Feature/reorg (#170)

* (wip) start moving core hydra files * (wip) rename package in code * finish moving core package files around * rename frontend class * rename backend class * rename lcd class * misc other renaming for configs * (wip) start moving hydra topology into hydra * fully drop hydra_topology package * rework reconstruction vs places namespace a little * move non-ros hydra utils to hydra package * get hydra ros code building again * move last of hydra_utils file into hydra_ros * move topology configs * drop config specializations for each enum * make hydra unit tests compile again * drop last ros package call * get hydra ros tests to compile * fix ros unit tests * (wip) fix config test resource filepaths * (wip) update lcd paths * (wip) fix loop closure tests with new convention * rework packages in launch files * update clang format file * reformat * update licenses and add dev scripts * fix cmake format * (wip) drop hydra msg defs from non-ros code * (wip) update cmake a little * adapt to frontend changes * (wip) fix ros compilation issues * address comments from Yun * minor cleanup to ros interface Co-authored-by: Nathan Hughes <[email protected]>
MIT-SPARK · Jun 26, 2023 · 6a80928 · 6a80928
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diff --git a/.clang-format b/.clang-format
@@ -1,94 +1,10 @@
 ---
-Language:        Cpp
-BasedOnStyle:  Google
-AccessModifierOffset: -1
-AlignAfterOpenBracket: Align
-AlignConsecutiveAssignments: false
-AlignConsecutiveDeclarations: false
-AlignOperands:   true
-AlignTrailingComments: true
-AllowAllParametersOfDeclarationOnNextLine: false
-AllowShortBlocksOnASingleLine: false
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AllowShortIfStatementsOnASingleLine: true
-AllowShortLoopsOnASingleLine: true
-AlwaysBreakAfterDefinitionReturnType: None
-AlwaysBreakAfterReturnType: None
-AlwaysBreakBeforeMultilineStrings: true
-AlwaysBreakTemplateDeclarations: true
+BasedOnStyle: Google
+---
+Language: Cpp
+DerivePointerAlignment: false
+PointerAlignment: Left
+ColumnLimit: 88
 BinPackArguments: false
 BinPackParameters: false
-BraceWrapping:
-  AfterClass:      false
-  AfterControlStatement: false
-  AfterEnum:       false
-  AfterFunction:   false
-  AfterNamespace:  false
-  AfterObjCDeclaration: false
-  AfterStruct:     false
-  AfterUnion:      false
-  BeforeCatch:     false
-  BeforeElse:      false
-  IndentBraces:    false
-BreakBeforeBinaryOperators: None
-BreakBeforeBraces: Attach
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-ColumnLimit:     88
-CommentPragmas:  '^ IWYU pragma:'
-ConstructorInitializerAllOnOneLineOrOnePerLine: true
-ConstructorInitializerIndentWidth: 4
-ContinuationIndentWidth: 4
-Cpp11BracedListStyle: true
-DerivePointerAlignment: true
-DisableFormat:   false
-ExperimentalAutoDetectBinPacking: false
-ForEachMacros:
-  - foreach
-  - Q_FOREACH
-  - BOOST_FOREACH
-IncludeCategories:
-  - Regex:           '^<ext/.*\.h>'
-    Priority:        2
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-  - Regex:           '^<.*'
-    Priority:        2
-  - Regex:           '.*'
-    Priority:        3
-IndentCaseLabels: true
-IndentWidth:     2
-IndentWrappedFunctionNames: false
-KeepEmptyLinesAtTheStartOfBlocks: false
-MacroBlockBegin: ''
-MacroBlockEnd:   ''
-MaxEmptyLinesToKeep: 1
-NamespaceIndentation: None
-ObjCBlockIndentWidth: 2
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: false
-PenaltyBreakBeforeFirstCallParameter: 1
-PenaltyBreakComment: 300
-PenaltyBreakFirstLessLess: 120
-PenaltyBreakString: 1000
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 200
-PointerAlignment: Left
-ReflowComments:  true
-SortIncludes:    true
-SpaceAfterCStyleCast: false
-SpaceBeforeAssignmentOperators: true
-SpaceBeforeParens: ControlStatements
-SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 2
-SpacesInAngles:  false
-SpacesInContainerLiterals: true
-SpacesInCStyleCastParentheses: false
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-Standard:        Auto
-TabWidth:        8
-UseTab:          Never
-...
-
+---
diff --git a/README.md b/README.md
@@ -202,12 +202,9 @@ Finally, build your workspace:
 catkin build
 ```
 
-### Components
+### Config Library
 
-See the following for more information:
-  - [hydra_dsg_builder](hydra_dsg_builder/README.md)
-  - [hydra_topology](hydra_topology/README.md)
-  - [hydra_utils](hydra_utils/README.md)
+Hydra has a wrapper around config parsing that is documented [here](doc/config_parsing.md).
 
 ### Filing Issues
 

diff --git a/dev/check-code.sh b/dev/check-code.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+pushd $(dirname $SCRIPT_DIR)
+
+find ./python -iname '*.py' | xargs python3 -m flake8
+
+popd
diff --git a/dev/check-licenses.sh b/dev/check-licenses.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+pushd $(dirname $SCRIPT_DIR)
+
+find . -iname *.h -o -iname *.cpp | xargs python3 $SCRIPT_DIR/check_license.py
+find . -iname '*.py' | xargs python3 $SCRIPT_DIR/check_license.py
+
+popd
diff --git a/dev/check_license.py b/dev/check_license.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python3
+"""Script to check source file for license info."""
+import difflib
+import pathlib
+import click
+
+
+def get_filetype(extension):
+    """Get filetype based on extension."""
+    if extension in [".cpp", ".h"]:
+        return "cpp"
+    elif extension == ".py":
+        return "python"
+    else:
+        return None
+
+
+@click.command()
+@click.argument("input_files", type=click.File("r"), nargs=-1)
+@click.option("--verbose", "-v", is_flag=True, help="show files checked")
+def main(input_files, verbose):
+    """Check if header of file matches license."""
+    parent_dir = pathlib.Path(__file__).absolute().parent
+    headers = {}
+    with (parent_dir / "cpp-header.txt").open("r") as fin:
+        headers["cpp"] = fin.read()
+
+    with (parent_dir / "python-header.txt").open("r") as fin:
+        headers["python"] = fin.read()
+
+    for input_file in input_files:
+        ext = pathlib.Path(input_file.name).suffix
+        filetype = get_filetype(ext)
+        if not filetype:
+            click.secho(f"unknown extension for {input_file.name}: {ext}", fg="yellow")
+            continue
+
+        target = headers[filetype]
+        num_lines = len(target.split("\n")) - 1
+
+        try:
+            lines = [next(input_file) for _ in range(num_lines)]
+        except StopIteration:
+            click.secho(f"{input_file.name}: missing", fg="red")
+            continue
+
+        if filetype == "python":
+            if lines and "#!" in lines[0]:
+                lines = lines[1:]
+                try:
+                    lines.append(next(input_file))
+                except StopIteration:
+                    click.secho(f"{input_file.name}: missing", fg="red")
+                    continue
+
+        header = "".join(lines)
+        if header != target:
+            click.secho(f"{input_file.name}: bad", fg="red")
+            if verbose:
+                diff = difflib.context_diff(
+                    header.splitlines(keepends=True),
+                    target.splitlines(keepends=True),
+                    fromfile=input_file.name,
+                    tofile="license",
+                )
+                diff_str = "".join(diff)
+                click.secho(f"{diff_str}", fg="red")
+        elif verbose:
+            click.secho(f"{input_file.name}: good", fg="green")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/dev/cpp-header.txt b/dev/cpp-header.txt
@@ -0,0 +1,34 @@
+/* -----------------------------------------------------------------------------
+ * Copyright 2022 Massachusetts Institute of Technology.
+ * All Rights Reserved
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *     this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright notice,
+ *     this list of conditions and the following disclaimer in the documentation
+ *     and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Research was sponsored by the United States Air Force Research Laboratory and
+ * the United States Air Force Artificial Intelligence Accelerator and was
+ * accomplished under Cooperative Agreement Number FA8750-19-2-1000. The views
+ * and conclusions contained in this document are those of the authors and should
+ * not be interpreted as representing the official policies, either expressed or
+ * implied, of the United States Air Force or the U.S. Government. The U.S.
+ * Government is authorized to reproduce and distribute reprints for Government
+ * purposes notwithstanding any copyright notation herein.
+ * -------------------------------------------------------------------------- */
diff --git a/dev/python-header.txt b/dev/python-header.txt
@@ -0,0 +1,32 @@
+# Copyright 2022, Massachusetts Institute of Technology.
+# All Rights Reserved
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  1. Redistributions of source code must retain the above copyright notice,
+#     this list of conditions and the following disclaimer.
+#
+#  2. Redistributions in binary form must reproduce the above copyright notice,
+#     this list of conditions and the following disclaimer in the documentation
+#     and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Research was sponsored by the United States Air Force Research Laboratory and
+# the United States Air Force Artificial Intelligence Accelerator and was
+# accomplished under Cooperative Agreement Number FA8750-19-2-1000. The views
+# and conclusions contained in this document are those of the authors and should
+# not be interpreted as representing the official policies, either expressed or
+# implied, of the United States Air Force or the U.S. Government. The U.S.
+# Government is authorized to reproduce and distribute reprints for Government
+# purposes notwithstanding any copyright notation herein.
diff --git a/dev/reformat.sh b/dev/reformat.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+pushd $(dirname $SCRIPT_DIR)
+
+find . -iname *.h -o -iname *.cpp | xargs clang-format -i
+python3 -m black .
+find . -iname *CMakeLists.txt* | xargs python3 -m cmakelang.format -i
+
+popd
diff --git a/hydra_utils/doc/config_parsing.md → doc/config_parsing.md b/hydra_utils/doc/config_parsing.md → doc/config_parsing.md
diff --git a/hydra_dsg_builder/.gitignore → hydra/.gitignore b/hydra_dsg_builder/.gitignore → hydra/.gitignore
diff --git a/hydra/CMakeLists.txt b/hydra/CMakeLists.txt
@@ -0,0 +1,100 @@
+cmake_minimum_required(VERSION 3.1)
+project(hydra)
+
+add_compile_options(-Wall -Wextra)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+option(HYDRA_USE_COVERAGE "Build core library with GCC --coverage option" OFF)
+option(HYDRA_GNN "build GNN interface" ON)
+if(HYDRA_GNN)
+  set(HYDRA_USE_GNN_CXX_VALUE 1)
+else()
+  set(HYDRA_USE_GNN_CXX_VALUE 0)
+endif()
+configure_file(hydra_build_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/hydra_build_config.h)
+
+find_package(Boost REQUIRED COMPONENTS timer)
+find_package(spark_dsg REQUIRED)
+find_package(teaserpp REQUIRED)
+find_package(GTSAM REQUIRED)
+find_package(Eigen3 REQUIRED)
+find_package(yaml-cpp REQUIRED)
+find_package(
+  catkin REQUIRED
+  COMPONENTS kimera_pgmo
+             kimera_semantics
+             tf2_eigen
+             voxblox
+)
+
+set(PCL_FIND_QUIETLY TRUE)
+find_package(PCL REQUIRED COMPONENTS common)
+
+configure_file(cmake/nanoflann.CMakeLists.txt.in nanoflann-download/CMakeLists.txt)
+execute_process(
+  COMMAND "${CMAKE_COMMAND}" -G "${CMAKE_GENERATOR}" .
+  WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/nanoflann-download"
+  OUTPUT_QUIET
+)
+execute_process(
+  COMMAND "${CMAKE_COMMAND}" --build .
+  WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/nanoflann-download"
+  OUTPUT_QUIET
+)
+
+set(NANOFLANN_BUILD_EXAMPLES
+    OFF
+    CACHE INTERNAL ""
+)
+set(NANOFLANN_BUILD_TESTS
+    OFF
+    CACHE INTERNAL ""
+)
+add_subdirectory(${CMAKE_BINARY_DIR}/nanoflann-src ${CMAKE_BINARY_DIR}/nanoflann-build)
+
+catkin_package(
+  CATKIN_DEPENDS
+  kimera_pgmo
+  kimera_semantics
+  tf2_eigen
+  voxblox
+  DEPENDS spark_dsg YAML_CPP
+  INCLUDE_DIRS include
+  LIBRARIES ${PROJECT_NAME} gtsam
+)
+
+add_library(${PROJECT_NAME})
+target_include_directories(
+  ${PROJECT_NAME}
+  PUBLIC include ${catkin_INCLUDE_DIRS}
+  PRIVATE ${CMAKE_CURRENT_BINARY_DIR} ${PCL_INCLUDE_DIRS}
+)
+target_link_libraries(
+  ${PROJECT_NAME}
+  PUBLIC ${catkin_LIBRARIES}
+         teaserpp::teaser_registration
+         spark_dsg::spark_dsg
+         yaml-cpp
+         gtsam
+  PRIVATE nanoflann::nanoflann ${PCL_LIBRARIES}
+)
+add_subdirectory(src)
+
+if(HYDRA_GNN)
+  add_subdirectory(src/gnn)
+  target_link_libraries(${PROJECT_NAME} PUBLIC ${PROJECT_NAME}_gnn)
+endif(HYDRA_GNN)
+
+if(HYDRA_USE_COVERAGE)
+  target_compile_options(${PROJECT_NAME} PRIVATE --coverage)
+  # TODO(nathan) once we have newer cmake, target link options
+  target_link_libraries(${PROJECT_NAME} PRIVATE --coverage)
+endif(HYDRA_USE_COVERAGE)
+
+if(CATKIN_ENABLE_TESTING)
+  add_subdirectory(tests)
+endif(CATKIN_ENABLE_TESTING)
+
+# TODO(nathan) handle install
diff --git a/hydra_dsg_builder/README.md → hydra/README.md b/hydra_dsg_builder/README.md → hydra/README.md