Merge topic 'gitlab_ci_doxygen'

930c3d2fb reproduce_ci_env better detects which stage a job is for 71d9d4311 Doxygen is now generated by gitlab and done on each master merge a652f7fe1 Update vtk-m doxygen to generate less warnings 97a2408fc Correct warnings for using TBB 2020 deprecated functions Acked-by: Kitware Robot <kwrobot@kitware.com> Merge-request: !2117
2024-09-08 21:33:55 +00:00 · 2020-06-03 14:00:45 +00:00 · 2020-06-03 14:00:45 +00:00 · 14338a559c
commit 14338a559c
parent 7c7b95e5b1 930c3d2fb0
17 changed files with 165 additions and 51 deletions
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@ -38,6 +38,11 @@
 #     - tbb
 #     - openmp
 #     - mpich2
+#   * .gitlab/ci/docker/ubuntu2004/doxygen/
+#     - gcc 9.3
+#     - tbb
+#     - openmp
+#     - mpich2

 .docker_image: &docker_image
  variables:
@ -78,6 +83,12 @@
  extends:
    - .docker_image

+.ubuntu2004_doxygen: &ubuntu2004_doxygen
+  image: "kitware/vtkm:ci-doxygen-20200601"
+  extends:
+    - .docker_image
+
+
 .only-default: &only-default
  only:
    - master
@ -88,12 +99,9 @@
  only:
    - master

+
 # General Longer Term Tasks:
-# - setup asan, and ubsan as sub-pipeline
-# - setup clang tidy as sub-pipeline
-#
-# Current Tasks:
-# - Determine if we can get sccache to work with CUDA
+# - Setup clang tidy as sub-pipeline
 # - Setup a machine to replicate the issue in https://gitlab.kitware.com/vtk/vtk-m/-/issues/447
 #   Note: Centos7 doesn't work as they ship separate standard library
 #   headers for each version. We will have to figure out something else
@ -165,6 +173,7 @@ stages:
 include:
  - local: '/.gitlab/ci/centos7.yml'
  - local: '/.gitlab/ci/centos8.yml'
+  - local: '/.gitlab/ci/doxygen.yml'
  - local: '/.gitlab/ci/rhel8.yml'
  - local: '/.gitlab/ci/ubuntu1604.yml'
  - local: '/.gitlab/ci/ubuntu1804.yml'
--- a/.gitlab/ci/docker/ubuntu2004/doxygen/Dockerfile
+++ b/.gitlab/ci/docker/ubuntu2004/doxygen/Dockerfile
@ -0,0 +1,33 @@
+FROM ubuntu:20.04
+LABEL maintainer "Robert Maynard<robert.maynard@kitware.com>"
+
+# Base dependencies for building VTK-m projects
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+      cmake \
+      curl \
+      doxygen \
+      g++ \
+      git \
+      git-lfs \
+      libmpich-dev \
+      libomp-dev \
+      libtbb-dev \
+      mpich \
+      ninja-build \
+      rsync \
+      ssh \
+      software-properties-common
+
+# Need to run git-lfs install manually on ubuntu based images when using the
+# system packaged version
+RUN git-lfs install
+
+# Provide CMake 3.17 so we can re-run tests easily
+# This will be used when we run just the tests
+RUN mkdir /opt/cmake/ && \
+    curl -L https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3-Linux-x86_64.sh > cmake-3.17.3-Linux-x86_64.sh && \
+    sh cmake-3.17.3-Linux-x86_64.sh --prefix=/opt/cmake/ --exclude-subdir --skip-license && \
+    rm cmake-3.17.3-Linux-x86_64.sh && \
+    ln -s /opt/cmake/bin/ctest /opt/cmake/bin/ctest-latest
+
+ENV PATH "${PATH}:/opt/cmake/bin"
--- a/.gitlab/ci/docker/update_all.sh
+++ b/.gitlab/ci/docker/update_all.sh
@ -34,6 +34,10 @@ cd ubuntu1804/cuda10.1
 sudo docker build -t kitware/vtkm:ci-ubuntu1804_cuda10.1-$date .
 cd ../..

+cd ubuntu2004/doxygen/
+sudo docker build -t kitware/vtkm:ci-doxygen-$date .
+cd ../..
+
 # sudo docker login --username=<docker_hub_name>
 sudo docker push kitware/vtkm
 sudo docker system prune
--- a/.gitlab/ci/doxygen.yml
+++ b/.gitlab/ci/doxygen.yml
@ -0,0 +1,34 @@
+
+# Build on documentation for VTK-m on ubuntu2004 with TBB and OpenMP
+# Uses gcc 9
+# Uses MPICH2
+doxygen:
+  stage: build
+  environment:
+    #establish that we need doxygen related
+    #env variables
+    name: doxygen-upload
+  only:
+    #make sure we are only trigged on
+    #the vtk-m primary project
+    variables:
+      - '$DOXYGEN_UPLOAD_ENABLE == "true"'
+  timeout:  30 minutes
+  interruptible: true
+  tags:
+    - vtkm
+    - docker
+    - linux
+  extends:
+    - .ubuntu2004_doxygen
+  before_script:
+    - "cmake -V -P .gitlab/ci/config/gitlab_ci_setup.cmake"
+    - "ctest -VV -S .gitlab/ci/ctest_configure.cmake"
+  script:
+    - eval `ssh-agent -s`
+    - ssh-add <(echo "$DOC_API_KEY_BASE64" | base64 --decode)
+    - doxygen build/docs/doxyfile
+    - rsync -tv --recursive --delete -e "ssh -o StrictHostKeyChecking=no" build/docs/doxygen/html/ vtkm.documentation
+  variables:
+    CMAKE_BUILD_TYPE: Release
+    VTKM_SETTINGS: "tbb+openmp+mpi+shared+docs"
--- a/CMake/doxyfile.in
+++ b/CMake/doxyfile.in
@ -357,8 +357,6 @@ ALLEXTERNALS           = NO

 EXTERNAL_GROUPS        = YES

-PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
--- a/CTestCustom.cmake.in
+++ b/CTestCustom.cmake.in
@ -10,10 +10,16 @@

 list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION
  ".*warning: ignoring loop annotation.*"
-  ".*warning: Included by graph for.*not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES."
+  ".*warning: Included by graph for.*not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES.*"
+
+  # disable doxygen warnings about no matching members caused by auto keyword
+  ".*warning: no matching file member found for.*"
+
+  # disable doxygen warning from VTKM_DEPRECATED usage
+  ".*warning: Found.*while parsing initializer list!.*"

  # disable doxygen warning about potential recursion.
-  ".*warning: Detected potential recursive class relation between class vtkm::exec::internal::ArrayPortalTransform"
+  ".*warning: Detected potential recursive class relation between .*"

  # disable doxygen warning about not generating graph
  ".*warning: Included by graph for"
--- a/Utilities/CI/reproduce_ci_env.py
+++ b/Utilities/CI/reproduce_ci_env.py
@ -57,23 +57,9 @@ def load_ci_file(ci_file_path):
          ci_state.update(yaml.safe_load(open(include_path)))
  return ci_state

-def ci_stages_and_jobs(ci_state):
-  stages = ci_state['stages']
-  jobs = dict((s,[]) for s in stages)
-  for key in ci_state:
-    maybe_stage = key.split(':')
-    if maybe_stage[0] in stages:
-      jobs[maybe_stage[0]].append(maybe_stage[1])
-  return jobs
-
-def subset_yml(ci_state, stage, name):
-  #given a stage and name generate a new yaml
-  #file that only contains information for stage and name.
-  #Does basic extend merging so that recreating the env is easier
-  runner_yml = {}
-  yml_name = stage+":"+name
-  runner_yml[yml_name] = ci_state[yml_name]
-  entry = runner_yml[yml_name]
+def flattened_entry_copy(ci_state, name):
+  import copy
+  entry = copy.deepcopy(ci_state[name])

  #Flatten 'extends' entries, only presume the first level of inheritance is
  #important
@ -86,6 +72,41 @@ def subset_yml(ci_state, stage, name):
    for e in entry['extends']:
      entry.update(ci_state[e])
    del entry['extends']
+  return entry
+
+def ci_stages_and_jobs(ci_state):
+  stages = ci_state['stages']
+  jobs = dict((s,[]) for s in stages)
+  for key in ci_state:
+    entry = flattened_entry_copy(ci_state, key)
+
+    is_job = False
+    if 'stage' in entry:
+      stage = entry['stage']
+      if stage in stages:
+        is_job = True
+
+    # if we have a job ( that isn't private )
+    if is_job and not key.startswith('.'):
+      # clean up the name
+      clean_name = key
+      if ':' in key:
+        clean_name = key.split(':')[1]
+      jobs[stage].append(clean_name)
+
+
+  return jobs
+
+def subset_yml(ci_state, stage, name):
+  #given a stage and name generate a new yaml
+  #file that only contains information for stage and name.
+  #Does basic extend merging so that recreating the env is easier
+  runner_yml = {}
+
+  if stage+":"+name in ci_state:
+    name = stage+":"+name
+
+  runner_yml[name] = flattened_entry_copy(ci_state, name)
  return runner_yml

 class CallMode(enum.Enum):
@ -147,8 +168,12 @@ def create_container(ci_file_path, *args):
  #fully expanded into a single definition
  subset = subset_yml(ci_state, stage, name)

+  job_name = name
+  if stage+":"+name in subset:
+    job_name = stage+":"+name
  runner_name = stage+":"+name
-  runner = subset[runner_name]
+
+  runner = subset[job_name]
  src_dir = get_root_dir()
  gitlab_env = [ k + '="' + v + '"' for k,v in runner['variables'].items()]

--- a/vtkm/Tuple.h
+++ b/vtkm/Tuple.h
@ -131,6 +131,7 @@ VTKM_EXEC_CONT auto make_tuple(Ts&&... args) -> decltype(vtkm::MakeTuple(std::fo
  return vtkm::MakeTuple(std::forward<Ts>(args)...);
 }

+/// @cond NONE
 namespace detail
 {
 struct TupleTransformFunctor
@ -171,6 +172,7 @@ VTKM_EXEC_CONT auto TupleForEach(TupleType&& tuple, Function&& f)
 }

 } // namespace detail
+/// @endcond

 template <>
 class Tuple<>
--- a/vtkm/VecTraits.h
+++ b/vtkm/VecTraits.h
@ -123,8 +123,8 @@ struct VTKM_NEVER_EXPORT VecTraits
  /// \brief Get a vector of the same type but with a different component.
  ///
  /// This type resolves to another vector with a different component type. For example,
-  /// vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> is vtkm::Vec<T2, N>.
-  /// This replacement is not recursive. So VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2>
+  /// @code vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> @endcode is vtkm::Vec<T2, N>.
+  /// This replacement is not recursive. So @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode
  /// is vtkm::Vec<T2, N>.
  ///
  template <typename NewComponentType>
@ -134,7 +134,7 @@ struct VTKM_NEVER_EXPORT VecTraits
  ///
  /// This type resolves to another vector with a different base component type. The replacement
  /// is recursive for nested types. For example,
-  /// VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> is Vec<Vec<T2, M>, N>.
+  /// @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode is Vec<Vec<T2, M>, N>.
  ///
  template <typename NewComponentType>
  using ReplaceBaseComponentType = VecTemplate<
@ -270,8 +270,8 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::Vec<T, Size>>
 /// \brief Get a vector of the same type but with a different component.
 ///
 /// This type resolves to another vector with a different component type. For example,
-/// vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> is vtkm::Vec<T2, N>.
-/// This replacement is not recursive. So VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2>
+/// @code vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> @endcode is vtkm::Vec<T2, N>.
+/// This replacement is not recursive. So @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode
 /// is vtkm::Vec<T2, N>.
 ///@{
 #if defined(VTKM_GCC) && (__GNUC__ <= 5)
@ -289,7 +289,7 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::Vec<T, Size>>
 ///
 /// This type resolves to another vector with a different base component type. The replacement
 /// is recursive for nested types. For example,
-/// VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> is Vec<Vec<T2, M>, N>.
+/// @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode is Vec<Vec<T2, M>, N>.
 ///@{
 #if defined(VTKM_GCC) && (__GNUC__ <= 5)
  // Silly workaround for bug in GCC <= 5
@ -381,8 +381,8 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::VecC<T>>
  /// \brief Get a vector of the same type but with a different component.
  ///
  /// This type resolves to another vector with a different component type. For example,
-  /// vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> is vtkm::Vec<T2, N>.
-  /// This replacement is not recursive. So VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2>
+  /// @code vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> @endcode is vtkm::Vec<T2, N>.
+  /// This replacement is not recursive. So @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode
  /// is vtkm::Vec<T2, N>.
  ///
  template <typename NewComponentType>
@ -392,7 +392,7 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::VecC<T>>
  ///
  /// This type resolves to another vector with a different base component type. The replacement
  /// is recursive for nested types. For example,
-  /// VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> is Vec<Vec<T2, M>, N>.
+  /// @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode is Vec<Vec<T2, M>, N>.
  ///
  template <typename NewComponentType>
  using ReplaceBaseComponentType = vtkm::VecC<
@ -470,8 +470,8 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::VecCConst<T>>
  /// \brief Get a vector of the same type but with a different component.
  ///
  /// This type resolves to another vector with a different component type. For example,
-  /// vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> is vtkm::Vec<T2, N>.
-  /// This replacement is not recursive. So VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2>
+  /// @code vtkm::VecTraits<vtkm::Vec<T, N>>::ReplaceComponentType<T2> @endcode is vtkm::Vec<T2, N>.
+  /// This replacement is not recursive. So @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode
  /// is vtkm::Vec<T2, N>.
  ///
  template <typename NewComponentType>
@ -481,7 +481,7 @@ struct VTKM_NEVER_EXPORT VecTraits<vtkm::VecCConst<T>>
  ///
  /// This type resolves to another vector with a different base component type. The replacement
  /// is recursive for nested types. For example,
-  /// VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> is Vec<Vec<T2, M>, N>.
+  /// @code VecTraits<Vec<Vec<T, M>, N>::ReplaceComponentType<T2> @endcode is Vec<Vec<T2, M>, N>.
  ///
  template <typename NewComponentType>
  using ReplaceBaseComponentType = vtkm::VecCConst<
--- a/vtkm/cont/Algorithm.h
+++ b/vtkm/cont/Algorithm.h
@ -23,7 +23,7 @@ namespace vtkm
 {
 namespace cont
 {
-
+/// @cond NONE
 namespace detail
 {
 template <typename Device, typename T>
@ -365,6 +365,7 @@ struct UpperBoundsFunctor
  }
 };
 } // namespace detail
+/// @endcond

 struct Algorithm
 {
--- a/vtkm/cont/ArrayHandle.h
+++ b/vtkm/cont/ArrayHandle.h
@ -83,7 +83,6 @@ using IsInValidArrayHandle =
 template <typename ArrayHandle>
 using IsWritableArrayHandle =
  vtkm::internal::PortalSupportsSets<typename std::decay<ArrayHandle>::type::WritePortalType>;
-/// @}

 /// Checks to see if the given object is an array handle. This check is
 /// compatible with C++11 type_traits. It a typedef named \c type that is
--- a/vtkm/cont/Logging.h
+++ b/vtkm/cont/Logging.h
@ -175,7 +175,7 @@
 /// \def VTKM_LOG_CAST_FAIL(inObj, outType)
 /// \brief Convenience macro for logging a failed cast of dynamic object.
 /// \param inObj The dynamic object.
-/// \param outObj The candidate type (or typelist) that was unsuccessful.
+/// \param outType The candidate type (or typelist) that was unsuccessful.

 /// \def VTKM_LOG_TRYEXECUTE_FAIL(errorMessage, functorName, deviceId)
 /// \brief Convenience macro for logging a TryExecute failure to the Error level.
--- a/vtkm/cont/StorageExtrude.h
+++ b/vtkm/cont/StorageExtrude.h
@ -290,9 +290,10 @@ struct VTKM_ALWAYS_EXPORT ArrayPortalExtrude
  vtkm::Int32 NumberOfPlanes;
  bool UseCylindrical;
 };
+
 template <typename PortalType>
-typename ArrayPortalExtrude<PortalType>::ValueType
-ArrayPortalExtrude<PortalType>::ArrayPortalExtrude::Get(vtkm::Id index) const
+typename ArrayPortalExtrude<PortalType>::ValueType ArrayPortalExtrude<PortalType>::Get(
+  vtkm::Id index) const
 {
  using CompType = typename ValueType::ComponentType;

@ -313,8 +314,8 @@ ArrayPortalExtrude<PortalType>::ArrayPortalExtrude::Get(vtkm::Id index) const
 }

 template <typename PortalType>
-typename ArrayPortalExtrude<PortalType>::ValueType
-ArrayPortalExtrude<PortalType>::ArrayPortalExtrude::Get(vtkm::Id2 index) const
+typename ArrayPortalExtrude<PortalType>::ValueType ArrayPortalExtrude<PortalType>::Get(
+  vtkm::Id2 index) const
 {
  using CompType = typename ValueType::ComponentType;

@ -336,7 +337,7 @@ ArrayPortalExtrude<PortalType>::ArrayPortalExtrude::Get(vtkm::Id2 index) const

 template <typename PortalType>
 vtkm::Vec<typename ArrayPortalExtrude<PortalType>::ValueType, 6>
-ArrayPortalExtrude<PortalType>::ArrayPortalExtrude::GetWedge(const IndicesExtrude& index) const
+ArrayPortalExtrude<PortalType>::GetWedge(const IndicesExtrude& index) const
 {
  using CompType = typename ValueType::ComponentType;

--- a/vtkm/cont/tbb/internal/ParallelSortTBB.cxx
+++ b/vtkm/cont/tbb/internal/ParallelSortTBB.cxx
@ -54,7 +54,7 @@
 #include <vtkm/internal/Windows.h>

 #include <tbb/task.h>
-#include <tbb/tbb_thread.h>
+#include <thread>

 #if defined(VTKM_MSVC)
 #pragma pop_macro("__TBB_NO_IMPLICITLINKAGE")
@ -69,7 +69,7 @@ namespace tbb
 namespace sort
 {

-const size_t MAX_CORES = ::tbb::tbb_thread::hardware_concurrency();
+const size_t MAX_CORES = std::thread::hardware_concurrency();

 // Simple TBB task wrapper around a generic functor.
 template <typename FunctorType>
--- a/vtkm/exec/arg/FetchTagArrayTopologyMapIn.h
+++ b/vtkm/exec/arg/FetchTagArrayTopologyMapIn.h
@ -41,6 +41,7 @@ struct FetchTagArrayTopologyMapIn
 {
 };

+/// @cond NONE
 namespace detail
 {

@ -188,6 +189,7 @@ struct FetchArrayTopologyMapInImplementation<
 };

 } // namespace detail
+/// @endcond

 template <typename ExecObjectType>
 struct Fetch<vtkm::exec::arg::FetchTagArrayTopologyMapIn,
--- a/vtkm/filter/ContourTreeUniformAugmented.h
+++ b/vtkm/filter/ContourTreeUniformAugmented.h
@ -197,7 +197,7 @@ struct GetRowsColsSlices
  /// Get the number of rows, cols, and slices of a vtkm::cont::CellSetStructured
  /// @param[in] cells  The input vtkm::cont::CellSetStructured
  /// @param[out] nRows  Number of rows (x) in the cell set
-  /// @param[out[ nCols  Number of columns (y) in the cell set
+  /// @param[out] nCols  Number of columns (y) in the cell set
  /// @param[out] nSlices Number of slices (z) in the cell set
  void operator()(const vtkm::cont::CellSetStructured<2>& cells,
                  vtkm::Id& nRows,
--- a/vtkm/worklet/KdTree3D.h
+++ b/vtkm/worklet/KdTree3D.h
@ -51,7 +51,7 @@ public:
  /// \param nearestNeighborIds Nearest neighbor in the traning data set for each points in the
  ///                           testing set
  /// \param distances Distances between query points and their nearest neighbors.
-  /// \param device Tag for selecting device adapter.
+  /// \param deviceId Tag for selecting device adapter.
  template <typename CoordType,
            typename CoordStorageTag1,
            typename CoordStorageTag2,