Release Appositionizer

.bbp-project.yaml

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+tools:
+  ClangFormat:
+    # >= 12.0.1 <12.0.2
+    version: ~=12.0.1

.ci/test_circuit1k-merged.sh

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+export BASE=$DATADIR/cellular/circuit-1k
+
+echo "SLURM_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK"
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export MPI_OPENMP_INTEROP=Yes
+
+srun appositionizer \
+    --tmp-dir=$PWD/tmp_dir \
+    --output=$PWD \
+    --appositionspace=axodendritic \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config_merged.json
+
+set +x
+hash module 2> /dev/null || . /etc/profile.d/modules.sh
+. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
+module load unstable py-pytouchreader
+module list
+set -xeo pipefail
+touchdiff --full --segment-precision 1 --distance-margin 1.0 --distance-precision=0.1 {$BASE/touches/binary,.}/touches.0 | head -n 500

.ci/test_circuit1k-sonata.sh

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+export BASE=$DATADIR/cellular/circuit-1k
+
+srun appositionizer \
+    --output=$PWD \
+    --output-population=All \
+    --appositionspace=axodendritic \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config.json
+
+set +x
+hash module 2> /dev/null || . /etc/profile.d/modules.sh
+. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
+module load unstable py-functionalizer parquetk
+module list
+set -xeo pipefail
+python ${SPACK_SOURCE_DIR}/tools/sonata_compare.py $BASE/touches/td_edges.h5 edges.h5

.ci/test_circuit1k.sh

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+export BASE=$DATADIR/cellular/circuit-1k
+
+srun appositionizer \
+    --output=$PWD \
+    --appositionspace=axodendritic \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config.json
+
+set +x
+hash module 2> /dev/null || . /etc/profile.d/modules.sh
+. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
+module load unstable py-pytouchreader
+module list
+set -xeo pipefail
+touchdiff --full --segment-precision 1 --distance-margin 1.0 --distance-precision=0.1 {$BASE/touches/binary,.}/touches.0 | head -n 500

.ci/test_circuit2k.sh

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+export BASE=$DATADIR/cellular/circuit-2k
+
+srun appositionizer \
+    --output=$PWD \
+    --appositionspace=axodendritic \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config.json
+
+set +x
+hash module 2> /dev/null || . /etc/profile.d/modules.sh
+. /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
+module load unstable py-pytouchreader
+module list
+set -xeo pipefail
+touchdiff --full --segment-precision 1 --distance-margin 1.0 --distance-precision=0.1 {$BASE/touches/binary,.}/touches.0 | head -n 500

.ci/test_nodesets.sh

@@ -0,0 +1,12 @@
+export BASE=$DATADIR/cellular/circuit-1k
+
+srun appositionizer \
+    --output=$PWD \
+    --from-nodeset test \
+    --to-nodeset test \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config.json |& tee output
+
+set +x
+
+grep "Number of cells written: 50" output &> /dev/null || exit 1

.ci/test_population.sh

@@ -0,0 +1,14 @@
+export BASE=$DATADIR/cellular/circuit-1k
+
+srun appositionizer \
+    --output=$PWD \
+    --from head \
+    --to tail \
+    --appositionspace=axodendritic \
+    --recipe $BASE/bioname/recipe.json \
+    --circuit-config $BASE/circuit_config_multipop.json |& tee output
+
+set +x
+
+# Output for 550 edeges between the (original 1k) ids <50 and >=900
+grep "Number of edeges written: 550" output &> /dev/null || exit 1

.clang-format

@@ -0,0 +1,93 @@
+---
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignConsecutiveMacros: true
+AlignEscapedNewlinesLeft: true
+AlignOperands: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BasedOnStyle: WebKit
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass: false
+  AfterControlStatement: false
+  AfterEnum: false
+  AfterExternBlock: false
+  AfterFunction: false
+  AfterNamespace: false
+  AfterStruct: false
+  AfterUnion: false
+  BeforeCatch: false
+  BeforeElse: false
+BreakBeforeBraces: Custom
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: true
+BreakStringLiterals: true
+ColumnLimit: 100
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+Language: Cpp
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+PenaltyBreakAssignment: 40
+PenaltyBreakBeforeFirstCallParameter: 100
+PenaltyBreakComment: 60
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+PointerBindsToType: true
+ReflowComments:  true
+SortIncludes: true
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: false
+SpaceBeforeInheritanceColon: false
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: false
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false # '< ' style
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false # '(' style
+SpacesInSquareBrackets: false
+Standard: c++17
+TabWidth: 4
+UseTab: Never
+...

.gitexternals

@@ -0,0 +1,2 @@
+# -*- mode: cmake -*-
+# CMake/common https://github.com/Eyescale/CMake.git 5397ec8

.gitignore

@@ -0,0 +1,14 @@
+*.bak
+.tox
+docs/build
+docs/source/_static/doxygen
+.idea/
+cmake-build-debug/
+tags
+spack-*
+.spack*
+.vscode
+.ccls-cache
+.bbp-project-venv
+build*
+deeps

.gitmodules

@@ -0,0 +1,12 @@
+[submodule "deps/hpc-coding-conventions"]
+	path = deps/hpc-coding-conventions
+	url = https://github.com/BlueBrain/hpc-coding-conventions.git
+[submodule "deps/cli11"]
+	path = deps/cli11
+	url = https://github.com/CLIUtils/CLI11.git
+[submodule "deps/fmt"]
+	path = deps/fmt
+	url = https://github.com/fmtlib/fmt.git
+[submodule "deps/nlohmann-json"]
+	path = deps/nlohmann-json
+	url = https://github.com/nlohmann/json.git

.gitreview

@@ -0,0 +1,5 @@
+[gerrit]
+host=bbpcode.epfl.ch
+project=building/TouchDetector
+defaultbranch=master
+port=22

CMake/config/CompilerFlagsHelpers.cmake

@@ -0,0 +1,150 @@
+# CompilerFlagsHelpers.cmake
+#
+# set of Convenience functions for portable compiler flags
+#
+# License: BSD 3
+#
+# Copyright (c) 2016, Adrien Devresse 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.
+#
+# 1. 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.
+#
+# 1. Neither the name of the copyright holder nor the names of its contributors may be used to
+#   endorse or promote products derived from this software without specific prior written
+#   permission.
+#
+# 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.
+
+set(SUPPORTED_COMPILER_LANGUAGE_LIST "C;CXX")
+
+# detect compiler
+foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
+
+  if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID STREQUAL "XL")
+    set(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_XLC ON)
+  elseif(CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID STREQUAL "Intel")
+    set(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_ICC ON)
+  elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
+    set(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_MSVC)
+  elseif(${CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID} STREQUAL "Clang")
+    set(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_CLANG ON)
+  else(CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID STREQUAL "GNU")
+    set(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_GCC ON)
+  endif()
+
+endforeach()
+
+foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
+  # preset default
+  set(CMAKE_${COMPILER_LANGUAGE}_FORTIFY "")
+
+  # XLC compiler
+  if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_XLC)
+
+    # XLC -qinfo=all is awfully verbose on any platforms that use the GNU STL Enable by default only
+    # the relevant one
+    set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL "-qformat=all -qinfo=lan:trx:ret:zea:cmp:ret")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_DEBUGINFO_FLAGS "-g")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NONE "-O0")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NORMAL "-O2")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_AGGRESSIVE "-O3")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_FASTEST "-O5")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_STACK_PROTECTION "-qstackprotect")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_FORTIFY "")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_POSITION_INDEPENDANT "-qpic=small")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_VECTORIZE "-qhot")
+
+    # Microsoft compiler
+  elseif(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_MSVC)
+
+    set(CMAKE_${COMPILER_LANGUAGE}_DEBUGINFO_FLAGS "-Zi")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NONE "")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NORMAL "-O2")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_AGGRESSIVE "-O2")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_FASTEST "-O2")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_STACK_PROTECTION "-GS")
+
+    # enable by default on MSVC
+    set(CMAKE_${COMPILER_LANGUAGE}_POSITION_INDEPENDANT "")
+
+    # ICC intel
+  elseif(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_ICC)
+
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NONE "-O0")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NORMAL "-O2")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_AGGRESSIVE "-O3")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_FASTEST "-Ofast")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_FORTIFY "-D_FORTIFY_SOURCE=2")
+    set(CMAKE_${COMPILER_LANGUAGE}_STACK_PROTECTION "-fstack-protector-strong")
+
+    # GCC, CLANG
+  elseif(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_CLANG OR CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_GCC)
+
+    set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL "-Wall -Wextra")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_DEBUGINFO_FLAGS "-g")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NONE "-O0")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_NORMAL "-O2")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_AGGRESSIVE "-O3")
+    set(CMAKE_${COMPILER_LANGUAGE}_OPT_FASTEST "-Ofast -march=native")
+
+    if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_GCC
+       AND (CMAKE_${COMPILER_LANGUAGE}_COMPILER_VERSION VERSION_GREATER "4.9.0"))
+      set(CMAKE_${COMPILER_LANGUAGE}_STACK_PROTECTION "-fstack-protector-strong")
+    else()
+      set(CMAKE_${COMPILER_LANGUAGE}_STACK_PROTECTION "-fstack-protector")
+    endif()
+
+    set(CMAKE_${COMPILER_LANGUAGE}_FORTIFY "-D_FORTIFY_SOURCE=2")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_POSITION_INDEPENDANT "-fPIC")
+
+    set(CMAKE_${COMPILER_LANGUAGE}_VECTORIZE "-ftree-vectorize")
+
+    if(CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_GCC
+       AND (CMAKE_${COMPILER_LANGUAGE}_COMPILER_VERSION VERSION_GREATER "4.7.0"))
+      set(CMAKE_${COMPILER_LANGUAGE}_LINK_TIME_OPT "-flto")
+    endif()
+
+    if((CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "^ppc")
+       OR (CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "^power"))
+      # ppc arch do not support -march= syntax
+      set(CMAKE_${COMPILER_LANGUAGE}_GEN_NATIVE "-mcpu=native")
+    else()
+      set(CMAKE_${COMPILER_LANGUAGE}_GEN_NATIVE "-march=native")
+    endif()
+
+  else() # rest of the world : Do nothing
+
+  endif()
+
+  # Common to all
+
+  # disable assert
+  set(CMAKE_${COMPILER_LANGUAGE}_DISABLE_ASSERT "-DNDEBUG")
+
+endforeach()