installed
-    WORKING_DIRECTORY ${BOOST_BUILD_DIR}
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.built
-    COMMENT "Installing Boost headers and libs")

modules/boost/boost_unpack.cmake

@@ -1,8 +0,0 @@
-# Unpack Boost
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.unpacked
-    COMMAND ${CMAKE_COMMAND} -E tar xzf ${BOOST_ARCHIVE_LOCATION}/${BOOST_ARCHIVE}
-    COMMAND ${CMAKE_COMMAND} -E touch boost.unpacked
-    DEPENDS ${BOOST_ARCHIVE_LOCATION}/${BOOST_ARCHIVE}
-    WORKING_DIRECTORY ${CUSTOM_BOOST_LOCATION}
-    COMMENT "Unpacking Boost")

modules/boost/boost_userconfig.cmake

@@ -1,15 +0,0 @@
-# To get boost to compile MPI we need to append "using mpi ;" to the end of the
-# user-config.jam file. MPI_SENT will be the command we append
-set(MPI_SENT "")
-if(ENABLE_MPI AND MPI_FOUND)
-    set(MPI_SENT "using mpi \;")
-endif()
-file(WRITE ${CUSTOM_BOOST_LOCATION}/user-config.jam ${MPI_SENT})
-# Write user-config.jam
-add_custom_command(
-    OUTPUT ${CUSTOM_BOOST_LOCATION}/boost.user-config
-    COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CUSTOM_BOOST_LOCATION}/user-config.jam ${BOOST_BUILD_DIR}/user-config.jam
-    COMMAND ${CMAKE_COMMAND} -E touch boost.user-config
-    DEPENDS ${CUSTOM_BOOST_LOCATION}/boost.unpacked
-    WORKING_DIRECTORY ${CUSTOM_BOOST_LOCATION}
-    COMMENT "Generating user-config.jam")

modules/cc.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds C support.
@@ -22,10 +25,7 @@
 #   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)
+#   define: "'-DCMAKE_C_COMPILER={0} -DEXTRA_CFLAGS=\"{1}\"'.format(arguments['--cc'], arguments['--extra-cc-flags'])"
 
 if(NOT DEFINED CMAKE_C_COMPILER_ID)
     message(FATAL_ERROR "CMAKE_C_COMPILER_ID variable is not defined!")
@@ -36,7 +36,9 @@ if(NOT CMAKE_C_COMPILER_WORKS)
 endif()
 
 if(DEFINED EXTRA_CFLAGS)
+  if(NOT EXTRA_CFLAGS STREQUAL "")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${EXTRA_CFLAGS}")
+  endif()
 endif()
 
 if(DEFINED ENV{CFLAGS})

modules/ccache.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds ccache support.

modules/code_coverage.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Enables code coverage by appending corresponding compiler flags.
@@ -10,30 +13,54 @@
 #
 # autocmake.yml configuration::
 #
-#   docopt: "--coverage Enable code coverage [default: False]."
+#   docopt: "--coverage Enable code coverage [default: OFF]."
 #   define: "'-DENABLE_CODE_COVERAGE={0}'.format(arguments['--coverage'])"
 
 option(ENABLE_CODE_COVERAGE "Enable code coverage" OFF)
 
 if(ENABLE_CODE_COVERAGE)
-    if(DEFINED CMAKE_Fortran_COMPILER_ID)
-        if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
-            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fprofile-arcs -ftest-coverage")
-        endif()
-    endif()
+  if(NOT CMAKE_BUILD_TYPE STREQUAL "debug")
+    message(WARNING "Code coverage analysis results with an optimized (non-Debug) build may be misleading")
+  endif()
 
-    if(DEFINED CMAKE_C_COMPILER_ID)
-        if(CMAKE_C_COMPILER_ID MATCHES GNU)
-            set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fprofile-arcs -ftest-coverage")
-        endif()
-    endif()
+  find_program(GCOV_PATH gcov)
+  if(NOT GCOV_PATH)
+    message(FATAL_ERROR "Code coverage analysis requires gcov!")
+  endif()
 
-    if(DEFINED CMAKE_CXX_COMPILER_ID)
-        if(CMAKE_CXX_COMPILER_ID MATCHES GNU)
-            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-        endif()
-        if(CMAKE_CXX_COMPILER_ID MATCHES Clang)
-            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-        endif()
+  if(DEFINED CMAKE_Fortran_COMPILER_ID)
+    if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+      set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fprofile-arcs -ftest-coverage")
+    else()
+      message(FATAL_ERROR "Code coverage analysis requires the GNU Fortran compiler!")
     endif()
+  endif()
+
+  if(DEFINED CMAKE_C_COMPILER_ID)
+    if(CMAKE_C_COMPILER_ID MATCHES "(Apple)?[Cc]lang")
+      if(CMAKE_C_COMPILER_VERSION VERSION_LESS 3)
+        message(FATAL_ERROR "Code coverage analysis on Mac OS X requires Clang version 3.0.0 or greater!")
+      else()
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fprofile-arcs -ftest-coverage")
+      endif()
+    elseif(CMAKE_C_COMPILER_ID MATCHES GNU)
+      set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fprofile-arcs -ftest-coverage")
+    else()
+      message(FATAL_ERROR "Code coverage analysis requires the GNU C compiler!")
+    endif()
+  endif()
+
+  if(DEFINED CMAKE_CXX_COMPILER_ID)
+    if(CMAKE_CXX_COMPILER_ID MATCHES "(Apple)?[Cc]lang")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3)
+        message(FATAL_ERROR "Code coverage analysis on Mac OS X requires Clang version 3.0.0 or greater!")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+      endif()
+    elseif(CMAKE_CXX_COMPILER_ID MATCHES GNU)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+    else()
+      message(FATAL_ERROR "Code coverage analysis requires the GNU C++ compiler!")
+    endif()
+  endif()
 endif()

modules/custom_color_messages.cmake

@@ -0,0 +1,63 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
+#.rst:
+#
+# Colorize CMake output.
+# Code was found on StackOverflow: http://stackoverflow.com/a/19578320
+#
+# Usage within CMake code:
+#   message("This is normal")
+#   message("${Red}This is Red${ColourReset}")
+#   message("${Green}This is Green${ColourReset}")
+#   message("${Yellow}This is Yellow${ColourReset}")
+#   message("${Blue}This is Blue${ColourReset}")
+#   message("${Magenta}This is Magenta${ColourReset}")
+#   message("${Cyan}This is Cyan${ColourReset}")
+#   message("${White}This is White${ColourReset}")
+#   message("${BoldRed}This is BoldRed${ColourReset}")
+#   message("${BoldGreen}This is BoldGreen${ColourReset}")
+#   message("${BoldYellow}This is BoldYellow${ColourReset}")
+#   message("${BoldBlue}This is BoldBlue${ColourReset}")
+#   message("${BoldMagenta}This is BoldMagenta${ColourReset}")
+#   message("${BoldCyan}This is BoldCyan${ColourReset}")
+#   message("${BoldWhite}This is BoldWhite\n\n${ColourReset}")
+#
+# Has no effect on WIN32.
+
+if(WIN32)
+    set(ColourReset "")
+    set(ColourBold  "")
+    set(Red         "")
+    set(Green       "")
+    set(Yellow      "")
+    set(Blue        "")
+    set(Magenta     "")
+    set(Cyan        "")
+    set(White       "")
+    set(BoldRed     "")
+    set(BoldGreen   "")
+    set(BoldYellow  "")
+    set(BoldBlue    "")
+    set(BoldMagenta "")
+    set(BoldCyan    "")
+    set(BoldWhite   "")
+else()
+    string(ASCII 27 Esc)
+    set(ColourReset "${Esc}[m")
+    set(ColourBold  "${Esc}[1m")
+    set(Red         "${Esc}[31m")
+    set(Green       "${Esc}[32m")
+    set(Yellow      "${Esc}[33m")
+    set(Blue        "${Esc}[34m")
+    set(Magenta     "${Esc}[35m")
+    set(Cyan        "${Esc}[36m")
+    set(White       "${Esc}[37m")
+    set(BoldRed     "${Esc}[1;31m")
+    set(BoldGreen   "${Esc}[1;32m")
+    set(BoldYellow  "${Esc}[1;33m")
+    set(BoldBlue    "${Esc}[1;34m")
+    set(BoldMagenta "${Esc}[1;35m")
+    set(BoldCyan    "${Esc}[1;36m")
+    set(BoldWhite   "${Esc}[1;37m")
+endif()

modules/cxx.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds C++ support.
@@ -22,21 +25,20 @@
 #   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'])"
+#   define: "'-DCMAKE_CXX_COMPILER={0} -DEXTRA_CXXFLAGS=\"{1}\"'.format(arguments['--cxx'], 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!")
+if(NOT DEFINED CMAKE_CXX_COMPILER_ID)
+    message(FATAL_ERROR "CMAKE_CXX_COMPILER_ID variable is not defined!")
 endif()
 
-if(NOT CMAKE_C_COMPILER_WORKS)
-    message(FATAL_ERROR "CMAKE_C_COMPILER_WORKS is false!")
+if(NOT CMAKE_CXX_COMPILER_WORKS)
+    message(FATAL_ERROR "CMAKE_CXX_COMPILER_WORKS is false!")
 endif()
 
 if(DEFINED EXTRA_CXXFLAGS)
+  if(NOT EXTRA_CXXFLAGS STREQUAL "")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${EXTRA_CXXFLAGS}")
+  endif()
 endif()
 
 if(DEFINED ENV{CXXFLAGS})

modules/default_build_paths.cmake

@@ -1,12 +1,19 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
-# Sets binary and library output directories to ${PROJECT_BINARY_DIR}/bin
-# and ${PROJECT_BINARY_DIR}/lib, respectively.
+# Sets binary and library output directories to ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
+# and ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}, respectively.
 #
 # Variables modified::
 #
-#   CMAKE_RUNTIME_OUTPUT_DIRECTORY
+#   CMAKE_ARCHIVE_OUTPUT_DIRECTORY
 #   CMAKE_LIBRARY_OUTPUT_DIRECTORY
+#   CMAKE_RUNTIME_OUTPUT_DIRECTORY
 
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+include(GNUInstallDirs)
+
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})

modules/definitions.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Add preprocessor definitions (example: --add-definitions="-DTHIS -DTHAT=137").

modules/export_header.cmake

@@ -0,0 +1,26 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
+#.rst:
+#
+# Generates export header for your API using best practices.
+# This module wraps https://cmake.org/cmake/help/v3.0/module/GenerateExportHeader.html and
+# it is needed because of these, Very Good Indeed, reasons: https://gcc.gnu.org/wiki/Visibility.
+# If you are not afraid of jargon, please also have a look at https://www.akkadia.org/drepper/dsohowto.pdf.
+#
+# Variables used::
+#
+#   PROJECT_NAME (defined by project())
+
+include(GenerateExportHeader)
+
+generate_export_header(${PROJECT_NAME}
+    BASE_NAME "${PROJECT_NAME}"
+    EXPORT_MACRO_NAME "${PROJECT_NAME}_EXPORT"
+    EXPORT_FILE_NAME "include/${PROJECT_NAME}_export.h"
+    DEPRECATED_MACRO_NAME "${PROJECT_NAME}_DEPRECATED"
+    NO_EXPORT_MACRO_NAME "${PROJECT_NAME}_NO_EXPORT"
+    STATIC_DEFINE "${PROJECT_NAME}_STATIC_DEFINE"
+    NO_DEPRECATED_MACRO_NAME "${PROJECT_NAME}_NO_DEPRECATED"
+    DEFINE_NO_DEPRECATED
+    )

modules/fc.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds Fortran support.
@@ -26,10 +29,7 @@
 #   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)
+#   define: "'-DCMAKE_Fortran_COMPILER={0} -DEXTRA_FCFLAGS=\"{1}\"'.format(arguments['--fc'], arguments['--extra-fc-flags'])"
 
 set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/modules)
 include_directories(${PROJECT_BINARY_DIR}/modules)
@@ -43,7 +43,9 @@ if(NOT CMAKE_Fortran_COMPILER_WORKS)
 endif()
 
 if(DEFINED EXTRA_FCFLAGS)
+  if(NOT EXTRA_FCFLAGS STREQUAL "")
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${EXTRA_FCFLAGS}")
+  endif()
 endif()
 
 if(DEFINED ENV{FCFLAGS})

modules/fc_optional.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds optional Fortran support.
@@ -32,9 +35,8 @@
 #     - "--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'])"
+#     - "'-DCMAKE_Fortran_COMPILER={0} -DEXTRA_FCFLAGS=\"{1}\"'.format(arguments['--fc'], arguments['--extra-fc-flags'])"
 #     - "'-DENABLE_FC_SUPPORT={0}'.format(arguments['--fc-support'])"
 
 option(ENABLE_FC_SUPPORT "Enable Fortran language support" ON)
@@ -54,7 +56,9 @@ if(ENABLE_FC_SUPPORT)
     endif()
 
     if(DEFINED EXTRA_FCFLAGS)
+      if(NOT EXTRA_FCFLAGS STREQUAL "")
         set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${EXTRA_FCFLAGS}")
+      endif()
     endif()
 
     if(DEFINED ENV{FCFLAGS})

modules/find/find_include_files.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 include(CheckIncludeFile)
 
 function(_find_include_dir _names _hints _result)

modules/find/find_libraries.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 include(CheckFunctionExists)
 
 function(_find_library _names _check_function _result)

modules/git_info/git_info.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Creates git_info.h in the build directory.
@@ -7,22 +10,65 @@
 #
 # autocmake.yml configuration::
 #
-#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   url_root: https://github.com/dev-cafe/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
-# workaround: create CMAKE_CURRENT_LIST_DIR 
-get_filename_component(CMAKE_CURRENT_LIST_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
-add_custom_command(
-    OUTPUT ${PROJECT_BINARY_DIR}/git_info.h
-    COMMAND ${CMAKE_COMMAND} -D_target_dir=${PROJECT_BINARY_DIR} -P git_info_sub.cmake
-    WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
+get_filename_component(_current_dir ${CMAKE_CURRENT_LIST_FILE} PATH)
+
+function(generate_git_info_header _header_location _header_name)
+  # _header_location: where the Git info header file should be generated
+  # _header_name: the Git info header name, complete with extension (.h, .hpp, .hxx or whatever)
+  find_package(Git)
+
+  set(_git_last_commit_hash "unknown")
+  set(_git_last_commit_author "unknown")
+  set(_git_last_commit_date "unknown")
+  set(_git_branch "unknown")
+
+  if(GIT_FOUND)
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} --no-pager show -s --pretty=format:%h -n 1
+      OUTPUT_VARIABLE _git_last_commit_hash
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+      ERROR_QUIET
+      )
+
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} --no-pager show -s --pretty=format:%aN -n 1
+      OUTPUT_VARIABLE _git_last_commit_author
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+      ERROR_QUIET
+      )
+
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} --no-pager show -s --pretty=format:%ad -n 1
+      OUTPUT_VARIABLE _git_last_commit_date
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+      ERROR_QUIET
+      )
+
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
+      OUTPUT_VARIABLE _git_branch
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+      ERROR_QUIET
+      )
+  endif()
+
+  configure_file(
+    ${_current_dir}/git_info.h.in
+    ${_header_location}/${_header_name}
+    @ONLY
     )
 
-add_custom_target(
+  unset(_git_last_commit_hash)
+  unset(_git_last_commit_author)
+  unset(_git_last_commit_date)
+  unset(_git_branch)
+
+  add_custom_target(
     git_info
-    ALL DEPENDS ${PROJECT_BINARY_DIR}/git_info.h
+    ALL DEPENDS ${_header_location}/${_header_name}
     )
+endfunction()

modules/git_info/git_info_sub.cmake

@@ -1,64 +0,0 @@
-#.rst:
-#
-# Creates git_info.h in the build directory.
-# This file can be included in sources to print
-# Git status information to the program output
-# for reproducibility reasons.
-
-find_package(Git)
-
-set(_git_last_commit_hash "unknown")
-set(_git_last_commit_author "unknown")
-set(_git_last_commit_date "unknown")
-set(_git_branch "unknown")
-
-if(GIT_FOUND)
-    execute_process(
-        COMMAND ${GIT_EXECUTABLE} rev-list --max-count=1 --abbrev-commit HEAD
-        OUTPUT_VARIABLE _git_last_commit_hash
-        ERROR_QUIET
-        )
-
-    if(_git_last_commit_hash)
-        string(STRIP ${_git_last_commit_hash} _git_last_commit_hash)
-    endif()
-
-    execute_process(
-        COMMAND ${GIT_EXECUTABLE} log --max-count=1 HEAD
-        OUTPUT_VARIABLE _git_last_commit
-        ERROR_QUIET
-        )
-
-    if(_git_last_commit)
-	string(REGEX MATCH "Author: +([^<]*) <" temp "${_git_last_commit}")
-        set(_git_last_commit_author ${CMAKE_MATCH_1})
-        string(STRIP ${_git_last_commit_author} _git_last_commit_author)
-        string(REGEX MATCH "Date: +(.+[0-9][0-9][0-9][0-9] [+-][0-9][0-9][0-9][0-9])" temp "${_git_last_commit}")
-        set(_git_last_commit_date ${CMAKE_MATCH_1})
-    endif()
-
-    execute_process(
-        COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
-        OUTPUT_VARIABLE _git_branch
-        ERROR_QUIET
-        )
-
-    if(_git_branch)
-        string(STRIP ${_git_branch} _git_branch)
-    endif()
-endif()
-
-# 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)
-configure_file(
-    ${CMAKE_CURRENT_LIST_DIR}/git_info.h.in
-    ${_target_dir}/git_info.h
-    @ONLY
-    )
-
-unset(_git_last_commit_hash)
-unset(_git_last_commit_author)
-unset(_git_last_commit_date)
-unset(_git_branch)

modules/googletest.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Includes Google Test sources and adds a library "googletest".

modules/int64.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Enables 64-bit integer support for Fortran projects.

modules/math/accelerate.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to ACCELERATE.
@@ -10,7 +13,7 @@
 #
 # autocmake.yml configuration::
 #
-#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   url_root: https://github.com/dev-cafe/autocmake/raw/master/
 #   docopt: "--accelerate Find and link to ACCELERATE [default: False]."
 #   define: "'-DENABLE_ACCELERATE={0}'.format(arguments['--accelerate'])"
 #   fetch:
@@ -20,8 +23,8 @@
 option(ENABLE_ACCELERATE "Find and link to ACCELERATE" OFF)
 
 if(ENABLE_ACCELERATE)
-    include(find_libraries)
-    include(find_include_files)
+    include(${CMAKE_CURRENT_LIST_DIR}/../find/find_libraries.cmake)
+    include(${CMAKE_CURRENT_LIST_DIR}/../find/find_include_files.cmake)
 
     set(ACCELERATE_FOUND FALSE)
     set(ACCELERATE_LIBRARIES "NOTFOUND")

modules/math/acml.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to ACML.

modules/math/atlas.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to ATLAS.

modules/math/blas.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to BLAS.

modules/math/cblas.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to CBLAS.
@@ -10,7 +13,7 @@
 #
 # autocmake.yml configuration::
 #
-#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   url_root: https://github.com/dev-cafe/autocmake/raw/master/
 #   docopt: "--cblas Find and link to CBLAS [default: False]."
 #   define: "'-DENABLE_CBLAS={0}'.format(arguments['--cblas'])"
 #   fetch:
@@ -20,8 +23,8 @@
 option(ENABLE_CBLAS "Find and link to CBLAS" OFF)
 
 if(ENABLE_CBLAS)
-    include(find_libraries)
-    include(find_include_files)
+    include(${CMAKE_CURRENT_LIST_DIR}/../find/find_libraries.cmake)
+    include(${CMAKE_CURRENT_LIST_DIR}/../find/find_include_files.cmake)
 
     set(CBLAS_FOUND FALSE)
     set(CBLAS_LIBRARIES "NOTFOUND")

modules/math/goto.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to Goto BLAS.

modules/math/lapack.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to LAPACK.

modules/math/lapacke.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Find and link to LAPACKE.
@@ -10,7 +13,7 @@
 #
 # autocmake.yml configuration::
 #
-#   url_root: https://github.com/coderefinery/autocmake/raw/master/
+#   url_root: https://github.com/dev-cafe/autocmake/raw/master/
 #   docopt: "--lapacke Find and link to LAPACKE [default: False]."
 #   define: "'-DENABLE_LAPACKE={0}'.format(arguments['--lapacke'])"
 #   fetch:
@@ -20,8 +23,8 @@
 option(ENABLE_LAPACKE "Find and link to LAPACKE" OFF)
 
 if(ENABLE_LAPACKE)
-    include(find_libraries)
-    include(find_include_files)
+    include(${CMAKE_CURRENT_LIST_DIR}/find_libraries.cmake)
+    include(${CMAKE_CURRENT_LIST_DIR}/find_include_files.cmake)
 
     set(LAPACKE_FOUND FALSE)
     set(LAPACKE_LIBRARIES "NOTFOUND")

modules/math_libs.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Detects and links to BLAS and LAPACK libraries.
@@ -43,6 +46,8 @@
 #     - "--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]."
+#     - "--scalapack=<SCALAPACK_LIBRARIES> Link line for ScaLAPACK libraries [default: ]"
+#     - "--blacs=<BLACS_IMPLEMENTATION> Implementation of BLACS for MKL ScaLAPACK (openmpi, intelmpi, sgimpt) [default: openmpi]"
 #   define:
 #     - "'-DENABLE_BLAS={0}'.format(arguments['--blas'])"
 #     - "'-DENABLE_LAPACK={0}'.format(arguments['--lapack'])"
@@ -50,8 +55,51 @@
 #     - "'-DMATH_LIB_SEARCH_ORDER=\"MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE\"'"
 #     - "'-DBLAS_LANG=Fortran'"
 #     - "'-DLAPACK_LANG=Fortran'"
+#     - "'-DSCALAPACK_LIBRARIES=\"{0}\"'.format(arguments['--scalapack'])"
+#     - "'-DBLACS_IMPLEMENTATION=\"{0}\"'.format(arguments['--blacs'])"
 #   warning: "the math_libs.cmake module is deprecated and will be removed in future versions"
 
+option_with_default(
+  NAME ENABLE_BLAS
+  MESSAGE "Enable BLAS autodetection"
+  DEFAULT "auto"
+  )
+option_with_default(
+  NAME ENABLE_LAPACK
+  MESSAGE "Enable LAPACK autodetection"
+  DEFAULT "auto"
+  )
+option_with_default(
+  NAME MKL_FLAG
+  MESSAGE "MKL flag for the Intel compiler and linker. Skips BLAS/LAPACK autodetection"
+  DEFAULT "off"
+  )
+option_with_default(
+  NAME MATH_LIB_SEARCH_ORDER
+  MESSAGE "Search order for autodetection of math libraries"
+  DEFAULT "MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE"
+  )
+option_with_default(
+  NAME BLAS_LANG
+  MESSAGE "Linker language for BLAS detection"
+  DEFAULT "Fortran"
+  )
+option_with_default(
+  NAME LAPACK_LANG
+  MESSAGE "Linker language for LAPACK detection"
+  DEFAULT "Fortran"
+  )
+option_with_default(
+  NAME SCALAPACK_LIBRARIES
+  MESSAGE "Link line for ScaLAPACK libraries"
+  DEFAULT ""
+  )
+option_with_default(
+  NAME BLACS_IMPLEMENTATION
+  MESSAGE "Implementation of BLACS for MKL ScaLAPACK"
+  DEFAULT "openmpi"
+  )
+
 #-------------------------------------------------------------------------------
 # ENABLE_STATIC_LINKING
 
@@ -194,7 +242,7 @@ if(${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "x86_64")
     endif()
 endif()
 
-if(ENABLE_SCALAPACK)
+if(ENABLE_SCALAPACK AND NOT SCALAPACK_LIBRARIES)
     set(_scalapack_lib      mkl_scalapack${_lib_suffix})
     if(${BLACS_IMPLEMENTATION} STREQUAL "intelmpi")
         set(_blacs_lib mkl_blacs_intelmpi${_lib_suffix})
@@ -208,6 +256,7 @@ if(ENABLE_SCALAPACK)
 else()
     set(_scalapack_lib)
     set(_blacs_lib)
+    set(BLACS_IMPLEMENTATION)
 endif()
 
 # MKL 10.0.1.014
@@ -429,7 +478,7 @@ foreach(_service BLAS LAPACK)
     endif()
 endforeach()
 
-if(NOT MKL_FLAG STREQUAL "off")
+if(MKL_FLAG AND NOT MKL_FLAG STREQUAL "off")
     set(EXTERNAL_LIBS ${EXTERNAL_LIBS} -mkl=${MKL_FLAG})
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mkl=${MKL_FLAG}")
     message(STATUS "User set explicit MKL flag which is passed to the compiler and linker: -mkl=${MKL_FLAG}")
@@ -492,12 +541,21 @@ foreach(_service BLAS LAPACK)
 endforeach()
 
 # first lapack, then blas as lapack might need blas routine
-set(MATH_LIBS
-    ${MATH_LIBS}
-    ${LAPACK_LIBRARIES}
-    ${BLAS_LIBRARIES}
-    CACHE STRING "Math libraries"
-    )
+if(SCALAPACK_LIBRARIES)
+  list(APPEND MATH_LIBS
+      ${MATH_LIBS}
+      ${SCALAPACK_LIBRARIES}
+      ${LAPACK_LIBRARIES}
+      ${BLAS_LIBRARIES}
+      )
+else()
+  list(APPEND MATH_LIBS
+      ${MATH_LIBS}
+      ${LAPACK_LIBRARIES}
+      ${BLAS_LIBRARIES}
+      )
+endif()
+set(MATH_LIBS ${MATH_LIBS} CACHE STRING "Math libraries")
 
 # further adaptation for the static linking
 if (ENABLE_STATIC_LINKING)

modules/mpi.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Enables MPI support.

modules/omp.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Enables OpenMP support.
@@ -21,25 +24,6 @@
 option(ENABLE_OPENMP "Enable OpenMP parallelization" OFF)
 
 if(ENABLE_OPENMP)
-    if(DEFINED CMAKE_Fortran_COMPILER_ID)
-        # we do this in a pedestrian way because the Fortran support is relatively recent
-        if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
-            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fopenmp")
-        endif()
-        if(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
-            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -openmp")
-        endif()
-        if(CMAKE_Fortran_COMPILER_ID MATCHES PGI)
-            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -mp")
-        endif()
-        if(CMAKE_Fortran_COMPILER_ID MATCHES XL)
-            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qsmp")
-        endif()
-        if(CMAKE_Fortran_COMPILER_ID MATCHES Cray)
-            # do nothing in this case
-        endif()
-        set(OPENMP_FOUND TRUE)
-    endif()
 
     if(NOT OPENMP_FOUND)
         find_package(OpenMP)
@@ -53,5 +37,35 @@ if(ENABLE_OPENMP)
         if(DEFINED CMAKE_CXX_COMPILER_ID)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
         endif()
+        if(DEFINED CMAKE_Fortran_COMPILER_ID)
+            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${OpenMP_Fortran_FLAGS}")
+        endif()
+    endif()
+
+    # this is only needed for CMake below 3.5
+    if(DEFINED CMAKE_Fortran_COMPILER_ID AND NOT DEFINED OpenMP_Fortran_FLAGS)
+        # we do this in a pedestrian way because the Fortran support is relatively recent
+        if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fopenmp")
+        endif()
+        if(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+            if(WIN32)
+                set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Qopenmp")
+            elseif("${CMAKE_Fortran_COMPILER_VERSION}" VERSION_LESS "15.0.0.20140528")
+                set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -openmp")
+            else()
+                set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qopenmp")
+            endif()
+        endif()
+        if(CMAKE_Fortran_COMPILER_ID MATCHES PGI)
+            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -mp")
+        endif()
+        if(CMAKE_Fortran_COMPILER_ID MATCHES XL)
+            set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qsmp=omp")
+        endif()
+        if(CMAKE_Fortran_COMPILER_ID MATCHES Cray)
+            # do nothing in this case
+        endif()
+        set(OPENMP_FOUND TRUE)
     endif()
 endif()

modules/profile.cmake

@@ -0,0 +1,33 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
+#.rst:
+#
+# Enable profiling by appending corresponding compiler flags.
+#
+# Variables modified (provided the corresponding language is enabled)::
+#
+#   CMAKE_Fortran_FLAGS
+#   CMAKE_C_FLAGS
+#   CMAKE_CXX_FLAGS
+#
+# autocmake.yml configuration::
+#
+#   docopt: "--profile Enable profiling [default: False]"
+#   define: "'-DENABLE_PROFILING={0}'.format(arguments['--profile'])"
+
+option(ENABLE_PROFILING "Enable profiling" OFF)
+
+message(STATUS "Enable profiling: ${ENABLE_PROFILING}")
+
+if(ENABLE_PROFILING)
+    if(DEFINED CMAKE_Fortran_COMPILER_ID)
+        set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -pg")
+    endif()
+    if(DEFINED CMAKE_C_COMPILER_ID)
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -pg")
+    endif()
+    if(DEFINED CMAKE_CXX_COMPILER_ID)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -pg")
+    endif()
+endif()

modules/python_interpreter.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Detects Python interpreter.

modules/python_libs.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Detects Python libraries and headers.
@@ -75,12 +78,9 @@ find_package_handle_standard_args(PythonLibs
     PYTHON_EXECUTABLE)
 
 if(NOT PYTHONLIBS_FOUND)
-    message(FATAL_ERROR "Could NOT find PythonLibs")
+    message(FATAL_ERROR "Could NOT find PythonLibs - did you install the python-dev package?")
 endif()
 
 # Hook-up script variables to cache variables
 set(PYTHON_LIBRARIES ${PYTHON_LIBRARY})
 set(PYTHON_INCLUDE_DIRS ${PYTHON_INCLUDE_DIR})
-
-include_directories(SYSTEM ${PYTHON_INCLUDE_DIRS})
-link_directories(${PYTHON_LIBRARIES})

modules/safeguards.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Provides safeguards against in-source builds and bad build types.
@@ -17,6 +20,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper)
 
 if(NOT cmake_build_type_tolower STREQUAL "debug" AND
    NOT cmake_build_type_tolower STREQUAL "release" AND
+   NOT cmake_build_type_tolower STREQUAL "minsizerel" AND
    NOT cmake_build_type_tolower STREQUAL "relwithdebinfo")
-    message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).")
+    message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo, and MinSizeRel (case-insensitive).")
 endif()

modules/save_flags.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Take care of updating the cache for fresh configurations.

modules/sccache.cmake

@@ -0,0 +1,30 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
+#.rst:
+#
+# Adds sccache support.
+# The user should export the appropriate environment variables to
+# tweak the program's behaviour, as described in its manpage.
+# Notice that some additional compiler flags might be needed in order
+# to avoid unnecessary warnings.
+#
+# Variables defined::
+#
+#   SCCACHE_FOUND
+#
+# autocmake.yml configuration::
+#
+#   docopt: "--sccache=<USE_SCCACHE> Toggle use of sccache <ON/OFF> [default: ON]."
+#   define: "'-DUSE_SCCACHE={0}'.format(arguments['--sccache'])"
+
+if(USE_SCCACHE)
+    find_program(SCCACHE_FOUND sccache)
+    if(SCCACHE_FOUND)
+        set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE sccache)
+        set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK sccache)
+        message(STATUS "Compiling with sccache")
+    else()
+        message(STATUS "sccache not available")
+    endif()
+endif()

modules/src.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Adds ${PROJECT_SOURCE_DIR}/src as subdirectory containing CMakeLists.txt.

modules/version.cmake

@@ -1,3 +1,6 @@
+# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md
+# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE
+
 #.rst:
 #
 # Determine program version from file "VERSION" (example: "14.1")

requirements.txt

@@ -1,3 +1,4 @@
-pep8
+pycodestyle
 pytest
 pyyaml
+sphinx

test/boost_header_only/cmake/autocmake.yml

@@ -1,14 +0,0 @@
-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_header_only/src/CMakeLists.txt

@@ -1 +0,0 @@
-add_executable(example example.cpp)

test/boost_header_only/src/example.cpp

@@ -1,17 +0,0 @@
-#include <iostream>
-#include <boost/version.hpp>
-
-int main()
-{
-    std::cout << "Boost version: "
-              << BOOST_VERSION / 100000
-              << "."
-              << BOOST_VERSION / 100 % 1000
-              << "."
-              << BOOST_VERSION % 100
-              << std::endl;
-
-    std::cout << "PASSED" << std::endl;
-
-    return 0;
-}

test/boost_libs/cmake/autocmake.yml

@@ -1,21 +0,0 @@
-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/boost_libs/src/CMakeLists.txt

@@ -1,8 +0,0 @@
-add_executable(example example.cpp)
-
-if(BUILD_CUSTOM_BOOST)
-    add_dependencies(example custom_boost)
-endif()
-
-target_link_libraries(example ${Boost_MPI_LIBRARY} ${Boost_SERIALIZATION_LIBRARY} ${MPI_CXX_LIBRARIES}
-                              ${Boost_PYTHON_LIBRARY} ${PYTHON_LIBRARIES})

test/boost_libs/src/example.cpp

@@ -1,45 +0,0 @@
-#include <iostream>
-
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/python.hpp>
-#include <boost/version.hpp>
-
-int main()
-{
-    using namespace boost::python;
-    namespace mpi = boost::mpi;
-
-    std::cout << "Boost version: "
-              << BOOST_VERSION / 100000
-              << "."
-              << BOOST_VERSION / 100 % 1000
-              << "."
-              << BOOST_VERSION % 100
-              << std::endl;
-
-    try {
-        Py_Initialize();
-
-        object main_module((
-                    handle<>(borrowed(PyImport_AddModule("__main__")))));
-
-        object main_namespace = main_module.attr("__dict__");
-
-        handle<> ignored(( PyRun_String( "print \"Hello, World\"",
-                        Py_file_input,
-                        main_namespace.ptr(),
-                        main_namespace.ptr() ) ));
-    } catch( error_already_set ) {
-        PyErr_Print();
-    }
-
-    mpi::environment env;
-    mpi::communicator world;
-    std::cout << "I am process " << world.rank() << " of " << world.size()
-        << "." << std::endl;
-
-    std::cout << "PASSED" << std::endl;
-
-    return 0;
-}

test/cxx/cmake/autocmake.yml

@@ -1,5 +1,7 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language: CXX
+default_build_type: debug
 modules:
 - cxx:
   - source: ../../../modules/cxx.cmake

test/cxx_accelerate/cmake/autocmake.yml

@@ -1,5 +1,9 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language:
+- CXX
+- C
+default_build_type: debug
 modules:
 - cxx:
   - source: ../../../modules/cxx.cmake

test/cxx_cblas/cmake/autocmake.yml

@@ -1,5 +1,9 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language:
+  - C
+  - CXX
+default_build_type: debug
 modules:
 - cxx:
   - source: ../../../modules/cxx.cmake

test/extra_cmake_options/cmake/autocmake.yml

@@ -1,5 +1,7 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language: CXX
+default_build_type: debug
 modules:
 - cxx:
   - source: ../../../modules/cxx.cmake

test/fc/cmake/autocmake.yml

@@ -1,5 +1,7 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language: Fortran
+default_build_type: debug
 modules:
 - fc:
   - source: ../../../modules/fc.cmake

test/fc_blas/cmake/autocmake.yml

@@ -1,5 +1,10 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language:
+  - Fortran
+  - C
+  - CXX
+default_build_type: debug
 modules:
 - fc:
   - source: ../../../modules/fc.cmake

test/fc_git_info/cmake/autocmake.yml

@@ -1,11 +1,13 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language: Fortran
+default_build_type: debug
 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
+- src:
+  - source: ../../../modules/src.cmake

test/fc_git_info/src/CMakeLists.txt

@@ -1,3 +1,5 @@
+generate_git_info_header(${PROJECT_BINARY_DIR} git_info.h)
+
 include_directories(${PROJECT_BINARY_DIR})
 
 add_executable(example example.F90)

test/fc_int64/cmake/autocmake.yml

@@ -1,5 +1,7 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language: Fortran
+default_build_type: debug
 modules:
 - fc:
   - source: ../../../modules/fc.cmake

test/fc_lapack/cmake/autocmake.yml

@@ -1,5 +1,10 @@
 name: example
-min_cmake_version: 2.8
+min_cmake_version: 3.1
+language:
+  - Fortran
+  - C
+  - CXX
+default_build_type: debug
 modules:
 - fc:
   - source: ../../../modules/fc.cmake