Squashed 'metaconfigure/' changes from d584ae2..77be710

77be710 Merge pull request #22 from njoy/feature/cleanup 7e115a7 Merge pull request #23 from njoy/feature/c++17 4fc7d82 Adding C++17 as C++ standard option. c2821b4 Just some small tweaks to fix spelling errors, and have no trailing whitespace on lines. 7fdf466 Merge pull request #21 from njoy/feature/signature 8d80475 Reverting some commands to make compatible wih Python 3.4 3ec3d00 Merge pull request #20 from njoy/feature/signature 61c791b Responding to Pull Request comments. a49258c Adding ability to do configuration files. 1fadec5 Adding ability to generate a signature. d6993d8 Making signature compatible with Python3 900549f Merge pull request #15 from njoy/feature/python3_to_python a348df3 Merge pull request #16 from njoy/feature/WindowsyLinux 24cd40e Added subobject linkage error exception in common flags. b3d6955 Merged. f22bae2 Adding Windows options for Cygwin and MinGW. 41786f5 Added check in CMakeLists.txt generated by cmake.py for python version. e72a44f Added version check of Git in constructed CMakeLists.txt. 0748844 Windows/Cygwin testing. 597ff74 Changing python3 to python. ca6c308 Added MinGW and CYGWIN environments to metaconfigure. ff293c6 Update cmake.py 6bda6e9 Update configuration.py 69647ab Update cmake.py 730615a Update index.md git-subtree-dir: metaconfigure git-subtree-split: 77be71034605196b158c64aa57a0e9b21696cf62
njoy · Feb 18, 2020 · 9e902dc · 9e902dc
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diff --git a/LICENSE b/LICENSE
@@ -7,4 +7,4 @@ Additionally, redistribution and use in source and binary forms, with or without
 2.      Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 3.      Neither the name of Los Alamos National Security, LLC, Los Alamos National Laboratory, LANL, the U.S. Government, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/cmake.py b/cmake.py
diff --git a/collect_subprojects.py b/collect_subprojects.py
@@ -25,7 +25,7 @@ def traverse_dependencies( destination, traversed ):
     """
     if not os.path.isdir( dependency_directory() ):
         return
-    
+
     os.chdir( dependency_directory() )
 
     for dependency in os.listdir( os.getcwd() ) :
@@ -48,14 +48,14 @@ def traverse_dependencies( destination, traversed ):
 
             traverse_dependencies( destination, traversed )
             os.chdir( ".." )
-            
+
     os.chdir( os.path.join( ".." ) )
 
 def collect_subprojects():
     destination = os.path.join( os.getcwd(), "subprojects" )
     if not os.path.isdir( destination ):
         os.makedirs( destination )
-        
+
     traverse_dependencies( destination, set() )
 
 collect_subprojects()
diff --git a/configuration.py b/configuration.py
@@ -2,20 +2,23 @@
 
 languages = {'c' : {}, 'c++' : {}, 'fortran' : {} }
 
-for langauge in languages.keys():
-    languages[langauge]['file extension'] = {}
-    languages[langauge]['compiler'] = {}
+for language in languages.keys():
+    languages[language]['file extension'] = {}
+    languages[language]['compiler'] = {}
 
 languages['c']['standards'] = ['c89', 'c99', 'c11']
-languages['c++']['standards'] = ['c++98', 'c++11', 'c++14']
+languages['c++']['standards'] = ['c++98', 'c++11', 'c++14', 'c++17']
 languages['fortran']['standards'] = ['fortran77', 'fortran90', 'fortran95', 'fortran2003', 'fortran2008']
 
 languages['c']['file extension']['implementation files'] = ['c']
 languages['c']['file extension']['header files'] = ['h']
-languages['c++']['file extension']['implementation files'] = ['c++', 'cxx', 'cpp', 'cc']
+languages['c']['file extension']['configure files'] = ['in']
+languages['c++']['file extension']['implementation files'] = ['c++', 'cxx', 'cpp', 'cc', 'C']
 languages['c++']['file extension']['header files'] = ['h++', 'hxx', 'hpp', 'hh', 'h']
+languages['c++']['file extension']['configure files'] = ['in']
 languages['fortran']['file extension']['implementation files'] = ['f', 'for', 'f90']
-
+languages['fortran']['file extension']['configure files'] = ['in']
+
 languages['c']['compiler']['gcc'] = {}
 languages['c']['compiler']['llvm clang'] = {}
 languages['c']['compiler']['apple clang'] = {}
@@ -25,16 +28,22 @@
 languages['fortran']['compiler']['gfortran'] = {}
 
 languages['c']['compiler']['gcc']['linux'] = {}
+languages['c']['compiler']['gcc']['cygwin'] = languages['c']['compiler']['gcc']['linux']
+languages['c']['compiler']['gcc']['mingw'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['gcc']['osx'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['gcc']['windows'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['llvm clang']['linux'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['llvm clang']['osx'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['llvm clang']['windows'] = languages['c']['compiler']['gcc']['linux']
+languages['c']['compiler']['llvm clang']['cygwin'] = languages['c']['compiler']['gcc']['linux']
+languages['c']['compiler']['llvm clang']['mingw'] = languages['c']['compiler']['gcc']['linux']
 languages['c']['compiler']['apple clang']['osx'] = languages['c']['compiler']['gcc']['linux']
 
 languages['fortran']['compiler']['gfortran']['linux'] = {}
 languages['fortran']['compiler']['gfortran']['osx'] = languages['fortran']['compiler']['gfortran']['linux']
 languages['fortran']['compiler']['gfortran']['windows'] = languages['fortran']['compiler']['gfortran']['linux']
+languages['fortran']['compiler']['gfortran']['cygwin'] = languages['fortran']['compiler']['gfortran']['linux']
+languages['fortran']['compiler']['gfortran']['mingw'] = languages['fortran']['compiler']['gfortran']['linux']
 
 languages['c']['compiler']['gcc']['linux']['standard'] = {'c89' : '-std=c90',
                                                           'c99' : '-std=c99',
@@ -43,7 +52,8 @@
 languages['c++']['compiler']['g++']['linux'] = {}
 languages['c++']['compiler']['g++']['linux']['standard'] = {'c++98' : '-std=c++98',
                                                             'c++11' : '-std=c++11',
-                                                            'c++14' : '-std=c++14'}
+                                                            'c++14' : '-std=c++14',
+                                                            'c++17' : '-std=c++17'}
 
 languages['fortran']['compiler']['gfortran']['linux']['standard'] = {'fortran77' : '-std=legacy' ,
                                                                      'fortran95' : '-std=f95',
@@ -93,13 +103,26 @@
 languages['fortran']['compiler']['gfortran']['linux']['flags']['profile use'] = languages['c']['compiler']['gcc']['linux']['flags']['profile use']
 
 languages['c++']['compiler']['g++']['linux']['flags'] = copy.deepcopy( languages['c']['compiler']['gcc']['linux']['flags'] )
+languages['c++']['compiler']['g++']['linux']['flags']['common'].append('-Wno-subobject-linkage')
 languages['c++']['compiler']['g++']['osx'] = copy.deepcopy( languages['c++']['compiler']['g++']['linux'] )
+languages['c++']['compiler']['g++']['cygwin'] = copy.deepcopy( languages['c++']['compiler']['g++']['linux'] )
+languages['c++']['compiler']['g++']['mingw'] = copy.deepcopy( languages['c++']['compiler']['g++']['linux'] )
 languages['c++']['compiler']['g++']['windows'] = languages['c++']['compiler']['g++']['linux']
 
 languages['c++']['compiler']['llvm clang++'] = copy.deepcopy( languages['c++']['compiler']['g++'])
 languages['c++']['compiler']['llvm clang++']['linux']['flags']['common'] = ['-stdlib=libstdc++']
 languages['c++']['compiler']['llvm clang++']['linux']['flags']['debug'].remove('-fsignaling-nans')
 
+languages['c++']['compiler']['llvm clang++']['cygwin']['standard'] = {'c++98' : '-std=gnu++98',
+                                                                      'c++11' : '-std=gnu++11',
+                                                                      'c++14' : '-std=gnu++14',
+                                                                      'c++17' : '-std=gnu++17'}
+
+languages['c++']['compiler']['g++']['cygwin']['standard'] = {'c++98' : '-std=gnu++98',
+                                                             'c++11' : '-std=gnu++11',
+                                                             'c++14' : '-std=gnu++14',
+                                                             'c++17' : '-std=gnu++17'}
+
 languages['c++']['compiler']['llvm clang++']['osx']['flags'] = copy.deepcopy(languages['c++']['compiler']['llvm clang++']['linux']['flags'])
 languages['c++']['compiler']['llvm clang++']['osx']['flags']['common'] = ['-stdlib=libc++']
 languages['c++']['compiler']['llvm clang++']['windows'] = languages['c++']['compiler']['llvm clang++']['osx']

diff --git a/docs/README-jekyll.md b/docs/README-jekyll.md
@@ -5,14 +5,14 @@ layout: page
 This repository contains the required stuff to make the NJOY website and keep it consistent across all the projects.
 
 ## Using jekyll-website
-For all projects under the NJOY organization, this repository should be created as a git 'subtree' in the `docs` directory. This will ensure consistency across all the projects as well as make the documentation for each accessible from the website. 
+For all projects under the NJOY organization, this repository should be created as a git 'subtree' in the `docs` directory. This will ensure consistency across all the projects as well as make the documentation for each accessible from the website.
 
 In order to prevent pushing to this repository one should set the push url for this remote in git like this:
 
 ```bash
 git remote set-url --push <name> no_push
 ```
-Here `<name>` is the name of the remote (probably `jekyll`). What this tells git is whenever you try to push to this remote, simply push to the url `no_push` which doesn't exist. 
+Here `<name>` is the name of the remote (probably `jekyll`). What this tells git is whenever you try to push to this remote, simply push to the url `no_push` which doesn't exist.
 
 Alternatively, you can set the push url to the url of the remote of the real repository like:
 

diff --git a/docs/Updating.md b/docs/Updating.md
@@ -35,18 +35,18 @@ These commands (unless otherwise specified) should be run from the top level of
    ```
 8. Inspect resulting `CMakelists.txt` file
 	 - Is the target of the expected type (executable, interface, or library)?
-	 
-	   An executable target will always be accompanied by a library or interface target in the CMake files generated by metaconfigure. A library target is a collection of soruce file which are to be compiled into a library file (either static or dynamic based on configuration settings) during the build process. This impllies that the project contains one or more implementation files (excluding an implementation file for any executable driver). Those declarations look something like this:
+
+	   An executable target will always be accompanied by a library or interface target in the CMake files generated by metaconfigure. A library target is a collection of source file which are to be compiled into a library file (either static or dynamic based on configuration settings) during the build process. This implies that the project contains one or more implementation files (excluding an implementation file for any executable driver). Those declarations look something like this:
        ```cmake
        add_library( <name> ${<name>_library_linkage} <source files> )
        ```
-       
+
        For targets that lack implementation files (`.cpp` files)—such as header-only libraries—there's nothing to compile. Interface declarations look like
        ```cmake
        add_library( <name> INTERFACE <source files> )
        ```
-       
-       Given a driver implementation file (defaults to `main.` but can be specified in the description), you should also see an exectuable target which links to the library or interface target.
+
+       Given a driver implementation file (defaults to `main.` but can be specified in the description), you should also see an executable target which links to the library or interface target.
        ```cmake
        add_executable( <name>_executable <driver> )
 	   set_target_properties( <name>_executable PROPERTIES OUTPUT_NAME <name> )
@@ -59,5 +59,3 @@ These commands (unless otherwise specified) should be run from the top level of
 10. Update `.travis.yml` and `.travis.sh`.
 11. Push to GitHub.
 12. Create pull request.
-
-
diff --git a/docs/index.md b/docs/index.md
@@ -2,7 +2,7 @@
 layout: page
 title: Metaconfigure
 ---
-## [Upating metaconfigure in a project](Updating.html)
+## [Updating metaconfigure in a project](Updating.html)
 
 ## Creating signatures
 Metaconfigure has the ability to create a "signature" for a project. A signature is a unique combination of the project and each of its dependencies---with their specific versions. The signature enables the ability to load a project from a point in time and ensure that you have the same version you had then.
@@ -15,8 +15,6 @@ To create a signature simply execute
 This will create a JSON file that contains the signature for the project as it currently stands. The `<filename>` is optional, but allows you to specify the JSON filename that is written.
 
 ### Collecting signatures
-A signature file is not automatically created. If one would like to be able to recreate a version at a specific time, you must create the signature file yourself. 
+A signature file is not automatically created. If one would like to be able to recreate a version at a specific time, you must create the signature file yourself.
 
 We have created and stored some signatures in a [repository](https://github.com/njoy/signatures) on GitHub. These signatures are created every time the `master` branch is updated. Thus, it is a collection of officially supported versions of the projects.
-
-
diff --git a/fetch_subprojects.py b/fetch_subprojects.py
@@ -30,35 +30,35 @@ def clone_submodule( relative_path ):
       ----------------------------------------
       """.format( relative_path = relative_path ) ) )
     invocation = [ "git", "submodule", "update", "-q","--init", "--", relative_path ]
-    if os.name == "nt":
-        invocation.insert( 0, "powershell" )
+#    if os.name == "nt":
+#        invocation.insert( 0, "powershell" )
 
     clone = subprocess.Popen( invocation )
     clone.communicate()
 
 def update_repository( git ):
     """
-    A function to update a submodule to lastest commit of the master branch
+    A function to update a submodule to latest commit of the master branch
     """
     if project_name() not in git:
         print("Updating to master branch...\n")
         invocation = ["git", "pull", "-q", "origin", "master"]
     else:
         print("Checking out revision {}...\n".format( git[ project_name() ] ) )
         invocation = ["git", "pull", "-q", "origin", git[ project_name() ] ]
-    if os.name == "nt":
-        invocation.insert( 0, "powershell" )
+#    if os.name == "nt":
+#        invocation.insert( 0, "powershell" )
     update = subprocess.Popen( invocation )
     update.communicate()
-  
+
 def traverse_dependencies( destination, traversed, git ):
     """
     Clone and update dependencies uniquely and collect links to dependency projects
     in a destination folder
     """
     if not os.path.isdir( dependency_directory() ):
         return
-    
+
     os.chdir( dependency_directory() )
 
     for dependency in os.listdir( os.getcwd() ) :
@@ -83,17 +83,17 @@ def traverse_dependencies( destination, traversed, git ):
 
             traverse_dependencies( destination, traversed, git )
             os.chdir( ".." )
-            
+
     os.chdir( os.path.join( ".." ) )
 
 def collect_subprojects( git ):
     if git:
         update_repository( git )
-    
+
     destination = os.path.join( os.getcwd(), "subprojects" )
     if not os.path.isdir( destination ):
         os.makedirs( destination )
-        
+
     traverse_dependencies( destination, set(), git )
 
 git = {}

diff --git a/generate.py b/generate.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python3
+#! /usr/bin/env python
 
 import sys
 

diff --git a/signature.py b/signature.py
@@ -8,33 +8,30 @@
 import sys
 import time
 
-def project_signature( git ):
-    project_name = os.path.split( os.getcwd() )[1]
+def project_signature():
     invocation = [ "git", "rev-parse", "HEAD" ]
     if os.name == "nt":
         invocation.insert( 0, "powershell" )
 
     process = subprocess.Popen( invocation, stdout=subprocess.PIPE )
     hash_value = process.communicate()
-    git[ project_name ] = str(hash_value[0].strip())
+    return hash_value[0].strip().decode("utf-8")
 
 def generate( name = None ):
+
+    project_name = os.path.split( os.getcwd() )[1]
     if name is None:
-        project_name = os.path.split( os.getcwd() )[1]
         name = project_name + str( time.time() )
 
     git = {}
-    project_signature( git )
-    if os.path.isdir( os.path.join( os.getcwd(), 'subprojects' ) ):
-        os.chdir( 'subprojects' )
-        root = os.getcwd()
-        for subproject in os.listdir( os.getcwd() ):
-            if os.path.isdir( os.path.join( os.getcwd(), subproject ) ):
-                os.chdir( subproject )
-                project_signature( git )
-                os.chdir( root )
-
-        os.chdir( '..' )
+    git[ project_name ] = project_signature()
+    root = os.getcwd()
+
+    if os.path.isdir( "subprojects" ):
+        for subproject in os.listdir( "subprojects" ):
+            os.chdir(os.path.join("subprojects", subproject))
+            git[subproject] = project_signature()
+            os.chdir(root)
 
     with open ( name + ".json", "w" ) as json_file:
         json_file.write( json.dumps( { 'git' : git }, indent=0 ) )