Merge remote-tracking branch 'ebra/dev' into noise

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,27 +1,30 @@
 ---
 name: Bug report
-about: Create a report to help us improve
-
+about: Report a bug to help us improve
+title: 'Bug report'
+labels: "Type: Bug"
 ---
 
 **Bug description**
-A clear and concise description of the bug.
+<A clear and concise description of the bug.>
 
 **To Reproduce**
+<Update the following list with your specific information.>
 Steps to reproduce the behavior:
 1. Compile with '...'
 2. Run '...' case with '...' settings
 3. Open '...' output
 4. See the error
 
 **Expected behavior**
-A clear and concise description of what you expected to happen.
+<A clear and concise description of what you expected to happen.>
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+**Screenshots, if applicable**
+<Add screenshots to help explain your problem.>
 
 **OpenFAST Version**
-Please provide as much detail as possible including git commit. The best information is a screenshot of the OpenFAST system description that prints when running OpenFAST:
+<Please provide as much detail as possible including git commit. The best information is a screenshot of the OpenFAST system description that prints when running OpenFAST:>
+
 ```
 **************************************************************************************************
  OpenFAST
@@ -45,9 +48,9 @@ Please provide as much detail as possible including git commit. The best informa
 ```
 
 **System Information (please complete the following information):**
- - OS: [e.g. Ubuntu 14.04 or macOS 10.12]
- - Compiler: [e.g. GFortran 4.4]
- - Compiler settings: [e.g. CMake flags or other settings]
+ - OS: <e.g. Ubuntu 14.04 or macOS 10.12>
+ - Compiler: <e.g. GFortran 4.4>
+ - Compiler settings: <e.g. CMake flags or other settings>
 
 **Additional context**
-Add any other context about the problem here.
+<Add any other context about the problem here.>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,18 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-
+title: 'Feature request'
+labels: 'Type: Enhancement'
 ---
 
 **Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+<A clear and concise description of the problem.>
 
 **Describe the solution you'd like**
-A clear and concise description of what you want to happen.
+<A clear and concise description of what you want to happen.>
 
 **Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
+<A clear and concise description of any alternative solutions or features youve considered.>
 
 **Additional context**
-Add any other context or screenshots about the feature request here.
+<Add any other context or screenshots about the feature request here.>

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,18 @@
+
+**Complete this sentence**
+THIS PULL REQUEST __ [IS/IS NOT] __ READY TO MERGE
+
+**Feature or improvement description**
+<A clear and concise description of the new code.>
+
+**Related issue, if one exists**
+<Link to a related GitHub Issue.>
+
+**Impacted areas of the software**
+<List any modules or other areas which should be impacted by this pull request. This helps to determine the verification tests.>
+
+**Additional supporting information**
+<Add any other context about the problem here.>
+
+**Test results, if applicable**
+<Add the results from unit tests and regression tests here along with justification for any failing test cases.>

.travis.yml

@@ -16,7 +16,7 @@ env:
     - FC=/usr/local/bin/gfortran-7; DOUBLE_PRECISION=OFF
     - FC=/usr/bin/gfortran; DOUBLE_PRECISION=ON
     - FC=/usr/bin/gfortran; DOUBLE_PRECISION=OFF
-    - FC=ifort; DOUBLE_PRECISION=ON; TRAVIS_BUILD_INTEL=YES
+    # - FC=ifort; DOUBLE_PRECISION=ON; TRAVIS_BUILD_INTEL=YES
 
 before_install:
     # mac configuration
@@ -25,6 +25,7 @@ before_install:
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gcc@7; fi
 
     # linux configuration
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install gfortran; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install libblas-dev liblapack-dev; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv shell 3.6.3; fi
@@ -54,8 +55,8 @@ matrix:
       env: FC=/usr/bin/gfortran; DOUBLE_PRECISION=ON
     - os: osx
       env: FC=/usr/bin/gfortran; DOUBLE_PRECISION=OFF
-    - os: osx
-      env: FC=ifort; DOUBLE_PRECISION=ON; TRAVIS_BUILD_INTEL=YES
+    # - os: osx
+    #   env: FC=ifort; DOUBLE_PRECISION=ON; TRAVIS_BUILD_INTEL=YES
 
 script:
     # beamdyn unit tests

CMakeLists.txt

@@ -22,12 +22,6 @@ include(${CMAKE_SOURCE_DIR}/cmake/OpenfastFortranOptions.cmake)
 
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 
-# Get the git info into the executable
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/")
-include(GetGitRevisionDescription)
-git_describe(GIT_DESCRIBE)
-add_definitions(-DGIT_VERSION_INFO="${GIT_DESCRIBE}")
-
 # CMake Configuration variables
 if (NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING
@@ -77,12 +71,12 @@ endif()
 ########################################################################
 # Build rules for OpenFAST Registry
 #
-add_subdirectory(modules-local/openfast-registry)
+add_subdirectory(modules/openfast-registry)
 
 ########################################################################
-# OpenFAST Core modules
+# OpenFAST modules
 #
-set(OPENFAST_MODULES_LOCAL
+set(OPENFAST_MODULES
   nwtc-library
   inflowwind
   aerodyn
@@ -98,12 +92,7 @@ set(OPENFAST_MODULES_LOCAL
   supercontroller
   turbsim
   openfast-library
-  )
-
-########################################################################
-# OpenFAST External modules
-#
-set(OPENFAST_MODULES_EXTERNAL
+  version
   feamooring
   moordyn
   icedyn
@@ -112,20 +101,15 @@ set(OPENFAST_MODULES_EXTERNAL
   )
 
 set(OPENFAST_REGISTRY_INCLUDES "" CACHE INTERNAL "Registry includes paths")
-set_registry_includes("modules-local" ${OPENFAST_MODULES_LOCAL})
-set_registry_includes("modules-ext" ${OPENFAST_MODULES_EXTERNAL})
+set_registry_includes("modules" ${OPENFAST_MODULES})
 # Fix non-standard path addition to OPENFAST_REGISTRY_INCLUDES in icefloe module
 set(OPENFAST_REGISTRY_INCLUDES
-  ${OPENFAST_REGISTRY_INCLUDES} -I ${CMAKE_SOURCE_DIR}/modules-ext/icefloe/src/interfaces/FAST/
+  ${OPENFAST_REGISTRY_INCLUDES} -I ${CMAKE_SOURCE_DIR}/modules/icefloe/src/interfaces/FAST/
   CACHE INTERNAL "Registry includes paths")
 
-foreach(IDIR IN ITEMS ${OPENFAST_MODULES_LOCAL})
-  add_subdirectory("${CMAKE_SOURCE_DIR}/modules-local/${IDIR}")
-endforeach(IDIR IN ITEMS ${OPENFAST_MODULES_LOCAL})
-
-foreach(IDIR IN ITEMS ${OPENFAST_MODULES_EXTERNAL})
-  add_subdirectory("${CMAKE_SOURCE_DIR}/modules-ext/${IDIR}")
-endforeach(IDIR IN ITEMS ${OPENFAST_MODULES_EXTERNAL})
+foreach(IDIR IN ITEMS ${OPENFAST_MODULES})
+  add_subdirectory("${CMAKE_SOURCE_DIR}/modules/${IDIR}")
+endforeach(IDIR IN ITEMS ${OPENFAST_MODULES})
 
 add_subdirectory(glue-codes)
 

cmake/OpenfastCmakeUtils.cmake

@@ -48,7 +48,7 @@ function(generate_f90_types regfile outfile)
   add_custom_command(
     OUTPUT ${output}
     DEPENDS openfast_registry ${input}
-    COMMAND ${CMAKE_BINARY_DIR}/modules-local/openfast-registry/openfast_registry
+    COMMAND ${CMAKE_BINARY_DIR}/modules/openfast-registry/openfast_registry
     ${input} ${OPENFAST_REGISTRY_INCLUDES} ${ARGN})
   set_source_files_properties(${output} PROPERTIES GENERATED TRUE)
 endfunction(generate_f90_types)

docs/Doxyfile.in

@@ -277,8 +277,7 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # Doxygen selects the parser to use depending on the extension of the files it
 # parses. With this tag you can assign which parser to use for a given
 # extension. Doxygen has a built-in mapping, but you can override or extend it
-# using this tag. The format is ext=language, where ext is a file extension, and
-# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# language is one of the parsers supported byen:IDL, Java, Javascript,
 # C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
 # FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
 # Fortran. In the later case the parser tries to guess whether the code is fixed
@@ -791,9 +790,7 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @CMAKE_SOURCE_DIR@/glue-codes/ \
-                         @CMAKE_SOURCE_DIR@/modules-local/ \
-                         @CMAKE_SOURCE_DIR@/modules-ext/
-
+                         @CMAKE_SOURCE_DIR@/modules/ \
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -849,8 +846,8 @@ EXCLUDE_PATTERNS       =  @CMAKE_SOURCE_DIR@/.git/* \
                           @CMAKE_SOURCE_DIR@/build/* \
                           @CMAKE_SOURCE_DIR@/cmake/* \
                           @CMAKE_SOURCE_DIR@/docs/* \
-                          @CMAKE_SOURCE_DIR@/modules-local/orcaflex-interface/src/OrcaFlexInterface.f90 \
-                          @CMAKE_SOURCE_DIR@/modules-local/servodyn/src/BladedInterface.f90
+                          @CMAKE_SOURCE_DIR@/modules/orcaflex-interface/src/OrcaFlexInterface.f90 \
+                          @CMAKE_SOURCE_DIR@/modules/servodyn/src/BladedInterface.f90
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -946,9 +943,7 @@ FILTER_SOURCE_FILES    = NO
 
 # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
 # pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
-# it is also possible to disable source filtering for a specific pattern using
-# *.ext= (so without naming a filter).
-# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+# it is also possible to disable source filtering for a specific pattern usihistag requires that the tag FILTER_SOURCE_FILES is set to YES.
 
 FILTER_SOURCE_PATTERNS =
 

docs/source/dev/build_doc.rst

@@ -1,36 +1,59 @@
 .. _build_doc:
 
+Developing Documentation
+========================
+OpenFAST documentation is hosted on
+`readthedocs <http://openfast.readthedocs.io/>`_. It is automatically generated
+through the readthedocs build system from both the ``master`` and ``dev``
+branches whenever new commits are added. This documentation uses the
+`restructured text <http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_
+markup language.
+
 Building this documentation locally
-===================================
+-----------------------------------
+The documentation is compiled with Sphinx, which is a Python based tool.
+Install it and the other required Python packages listed in
+``docs/requirements.txt`` with pip or another python package manager.
+
+These packages are optional:
+- `Doxygen <http://www.stack.nl/~dimitri/doxygen/>`__
+- `Doxylink <https://pythonhosted.org/sphinxcontrib-doxylink/>`__
+- `Graphviz <http://www.graphviz.org>`__
+
+Doxygen and Graphviz can be installed directly from their website or with a
+package manager like ``brew``, ``yum``, or ``apt``.
 
-This document describes how to build the OpenFAST documentation on your local machine. The official documentation is automatically built
-and updated on `readthedocs <http://openfast.readthedocs.io/en/latest/>`__ when new material is pushed to the github repo.
-However, while developing documentation, it is helpful to build locally in order to see changes quickly and without needing
-to publish your changes to the public facing site.
+Pure python build
+-----------------
+If CMake and Make are not available on your system, the documentation can
+be generated directly with `sphinx`.
+**Note: This method does not generate the API documentation through Doxygen.**
 
-Dependencies
-------------
-The documentation is built in `Sphinx <http://www.sphinx-doc.org/en/master/>`__ with optional support for 
-`Doxygen <http://www.stack.nl/~dimitri/doxygen/>`__, `Doxylink <https://pythonhosted.org/sphinxcontrib-doxylink/>`__, and
-`Graphviz <http://www.graphviz.org>`__. Therefore users will need to install these tools as well as several extensions of Sphinx that are utilized.
+First, align your build structure to the standard OpenFAST build by creating
+a directory  at ``openfast/build``.
 
-Doxygen and Graphviz can be installed directly from their website or with a package manager like ``brew``, ``yum``, or ``apt``.
+If all tools are available, move into ``openfast/build`` and run the `sphinx`
+command:
 
-The remaining tools are Python based and should be installed with `pip` using the requirements file at
-``docs/requirements.txt``.
+::
 
-With CMake and Make
--------------------
-In the OpenFAST repository checkout, if it has not been created yet,
-create a ``build`` directory.  Change
-to the build directory and run CMake with ``BUILD_DOCUMENTATION`` on.  If all
+    # sphinx-build -b <builder-name> <source-directory> <output-directory>
+    sphinx-build -b html ../docs ./docs/html
+
+If this completes successfully, a html file will be created at
+``build/docs/html/index.html`` which can be opened with any web browser.
+
+Building with CMake and Make
+----------------------------
+In the OpenFAST directory, create a ``build`` directory and move into it.
+Then, run CMake with this flag: ``-DBUILD_DOCUMENTATION=ON``.  If all
 of the required tools are found successfully, CMake will configure with the
 ability to build the documentation.
 
-Issue the command ``make docs`` which will first build the Doxygen
+Next, run the command ``make docs`` which will first build the Doxygen
 documentation and then the Sphinx documentation. If this completes
-successfully, the entry point to the documentation will be in
-``build/docs/html/index.html``.
+successfully, a html file will be created at ``build/docs/html/index.html``
+which can be opened with any web browser.
 
 For example, from the OpenFAST directory:
 
@@ -41,42 +64,20 @@ For example, from the OpenFAST directory:
     cmake .. -DBUILD_DOCUMENTATION=ON
     make docs
 
-If you modify document source files in ``OpenFAST/docs/source``, you can simply update the html files through another ``make docs`` in ``OpenFAST/build``:
+If you modify document source files in ``openfast/docs/source``, you can simply
+update the html files through another ``make docs`` in ``openfast/build``:
 
 ::
 
     make docs
 
-Pure python
------------
-If CMake and Make are not available on your system, the documentation can be generated directly
-with `sphinx`. **Note: This method does not generate the API documentation through Doxygen.**
-
-First, align your build structure to the standard OpenFAST build by creating a directory 
-at ``openfast/build``.
-
-If all tools are available, move into ``openfast/build`` and run the `sphinx` command:
-
-::
-
-    # sphinx-build -b <builder-name> <source-directory> <output-directory>
-    sphinx-build -b html ../docs ./docs/html
-
-
-
-Documentation Output
---------------------
-
-After building the documentation, it can be accessed by opening the output in a browser.
-Open the high level html file generated at ``openfast/build/docs/html/index.html``
-and begin using the page as any other web page.
-
-
-Additional Build Targets
-------------------------
-
-The html portion of the documentation can be built with ``make sphinx-html``, and
-the output is available at ``openfast/build/docs/html/index.html``.
+Building only the html
+~~~~~~~~~~~~~~~~~~~~~~
+Generating the only html is much faster than compiling all components of the
+documentation. This can be done with ``make sphinx-html``.
 
+Building the PDF
+~~~~~~~~~~~~~~~~
 If LaTeX is installed, a pdf version of the documentation can be built with
-``make sphinx-pdf``, and the output is available at ``openfast/build/docs/latex/Openfast.pdf``.
+``make sphinx-pdf``, and the output is available at
+``OpenFAT/build/docs/latex/Openfast.pdf``.