Merge pull request #36 from henryleberre/master

Close #31, #32, #33, #34, and #35

Author: sbryngelson

.github/workflows/doc.yml

@@ -30,17 +30,18 @@ jobs:
         git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q
         code=$?
         if [ "$code" -ne "0" ]; then exit 0; fi
-        git config --global user.name  "MFC Action"
-        git config --global user.email "MFC Action"
+        git config --global user.name  'MFC Action'
+        git config --global user.email '<>'
         git clone "${{ secrets.DOC_PUSH_URL }}"
         cd "$(find . -name '*.github.io')"
         mv .github ..
         rm -rf $(pwd)/*
         mv ../.github       .
         mv ../install/doc/mfc/* .
         git add -A
-        git commit -m "${GITHUB_SHA::7}: $(date +%d/%m/%Y-%H:%M:%S)" || true
+        git commit -m "Docs @ ${GITHUB_SHA::7}" || true
         git push
 
 # DOC_PUSH_URL should be of the format:
-# - "https://${{ github.repository_owner }}:${{ TOKEN }}@github.com/${{ github.repository_owner }}/${{ github.repository_owner }}.github.io"
+# --> https://<username>:<token>@github.com/<username>/<repository>
+

CMakeLists.txt

@@ -216,7 +216,13 @@ if (MFC_BUILD_SIMULATION)
 
 
     if (MFC_WITH_OPEN_ACC)
-        find_package(OpenACC REQUIRED)
+        find_package(OpenACC)
+
+        # This should be equivalent to if (NOT OpenACC_FC_FOUND)
+        if (NOT TARGET OpenACC::OpenACC_Fortran)
+            message(FATAL_ERROR "OpenACC + Fortran is unsupported.")
+        endif()
+
         target_link_libraries(simulation PRIVATE OpenACC::OpenACC_Fortran)
 
 
@@ -315,26 +321,23 @@ macro(GEN_DOCS target name)
     set(DOXYGEN_PROJECT_NAME "${name}")
     set(DOXYGEN_INPUT        "${CMAKE_CURRENT_SOURCE_DIR}/src/${target}/ ${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/")
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/${target}"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/${target}"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/doxygen"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}")
 
     configure_file(
         "${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in"
         "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/Doxyfile"
         @ONLY
     )
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/res"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/res"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/config.js"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/config.js"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
 
     add_custom_command(
         OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/html/index.html"
@@ -382,7 +385,7 @@ if (MFC_BUILD_DOC)
     ExternalProject_Add(doxygen-awesome-css
         PREFIX            doxygen-awesome-css
         GIT_REPOSITORY    "https://github.com/jothepro/doxygen-awesome-css"
-        GIT_TAG           "a5efba07a3d4fd6317d95657b3095b97e134b791"
+        GIT_TAG           "8a34f701d3435309a21080f44fbd4a466979aa19"
         CONFIGURE_COMMAND ""
         BUILD_COMMAND     ""
         INSTALL_COMMAND   ""
@@ -398,6 +401,6 @@ if (MFC_BUILD_DOC)
     GEN_DOCS(post_process "MFC: Post-Process")
 
     # === === Generate Landing Page
-    GEN_DOCS(landing "MFC")
+    GEN_DOCS(documentation "MFC")
 
 endif()

README.md

@@ -34,7 +34,7 @@ Please contact the developers, like [Spencer](mailto:[email protected]), if you hav
 We have an active Slack channel to help ease in new MFC users and support development.
 
 MFC has both API and high-level documentation. 
-It is available on [the website](https://mflowcode.github.io/) and in markdown format at [doc/landing/readme.md](doc/landing/readme.md).
+It is available on [the website](https://mflowcode.github.io/) and in markdown format at [doc/documentation/readme.md](doc/documentation/readme.md).
 
 If you use MFC, consider citing it:
 * <a href="https://doi.org/10.1016/j.cpc.2020.107396">

doc/Doxyfile.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "@DOXYGEN_PROJECT_NAME@"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.0.0
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1166,7 +1166,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = doxygen/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1176,7 +1176,7 @@ HTML_HEADER            =
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =
+HTML_FOOTER            = doxygen/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1211,7 +1211,7 @@ HTML_EXTRA_STYLESHEET  = @DOXYGEN_HTML_EXTRA_STYLESHEET@
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES       = 
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to

doc/landing/CODE_OF_CONDUCT.md renamed to doc/documentation/CODE_OF_CONDUCT.md

@@ -81,9 +81,9 @@ Ph.D. Disserations:
     V. Coralic (2014) Ph.D. thesis, California Institute of Technology
   </a>
 
-### User Configuration (`defaults.yaml`)
+### User Configuration
 
-The `mfc.sh` script used in the previous section is configured through the file named `defaults.yaml`.
+The [mfc.sh](https://github.com/MFlowCode/MFC/blob/master/mfc.sh) script used in the previous section is configured through the [defaults.yaml](https://github.com/MFlowCode/MFC/blob/master/defaults.yaml) file.
 
 ## Development
 
@@ -112,7 +112,7 @@ You can append `-DMFC_MEMORY_DUMP` to `release-gpu`'s Fortran compiler options i
 ## License
 
 Copyright 2022.
-MFC is under the MIT license (see [LICENSE](LICENSE) file for full text).
+MFC is under the MIT license (see [LICENSE](https://github.com/MFlowCode/MFC/blob/master/LICENSE) file for full text).
 
 ## Acknowledgements