diff --git a/.cmake-format.py b/.cmake-format.py
new file mode 100644
index 0000000000000000000000000000000000000000..94457f5b233fd324995fef4e7a2a39e6bef5ec42
--- /dev/null
+++ b/.cmake-format.py
@@ -0,0 +1,240 @@
+# ----------------------------------
+# Options affecting listfile parsing
+# ----------------------------------
+with section("parse"):
+
+ # Specify structure for custom cmake functions
+ additional_commands = { 'foo': { 'flags': ['BAR', 'BAZ'],
+ 'kwargs': {'DEPENDS': '*', 'HEADERS': '*', 'SOURCES': '*'}}}
+
+ # Override configurations per-command where available
+ override_spec = {}
+
+ # Specify variable tags.
+ vartags = []
+
+ # Specify property tags.
+ proptags = []
+
+# -----------------------------
+# Options affecting formatting.
+# -----------------------------
+with section("format"):
+
+ # Disable formatting entirely, making cmake-format a no-op
+ disable = False
+
+ # How wide to allow formatted cmake files
+ line_width = 80
+
+ # How many spaces to tab for indent
+ tab_size = 2
+
+ # If true, lines are indented using tab characters (utf-8 0x09) instead of
+ # <tab_size> space characters (utf-8 0x20). In cases where the layout would
+ # require a fractional tab character, the behavior of the fractional
+ # indentation is governed by <fractional_tab_policy>
+ use_tabchars = False
+
+ # If <use_tabchars> is True, then the value of this variable indicates how
+ # fractional indentions are handled during whitespace replacement. If set to
+ # 'use-space', fractional indentation is left as spaces (utf-8 0x20). If set
+ # to `round-up` fractional indentation is replaced with a single tab character
+ # (utf-8 0x09) effectively shifting the column to the next tabstop
+ fractional_tab_policy = 'use-space'
+
+ # 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 = False
+
+ # 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"):
+
+ # 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 = False
+
+ # 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 = False
+
+# ----------------------------
+# Options affecting the linter
+# ----------------------------
+with section("lint"):
+
+ # a list of lint codes to disable
+ disabled_codes = []
+
+ # 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"):
+
+ # 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"):
+
+ # A dictionary containing any per-command configuration overrides. Currently
+ # only `command_case` is supported.
+ per_command = {}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0565e481ccf9ec38dae2e555bb8a15c7d4e52aeb..12b29f1aac04ed5556a2c1b878219d3308295a1f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -160,9 +160,10 @@ build-package:
linting:
stage: linting
extends: .failable
+ needs: ["build-base"]
image: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA
script:
- - ./scripts/run-clang-format.sh
+ - ./scripts/run-format.sh
unit-test:
stage: test
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2aab7b28724e693c0544ed50877dcc79814ffb26..e72bd52b14c955d945e62dad3085e654f12021cd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,12 +1,11 @@
# Copyright (C) 2020 ASTRON (Netherlands Institute for Radio Astronomy)
# SPDX-License-Identifier: GPL-3.0-or-later
-# FindHDF5 uses NATIVE_COMMAND in separate_arguments, which requires
-# CMake 3.9.
+# FindHDF5 uses NATIVE_COMMAND in separate_arguments, which requires CMake 3.9.
cmake_minimum_required(VERSION 3.9)
# CMake >= 3.19.1 gives a warning when this policy is not 'NEW'.
-if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.19.1")
+if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.19.1")
cmake_policy(SET CMP0074 NEW)
endif()
@@ -59,7 +58,6 @@ if(BUILD_PACKAGES)
add_subdirectory(CPack)
endif()
-
# === Load external packages ===
# DDECal dependencies
@@ -68,27 +66,36 @@ if(${ARMADILLO_FOUND})
add_definitions(-DHAVE_ARMADILLO)
include_directories(${ARMADILLO_INCLUDE_DIRS})
set(DDE_ARMADILLO_FILES
- ddecal/constraints/KLFitter.cc
- ddecal/constraints/PiercePoint.cc
- ddecal/constraints/ScreenConstraint.cc)
+ ddecal/constraints/KLFitter.cc ddecal/constraints/PiercePoint.cc
+ ddecal/constraints/ScreenConstraint.cc)
else()
- message(WARNING "Armadillo was not found, not including screenfitter inside DDECal")
+ message(
+ WARNING "Armadillo was not found, not including screenfitter inside DDECal")
set(DDE_ARMADILLO_FILES)
endif()
# Casacore depends on HDF5 -> First load HDF5.
-find_package(HDF5 COMPONENTS C CXX REQUIRED)
+find_package(
+ HDF5
+ COMPONENTS C CXX
+ REQUIRED)
add_definitions(${HDF5_DEFINITIONS})
include_directories(${HDF5_INCLUDE_DIRS})
-find_package(Casacore COMPONENTS casa ms tables fits REQUIRED)
+find_package(
+ Casacore
+ COMPONENTS casa ms tables fits
+ REQUIRED)
include_directories(${CASACORE_INCLUDE_DIR})
find_package(CFITSIO REQUIRED)
include_directories(${CFITSIO_INCLUDE_DIRS})
-if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12")
- find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.12")
+ find_package(
+ Python3
+ COMPONENTS Interpreter Development
+ REQUIRED)
find_package(Python3 COMPONENTS NumPy)
else() # Use old, deprecated means of detecting python.
find_package(PythonInterp 3 REQUIRED)
@@ -109,44 +116,56 @@ message(STATUS "Using python version ${Python3_VERSION}")
include_directories(${Python3_INCLUDE_DIRS})
if(BUILD_PACKAGES)
- set(PYTHON_INSTALL_DIR lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/dist-packages)
+ set(PYTHON_INSTALL_DIR
+ lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/dist-packages)
else()
- set(PYTHON_INSTALL_DIR lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/site-packages)
+ set(PYTHON_INSTALL_DIR
+ lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/site-packages)
endif()
-#Prevent accidentally finding old BoostConfig.cmake file from casapy
+# Prevent accidentally finding old BoostConfig.cmake file from casapy
set(Boost_NO_BOOST_CMAKE ON)
-find_package(Boost COMPONENTS filesystem program_options system unit_test_framework REQUIRED)
+find_package(
+ Boost
+ COMPONENTS filesystem program_options system unit_test_framework
+ REQUIRED)
include_directories(${Boost_INCLUDE_DIR})
find_package(Threads REQUIRED)
-
# === Load astron packages ===
find_package(AOFlagger 3.0.1 REQUIRED)
include_directories(${AOFLAGGER_INCLUDE_DIR})
-# We could use find_package(EveryBeam 0.1.1 REQUIRED),
-# however conditions below make it somewhat more explicit
+# We could use find_package(EveryBeam 0.1.1 REQUIRED), however conditions below
+# make it somewhat more explicit
find_package(EveryBeam NO_MODULE)
if(${EVERYBEAM_FOUND})
- if(${EVERYBEAM_VERSION} VERSION_LESS "0.2.0" OR ${EVERYBEAM_VERSION} VERSION_GREATER_EQUAL "0.3.0")
- message(FATAL_ERROR "DP3 needs EveryBeam version 0.2.x - with x >= 0 - but found version ${EveryBeam_VERSION}")
+ if(${EVERYBEAM_VERSION} VERSION_LESS "0.2.0" OR ${EVERYBEAM_VERSION}
+ VERSION_GREATER_EQUAL "0.3.0")
+ message(
+ FATAL_ERROR
+ "DP3 needs EveryBeam version 0.2.x - with x >= 0 - but found version ${EveryBeam_VERSION}"
+ )
endif()
-include_directories(${EVERYBEAM_INCLUDE_DIR})
+ include_directories(${EVERYBEAM_INCLUDE_DIR})
else(${EVERYBEAM_FOUND})
- message(FATAL_ERROR "DP3 requires EveryBeam, but EveryBeam was not found. "
- "Please install https://git.astron.nl/RD/EveryBeam and make sure that "
- "EveryBeam is added to the CMAKE_PREFIX_PATH")
+ message(
+ FATAL_ERROR
+ "DP3 requires EveryBeam, but EveryBeam was not found. "
+ "Please install https://git.astron.nl/RD/EveryBeam and make sure that "
+ "EveryBeam is added to the CMAKE_PREFIX_PATH")
endif(${EVERYBEAM_FOUND})
find_package(IDGAPI NO_MODULE QUIET)
if(IDGAPI_FOUND)
# Throw error if IDG version < 0.8 or version not provided at all
if((IDGAPI_VERSION VERSION_LESS "0.8") OR (NOT DEFINED IDGAPI_VERSION))
- message(FATAL_ERROR "IDGAPI was found, but DP3 requires IDGAPI to have version >= 0.8. "
- "Please compile IDG repository at a version >= 0.8")
+ message(
+ FATAL_ERROR
+ "IDGAPI was found, but DP3 requires IDGAPI to have version >= 0.8. "
+ "Please compile IDG repository at a version >= 0.8")
endif()
endif()
if(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
@@ -156,10 +175,12 @@ if(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
message(STATUS "Image domain gridder API libraries found.")
else(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
set(IDGAPI_LIBRARIES "")
- message(WARNING "Image domain gridder API libraries NOT found. IDG prediction will not be available.")
+ message(
+ WARNING
+ "Image domain gridder API libraries NOT found. IDG prediction will not be available."
+ )
endif(IDGAPI_LIBRARIES AND IDGAPI_INCLUDE_DIRS)
-
# === Load internal submodule packages. ===
# Update submodules as needed
@@ -169,19 +190,27 @@ if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
if(GIT_SUBMODULE)
message(STATUS "Syncing submodules")
# Account for potential changes in git repo URL's
- execute_process(COMMAND ${GIT_EXECUTABLE} submodule sync --recursive
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- RESULT_VARIABLE GIT_SUBMOD_RESULT)
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} submodule sync --recursive
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+ RESULT_VARIABLE GIT_SUBMOD_RESULT)
if(NOT GIT_SUBMOD_RESULT EQUAL "0")
- message(FATAL_ERROR "Syncing submodules did not succeed"
- "command '${GIT_EXECUTABLE} submodule sync --recursive' failed with exit code ${GIT_SUBMOD_RESULT}")
+ message(
+ FATAL_ERROR
+ "Syncing submodules did not succeed"
+ "command '${GIT_EXECUTABLE} submodule sync --recursive' failed with exit code ${GIT_SUBMOD_RESULT}"
+ )
endif()
message(STATUS "Updating submodules")
- execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive --checkout
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- RESULT_VARIABLE GIT_SUBMOD_RESULT)
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive --checkout
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ RESULT_VARIABLE GIT_SUBMOD_RESULT)
if(NOT GIT_SUBMOD_RESULT EQUAL "0")
- message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+ message(
+ FATAL_ERROR
+ "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules"
+ )
endif()
endif()
endif()
@@ -202,9 +231,10 @@ include_directories("${CMAKE_SOURCE_DIR}/external/schaapcommon/include")
configure_file(base/Version.h.in base/Version.h)
include_directories(${CMAKE_CURRENT_BINARY_DIR}/base)
-if (USE_LSMR)
+if(USE_LSMR)
add_definitions(-DUSE_LSMR)
- add_library(LSMR OBJECT
+ add_library(
+ LSMR OBJECT
external/clsmr/lsmrblas.f90
external/clsmr/lsmrblasInterface.f90
external/clsmr/lsmrCheckModule.f90
@@ -216,21 +246,21 @@ if (USE_LSMR)
external/clsmr/clsmrblas.f90
external/clsmr/clsmrblasInterface.f90
external/clsmr/clsmrDataModule.f90
- external/clsmr/clsmrModule.f90
- )
+ external/clsmr/clsmrModule.f90)
endif()
-add_library(Blob OBJECT
+add_library(
+ Blob OBJECT
blob/BlobAipsIO.cc
blob/BlobArray.cc
blob/BlobHeader.cc
blob/BlobIBufStream.cc
blob/BlobIStream.cc
blob/BlobOBufStream.cc
- blob/BlobOStream.cc
-)
+ blob/BlobOStream.cc)
-add_library(Common OBJECT
+add_library(
+ Common OBJECT
common/BaselineSelect.cc
common/ClusterDesc.cc
common/DataConvert.cc
@@ -248,10 +278,10 @@ add_library(Common OBJECT
common/TypeNames.cc
common/VdsDesc.cc
common/VdsMaker.cc
- common/VdsPartDesc.cc
-)
+ common/VdsPartDesc.cc)
-add_library(DDECal OBJECT
+add_library(
+ DDECal OBJECT
steps/DDECal.cc
ddecal/Settings.cc
ddecal/constraints/Constraint.cc
@@ -278,7 +308,8 @@ add_library(DDECal OBJECT
ddecal/linear_solvers/LLSSolver.cc
${DDE_ARMADILLO_FILES})
-add_library(DP3_OBJ OBJECT
+add_library(
+ DP3_OBJ OBJECT
base/Apply.cc
base/BaselineSelection.cc
base/BDABuffer.cc
@@ -345,10 +376,10 @@ add_library(DP3_OBJ OBJECT
steps/Upsample.cc
steps/UVWFlagger.cc
steps/ApplyBeam.cc
- steps/DemixerNew.cc
-)
+ steps/DemixerNew.cc)
-add_library(ParmDB OBJECT
+add_library(
+ ParmDB OBJECT
parmdb/Axis.cc
parmdb/AxisMapping.cc
parmdb/Box.cc
@@ -370,46 +401,40 @@ add_library(ParmDB OBJECT
parmdb/SourceDB.cc
parmdb/SourceDBBlob.cc
parmdb/SourceDBCasa.cc
- parmdb/SourceInfo.cc
-)
+ parmdb/SourceInfo.cc)
-add_library(PythonDP3 OBJECT
- pythondp3/PyStep.cc
-)
+add_library(PythonDP3 OBJECT pythondp3/PyStep.cc)
# dp3_testdyndp3 requires using position independent code.
set_property(TARGET Blob Common DDECal DP3_OBJ ParmDB PythonDP3
PROPERTY POSITION_INDEPENDENT_CODE ON)
if(USE_LSMR)
-set_property(TARGET LSMR
- PROPERTY POSITION_INDEPENDENT_CODE ON)
+ set_property(TARGET LSMR PROPERTY POSITION_INDEPENDENT_CODE ON)
endif()
set(DP3_OBJECTS
- $<TARGET_OBJECTS:Blob>
- $<TARGET_OBJECTS:Common>
- $<TARGET_OBJECTS:DDECal>
- $<TARGET_OBJECTS:DP3_OBJ>
- $<TARGET_OBJECTS:ParmDB>
- $<TARGET_OBJECTS:PythonDP3>)
+ $<TARGET_OBJECTS:Blob> $<TARGET_OBJECTS:Common> $<TARGET_OBJECTS:DDECal>
+ $<TARGET_OBJECTS:DP3_OBJ> $<TARGET_OBJECTS:ParmDB>
+ $<TARGET_OBJECTS:PythonDP3>)
if(USE_LSMR)
list(APPEND DP3_OBJECTS $<TARGET_OBJECTS:LSMR>)
endif()
set(DP3_LIBRARIES
- ${AOFLAGGER_LIB}
- ${ARMADILLO_LIBRARIES}
- ${Boost_LIBRARIES}
- ${CASACORE_LIBRARIES}
- ${CFITSIO_LIBRARY}
- ${EVERYBEAM_LIB}
- ${HDF5_LIBRARIES} ${HDF5_CXX_LIBRARIES}
- ${IDGAPI_LIBRARIES}
- ${Python3_LIBRARIES}
- schaapcommon
- Threads::Threads
- pybind11::embed)
+ ${AOFLAGGER_LIB}
+ ${ARMADILLO_LIBRARIES}
+ ${Boost_LIBRARIES}
+ ${CASACORE_LIBRARIES}
+ ${CFITSIO_LIBRARY}
+ ${EVERYBEAM_LIB}
+ ${HDF5_LIBRARIES}
+ ${HDF5_CXX_LIBRARIES}
+ ${IDGAPI_LIBRARIES}
+ ${Python3_LIBRARIES}
+ schaapcommon
+ Threads::Threads
+ pybind11::embed)
add_subdirectory(base)
@@ -417,14 +442,10 @@ if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
add_subdirectory(pythondp3)
endif()
-set(SOURCEDB_OBJECTS
- $<TARGET_OBJECTS:Blob>
- $<TARGET_OBJECTS:Common>
- $<TARGET_OBJECTS:ParmDB>)
+set(SOURCEDB_OBJECTS $<TARGET_OBJECTS:Blob> $<TARGET_OBJECTS:Common>
+ $<TARGET_OBJECTS:ParmDB>)
-set(SOURCEDB_LIBRARIES
- ${CASACORE_LIBRARIES}
- ${Boost_SYSTEM_LIBRARY})
+set(SOURCEDB_LIBRARIES ${CASACORE_LIBRARIES} ${Boost_SYSTEM_LIBRARY})
add_executable(makesourcedb parmdb/makesourcedb.cc ${SOURCEDB_OBJECTS})
target_link_libraries(makesourcedb ${SOURCEDB_LIBRARIES})
@@ -435,74 +456,79 @@ target_link_libraries(showsourcedb ${SOURCEDB_LIBRARIES})
install(TARGETS makesourcedb showsourcedb DESTINATION bin)
# Install a script that warns users that DP3 is the new name of the executable
-install(PROGRAMS scripts/DPPP-deprecation.sh DESTINATION bin RENAME DPPP)
+install(
+ PROGRAMS scripts/DPPP-deprecation.sh
+ DESTINATION bin
+ RENAME DPPP)
include(docs/CMakeLists.txt)
-if (BUILD_TESTING)
+if(BUILD_TESTING)
include(CTest)
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(OS_SPECIFIC_TESTS) # No specific tests for Apple
else()
# These run only on Linux
- set(OS_SPECIFIC_TESTS
- # steps/dynamic_test_step/test/tDynamicTestStep.cc # This test still fails
- )
- add_library(dp3_testdyndp3 SHARED
- steps/dynamic_test_step/DynamicTestStep.cc ${DP3_OBJECTS}
+ set(OS_SPECIFIC_TESTS # steps/dynamic_test_step/test/tDynamicTestStep.cc #
+ # This test still fails
)
+ add_library(dp3_testdyndp3 SHARED steps/dynamic_test_step/DynamicTestStep.cc
+ ${DP3_OBJECTS})
target_link_libraries(dp3_testdyndp3 ${DP3_LIBRARIES})
add_dependencies(dp3_testdyndp3 schaapcommon)
endif()
set(TEST_FILENAMES
- common/test/unit/tProximityClustering.cc
- base/test/runtests.cc
- base/test/unit/tBaselineSelection.cc
- base/test/unit/tBDABuffer.cc
- base/test/unit/tDPBuffer.cc
- # base/test/unit/tDemixer.cc # Parset is no longer valid in this test
- base/test/unit/tDP3.cc
- base/test/unit/tMirror.cc
- base/test/unit/tSolutionInterval.cc
- base/test/unit/tSourceDBUtil.cc
- ddecal/test/unit/SolverTester.cc
- ddecal/test/unit/tBDASolverBuffer.cc
- ddecal/test/unit/tLLSSolver.cc
- ddecal/test/unit/tRotationConstraint.cc
- ddecal/test/unit/tSmoothnessConstraint.cc
- ddecal/test/unit/tSolvers.cc
- ddecal/test/unit/tBdaSolvers.cc
- steps/test/unit/mock/MockInput.cc
- steps/test/unit/mock/MockStep.cc
- steps/test/unit/fixtures/fDirectory.cc
- steps/test/unit/tAOFlaggerStep.cc
- steps/test/unit/tApplyCal.cc
- steps/test/unit/tApplyCalH5.cc
- steps/test/unit/tAverager.cc
- steps/test/unit/tBDAResultStep.cc
- steps/test/unit/tFilter.cc
- steps/test/unit/tInterpolate.cc
- steps/test/unit/tMedFlagger.cc
- steps/test/unit/tMSReader.cc
- steps/test/unit/tPreFlagger.cc
- steps/test/unit/tPhaseShift.cc
- steps/test/unit/tUpsample.cc
- steps/test/unit/tUVWFlagger.cc
- steps/test/unit/tPSet.cc
- steps/test/unit/tScaleData.cc
- steps/test/unit/tStationAdder.cc
- )
+ common/test/unit/tProximityClustering.cc
+ base/test/runtests.cc
+ base/test/unit/tBaselineSelection.cc
+ base/test/unit/tBDABuffer.cc
+ base/test/unit/tDPBuffer.cc
+ # base/test/unit/tDemixer.cc # Parset is no longer valid in this test
+ base/test/unit/tDP3.cc
+ base/test/unit/tMirror.cc
+ base/test/unit/tSolutionInterval.cc
+ base/test/unit/tSourceDBUtil.cc
+ ddecal/test/unit/SolverTester.cc
+ ddecal/test/unit/tBDASolverBuffer.cc
+ ddecal/test/unit/tLLSSolver.cc
+ ddecal/test/unit/tRotationConstraint.cc
+ ddecal/test/unit/tSmoothnessConstraint.cc
+ ddecal/test/unit/tSolvers.cc
+ ddecal/test/unit/tBdaSolvers.cc
+ steps/test/unit/mock/MockInput.cc
+ steps/test/unit/mock/MockStep.cc
+ steps/test/unit/fixtures/fDirectory.cc
+ steps/test/unit/tAOFlaggerStep.cc
+ steps/test/unit/tApplyCal.cc
+ steps/test/unit/tApplyCalH5.cc
+ steps/test/unit/tAverager.cc
+ steps/test/unit/tBDAResultStep.cc
+ steps/test/unit/tFilter.cc
+ steps/test/unit/tInterpolate.cc
+ steps/test/unit/tMedFlagger.cc
+ steps/test/unit/tMSReader.cc
+ steps/test/unit/tPreFlagger.cc
+ steps/test/unit/tPhaseShift.cc
+ steps/test/unit/tUpsample.cc
+ steps/test/unit/tUVWFlagger.cc
+ steps/test/unit/tPSet.cc
+ steps/test/unit/tScaleData.cc
+ steps/test/unit/tStationAdder.cc)
if(${Python3_NumPy_FOUND})
- list(APPEND TEST_FILENAMES "steps/test/unit/tPyStep.cc")
+ list(APPEND TEST_FILENAMES "steps/test/unit/tPyStep.cc")
else(${Python3_NumPy_FOUND})
- message(WARNING "NumPy not found on machine, tPyStep test is excluded from tests.")
+ message(
+ WARNING "NumPy not found on machine, tPyStep test is excluded from tests."
+ )
endif()
# Boost 1.59 introduced BOOST_TEST. The tests below use this feature.
if(Boost_VERSION_STRING VERSION_GREATER_EQUAL "1.59")
- list(APPEND TEST_FILENAMES
+ list(
+ APPEND
+ TEST_FILENAMES
common/test/unit/tMemory.cc
common/test/unit/tStringTools.cc
base/test/unit/tDPInfo.cc
@@ -522,93 +548,82 @@ if (BUILD_TESTING)
# Add boost dynamic link flag for all test files.
# https://www.boost.org/doc/libs/1_66_0/libs/test/doc/html/boost_test/usage_variants.html
- # Without this flag, linking is incorrect and boost performs duplicate delete()
- # calls after running all tests, in the cleanup phase.
+ # Without this flag, linking is incorrect and boost performs duplicate
+ # delete() calls after running all tests, in the cleanup phase.
set_source_files_properties(
- ${TEST_FILENAMES} PROPERTIES COMPILE_DEFINITIONS "BOOST_TEST_DYN_LINK"
- )
+ ${TEST_FILENAMES} PROPERTIES COMPILE_DEFINITIONS "BOOST_TEST_DYN_LINK")
set(DP3_RESOURCE_DIR ${CMAKE_SOURCE_DIR}/resources)
set(EXTRACT_CMD ${CMAKE_COMMAND} -E tar xzf)
- add_custom_target(extract_test_resources
+ add_custom_target(
+ extract_test_resources
COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tApplyCal_tmp.parmdb.tgz
COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tIDGPredict.sources.tgz
COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tNDPPP.in_MS.tgz
COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tNDPPP_bda.in_MS.tgz
COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tNDPPP-generic.MS.tgz
- COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tOSKAR.in_MS.tgz
- )
+ COMMAND ${EXTRACT_CMD} ${DP3_RESOURCE_DIR}/tOSKAR.in_MS.tgz)
- add_test(
- NAME extract_resources
- COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target extract_test_resources
- )
- set_tests_properties(extract_resources PROPERTIES FIXTURES_SETUP extract_resources)
+ add_test(NAME extract_resources
+ COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target
+ extract_test_resources)
+ set_tests_properties(extract_resources PROPERTIES FIXTURES_SETUP
+ extract_resources)
- add_executable(
- unittests
- ${TEST_FILENAMES} ${OS_SPECIFIC_TESTS} ${DP3_OBJECTS}
- )
+ add_executable(unittests ${TEST_FILENAMES} ${OS_SPECIFIC_TESTS}
+ ${DP3_OBJECTS})
set_target_properties(unittests PROPERTIES ENABLE_EXPORTS ON)
target_link_libraries(unittests ${DP3_LIBRARIES})
add_dependencies(unittests schaapcommon)
# Automatically (re)build the unit tests on every ctest run.
- add_test(buildunittests ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target unittests)
+ add_test(buildunittests ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target
+ unittests)
set_tests_properties(buildunittests PROPERTIES FIXTURES_SETUP unittests)
# unittests.sh adjusts the PYTHONPATH to make tPyStep working.
configure_file(scripts/unittests.sh.in unittests.sh)
- add_test(
- NAME unittests
- COMMAND unittests.sh -t !@slow -f JUNIT -k unittests.xml --catch_system_error=yes
- )
- set_tests_properties(
- unittests PROPERTIES LABELS unit
- FIXTURES_REQUIRED "unittests;extract_resources"
- )
-
- # Long running tests are labeled 'slow' and use a separate add_test call,
- # so ctest can run them in parallel.
- # Unfortunately there is no easy means of retreiving a list of all slow tests.
+ add_test(NAME unittests COMMAND unittests.sh -t !@slow -f JUNIT -k
+ unittests.xml --catch_system_error=yes)
+ set_tests_properties(unittests PROPERTIES LABELS unit FIXTURES_REQUIRED
+ "unittests;extract_resources")
+
+ # Long running tests are labeled 'slow' and use a separate add_test call, so
+ # ctest can run them in parallel. Unfortunately there is no easy means of
+ # retreiving a list of all slow tests.
set(SLOW_TESTS
- bda_solvers/diagonal
- bda_solvers/hybrid
- bda_solvers/iterative_diagonal
- bda_solvers/iterative_scalar
- bda_solvers/scalar
- idgpredict/process
- idgpredict/process_beam
- msbdawriter/process_simple
- msbdawriter/create_default_subtables
- msbdawriter/different_bda_intervals
- solvers/scalar_solver
- solvers/iterative_scalar_solver
- solvers/scalar_solver_normaleq
- solvers/diagonal_solver
- solvers/iterative_diagonal_solver
- solvers/hybrid_solver
- solvers/full_jones_solver
- solvers/min_iterations
- )
+ bda_solvers/diagonal
+ bda_solvers/hybrid
+ bda_solvers/iterative_diagonal
+ bda_solvers/iterative_scalar
+ bda_solvers/scalar
+ idgpredict/process
+ idgpredict/process_beam
+ msbdawriter/process_simple
+ msbdawriter/create_default_subtables
+ msbdawriter/different_bda_intervals
+ solvers/scalar_solver
+ solvers/iterative_scalar_solver
+ solvers/scalar_solver_normaleq
+ solvers/diagonal_solver
+ solvers/iterative_diagonal_solver
+ solvers/hybrid_solver
+ solvers/full_jones_solver
+ solvers/min_iterations)
if(USE_LSMR)
- list(APPEND SLOW_TESTS
- solvers/scalar_solver_lsmr
- solvers/diagonal_solver_lsmr
- )
+ list(APPEND SLOW_TESTS solvers/scalar_solver_lsmr
+ solvers/diagonal_solver_lsmr)
endif()
foreach(TEST ${SLOW_TESTS})
string(REPLACE "/" "_" XMLNAME ${TEST})
set(XMLNAME "unittest_${XMLNAME}.xml")
- add_test(
- NAME ${TEST}
- COMMAND unittests -t ${TEST} -f JUNIT -k ${XMLNAME} --catch_system_error=yes
- )
+ add_test(NAME ${TEST} COMMAND unittests -t ${TEST} -f JUNIT -k ${XMLNAME}
+ --catch_system_error=yes)
set_tests_properties(
- ${TEST} PROPERTIES LABELS "unit;slow" FIXTURES_REQUIRED "unittests;extract_resources"
- )
+ ${TEST} PROPERTIES LABELS "unit;slow" FIXTURES_REQUIRED
+ "unittests;extract_resources")
endforeach()
add_subdirectory(steps/test/integration)
diff --git a/CPack/CMakeLists.txt b/CPack/CMakeLists.txt
index 25f8a928a000fd2905a265165ef97d4f75c5f008..0101855adff78cce3fd0c8e69c19d44d1dc7356d 100644
--- a/CPack/CMakeLists.txt
+++ b/CPack/CMakeLists.txt
@@ -43,16 +43,16 @@ set(CPACK_SOURCE_GENERATOR "TGZ")
set(CPACK_DEBIAN_FILE_NAME DEB-DEFAULT)
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
-set(CPACK_DEBIAN_PACKAGE_DEPENDS
-"aoflagger (>= 3.0.1),\
+set(CPACK_DEBIAN_PACKAGE_DEPENDS
+ "aoflagger (>= 3.0.1),\
everybeam (>= 0.2), everybeam (<< 0.3),\
idg-api (>= 0.8)")
set(CPACK_DEBIAN_PACKAGE_MAINTAINER "deb-packages@astron.nl")
set(CPACK_DEBIAN_PACKAGE_SECTION "science")
set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
-# Determine list of conflicting package names.
-# Packages not built for current target CPU always conflict.
+# Determine list of conflicting package names. Packages not built for current
+# target CPU always conflict.
if(DEFINED IDENTIFIED_TARGET_CPU)
set(_conflicts dp3)
else()
@@ -73,4 +73,3 @@ include(CPack)
message(STATUS "Package name: ${CPACK_PACKAGE_NAME}")
message(STATUS "Package version: ${CPACK_PACKAGE_VERSION}")
-
diff --git a/CPack/DetermineTargetCPU.cmake b/CPack/DetermineTargetCPU.cmake
index fbe8ee314912f788a57077d9b7206f0c5ebcb9fb..72121d72eeb6530307bfb35e8d09e79f911de22c 100644
--- a/CPack/DetermineTargetCPU.cmake
+++ b/CPack/DetermineTargetCPU.cmake
@@ -24,25 +24,58 @@ This modules sets the following ``INTERNAL`` variables:
#]=======================================================================]
-# List of target CPUs known by both GCC and Clang
-# This list was produced as follows (note: requires llc to be installed):
-# comm -12 \
-# <(g++ -march=foo -E - < /dev/null |& grep '^cc1: note' | \
-# sed -nE 's,^.*: *([^;]*).*$,\1,p' | tr ' ' '\n' | sort -u) \
-# <(llc -mattr=help |& grep processor. | awk '{print $1}' | sort -u)
+# List of target CPUs known by both GCC and Clang This list was produced as
+# follows (note: requires llc to be installed): comm -12 \ <(g++ -march=foo -E -
+# < /dev/null |& grep '^cc1: note' | \ sed -nE 's,^.*: *([^;]*).*$,\1,p' | tr '
+# ' '\n' | sort -u) \ <(llc -mattr=help |& grep processor. | awk '{print $1}' |
+# sort -u)
set(KNOWN_TARGET_CPUS
- amdfam10 athlon64 athlon64-sse3 athlon-fx atom barcelona bdver1 bdver2
- bdver3 bdver4 bonnell broadwell btver1 btver2 core2 core-avx2 core-avx-i
- corei7 corei7-avx haswell ivybridge k8 k8-sse3 knl nehalem nocona opteron
- opteron-sse3 sandybridge silvermont skylake skylake-avx512 slm westmere
- x86-64 znver1 CACHE INTERNAL "Known target CPUs")
+ amdfam10
+ athlon64
+ athlon64-sse3
+ athlon-fx
+ atom
+ barcelona
+ bdver1
+ bdver2
+ bdver3
+ bdver4
+ bonnell
+ broadwell
+ btver1
+ btver2
+ core2
+ core-avx2
+ core-avx-i
+ corei7
+ corei7-avx
+ haswell
+ ivybridge
+ k8
+ k8-sse3
+ knl
+ nehalem
+ nocona
+ opteron
+ opteron-sse3
+ sandybridge
+ silvermont
+ skylake
+ skylake-avx512
+ slm
+ westmere
+ x86-64
+ znver1
+ CACHE INTERNAL "Known target CPUs")
if(NOT PORTABLE)
get_directory_property(_compile_options COMPILE_OPTIONS)
string(REPLACE ";" " " _compile_options "${_compile_options}")
- execute_process(COMMAND bash -c
- # Executed command is printed on stderr; we can discard stdout
- "echo | ${CMAKE_CXX_COMPILER} ${_compile_options} -E -v - >/dev/null"
+ execute_process(
+ COMMAND
+ bash -c
+ # Executed command is printed on stderr; we can discard stdout
+ "echo | ${CMAKE_CXX_COMPILER} ${_compile_options} -E -v - >/dev/null"
ERROR_VARIABLE _command
RESULT_VARIABLE _result)
if(NOT _result EQUAL 0)
@@ -50,13 +83,17 @@ if(NOT PORTABLE)
"target CPU '${TARGET_CPU}'")
else()
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
- execute_process(COMMAND bash -c
- "echo '${_command}' | sed -nE '/cc1/s/^.*-march=([^ ]+).*$/\\1/p'"
+ execute_process(
+ COMMAND
+ bash -c
+ "echo '${_command}' | sed -nE '/cc1/s/^.*-march=([^ ]+).*$/\\1/p'"
OUTPUT_VARIABLE _target_cpu
OUTPUT_STRIP_TRAILING_WHITESPACE)
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
- execute_process(COMMAND bash -c
- "echo '${_command}' | sed -nE '/cc1/s/^.*-target-cpu ([^ ]+).*$/\\1/p'"
+ execute_process(
+ COMMAND
+ bash -c
+ "echo '${_command}' | sed -nE '/cc1/s/^.*-target-cpu ([^ ]+).*$/\\1/p'"
OUTPUT_VARIABLE _target_cpu
OUTPUT_STRIP_TRAILING_WHITESPACE)
else()
@@ -67,15 +104,17 @@ if(NOT PORTABLE)
endif()
if(DEFINED _target_cpu)
- set(IDENTIFIED_TARGET_CPU ${_target_cpu} CACHE INTERNAL "")
+ set(IDENTIFIED_TARGET_CPU
+ ${_target_cpu}
+ CACHE INTERNAL "")
else()
unset(IDENTIFIED_TARGET_CPU CACHE)
endif()
-if(DEFINED IDENTIFIED_TARGET_CPU AND
- NOT IDENTIFIED_TARGET_CPU IN_LIST KNOWN_TARGET_CPUS)
- message(AUTHOR_WARNING
- "'${IDENTIFIED_TARGET_CPU}' is not in the list KNOWN_TARGET_CPUS. "
- "Please check if this list is still up-to-date")
+if(DEFINED IDENTIFIED_TARGET_CPU AND NOT IDENTIFIED_TARGET_CPU IN_LIST
+ KNOWN_TARGET_CPUS)
+ message(
+ AUTHOR_WARNING
+ "'${IDENTIFIED_TARGET_CPU}' is not in the list KNOWN_TARGET_CPUS. "
+ "Please check if this list is still up-to-date")
endif()
-
diff --git a/base/CMakeLists.txt b/base/CMakeLists.txt
index 94ebdb259bf53c042125dac16a5a42d1f85e4c22..51d4ccdd301905d9c37334d9411d8290d62d718f 100644
--- a/base/CMakeLists.txt
+++ b/base/CMakeLists.txt
@@ -6,11 +6,11 @@ target_link_libraries(DP3 ${DP3_LIBRARIES})
add_dependencies(DP3 schaapcommon)
set_target_properties(DP3 PROPERTIES ENABLE_EXPORTS ON)
-set_target_properties(DP3 PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+set_target_properties(DP3 PROPERTIES RUNTIME_OUTPUT_DIRECTORY
+ ${CMAKE_BINARY_DIR})
install(TARGETS DP3 DESTINATION bin)
# Data files
-install(
- FILES share/LOFAR-LBA-default.rfis share/LOFAR-HBA-default.rfis
- DESTINATION share/rfistrategies)
+install(FILES share/LOFAR-LBA-default.rfis share/LOFAR-HBA-default.rfis
+ DESTINATION share/rfistrategies)
diff --git a/base/etc/CMakeLists.txt b/base/etc/CMakeLists.txt
index ce203d7616d9d31169e9f64db88f31ad08b43c38..569deaf21576fbf5800b82b569a50144732b08de 100644
--- a/base/etc/CMakeLists.txt
+++ b/base/etc/CMakeLists.txt
@@ -2,6 +2,4 @@
# SPDX-License-Identifier: GPL-3.0-or-later
# Logger configuration
-install(FILES
- DPPP.log_prop
- DESTINATION etc)
+install(FILES DPPP.log_prop DESTINATION etc)
diff --git a/ddecal/test/integration/CMakeLists.txt b/ddecal/test/integration/CMakeLists.txt
index 7eee00920deee349435fa4f360f12cb2fcdfdaa7..4057a569e60ad2834523861b979458f0f3f0f432 100644
--- a/ddecal/test/integration/CMakeLists.txt
+++ b/ddecal/test/integration/CMakeLists.txt
@@ -5,17 +5,16 @@ configure_file(testInit.sh.in testInit.sh)
# The 'source' symbolic link simplifies running the tests manually inside
# ${CMAKE_CURRENT_BINARY_DIR}: It allows using 'source/tApplyBeam.sh' instead of
-# '../../../../DP3/steps/test/integration/tApplyBeam.sh.
-# (Using 'RESULT', fatal errors won't occur on systems without symlink support.)
+# '../../../../DP3/steps/test/integration/tApplyBeam.sh. (Using 'RESULT', fatal
+# errors won't occur on systems without symlink support.)
if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14")
- file(CREATE_LINK ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/source
- RESULT DUMMY_RESULT SYMBOLIC)
+ file(
+ CREATE_LINK ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/source
+ RESULT DUMMY_RESULT
+ SYMBOLIC)
endif()
-set(INTEGRATION_TESTS
- tDDECal
- tIDGPredict
-)
+set(INTEGRATION_TESTS tDDECal tIDGPredict)
foreach(TEST ${INTEGRATION_TESTS})
# Use ${CMAKE_CURRENT_SOURCE_DIR} instead of 'source' since not all systems
diff --git a/docker/ubuntu_20_04_base b/docker/ubuntu_20_04_base
index bf116824c7f877dd6f0a2e60ae3c8dbad4719883..471d56cfe5c2713c2341ae4b6071f5eccfc8fe33 100644
--- a/docker/ubuntu_20_04_base
+++ b/docker/ubuntu_20_04_base
@@ -50,6 +50,6 @@ RUN export DEBIAN_FRONTEND=noninteractive && apt-get update && \
&& tar xfz /WSRT_Measures.ztar \
&& rm /WSRT_Measures.ztar \
# Install pip dependencies
- && pip3 install gcovr clang-format==9.0.0 h5py \
+ && pip3 install gcovr clang-format==9.0.0 cmake-format h5py \
# build-doc dependencies
autosemver==0.5.5 jsonschema2rst==0.1.0 sphinx sphinx-rtd-theme
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 838f6ffc07006cb89a6b077543efab1de7c21ccc..cc5497431f02c0868da9e9ec0f10a721df7657ab 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -10,43 +10,50 @@ find_package(Doxygen)
if(NOT DP3_VERSION)
# Building docs standalone, get version from top level CMakelists
- FILE(READ "../CMakeLists.txt" TOPLEVEL_CMAKELISTS)
- set(DP3_VERSION_REGEX ".*set\\(DP3_VERSION ([0-9]+)\\.([0-9]+)\\.([0-9]+).*\\)")
- if ("${TOPLEVEL_CMAKELISTS}" MATCHES ${DP3_VERSION_REGEX})
+ file(READ "../CMakeLists.txt" TOPLEVEL_CMAKELISTS)
+ set(DP3_VERSION_REGEX
+ ".*set\\(DP3_VERSION ([0-9]+)\\.([0-9]+)\\.([0-9]+).*\\)")
+ if("${TOPLEVEL_CMAKELISTS}" MATCHES ${DP3_VERSION_REGEX})
set(DP3_VERSION_MAJOR "${CMAKE_MATCH_1}")
set(DP3_VERSION_MINOR "${CMAKE_MATCH_2}")
set(DP3_VERSION_PATCH "${CMAKE_MATCH_3}")
else()
- message(FATAL_ERROR "Failed to parse DP3_VERSION from top level CMakeLists.txt")
+ message(
+ FATAL_ERROR "Failed to parse DP3_VERSION from top level CMakeLists.txt")
endif()
endif()
-
if(DOXYGEN_FOUND)
- configure_file(${CMAKE_CURRENT_LIST_DIR}/doxygen/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
- add_custom_target(doc
+ configure_file(${CMAKE_CURRENT_LIST_DIR}/doxygen/Doxyfile.in
+ ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+ add_custom_target(
+ doc
${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating API documentation with Doxygen" VERBATIM)
+ COMMENT "Generating API documentation with Doxygen"
+ VERBATIM)
endif(DOXYGEN_FOUND)
find_package(Sphinx)
-find_program(JSONSCHEMA2RST_EXECUTABLE
- NAMES jsonschema2rst
- DOC "Path to jsonschema2rst executable")
+find_program(
+ JSONSCHEMA2RST_EXECUTABLE
+ NAMES jsonschema2rst
+ DOC "Path to jsonschema2rst executable")
if(SPHINX_FOUND AND JSONSCHEMA2RST_EXECUTABLE)
set(SPHINX_SOURCE ${CMAKE_CURRENT_BINARY_DIR})
set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}/docs/)
- configure_file(${CMAKE_CURRENT_LIST_DIR}/index.rst ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
- configure_file(${CMAKE_CURRENT_LIST_DIR}/conf.py ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
- add_custom_target(userdoc
- COMMAND
- ${SPHINX_EXECUTABLE} -b html
- ${SPHINX_SOURCE} ${SPHINX_BUILD}
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating user documentation with Sphinx"
- )
+ configure_file(${CMAKE_CURRENT_LIST_DIR}/index.rst
+ ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
+ configure_file(${CMAKE_CURRENT_LIST_DIR}/conf.py ${CMAKE_CURRENT_BINARY_DIR}
+ COPYONLY)
+ add_custom_target(
+ userdoc
+ COMMAND ${SPHINX_EXECUTABLE} -b html ${SPHINX_SOURCE} ${SPHINX_BUILD}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMENT "Generating user documentation with Sphinx")
else()
- message("Sphinx (sphinx-build) and jsonschema2rst are necessary for building user docs")
+ message(
+ "Sphinx (sphinx-build) and jsonschema2rst are necessary for building user docs"
+ )
endif(SPHINX_FOUND AND JSONSCHEMA2RST_EXECUTABLE)
diff --git a/scripts/format.sh b/scripts/format.sh
new file mode 100644
index 0000000000000000000000000000000000000000..5c0d8261a9dc56936931f97f225ebea8fca48a85
--- /dev/null
+++ b/scripts/format.sh
@@ -0,0 +1,78 @@
+# Copyright (C) 2021 ASTRON (Netherlands Institute for Radio Astronomy)
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+# format.sh: Formats source code in a repository in accordance with
+# .clang-format and .cmake-format.py files.
+#
+# This script uses the following variables:
+# - SOURCE_DIR: The directory that contains the source files.
+# - EXCLUDE_DIRS: (Optional) directories that must be excluded from formatting.
+# These paths are relative to SOURCE_DIR.
+# - CXX_SOURCES: Patterns of the C++ files, which clang-format should format.
+# - CMAKE_SOURCES: Patterns of the CMake files, which cmake-format should format.
+#
+# A repository that uses format.sh should define its own run-format.sh script
+# that defines these variables and then sources this script.
+# If you want to automatically check formatting in each commit, include the line
+# "./scripts/run-format.sh" to .git/hooks/pre-commit
+# and make sure pre-commit is an executable shell script.
+
+# Disable globbing
+set -e -f
+
+# Check arguments
+if [ -z "$SOURCE_DIR" -o -z "$CXX_SOURCES" -o -z "$CMAKE_SOURCES" ]; then
+ echo "Please define SOURCE_DIR, CXX_SOURCES and CMAKE_SOURCES when using $BASH_SOURCE"
+ exit 1
+fi
+
+# Detect run environment.
+if [ -n "$CI" ]; then
+ DRYRUN=" (dry run on CI)"
+elif [ -n "$GIT_AUTHOR_DATE" ]; then
+ DRYRUN=" (dry run in git hook)"
+fi
+
+# print in bold-face
+echo -e "\e[1mRunning formatters$DRYRUN...\e[0m"
+
+# Convert SOURCES into "-name ext1 -o -name ext2 -o name ext3 ..."
+CXX_FIND_NAMES="-name ${CXX_SOURCES[0]}"
+for i in `seq 1 $((${#CXX_SOURCES[*]} - 1))`; do
+ CXX_FIND_NAMES+=" -o -name ${CXX_SOURCES[$i]}"
+done
+
+CMAKE_FIND_NAMES="-name ${CMAKE_SOURCES[0]}"
+for i in `seq 1 $((${#CMAKE_SOURCES[*]} - 1))`; do
+ CMAKE_FIND_NAMES+=" -o -name ${CMAKE_SOURCES[$i]}"
+done
+
+# Convert EXCLUDE_DIRS into "-path ./dir1 -prune -o -path ./dir2 -prune -o ..."
+FIND_EXCLUDES=
+for e in ${EXCLUDE_DIRS[*]}; do
+ FIND_EXCLUDES+="-path ./$e -prune -o "
+done
+
+cd $SOURCE_DIR
+CXX_FILES=$(find . $FIND_EXCLUDES -type f \( $CXX_FIND_NAMES \) -print)
+CMAKE_FILES=$(find . $FIND_EXCLUDES -type f \( $CMAKE_FIND_NAMES \) -print)
+
+if [ -n "$DRYRUN" ]; then
+ # If the clang-format xml has no replacement entries, all files are formatted.
+ if !(clang-format -style=file --output-replacements-xml $CXX_FILES |
+ grep -q "<replacement ") && cmake-format --check $CMAKE_FILES; then
+ # print in bold-face green
+ echo -e "\e[1m\e[32mGreat job, all files are properly formatted!\e[0m"
+ exit 0;
+ else
+ # Print in bold-face red
+ echo -e "\e[1m\e[31mAt least one file is not properly formatted!\e[0m"
+ echo -e "\e[1m\e[31mRun $0 for formatting all files!\e[0m"
+ exit 1;
+ fi
+else
+ clang-format -i -style=file $CXX_FILES
+ cmake-format -i $CMAKE_FILES
+ # print in bold-face
+ echo -e "\e[1mSuccessfully formatted all files.\e[0m"
+fi
diff --git a/scripts/run-clang-format.sh b/scripts/run-clang-format.sh
deleted file mode 100755
index 7a939c468a88a08ad5a92bf8eadc31cb80349a2a..0000000000000000000000000000000000000000
--- a/scripts/run-clang-format.sh
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/bin/bash
-
-# Copyright (C) 2020 ASTRON (Netherlands Institute for Radio Astronomy)
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-# run-clang-format.sh: Formats source code in this repo in accordance with .clang-format file.
-#
-# To hook this script to pre-commit include the line
-# "./scripts/run-clang-format.sh" to .git/hooks/pre-commit
-# and make sure pre-commit is an executable shell script.
-
-# Disable globbing
-set -e -f
-
-#Script configuration for this repo. Adjust it when copying to a different repo.
-
-#The directory that contains the source files, which clang-format should format.
-SOURCE_DIR=$(dirname "$0")/..
-
-#Directories that must be excluded from formatting. These paths are
-#relative to SOURCE_DIR.
-EXCLUDE_DIRS=(external build)
-
-#The extensions of the source files, which clang-format should format.
-SOURCE_EXT=(*.cc *.h)
-
-#End script configuration.
-
-# Detect run environment.
-if [ -n "$CI" ]; then
- DRYRUN=" (dry run on CI)"
-elif [ -n "$GIT_AUTHOR_DATE" ]; then
- DRYRUN=" (dry run in git hook)"
-fi
-
-# print in bold-face
-echo -e "\e[1mRunning clang-format$DRYRUN...\e[0m"
-
-# Convert SOURCE_EXT into "-name ext1 -o -name ext2 -o name ext3 ..."
-FIND_NAMES="-name ${SOURCE_EXT[0]}"
-for i in `seq 1 $((${#SOURCE_EXT[*]} - 1))`; do
- FIND_NAMES+=" -o -name ${SOURCE_EXT[$i]}"
-done
-
-# Convert EXCLUDE_DIRS into "-path ./dir1 -prune -o -path ./dir2 -prune -o ..."
-FIND_EXCLUDES=
-for e in ${EXCLUDE_DIRS[*]}; do
- FIND_EXCLUDES+="-path ./$e -prune -o "
-done
-
-cd $SOURCE_DIR
-FILES=$(find . $FIND_EXCLUDES -type f \( $FIND_NAMES \) -print)
-
-if [ -n "$DRYRUN" ]; then
- # If the xml has no replacement entries, all files are formatted.
- if clang-format -style=file --output-replacements-xml $FILES |
- grep -q "<replacement "; then
- # Print in bold-face red
- echo -e "\e[1m\e[31mAt least one file is not properly formatted!\e[0m"
- echo -e "\e[1m\e[31mRun $0 for formatting all files!\e[0m"
- exit 1;
- else
- # print in bold-face green
- echo -e "\e[1m\e[32mGreat job, all files are properly formatted!\e[0m"
- exit 0;
- fi
-else
- clang-format -i -style=file $FILES
- # print in bold-face
- echo -e "\e[1mSuccessfully formatted all files.\e[0m"
-fi
diff --git a/scripts/run-format.sh b/scripts/run-format.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f851bdf4b0172be062ae5b1d23f98c394ef690a0
--- /dev/null
+++ b/scripts/run-format.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Copyright (C) 2021 ASTRON (Netherlands Institute for Radio Astronomy)
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+#Script configuration for this repo. Adjust it when copying to a different repo.
+
+#The directory that contains the source files.
+SOURCE_DIR=$(dirname "$0")/..
+
+#Directories that must be excluded from formatting. These paths are
+#relative to SOURCE_DIR.
+EXCLUDE_DIRS=(external build CMake)
+
+#The patterns of the C++ source files, which clang-format should format.
+CXX_SOURCES=(*.cc *.h)
+
+#The patterns of the CMake source files, which cmake-format should format.
+CMAKE_SOURCES=(CMakeLists.txt *.cmake)
+
+#End script configuration.
+
+#The common formatting script has further documentation.
+source $(dirname "$0")/format.sh
diff --git a/steps/test/integration/CMakeLists.txt b/steps/test/integration/CMakeLists.txt
index 397277dbd0d1d87ee3fc3ffbded2c72cbaa51d3f..6aff263f202ca4779f404efd8daef02a94449c9a 100644
--- a/steps/test/integration/CMakeLists.txt
+++ b/steps/test/integration/CMakeLists.txt
@@ -5,25 +5,26 @@ configure_file(testInit.sh.in testInit.sh)
# The 'source' symbolic link simplifies running the tests manually inside
# ${CMAKE_CURRENT_BINARY_DIR}: It allows using 'source/tApplyBeam.sh' instead of
-# '../../../../DP3/steps/test/integration/tApplyBeam.sh.
-# (Using 'RESULT', fatal errors won't occur on systems without symlink support.)
+# '../../../../DP3/steps/test/integration/tApplyBeam.sh. (Using 'RESULT', fatal
+# errors won't occur on systems without symlink support.)
if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.14")
- file(CREATE_LINK ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/source
- RESULT DUMMY_RESULT SYMBOLIC)
+ file(
+ CREATE_LINK ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/source
+ RESULT DUMMY_RESULT
+ SYMBOLIC)
endif()
set(INTEGRATION_TESTS
- tApplyBeam
- tApplyCal2
- tBdaPredict
- tDemix
- tGainCal
- tGainCalH5Parm
- tMultiApplyCal
- tPredict
- tReadOnly
- tSplit
-)
+ tApplyBeam
+ tApplyCal2
+ tBdaPredict
+ tDemix
+ tGainCal
+ tGainCalH5Parm
+ tMultiApplyCal
+ tPredict
+ tReadOnly
+ tSplit)
foreach(TEST ${INTEGRATION_TESTS})
# Use ${CMAKE_CURRENT_SOURCE_DIR} instead of 'source' since not all systems