nasa
diff --git a/‎.flake8
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diff --git a/‎.gitignore
Lines changed: 4 additions & 0 deletions b/‎.gitignore
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diff --git a/‎CMakeLists.txt
Lines changed: 54 additions & 210 deletions b/‎CMakeLists.txt
Lines changed: 54 additions & 210 deletions
@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 88
@@ -2,3 +2,7 @@ __pycache__
 *.pyc
 *.egg-info
 
+# scikit-build artifacts
+_skbuild/
+python/upsp/_version.py
+
@@ -2,20 +2,50 @@ cmake_minimum_required(VERSION 3.20)
 project(upsp) 
 cmake_policy(SET CMP0074 NEW)
 
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules")
-
-set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH True)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-# Direct inclusion of open-source tools for
-# integrating pandoc w/ CMake, copied into cmake/Modules. Ref:
-# https://github.com/jeetsukumaran/cmake-pandocology/
-# (SHA: 10900f9aec4431b504fa8979576f950533cf20d9)
-include(pandocology)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules")
 
+# This ensures any link paths used at build time are preserved in
+# the installed targets. This supports cases where the user has
+# supplied third-party libraries in non-system locations (for
+# instance, if making use of a local vcpkg setup)
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+if (DEFINED SKBUILD)
+  # prevent an unused variable warning
+  set(ignoreMe "${SKBUILD}")
+
+  # TODO this is ugly but it works for now.
+  #
+  # When the project is built by scikit-build for deployment as a
+  # Python package, libraries are dropped in the lib/ folder and there's
+  # multiple consumers of those libraries that need to resolve them at runtime:
+  #
+  # - Executables, installed to bin/, need to look in $ORIGIN/../lib
+  # - Python extension modules, installed to lib/pythonX/site-packages/upsp,
+  #   need to look in $ORIGIN/../../..
+  #
+  # Lastly, there's some build-tree-only artifacts (eg gtest unit tests),
+  # those need to look in their own build directory ($ORIGIN).
+  #
+  # We could do this on a per-target basis but I'd rather just leave
+  # the hack in one spot for now instead of being peppered all over
+  # this build file.
+  #
+  # A "better/cleaner" example of this setup can be found here (although
+  # I don't think it handles all the use cases I listed above, it's
+  # a small sample project):
+  #
+  # https://github.com/scikit-build/scikit-build-sample-projects/blob/master/projects/hello-cmake-package/CMakeLists.txt#L92
+  #
+  set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+  set(CMAKE_INSTALL_RPATH "\$ORIGIN:\$ORIGIN/../lib:\$ORIGIN/../../../")
+endif()
+ 
 find_package(Eigen3 CONFIG REQUIRED)
 find_package(Boost REQUIRED)
 find_package(OpenCV CONFIG REQUIRED COMPONENTS core imgproc imgcodecs calib3d videoio tracking)
@@ -26,14 +56,16 @@ find_package(pybind11 REQUIRED)
 find_library(LIBRT rt)
 find_package(hdf5 CONFIG REQUIRED)
 find_package(IlmBase CONFIG REQUIRED)
+find_package(PythonExtensions)
+
+include_directories(cpp/include)
 
 pybind11_add_module(cine cpp/pybind11/cine.cpp)
 target_link_libraries(cine PRIVATE upsp_video)
+
 pybind11_add_module(raycast cpp/pybind11/raycast.cpp)
 target_link_libraries(raycast PRIVATE upsp_kdtree)
 
-include_directories(cpp/include)
-
 add_library(
     upsp_video
     SHARED
@@ -121,9 +153,6 @@ add_executable(upsp_matrix_transpose cpp/exec/upsp_matrix_transpose.cpp)
 target_link_libraries(upsp_matrix_transpose MPI::MPI_CXX)
 target_link_libraries(upsp_matrix_transpose OpenMP::OpenMP_CXX)
 
-
-# GTest::gmock GTest::gtest GTest::gmock_main GTest::gtest_main
-# TODO could automate smoke tests and gtest unit tests leveraging CTest
 find_package(GTest CONFIG REQUIRED)
 upsp_add_executable(
     run_tests
@@ -143,91 +172,6 @@ target_link_libraries(run_tests GTest::gtest GTest::gtest_main)
 target_link_libraries(run_tests OpenMP::OpenMP_CXX)
 target_link_libraries(run_tests hdf5::hdf5_cpp-shared hdf5::hdf5_hl_cpp-shared)
 
-# Documentation (custom cmake macros from pandocology)
-# NOTE: pandoc options ref: https://pandoc.org/MANUAL.html
-string(TIMESTAMP TODAY "%Y-%m-%d")
-function(upsp_add_document TARGET FILENAME)
-    list(APPEND UPSP_ADD_DOCUMENT_TARGETS ${TARGET})
-    set(UPSP_ADD_DOCUMENT_TARGETS ${UPSP_ADD_DOCUMENT_TARGETS} PARENT_SCOPE)
-    get_filename_component(BASENAME_WE ${FILENAME} NAME_WE)
-    add_document(
-        TARGET ${TARGET}_docx
-        OUTPUT_FILE ${BASENAME_WE}.docx
-        SOURCES ${FILENAME}
-        RESOURCE_DIRS docs/md/static
-        PANDOC_DIRECTIVES --to docx
-                        --from markdown+pandoc_title_block+table_captions+simple_tables+yaml_metadata_block
-                        --filter pandoc-xnos
-                        --mathjax
-                        --standalone
-                        --toc
-                        --number-sections
-                        --metadata date=${TODAY}
-        NO_EXPORT_PRODUCT
-    )
-
-    add_document(
-        TARGET ${TARGET}_html
-        OUTPUT_FILE ${BASENAME_WE}.html
-        SOURCES ${FILENAME}
-        RESOURCE_DIRS docs/md/static
-        PANDOC_DIRECTIVES --to html
-                        --from markdown+pandoc_title_block+table_captions+simple_tables+yaml_metadata_block
-                        --filter pandoc-xnos
-                        --mathjax
-                        --standalone
-                        --toc
-                        --number-sections
-                        --metadata date=${TODAY}
-                        -c static/upsp-styles.css
-                        -A static/upsp-footer.html
-        NO_EXPORT_PRODUCT
-    )
-
-    add_dependencies(${TARGET}_html ${TARGET}_docx)
-endfunction()
-
-function(upsp_serialize_document_depends)
-    list(LENGTH UPSP_ADD_DOCUMENT_TARGETS NUMBER_TARGETS)
-    if (${NUMBER_TARGETS} LESS_EQUAL 1)
-        return()
-    endif()
-    math(EXPR START "1")
-    math(EXPR STOP "${NUMBER_TARGETS} - 1")
-    foreach(THIS_IDX RANGE ${START} ${STOP})
-        math(EXPR PREV_IDX "${THIS_IDX} - 1")
-        list(GET UPSP_ADD_DOCUMENT_TARGETS ${THIS_IDX} THIS_TGT)
-        list(GET UPSP_ADD_DOCUMENT_TARGETS ${PREV_IDX} PREV_TGT)
-        add_dependencies(${THIS_TGT}_docx ${PREV_TGT}_html)
-    endforeach()
-endfunction()
-
-upsp_add_document(upsp_user_manual docs/md/upsp-user-manual.md)
-upsp_add_document(upsp_swdd docs/md/upsp-swdd.md)
-upsp_add_document(upsp_third_party_dependencies docs/md/upsp-third-party-dependencies.md)
-upsp_serialize_document_depends()
-
-# INSTALLATION TARGETS
-
-# Documentation install targets
-# A bit hacky but it works. Grab outputs from the build directory
-# after pandoc has been run (pandoc configured by the various
-# cmake pandocology macros) and copy them "by hand" to install location.
-install(
-    FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-swdd.docx
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-swdd.html
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-third-party-dependencies.docx
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-third-party-dependencies.html
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-user-manual.docx
-    ${CMAKE_CURRENT_BINARY_DIR}/upsp-user-manual.html
-    DESTINATION docs
-)
-install(
-    DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/static
-    DESTINATION docs
-)
-
 install(
     TARGETS
     add_field
@@ -248,120 +192,20 @@ install(
     scripts/upsp-make-processing-tree
     scripts/upsp-kulite-comparison
     scripts/upsp-plotting
-    scripts/upsp-unity-export
+    scripts/upsp-qsub-args
     DESTINATION
     bin
 )
 
-# Python install process could be a bit cleaner.
-# - Ideally we would make use of setuputils.
-# - However, there are a couple modules built with
-#   pybind11 (e.g., raycast.so) that rely on other
-#   solibs built by the project. If a user wants
-#   to import them in Python, then either
-#   a) raycast.so has to have its RPATH populated with
-#      the path to the folder containing the solib
-#      dependencies, or
-#   b) the user has to have their LD_LIBRARY_PATH set.
-#   Clearly, option (a) is preferred for Python
-#   development, and option (b) is an annoying
-#   workaround.
-# - By using the CMake install() command on the pybind11
-#   CMake targets, their RPATH's are updated correctly
-#   so option (a) works. However, this precludes using
-#   setuputils.
-# - There is probably a way to configure CMake via
-#   setuputils calls to properly replicate the behavior
-#   but I haven't figured it out yet.
-install(TARGETS cine raycast LIBRARY DESTINATION python/upsp)
-
-# The rest of the non-pybind11 Python modules are then
-# just manually copied here. We explicitly list out all files
-# for safety (in general, globs in build scripts aren't best
-# practice).
+# TODO I think this works in a fairly brittle fashion right now.
+# It just so happens that the cmake_install_dir staging directory
+# created by scikit-build has a "python/upsp" folder mimicking the
+# source tree layout... so these extensions are just "dropped" into the
+# right spot. There's probably a more robust way to specify their
+# install location, probably some CMAKE_ variable I'm ignorant of.
 install(
-    FILES
-    python/upsp/__init__.py
-    DESTINATION
-    python/upsp
-)
-
-install(
-    FILES
-    python/upsp/processing/context.py
-    python/upsp/processing/grids.py
-    python/upsp/processing/io.py
-    python/upsp/processing/kulite_processing.py
-    python/upsp/processing/kulite_utilities.py
-    python/upsp/processing/p3d_conversions.py
-    python/upsp/processing/p3d_utilities.py
-    python/upsp/processing/plot3d.py
-    python/upsp/processing/tree.py
-    python/upsp/processing/unity_conversions.py
-    DESTINATION
-    python/upsp/processing
-)
-
-install(
-    FILES
-    python/upsp/cam_cal_utils/external_calibrate.py
-    python/upsp/cam_cal_utils/img_utils.py
-    python/upsp/cam_cal_utils/parsers.py
-    python/upsp/cam_cal_utils/photogrammetry.py
-    python/upsp/cam_cal_utils/target_bumping.py
-    python/upsp/cam_cal_utils/visibility.py
-    python/upsp/cam_cal_utils/visualization.py
-    DESTINATION
-    python/upsp/cam_cal_utils
-)
-
-install(
-    FILES
-    python/upsp/target_localization/blob_detector_methods.py
-    python/upsp/target_localization/gaussian_fitting_methods.py
-    DESTINATION
-    python/upsp/target_localization
-)
-
-install(
-    FILES
-    python/upsp/kulite_comparison/plotting.py
-    python/upsp/kulite_comparison/selection.py
-    python/upsp/kulite_comparison/spatial_queries.py
-    DESTINATION
-    python/upsp/kulite_comparison
-)
-
-install(
-    FILES
-    python/upsp/processing/templates/add-field.sh.template
-    python/upsp/processing/templates/gltf-viewer.html.template
-    python/upsp/processing/templates/launcher.sh.template
-    python/upsp/processing/templates/run-step-parallel.sh.template
-    python/upsp/processing/templates/run-step-serial.sh.template
-    DESTINATION
-    python/upsp/processing/templates
-)
-
-# Define the two required variables before including
-# the source code for watching a git repository.
-set(PRE_CONFIGURE_FILE "scripts/version")
-set(POST_CONFIGURE_FILE "${CMAKE_BINARY_DIR}/version")
-include(cmake/git_watcher.cmake)
-
-install(
-    PROGRAMS
-    ${CMAKE_BINARY_DIR}/version
-    DESTINATION
-    ${CMAKE_INSTALL_PREFIX}
-)
-
-install(
-    FILES
-    scripts/activate.sh
-    scripts/activate.csh
-    RELEASE.md
-    DESTINATION
-    ${CMAKE_INSTALL_PREFIX}
+    TARGETS
+    cine
+    raycast
+    LIBRARY DESTINATION python/upsp
 )
-