Merge remote-tracking branch 'upstream/develop' into query_system_load

.clang-format

@@ -61,7 +61,7 @@ ForEachMacros:
   - BOOST_FOREACH
 IncludeBlocks:   Preserve
 IncludeCategories:
-  - Regex:           '^"(c4|cdi|cdi_analytic|cdi_CPEloss|cdi_eospac|cdi_ipcress|cdi_ndi|compton_interface|compton_tools|device|diagnostics|ds\+\+|experimental|fit|linear|memory|mesh|mesh_element|meshReaders|min|norms|ode|parser|quadrature|rng|roots|RTT_Format_Reader|special_functions|timestep|units|viz)/'
+  - Regex:           '^"(c4|cdi|cdi_analytic|cdi_CPEloss|cdi_eospac|cdi_ipcress|cdi_ndi|compton_interface|compton_tools|device|diagnostics|ds\+\+|experimental|fit|linear|memory|mesh|mesh_element|meshReaders|min|norms|ode|parser|quadrature|rng|roots|RTT_Format_Reader|special_functions|units|viz)/'
     Priority:        2
   - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
     Priority:        3

.cmake-format.py

@@ -0,0 +1,243 @@
+# ----------------------------------
+# Options affecting listfile parsing
+#
+# https://cmake-format.readthedocs.io/en/latest/configuration.html
+# ----------------------------------
+with section("parse"):  # noqa: F821
+
+    # Specify structure for custom cmake functions
+    additional_commands = {
+
+        "add_component_library": {
+            "pargs": 1,
+            "flags": ["NOEXPORT"],
+            "kwargs": {"TARGET": '*', "LIBRARY_NAME": '*', "SOURCES": '*', "HEADERS": '*',
+                       "INCLUDE_DIRS": '*', "TARGET_DEPS": '*', "LINK_LANGUAGE": '*',
+                       "LIBRARY_TYPE": '*'}},
+
+        "add_component_executable": {
+            "kwargs": {"TARGET": '*', "LIBRARY_NAME": '*', "SOURCES": '*', "HEADERS": '*',
+                       "INCLUDE_DIRS": '*', "TARGET_DEPS": '*', "EXE_NAME": '*', "FOLDER": '*'}},
+
+        "add_scalar_tests": {
+            "kwargs": {"SOURCES": '*', "DEPS": '*', "TEST_ARGS": '*', "PASS_REGEX": '*', "LABELS":
+                       '*'}},
+
+        "add_parallel_tests": {
+            "flags": ["MPI_PLUS_OMP"],
+            "kwargs": {"SOURCES": '*', "DEPS": '*', "TEST_ARGS": '*', "PASS_REGEX": '*',
+                       "FAIL_REGEX": '*', "LABEL": '*', "PE_LIST": '*'}},
+
+        "add_app_unit_test": {
+            "kwargs": {"DRIVER": '*', "APPS": '*', "TEST_ARGS": '*', "LABELS": '*', "APP": '*',
+                       "PE_LIST": '*', "STDINFILE": '*', "GOLDFILE": '*'}},
+
+        "cmake_add_fortran_subdirectory": {
+            "pargs": 1,
+            "flags": ["VERBOSE", "NO_EXTERNAL_INSTALL"],
+            "kwargs": {"PROJECT": '*', "ARCHIVE_DIR": '*', "RUNTIME_DIR": '*', "LIBRARIES": '*',
+                       "TARGET_NAMES": '*', "DEPENDS": '*', "CMAKE_COMMAND_LINE": '*'}},
+
+    }
+
+    # Specify variable tags.
+    vartags = []
+
+    # Specify property tags.
+    proptags = []
+
+# -----------------------------
+# Options affecting formatting.
+# -----------------------------
+with section("format"):  # noqa: F821
+
+    # How wide to allow formatted cmake files
+    line_width = 100
+
+    # How many spaces to tab for indent
+    tab_size = 2
+
+    # If an argument group contains more than this many sub-groups (parg or kwarg groups) then force
+    # it to a vertical layout.
+    max_subgroups_hwrap = 2
+
+    # If a positional argument group contains more than this many arguments, then force it to a
+    # vertical layout.
+    max_pargs_hwrap = 6
+
+    # If a cmdline positional group consumes more than this many lines without nesting, then
+    # invalidate the layout (and nest)
+    max_rows_cmdline = 2
+
+    # If true, separate flow control names from their parentheses with a space
+    separate_ctrl_name_with_space = False
+
+    # If true, separate function names from parentheses with a space
+    separate_fn_name_with_space = False
+
+    # If a statement is wrapped to more than one line, than dangle the closing parenthesis on its
+    # own line.
+    dangle_parens = False
+
+    # If the trailing parenthesis must be 'dangled' on its on line, then align it to this reference:
+    # `prefix`: the start of the statement, `prefix-indent`: the start of the statement, plus one
+    # indentation level, `child`: align to the column of the arguments
+    dangle_align = 'prefix'
+
+    # If the statement spelling length (including space and parenthesis) is smaller than this
+    # amount, then force reject nested layouts.
+    min_prefix_chars = 4
+
+    # If the statement spelling length (including space and parenthesis) is larger than the tab
+    # width by more than this amount, then force reject un-nested layouts.
+    max_prefix_chars = 10
+
+    # If a candidate layout is wrapped horizontally but it exceeds this many lines, then reject the
+    # layout.
+    max_lines_hwrap = 2
+
+    # What style line endings to use in the output.
+    line_ending = 'unix'
+
+    # Format command names consistently as 'lower' or 'upper' case
+    command_case = 'canonical'
+
+    # Format keywords consistently as 'lower' or 'upper' case
+    keyword_case = 'unchanged'
+
+    # A list of command names which should always be wrapped
+    always_wrap = []
+
+    # If true, the argument lists which are known to be sortable will be sorted lexicographicall
+    enable_sort = True
+
+    # If true, the parsers may infer whether or not an argument list is sortable (without
+    # annotation).
+    autosort = True
+
+    # By default, if cmake-format cannot successfully fit everything into the desired linewidth it
+    # will apply the last, most agressive attempt that it made. If this flag is True, however,
+    # cmake-format will print error, exit with non-zero status code, and write-out nothing
+    require_valid_layout = False
+
+    # A dictionary mapping layout nodes to a list of wrap decisions. See the documentation for more
+    # information.
+    layout_passes = {}
+
+# ------------------------------------------------
+# Options affecting comment reflow and formatting.
+# ------------------------------------------------
+with section("markup"):  # noqa: F821
+
+    # What character to use for bulleted lists
+    bullet_char = '*'
+
+    # What character to use as punctuation after numerals in an enumerated list
+    enum_char = '.'
+
+    # If comment markup is enabled, don't reflow the first comment block in each listfile. Use this
+    # to preserve formatting of your copyright/license statements.
+    first_comment_is_literal = True
+
+    # If comment markup is enabled, don't reflow any comment block which matches this (regex)
+    # pattern. Default is `None` (disabled).
+    literal_comment_pattern = None
+
+    # Regular expression to match preformat fences in comments default=
+    # ``r'^\s*([`~]{3}[`~]*)(.*)$'``
+    fence_pattern = '^\\s*([`~]{3}[`~]*)(.*)$'
+
+    # Regular expression to match rulers in comments default= ``r'^\s*[^\w\s]{3}.*[^\w\s]{3}$'``
+    ruler_pattern = '^\\s*[^\\w\\s]{3}.*[^\\w\\s]{3}$'
+
+    # If a comment line matches starts with this pattern then it is explicitly a trailing comment
+    # for the preceeding argument. Default is '#<'
+    explicit_trailing_pattern = '#<'
+
+    # If a comment line starts with at least this many consecutive hash characters, then don't
+    # lstrip() them off. This allows for lazy hash rulers where the first hash char is not separated
+    # by space
+    hashruler_min_length = 10
+
+    # If true, then insert a space between the first hash char and remaining hash chars in a hash
+    # ruler, and normalize its length to fill the column
+    canonicalize_hashrulers = True
+
+    # enable comment markup parsing and reflow
+    enable_markup = True
+
+# ----------------------------
+# Options affecting the linter
+# ----------------------------
+with section("lint"):  # noqa: F821
+
+    # a list of lint codes to disable
+    disabled_codes = ["C0103"]
+
+    # regular expression pattern describing valid function names
+    function_pattern = '[0-9a-z_]+'
+
+    # regular expression pattern describing valid macro names
+    macro_pattern = '[0-9A-Z_]+'
+
+    # regular expression pattern describing valid names for variables with global (cache) scope
+    global_var_pattern = '[A-Z][0-9A-Z_]+'
+
+    # regular expression pattern describing valid names for variables with global scope (but
+    # internal semantic)
+    internal_var_pattern = '_[A-Z][0-9A-Z_]+'
+
+    # regular expression pattern describing valid names for variables with local scope
+    local_var_pattern = '[a-z][a-z0-9_]+'
+
+    # regular expression pattern describing valid names for privatedirectory variables
+    private_var_pattern = '_[0-9a-z_]+'
+
+    # regular expression pattern describing valid names for public directory variables
+    public_var_pattern = '[A-Z][0-9A-Z_]+'
+
+    # regular expression pattern describing valid names for function/macro arguments and loop
+    # variables.
+    argument_var_pattern = '[a-z][a-z0-9_]+'
+
+    # regular expression pattern describing valid names for keywords used in functions or macros
+    keyword_pattern = '[A-Z][0-9A-Z_]+'
+
+    # In the heuristic for C0201, how many conditionals to match within a loop in before considering
+    # the loop a parser.
+    max_conditionals_custom_parser = 2
+
+    # Require at least this many newlines between statements
+    min_statement_spacing = 1
+
+    # Require no more than this many newlines between statements
+    max_statement_spacing = 2
+    max_returns = 6
+    max_branches = 12
+    max_arguments = 5
+    max_localvars = 15
+    max_statements = 50
+
+# -------------------------------
+# Options affecting file encoding
+# -------------------------------
+with section("encode"):  # noqa: F821
+
+    # If true, emit the unicode byte-order mark (BOM) at the start of the file
+    emit_byteorder_mark = False
+
+    # Specify the encoding of the input file. Defaults to utf-8
+    input_encoding = 'utf-8'
+
+    # Specify the encoding of the output file. Defaults to utf-8. Note that cmake only claims to
+    # support utf-8 so be careful when using anything else
+    output_encoding = 'utf-8'
+
+# -------------------------------------
+# Miscellaneous configurations options.
+# -------------------------------------
+with section("misc"):  # noqa: F821
+
+    # A dictionary containing any per-command configuration overrides. Currently only `command_case`
+    # is supported.
+    per_command = {}

.fprettify.rc

@@ -0,0 +1,12 @@
+indent = 2
+line-length = 100
+whitespace = 2
+whitespace-comma = true
+whitespace-assignment = true
+whitespace-relational = true
+whitespace-logical = false
+whitespace-plusminus = true
+whitespace-multdiv = true
+whitespace-print = true
+whitespace-type = true
+whitespace-intrinsics = true

.github/PULL_REQUEST_TEMPLATE

@@ -20,7 +20,7 @@
 * Checks
   * [ ] Travis/Appveyor CI checks pass
   * [ ] Code coverage does not decrease
-  * [ ] [Valgrind test passes](https://rtt.lanl.gov/CDash/index.php?project=Draco)
-  * [ ] [Toss3 checks pass](https://rtt.lanl.gov/CDash/index.php?project=Draco)
-  * [ ] [Trinitite checks pass](https://rtt.lanl.gov/CDash/index.php?project=Draco)
+  * [ ] [Valgrind test passes](https://rtt.lanl.gov/cdash3/index.php?project=Draco)
+  * [ ] [Toss3 checks pass](https://rtt.lanl.gov/cdash3/index.php?project=Draco)
+  * [ ] [Trinitite checks pass](https://rtt.lanl.gov/cdash3/index.php?project=Draco)
   * [ ] Code reviewed/approved, sufficient DbC checks, testing, documentation

.github/workflows/ci-autodoc.yml

@@ -0,0 +1,55 @@
+name: CI autodoc
+
+#
+# Documentation:
+# - https://help.github.com/en/articles/workflow-syntax-for-github-actions
+# - https://github.com/lanl/Draco/new/develop?filename=.github%2Fworkflows%2Fmain.yml&workflow_template=blank
+#
+
+#############################
+# Start the job on all push #
+#############################
+on:
+  # Triggers the workflow on push or pull request events but only for the develop branch
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  PYTHONPATH: /home/runner/work/Draco/Draco/config
+
+###############
+# Set the Job #
+###############
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v2
+        with:
+          # Full git history is needed to get a proper list of changed files within `super-linter`
+          fetch-depth: 0
+          # submodules: true
+
+      - name: Fetch Docker image for CI
+        uses: docker://kinetictheory/draco-ci-2020nov:autodoc
+
+      - name: Autodoc
+        env:
+          DOCKER_TAG: autodoc
+          AUTODOC: ON
+          COMPILER: GCC
+          DRACO_C4: MPI
+          WERROR: ON
+        run: |
+          echo "docker run -v ${GITHUB_WORKSPACE}:/home/travis/Draco -e COMPILER=${COMPILER} -e VENDOR_DIR=/vendors  -e BUILD_DIR=/home/travis/Draco/build -e SOURCE_DIR=/home/travis/Draco -e STYLE=${STYLE} -e COVERAGE=${COVERAGE} -e WERROR=${WERROR} -e DRACO_C4=${DRACO_C4} -e AUTODOC=${AUTODOC} -e CLANGTIDY=${CLANGTIDY} -e CI=${CI} kinetictheory/draco-ci-2020nov:${DOCKER_TAG} /bin/bash -l -c /home/travis/Draco/tools/travis-run-tests.sh"
+          docker run -v ${GITHUB_WORKSPACE}:/home/travis/Draco -e COMPILER=${COMPILER} -e VENDOR_DIR=/vendors -e BUILD_DIR=/home/travis/Draco/build -e SOURCE_DIR=/home/travis/Draco -e STYLE=${STYLE} -e COVERAGE=${COVERAGE} -e WERROR=${WERROR} -e DRACO_C4=${DRACO_C4} -e AUTODOC=${AUTODOC} -e CLANGTIDY=${CLANGTIDY} -e CI=${CI} kinetictheory/draco-ci-2020nov:${DOCKER_TAG} /bin/bash -l -c '/home/travis/Draco/tools/travis-run-tests.sh'
+
+# cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+# cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+# ctest -C ${{env.BUILD_TYPE}}

.github/workflows/ci-clang-tidy.yml

@@ -0,0 +1,55 @@
+name: CI clang-tidy
+
+#
+# Documentation:
+# - https://help.github.com/en/articles/workflow-syntax-for-github-actions
+# - https://github.com/lanl/Draco/new/develop?filename=.github%2Fworkflows%2Fmain.yml&workflow_template=blank
+#
+
+#############################
+# Start the job on all push #
+#############################
+on:
+  # Triggers the workflow on push or pull request events but only for the develop branch
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  PYTHONPATH: /home/runner/work/Draco/Draco/config
+
+###############
+# Set the Job #
+###############
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v2
+        with:
+          # Full git history is needed to get a proper list of changed files within `super-linter`
+          fetch-depth: 0
+          # submodules: true
+
+      - name: Fetch Docker image for CI
+        uses: docker://kinetictheory/draco-ci-2020nov:spack-llvm
+
+      - name: clang-tidy
+        env:
+          DOCKER_TAG: spack-llvm
+          CLANGTIDY: ON
+          COMPILER: LLVM
+          DRACO_C4: MPI
+          WERROR: ON
+        run: |
+          echo "docker run -v ${GITHUB_WORKSPACE}:/home/travis/Draco -e COMPILER=${COMPILER} -e VENDOR_DIR=/vendors  -e BUILD_DIR=/home/travis/Draco/build -e SOURCE_DIR=/home/travis/Draco -e STYLE=${STYLE} -e COVERAGE=${COVERAGE} -e WERROR=${WERROR} -e DRACO_C4=${DRACO_C4} -e AUTODOC=${AUTODOC} -e CLANGTIDY=${CLANGTIDY} -e CI=${CI} kinetictheory/draco-ci-2020nov:${DOCKER_TAG} /bin/bash -l -c /home/travis/Draco/tools/travis-run-tests.sh"
+          docker run -v ${GITHUB_WORKSPACE}:/home/travis/Draco -e COMPILER=${COMPILER} -e VENDOR_DIR=/vendors -e BUILD_DIR=/home/travis/Draco/build -e SOURCE_DIR=/home/travis/Draco -e STYLE=${STYLE} -e COVERAGE=${COVERAGE} -e WERROR=${WERROR} -e DRACO_C4=${DRACO_C4} -e AUTODOC=${AUTODOC} -e CLANGTIDY=${CLANGTIDY} -e CI=${CI} kinetictheory/draco-ci-2020nov:${DOCKER_TAG} /bin/bash -l -c '/home/travis/Draco/tools/travis-run-tests.sh'
+
+# cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+# cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+# ctest -C ${{env.BUILD_TYPE}}