Merge pull request OpenFAST#11 from andrew-platt/MDv2-farm into matte…

…hall/MDv2-farm

Update to OpenFAST/dev branch, and some SrvD_Linearization updates

.github/workflows/automated-dev-tests.yml

@@ -106,7 +106,7 @@ jobs:
             install_deps: brew install gcovr
           - os: ubuntu-20.04
             FORTRAN_COMPILER: gfortran-10
-            install_deps: sudo apt-get install -y gcovr
+            install_deps: sudo apt-get update && sudo apt-get install -y gcovr
 
     name: regression-test-debug-${{ matrix.os }}-${{ matrix.FORTRAN_COMPILER }}
     steps:
@@ -137,7 +137,6 @@ jobs:
             -DCMAKE_C_COMPILER:STRING=${{env.C_COMPILER}} \
             -DCMAKE_BUILD_TYPE:STRING=Debug \
             -DBUILD_TESTING:BOOL=ON \
-            -DCODECOV:BOOL=ON \
             -DCTEST_PLOT_ERRORS:BOOL=ON \
             ${GITHUB_WORKSPACE}
 
@@ -167,35 +166,26 @@ jobs:
         with:
           test-target: regression
 
-      - name: Generate coverage report
-        working-directory: ${{runner.workspace}}/openfast/build
-        run: |
-          find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
-          cd ..
-          gcovr -g -k -r . --xml regressioncov.xml  # --html --html-details -o regressioncov.html # -v
-
-          # cp `find . -name *.gcno` .
-          # cp `find . -name *.gcda` .
-          # ${{env.GCOV_EXE}} -b -l -p -c *.gcno
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
-        with:
-          dry_run: false
-          # token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          files: ./regressioncov.xml # optional
-          flags: regtests # optional
-          # name: codecov-umbrella # optional
-          fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
-          directory: ${{runner.workspace}}/openfast
-
-      - name: Success artifacts
-        uses: actions/upload-artifact@v2
-        if: success()
-        with:
-          name: regression-tests-debug
-          path: |
-            ${{runner.workspace}}/openfast/regressioncov.xml
+      # Disabled Codecov since the dashboard and GitHub comments were buggy,
+      # but it may be useful to post the gcov coverage reports to GitHub Actions
+      # artifacts.
+      # Note: if reenabling Codecov, the reports must be in xml format not html.
+      # - name: Generate coverage report
+      #   working-directory: ${{runner.workspace}}/openfast/build
+      #   run: |
+      #     find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
+      #     cd ..
+      #     gcovr -g -k -r . --html --html-details -o regressioncov.html # -v
+      #     # cp `find . -name *.gcno` .
+      #     # cp `find . -name *.gcda` .
+      #     # ${{env.GCOV_EXE}} -b -l -p -c *.gcno
+      # - name: Success artifacts
+      #   uses: actions/upload-artifact@v2
+      #   if: success()
+      #   with:
+      #     name: regression-tests-debug
+      #     path: |
+      #       ${{runner.workspace}}/openfast/regressioncov.html
       - name: Failing test artifacts
         uses: actions/upload-artifact@v2
         if: failure()
@@ -288,7 +278,6 @@ jobs:
             -DCMAKE_C_COMPILER:STRING=${{env.C_COMPILER}} \
             -DCMAKE_BUILD_TYPE:STRING=Debug \
             -DBUILD_TESTING:BOOL=ON \
-            -DCODECOV:BOOL=ON \
             ${GITHUB_WORKSPACE}
 
       - name: Build unit tests
@@ -310,31 +299,23 @@ jobs:
         with:
           test-target: unit
 
-      - name: Generate coverage report
-        working-directory: ${{runner.workspace}}/openfast/build
-        run: |
-          find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
-          cd ..
-          gcovr -g -k -r . --xml unitcov.xml
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
-        with:
-          dry_run: false
-          # token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          files: ./unitcov.xml # optional
-          flags: unittests # optional
-          # name: codecov-umbrella # optional
-          fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
-          directory: ${{runner.workspace}}/openfast
-
-      - name: Success artifacts
-        uses: actions/upload-artifact@v2
-        if: success()
-        with:
-          name: unit-tests
-          path: |
-            ${{runner.workspace}}/openfast/unitcov.xml
+      # Disabled Codecov since the dashboard and GitHub comments were buggy,
+      # but it may be useful to post the gcov coverage reports to GitHub Actions
+      # artifacts.
+      # Note: if reenabling Codecov, the reports must be in xml format not html.
+      # - name: Generate coverage report
+      #   working-directory: ${{runner.workspace}}/openfast/build
+      #   run: |
+      #     find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
+      #     cd ..
+      #     gcovr -g -k -r . --html --html-details unitcov.html
+      # - name: Success artifacts
+      #   uses: actions/upload-artifact@v2
+      #   if: success()
+      #   with:
+      #     name: unit-tests
+      #     path: |
+      #       ${{runner.workspace}}/openfast/unitcov.html
 
       - name: Failing test artifacts
         uses: actions/upload-artifact@v2
@@ -411,7 +392,6 @@ jobs:
             -DBUILD_SHARED_LIBS:BOOL=ON \
             -DBUILD_TESTING:BOOL=ON \
             -DCTEST_PLOT_ERRORS:BOOL=ON \
-            -DCODECOV:BOOL=ON \
             ${GITHUB_WORKSPACE}
 
       - name: Build OpenFAST C-Interfaces
@@ -432,31 +412,23 @@ jobs:
         run: |
           ctest -VV -L python
 
-      - name: Generate coverage report
-        working-directory: ${{runner.workspace}}/openfast/build
-        run: |
-          find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
-          cd ..
-          gcovr -g -k -r . --xml regressioncov.xml
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
-        with:
-          dry_run: false
-          # token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          files: ./regressioncov.xml # optional
-          flags: regtests # optional
-          # name: codecov-umbrella # optional
-          fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
-          directory: ${{runner.workspace}}/openfast
-
-      - name: Success artifacts
-        uses: actions/upload-artifact@v2
-        if: success()
-        with:
-          name: c-interface-reg-tests
-          path: |
-            ${{runner.workspace}}/openfast/regressioncov.xml
+      # Disabled Codecov since the dashboard and GitHub comments were buggy,
+      # but it may be useful to post the gcov coverage reports to GitHub Actions
+      # artifacts.
+      # Note: if reenabling Codecov, the reports must be in xml format not html.
+      # - name: Generate coverage report
+      #   working-directory: ${{runner.workspace}}/openfast/build
+      #   run: |
+      #     find . -type f -name '*.gcno' -not -path "**tests**" -exec ${{env.GCOV_EXE}} -pb {} +
+      #     cd ..
+      #     gcovr -g -k -r . --html --html-details regressioncov.html
+      # - name: Success artifacts
+      #   uses: actions/upload-artifact@v2
+      #   if: success()
+      #   with:
+      #     name: c-interface-reg-tests
+      #     path: |
+      #       ${{runner.workspace}}/openfast/regressioncov.html
 
       - name: Failing test artifacts
         uses: actions/upload-artifact@v2

CMakeLists.txt

@@ -49,7 +49,7 @@ endif()
 # Do this before configuring modules so that the flags are included
 option(BUILD_TESTING "Build the testing tree." OFF)
 if(BUILD_TESTING)
-  option(CODECOV "Enable infrastructure for measuring code coverage." OFF)
+  option(CODECOVERAGE "Enable infrastructure for measuring code coverage." OFF)
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DUNIT_TEST")
 endif()
 option(BUILD_OPENFAST_SIMULINK_API "Enable building OpenFAST for use with Simulink" off)
@@ -61,21 +61,21 @@ endif()
 set_fast_fortran()
 
 # Configure measuring code coverage in tests
-if(CODECOV)
+if(CODECOVERAGE)
   # Only supports GNU
   if(NOT CMAKE_Fortran_COMPILER_ID MATCHES GNU)
-    message(WARNING "CODECOV is only support with GNU Compilers. The current Fortran compiler is ${CMAKE_Fortran_COMPILER_ID}.")
+    message(WARNING "CODECOVERAGE is only support with GNU Compilers. The current Fortran compiler is ${CMAKE_Fortran_COMPILER_ID}.")
   endif()
   if(NOT CMAKE_CXX_COMPILER_ID MATCHES GNU)
-    message(WARNING "CODECOV is only support with GNU Compilers. The current C++ compiler is ${CMAKE_CXX_COMPILER_ID}.")
+    message(WARNING "CODECOVERAGE is only support with GNU Compilers. The current C++ compiler is ${CMAKE_CXX_COMPILER_ID}.")
   endif()
   if(NOT CMAKE_C_COMPILER_ID MATCHES GNU)
-    message(WARNING "CODECOV is only support with GNU Compilers. The current C compiler is ${CMAKE_C_COMPILER_ID}.")
+    message(WARNING "CODECOVERAGE is only support with GNU Compilers. The current C compiler is ${CMAKE_C_COMPILER_ID}.")
   endif()
 
   string(TOUPPER ${CMAKE_BUILD_TYPE} _build_type)
   if (NOT ${_build_type} STREQUAL "DEBUG")
-    message(WARNING "CODECOV reporting may be inaccurate with compiler optimizations on. Please run with CMAKE_BUILD_TYPE=DEBUG.")
+    message(WARNING "CODECOVERAGE reporting may be inaccurate with compiler optimizations on. Please run with CMAKE_BUILD_TYPE=DEBUG.")
   endif()
 
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} --coverage")

README.rst

@@ -1,13 +1,11 @@
 OpenFAST
 ========
 
-|actions| |nbsp| |rtfd| |regtest-coverage|
+|actions| |nbsp| |rtfd|
 
 .. |actions| image:: https://github.com/openfast/openfast/actions/workflows/automated-dev-tests.yml/badge.svg?branch=dev
    :target: https://github.com/OpenFAST/openfast/actions/workflows/automated-dev-tests.yml?query=workflow%3A%22Development+Pipeline%22
    :alt: Build Status
-.. |regtest-coverage| image:: https://codecov.io/gh/openfast/openfast/branch/dev/graph/badge.svg?token=lZzalptLMO
-   :target: https://codecov.io/gh/openfast/openfast
 .. |rtfd| image:: https://readthedocs.org/projects/openfast/badge/?version=dev
    :target: https://openfast.readthedocs.io/en/dev
    :alt: Documentation Status

docs/conf.py

@@ -67,6 +67,17 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
     'sphinxcontrib.bibtex',
     'sphinxcontrib.mermaid',
 ]
+bibtex_bibfiles = [
+    'source/user/aerodyn-aeroacoustics/references.bib',
+    'source/user/aerodyn-olaf/bibliography.bib',
+    'source/user/aerodyn/bibliography.bib',
+    'source/user/beamdyn/references.bib',
+    'source/user/extptfm/bibliography.bib',
+    'source/user/fast.farm/bibliography.bib',
+    'source/user/hydrodyn/references.bib',
+    'source/user/servodyn-stc/StC_Refs.bib',
+    'source/user/subdyn/references_SD.bib'
+]
 
 autodoc_default_flags = [
     'members',
@@ -117,9 +128,9 @@ def runDoxygen(sourcfile, doxyfileIn, doxyfileOut):
 # built documents.
 #
 # The short X.Y version.
-version = u'3.0'
+version = u'3.1'
 # The full version, including alpha/beta/rc tags.
-release = u'v3.0.0'
+release = u'v3.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/requirements.txt

@@ -3,7 +3,7 @@ docutils==0.16
 Pygments>=2.2
 pyparsing>=2.1
 Sphinx>=1.8.5
-sphinxcontrib-bibtex>=0.3.3,<2.0.0
+sphinxcontrib-bibtex>=2.0.0
 sphinxcontrib-doxylink>=1.3
 sphinxcontrib-mermaid>=0.6
 sphinx_rtd_theme>=0.3

docs/source/testing/index.rst

@@ -27,14 +27,7 @@ to automatically execute the test suite for new commits and pull
 requests. This cloud computing resource is available to all
 GitHub users and is highly recommended as part of the development
 workflow. After enabling GitHub Actions in an OpenFAST repository, simply
-pushing new commits will trigger the tests. The GitHub Actions pipeline
-is configured to measure the level of code coverage in the included
-tests. These reports are currently available only for the module-level
-regression tests and the unit tests, and they are available for viewing
-on the `OpenFAST Codecov.io dashboard <https://app.codecov.io/gh/openfast/openfast>`_.
-For any fork of OpenFAST where the GitHub Actions workflow successfully
-completes, a unique Codecov.io dashboard will be available at
-`https://app.codecov.io/gh/<github account>/openfast`.
+pushing new commits will trigger the tests.
 
 Test specific documentation
 ---------------------------

docs/source/this_doc.rst

@@ -10,7 +10,7 @@ generated from both the
 `dev <http://github.com/openfast/openfast/tree/dev/>`_ branches whenever
 new commits are added. Clicking on the bar on the lower left corner of the
 page reveals a panel (see image below) containing options to select the branch
-of the repository, download the documentation other formats (PFD, HTML, EPub),
+of the repository, download the documentation other formats (PDF, HTML, EPub),
 and link to other relevant websites.
 
 .. image:: ../_static/docs_options.png

docs/source/user/aerodyn-aeroacoustics/example/AD15.ipt

@@ -1,12 +1,12 @@
-------- AERODYN v15.03.\* INPUT FILE ------------------------------------------------
+------- AERODYN INPUT FILE -----------------------------------------------
 IEA Wind Task 37 land-based reference wind turbine
 ====== General Options ===================================================
 False          Echo        - Echo the input to "<rootname>.AD.ech"? (flag)
 "default"      DT_AA       - Time interval for aerodynamic calculations {or "default"} (s)
 1              WakeMod     - Type of wake/induction model (switch) {0=none, 1=BEMT}
 2              AFAeroMod   - Type of blade airfoil aerodynamics model (switch
-0              TwrPotent   - Type tower influence on wind around the tower (switch)
-False          TwrShadow   - Calculate tower influence on wind (flag)
+0              TwrPotent   - Type of tower influence on wind around the tower (switch)
+0              TwrShadow   - Type of tower influence on wind based on downstream tower shadow (switch) {0=none, 1=Powles model, 2=Eames model}
 False          TwrAero     - Calculate tower aerodynamic loads? (flag)
 False          FrozenWake  - Assume frozen wake during linearization? (flag
 False          CavitCheck  - Perform cavitation check? (flag)

docs/source/user/aerodyn-aeroacoustics/example/AFtab.dat

@@ -1,12 +1,12 @@
-! ------------ AirfoilInfo v1.01.x Input File ----------------------------------
+! ------------ AirfoilInfo Input File ------------------------------------------
 ! AeroElasticSE FAST driver
 !
 !
 ! ------------------------------------------------------------------------------
-DEFAULT                  InterpOrd   ! Interpolation order to use for quasi-steady table lookup {1=linear; 3=cubic spline; "default"} [default=3]
+DEFAULT                  InterpOrd   ! Interpolation order to use for quasi-steady table lookup {1=linear; 3=cubic spline; "default"} [default=1]
 1                        NonDimArea  ! The non-dimensional area of the airfoil (area/chord^2) (set to 1.0 if unsure or unneeded)
 @"AF20_Coords.txt"       NumCoords   ! The number of coordinates in the airfoil shape file. Set to zero if coordinates not included.
-AF20_BL.txt              BL_file     ! The file name including the boundary layer characteristics of the profile. Ignored if the aeroacoustic module is not called.
+AF20_BL.txt              BL_file     ! The file name including the boundary layer characteristics of the profile. Optional and ignored if the aeroacoustic module is not called.
 1                        NumTabs     ! Number of airfoil tables in this file.  Each table must have lines for Re and Ctrl.
 ! ------------------------------------------------------------------------------
 ! data for table 1

docs/source/user/aerodyn-aeroacoustics/example/AeroAcousticsInput.dat

@@ -1,7 +1,7 @@
-------- AeroAcoustics Module v1.00.* INPUT FILE ------------------------------------------------
+------- AeroAcoustics Module INPUT FILE -------------------------------------------------------------
 IEA task 37 RWT turbine -- https://github.com/IEAWindTask37/IEA-3.4-130-RWT
 ======  General Options  ============================================================================
-False        Echo         - Echo the input to "<rootname>.AD.ech"?  (flag)
+False        Echo         - Echo the input to "<rootname>.AD.NN.ech"?  (flag)
 0.1          DT_AA        - Time interval for aeroacoustics calculations (s), must be a multiple of DT_Aero from AeroDyn15  (or "default")
 0            AAStart      - Time after which the AeroAcoustics module is run (s)
 70           BldPrcnt     - Percentage of the blade span, starting from the tip, that will contribute to the overall noise levels. (float)