pax_global_header 0000666 0000000 0000000 00000000064 14420461415 0014513 g ustar 00root root 0000000 0000000 52 comment=f729744ef92891a0417b8298e8a6978f20017f90
nmodl-0.6/ 0000775 0000000 0000000 00000000000 14420461415 0012471 5 ustar 00root root 0000000 0000000 nmodl-0.6/.bbp-project.yaml 0000664 0000000 0000000 00000000503 14420461415 0015640 0 ustar 00root root 0000000 0000000 tools:
ClangFormat:
enable: True
exclude:
match:
- ext/.*
- src/language/templates/*
ClangTidy:
enable: true
option: ''
exclude:
match:
- src/language/templates/*
CMakeFormat:
enable: True
exclude:
match:
- ext/.*
- src/language/templates/*
nmodl-0.6/.clang-format.changes 0000664 0000000 0000000 00000000062 14420461415 0016451 0 ustar 00root root 0000000 0000000 StatementMacros: [nrn_pragma_acc, nrn_pragma_omp]
nmodl-0.6/.clang-tidy 0000664 0000000 0000000 00000001315 14420461415 0014525 0 ustar 00root root 0000000 0000000 Checks: >
boost-*,
bugprone-*,
clang-analyzer-*,
cppcoreguidelines-*,
misc-*,
mpi-*,
performance-*,
portability-*,
readability-*,
-bugprone-easily-swappable-parameters,
-bugprone-exception-escape,
-cppcoreguidelines-owning-memory,
-cppcoreguidelines-pro-bounds-array-to-pointer-decay,
-misc-no-recursion,
-misc-non-private-member-variables-in-classes,
-readability-else-after-return,
-readability-identifier-length,
-readability-implicit-bool-conversion,
-readability-isolate-declaration,
-readability-qualified-auto,
-readability-uppercase-literal-suffix,
CheckOptions:
- key: readability-function-cognitive-complexity.IgnoreMacros
value: true
FormatStyle: none
nmodl-0.6/.github/ 0000775 0000000 0000000 00000000000 14420461415 0014031 5 ustar 00root root 0000000 0000000 nmodl-0.6/.github/problem-matchers/ 0000775 0000000 0000000 00000000000 14420461415 0017275 5 ustar 00root root 0000000 0000000 nmodl-0.6/.github/problem-matchers/address-leak.json 0000664 0000000 0000000 00000000457 14420461415 0022535 0 ustar 00root root 0000000 0000000
{
"problemMatcher": [
{
"owner": "asan-problem-matcher",
"severity": "warning",
"pattern": [
{
"regexp": "^.*AddressSanitizer: (.*)$",
"message": 1
}
]
}
]
}
nmodl-0.6/.github/problem-matchers/gcc.json 0000664 0000000 0000000 00000001011 14420461415 0020715 0 ustar 00root root 0000000 0000000 {
"__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule",
"problemMatcher": [
{
"owner": "gcc-problem-matcher",
"pattern": [
{
"regexp": "^\\.\\./(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$",
"file": 1,
"line": 2,
"column": 3,
"severity": 4,
"message": 5
}
]
}
]
}
nmodl-0.6/.github/problem-matchers/undefined.json 0000664 0000000 0000000 00000001017 14420461415 0022130 0 ustar 00root root 0000000 0000000 {
"problemMatcher": [
{
"owner": "ubsan-problem-matcher",
"severity": "warning",
"pattern": [
{
"regexp": "^.*\\/(src\\/.*):(\\d+):(\\d+): runtime error: (.*)$",
"file": 1,
"line": 2,
"column": 3,
"message": 4
},
{
"regexp": "^.*UndefinedBehaviorSanitizer:.*$"
}
]
}
]
}
nmodl-0.6/.github/workflows/ 0000775 0000000 0000000 00000000000 14420461415 0016066 5 ustar 00root root 0000000 0000000 nmodl-0.6/.github/workflows/coverage.yml 0000664 0000000 0000000 00000005137 14420461415 0020412 0 ustar 00root root 0000000 0000000 name: Coverage
concurrency:
group: ${{ github.workflow }}#${{ github.ref }}
cancel-in-progress: true
on:
push:
branches:
- master
- live-debug*
- release/**
pull_request:
branches:
- master
- release/**
env:
CMAKE_BUILD_PARALLEL_LEVEL: 3
CTEST_PARALLEL_LEVEL: 1
DESIRED_CMAKE_VERSION: 3.15.0
PYTHON_VERSION: 3.8
jobs:
coverage:
runs-on: ubuntu-20.04
name: "Coverage Test"
steps:
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v1
with:
cmake-version: ${{ env.DESIRED_CMAKE_VERSION }}
- name: Install packages
run: |
sudo apt-get install bison ccache flex lcov libfl-dev ninja-build \
python3-dev python3-pip
shell: bash
- name: Set up Python3
uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
- uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Install Python3 dependencies
working-directory: ${{runner.workspace}}/nmodl
run: |
pip3 install -U pip setuptools scikit-build
pip3 install --user -r requirements.txt
- name: Restore compiler cache
uses: actions/cache@v3
with:
path: |
${{runner.workspace}}/ccache
key: cov-${{github.ref}}-${{github.sha}}
restore-keys: |
cov-${{github.ref}}-
cov-
- name: Build and Test for Coverage
id: codecov
shell: bash
working-directory: ${{runner.workspace}}/nmodl
run: |
mkdir build && cd build
cmake .. -G Ninja \
-DPYTHON_EXECUTABLE=$(which python3) \
-DCMAKE_BUILD_TYPE=Debug \
-DCMAKE_CXX_FLAGS="-coverage" \
-DCMAKE_CXX_COMPILER_LAUNCHER=ccache
ccache -z
ccache -s
cmake --build .
ccache -s
(cd ..; lcov --capture --initial --directory . --no-external --output-file build/coverage-base.info --exclude "*/ext/*")
ctest --output-on-failure
(cd ..; lcov --capture --directory . --no-external --output-file build/coverage-run.info --exclude "*/ext/*")
lcov --add-tracefile coverage-base.info --add-tracefile coverage-run.info --output-file coverage.info
lcov --list coverage.info
env:
CCACHE_DIR: ${{runner.workspace}}/ccache
- uses: codecov/codecov-action@v3
with:
files: ./build/coverage.info
fail_ci_if_error: true
verbose: true
token: ${{ secrets.CODECOV_TOKEN }}
nmodl-0.6/.github/workflows/formatting.yml 0000664 0000000 0000000 00000001145 14420461415 0020764 0 ustar 00root root 0000000 0000000 name: Check formatting
concurrency:
group: ${{ github.workflow }}#${{ github.ref }}
cancel-in-progress: true
on:
pull_request:
branches:
- master
- release/**
jobs:
all:
name: C/C++, CMake and Python
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- name: Update submodule
working-directory: ${{runner.workspace}}/nmodl
run: git submodule update --init cmake/hpc-coding-conventions
- name: Check formatting
working-directory: ${{runner.workspace}}/nmodl
run: cmake/hpc-coding-conventions/bin/format -v --dry-run
nmodl-0.6/.github/workflows/nmodl-ci.yml 0000664 0000000 0000000 00000014267 14420461415 0020325 0 ustar 00root root 0000000 0000000 name: NMODL CI
concurrency:
group: ${{ github.workflow }}#${{ github.ref }}
cancel-in-progress: true
on:
push:
branches:
- master
- release/**
pull_request:
branches:
- master
- release/**
env:
CTEST_PARALLEL_LEVEL: 1
PYTHON_VERSION: 3.8
DESIRED_CMAKE_VERSION: 3.15.0
jobs:
ci:
runs-on: ${{matrix.config.os}}
name: ${{toJson(matrix.config)}}
strategy:
matrix:
include:
- config:
os: ubuntu-20.04
- config:
flag_warnings: ON
os: ubuntu-22.04
- config:
os: macos-11
# TODO: might be interesting to add the thread sanitizer too
- config:
os: ubuntu-22.04
# Hyphens here will be replaced with commas before the value is
# passed to NMODL_SANITIZERS
sanitizer: address-leak
- config:
flag_warnings: ON
os: ubuntu-22.04
sanitizer: undefined
fail-fast: true
steps:
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v1
with:
cmake-version: ${{ env.DESIRED_CMAKE_VERSION }}
- name: Install homebrew packages
if: startsWith(matrix.config.os, 'macOS')
run: |
brew install ccache coreutils bison boost flex ninja
echo /usr/local/opt/flex/bin:/usr/local/opt/bison/bin >> $GITHUB_PATH
# Taken from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
shell: bash
- name: Install apt packages
if: startsWith(matrix.config.os, 'ubuntu')
run: |
sudo apt-get install bison ccache flex libfl-dev ninja-build python3-dev python3-pip
# Taken from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV
shell: bash
- name: Set up Python3
uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
- uses: actions/checkout@v3
- name: Install Python3 dependencies
working-directory: ${{runner.workspace}}/nmodl
run: |
python3 -m pip install -U pip setuptools
python3 -m pip install --user -r requirements.txt
- name: Register compiler warning problem matcher
if: ${{matrix.config.flag_warnings == 'ON'}}
run: echo "::add-matcher::.github/problem-matchers/gcc.json"
- name: Register sanitizer problem matcher
if: ${{matrix.config.sanitizer}}
run: echo "::add-matcher::.github/problem-matchers/${{matrix.config.sanitizer}}.json"
- name: Configure
shell: bash
working-directory: ${{runner.workspace}}/nmodl
run: |
echo "------- Configure -------"
mkdir build && pushd build
cmake_args=(-G Ninja
-DPYTHON_EXECUTABLE=$(which python3) \
-DCMAKE_INSTALL_PREFIX=$INSTALL_DIR)
if [[ -n "${{matrix.config.flag_warnings}}" ]]; then
cmake_args+=(-DNMODL_EXTRA_CXX_FLAGS="-Wall \
-Wno-reorder \
-Wno-unknown-pragmas \
-Wno-sign-compare \
-Wno-overloaded-virtual")
fi
if [[ -n "${{matrix.config.sanitizer}}" ]]; then
cmake_args+=(-DCMAKE_BUILD_TYPE=Custom \
-DCMAKE_CXX_FLAGS="-O1 -g" \
-DNMODL_SANITIZERS=$(echo ${{matrix.config.sanitizer}} | sed -e 's/-/,/g'))
CXX=$(command -v clang++-14)
else
CXX=${CXX:-g++}
fi
cmake_args+=(-DCMAKE_CXX_COMPILER=${CXX} \
-DCMAKE_CXX_COMPILER_LAUNCHER=ccache)
cmake .. "${cmake_args[@]}"
env:
INSTALL_DIR: ${{ runner.workspace }}/install
- name: Dump config dictionary
run: |
cat << EOF > matrix.json
${{toJSON(matrix.config)}}
EOF
echo matrix.config JSON:
cat matrix.json
echo -----
- name: Restore compiler cache
uses: pat-s/always-upload-cache@v3
with:
path: |
${{runner.workspace}}/ccache
key: ${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}}
restore-keys: |
${{hashfiles('matrix.json')}}-${{github.ref}}-
${{hashfiles('matrix.json')}}-
- name: Build, Test and Install
shell: bash
working-directory: ${{runner.workspace}}/nmodl/build
env:
CCACHE_BASEDIR: ${{runner.workspace}}/nmodl
CCACHE_DIR: ${{runner.workspace}}/ccache
run: |
if ccache --version | grep -E '^ccache version 4\.(4|4\.1)$'
then
echo "------- Disable ccache direct mode -------"
# https://github.com/ccache/ccache/issues/935
export CCACHE_NODIRECT=1
fi
echo "------- Building -------"
ccache -z
# Older versions don't support -v (verbose)
ccache -vs 2>/dev/null || ccache -s
cmake --build .
ccache -vs 2>/dev/null || ccache -s
echo "------- Testing -------"
ctest --output-on-failure -T Test
echo "------- Installing -------"
cmake --build . --target install
- uses: actions/upload-artifact@v3
with:
name: ctest-results-${{hashfiles('matrix.json')}}
path: ${{runner.workspace}}/nmodl/build/Testing/*/Test.xml
# This step will set up an SSH connection on tmate.io for live debugging.
# To enable it, you have to:
# * add 'live-debug-tests' to your PR title
# * push something to your PR branch (note that just re-running disregards the title update)
- name: live debug session on failure (manual steps required, check `nmodl-ci.yml`)
if: failure() && contains(github.event.pull_request.title, 'live-debug-tests')
uses: mxschmitt/action-tmate@v3
timeout-minutes: 60
nmodl-0.6/.github/workflows/nmodl-doc.yml 0000664 0000000 0000000 00000006026 14420461415 0020471 0 ustar 00root root 0000000 0000000 name: NMODL Documentation
concurrency:
group: ${{ github.workflow }}#${{ github.ref }}
cancel-in-progress: true
on:
push:
branches:
- master
- release/**
pull_request:
branches:
- master
- release/**
env:
BUILD_TYPE: Release
PYTHON_VERSION: 3.8
DESIRED_CMAKE_VERSION: 3.15.0
jobs:
ci:
runs-on: ubuntu-20.04
name: documentation
env:
INSTALL_DIR: install
strategy:
fail-fast: true
steps:
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v1
with:
cmake-version: ${{ env.DESIRED_CMAKE_VERSION }}
- name: Install apt packages
run: |
sudo apt-get update
sudo apt-get install bison ccache dvipng doxygen flex libfl-dev \
ninja-build pandoc python3-dev python3-pip \
texlive-latex-recommended texlive-latex-extra
shell: bash
- name: Set up Python3
uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
- uses: actions/checkout@v3
- name: Install Python3 dependencies
working-directory: ${{runner.workspace}}/nmodl
run: |
pip3 install -U pip setuptools scikit-build
pip3 install --user -r requirements.txt
# This step will set up an SSH connection on tmate.io for live debugging.
# To trigger it, simply add 'live-debug-docs' to your last pushed commit message.
- name: live debug session on failure
if: failure() && contains(github.event.head_commit.message, 'live-debug-docs')
uses: mxschmitt/action-tmate@v3
- name: Restore compiler cache
uses: actions/cache@v3
with:
path: |
${{runner.workspace}}/ccache
key: docs-${{github.ref}}-${{github.sha}}
restore-keys: |
docs-${{github.ref}}-
docs-
- name: Documentation
id: documentation
working-directory: ${{runner.workspace}}/nmodl
run: |
echo "------- Build Documentation -------";
ccache -z
ccache -s
python3 setup.py build_ext --inplace docs -j 2 -G Ninja \
-- -DCMAKE_CXX_COMPILER_LAUNCHER=ccache;
ccache -s
cd _skbuild/linux-x86_64-3.8/setuptools/sphinx;
rm -rf doctest doctrees && touch .nojekyll;
echo "" > index.html;
echo ::set-output name=status::done
env:
CCACHE_DIR: ${{runner.workspace}}/ccache
- name: Deploy 🚀
uses: JamesIves/github-pages-deploy-action@v4
if: steps.documentation.outputs.status == 'done' && startsWith(github.ref, 'refs/heads/master')
with:
branch: gh-pages # The branch the action should deploy to.
folder: ${{runner.workspace}}/nmodl/_skbuild/linux-x86_64-3.8/setuptools/sphinx # The folder the action should deploy.
clean: false # Automatically remove deleted files from the deploy branch
nmodl-0.6/.gitignore 0000664 0000000 0000000 00000001021 14420461415 0014453 0 ustar 00root root 0000000 0000000 *build*
spconfig.*
*~
.DS_Store
*.swp
.idea
docs/Doxyfile
*.srctrl*
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# HPC coding conventions
.clang-format
.cmake-format.yaml
.pre-commit-config.yaml
.ipynb_checkpoints
.bbp-project-venv/
nmodl-0.6/.gitlab-ci.yml 0000664 0000000 0000000 00000005264 14420461415 0015134 0 ustar 00root root 0000000 0000000 include:
- project: hpc/gitlab-pipelines
file:
- spack-build-components.gitlab-ci.yml
- github-project-pipelines.gitlab-ci.yml
- project: hpc/gitlab-upload-logs
file: enable-upload.yml
variables:
CVF_BRANCH:
description: Branch of the channel validation framework (CVF) to trigger the CI of
value: main
SPACK_BRANCH:
description: Branch of BlueBrain Spack to use for the CI pipeline
value: develop
SPACK_DEPLOYMENT_SUFFIX:
description: Extra path component used when finding deployed software. Set to something like `pulls/1497` use software built for https://github.com/BlueBrain/spack/pull/1497. You probably want to set SPACK_BRANCH to the branch used in the relevant PR if you set this.
value: ''
trigger cvf:
# Stop the globally-defined CVF_BRANCH above from being set in the child pipeline
inherit:
variables: false
needs: [spack_setup] # for SPACK_SETUP_COMMIT_MAPPING_URL
stage: .pre
rules:
# Don't run on PRs targeting the LLVM development branch
- if: '$CI_EXTERNAL_PULL_REQUEST_TARGET_BRANCH_NAME == "llvm"'
when: never
# Otherwise always run this
- when: always
trigger:
branch: ${CVF_BRANCH}
project: hpc/cvf
# Make the NMODL CI status depend on the CVF CI status
strategy: depend
variables:
# Tell CVF to use the same commits/branches as NMODL.
SPACK_ENV_FILE_URL: $SPACK_SETUP_COMMIT_MAPPING_URL
.spack_nmodl:
variables:
SPACK_PACKAGE: nmodl
SPACK_PACKAGE_SPEC: ~legacy-unit+python
spack_setup:
extends: .spack_setup_ccache
script:
- !reference [.spack_setup_ccache, script]
# Setting CVF_BRANCH in the PR description will cause it to be set in the
# environment of this job, but because we put CVF in
# SPACK_SETUP_IGNORE_PACKAGE_VARIABLES then nothing will be done with it.
- echo "CVF_BRANCH=${CVF_BRANCH}" >> spack_clone_variables.env
variables:
NMODL_COMMIT: ${CI_COMMIT_SHA}
# Enable fetching GitHub PR descriptions and parsing them to find out what
# branches to build of other projects.
PARSE_GITHUB_PR_DESCRIPTIONS: "true"
SPACK_SETUP_IGNORE_PACKAGE_VARIABLES: CVF
build:intel:
extends:
- .spack_build
- .spack_nmodl
variables:
SPACK_PACKAGE_COMPILER: intel
build:nvhpc:
extends:
- .spack_build
- .spack_nmodl
variables:
SPACK_PACKAGE_COMPILER: nvhpc
SPACK_PACKAGE_DEPENDENCIES: ^bison%gcc^flex%gcc^py-jinja2%gcc^py-sympy%gcc^py-pyyaml%gcc
.nmodl_tests:
variables:
# https://github.com/BlueBrain/nmodl/issues/737
bb5_ntasks: 1
test:intel:
extends:
- .ctest
- .nmodl_tests
needs: ["build:intel"]
test:nvhpc:
extends:
- .ctest
- .nmodl_tests
needs: ["build:nvhpc"]
nmodl-0.6/.gitmodules 0000664 0000000 0000000 00000001354 14420461415 0014651 0 ustar 00root root 0000000 0000000 [submodule "ext/pybind11"]
path = ext/pybind11
url = https://github.com/pybind/pybind11.git
[submodule "cmake/hpc-coding-conventions"]
path = cmake/hpc-coding-conventions
url = https://github.com/BlueBrain/hpc-coding-conventions.git
[submodule "ext/cli11"]
path = ext/cli11
url = https://github.com/CLIUtils/CLI11.git
[submodule "ext/spdlog"]
path = ext/spdlog
url = https://github.com/gabime/spdlog
[submodule "ext/fmt"]
path = ext/fmt
url = https://github.com/fmtlib/fmt.git
[submodule "ext/eigen"]
path = ext/eigen
url = https://gitlab.com/libeigen/eigen.git
[submodule "ext/json"]
path = ext/json
url = https://github.com/nlohmann/json.git
[submodule "ext/catch2"]
path = ext/catch2
url = https://github.com/catchorg/Catch2.git
nmodl-0.6/.sanitizers/ 0000775 0000000 0000000 00000000000 14420461415 0014742 5 ustar 00root root 0000000 0000000 nmodl-0.6/.sanitizers/leak.supp 0000664 0000000 0000000 00000000074 14420461415 0016570 0 ustar 00root root 0000000 0000000 leak:nmodl::parser::NmodlParser::parse()
leak:PyInit__nmodl
nmodl-0.6/.sanitizers/undefined.supp 0000664 0000000 0000000 00000000530 14420461415 0017612 0 ustar 00root root 0000000 0000000 implicit-integer-sign-change:double vector[2] Eigen::internal::pabs(double vector[2] const&)
unsigned-integer-overflow:nmodl::fast_math::vexp(double)
unsigned-integer-overflow:nmodl::fast_math::vexpm1(double)
unsigned-integer-overflow:std::mersenne_twister_engine
unsigned-integer-overflow:fmt::v9::detail::make_write_int_arg
nmodl-0.6/AUTHORS.txt 0000664 0000000 0000000 00000000514 14420461415 0014357 0 ustar 00root root 0000000 0000000 Alessandro Cattabiani
Alexandru Săvulescu
Antonio Bellota
Christos Kotsalos
Fernando L. Pereira
Francesco Cremonesi
Ioannis Magkanaris
Jeremy Fouriaux
Jorge Blanco Alonso
Liam Keegan
Matthias Wolf
Michael Hines
Mike Gevaert
Nicolas Cornu
Olli Lupton
Omar Awile
Pramod Kumbhar (maintainer)
Sergio Rivas-Gomez
Tristan Carel
Weina Ji
nmodl-0.6/CMakeLists.txt 0000664 0000000 0000000 00000031013 14420461415 0015227 0 ustar 00root root 0000000 0000000 # =============================================================================
# Copyright (C) 2018-2022 Blue Brain Project
#
# This file is part of NMODL distributed under the terms of the GNU Lesser General Public License.
# See top-level LICENSE file for details.
# =============================================================================
cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
project(NMODL LANGUAGES CXX)
# =============================================================================
# CMake common project settings
# =============================================================================
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
# =============================================================================
# Build options for NMODL
# =============================================================================
option(NMODL_ENABLE_PYTHON_BINDINGS "Enable pybind11 based python bindings" ON)
option(NMODL_ENABLE_LEGACY_UNITS "Use original faraday, R, etc. instead of 2019 nist constants" OFF)
if(NMODL_ENABLE_LEGACY_UNITS)
add_definitions(-DUSE_LEGACY_UNITS)
endif()
set(NMODL_EXTRA_CXX_FLAGS
""
CACHE STRING "Add extra compile flags for NMODL sources")
separate_arguments(NMODL_EXTRA_CXX_FLAGS)
# =============================================================================
# Settings to enable project as submodule
# =============================================================================
set(NMODL_PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
set(NMODL_PROJECT_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR})
set(NMODL_AS_SUBPROJECT OFF)
if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
set(NMODL_AS_SUBPROJECT ON)
# output targets into top level build directory
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
endif()
# =============================================================================
# Compile static libraries with hidden visibility
# =============================================================================
set(CMAKE_CXX_VISIBILITY_PRESET hidden)
# =============================================================================
# Find required packages
# =============================================================================
message(STATUS "CHECKING FOR FLEX/BISON")
find_package(FLEX 2.6 REQUIRED)
find_package(BISON 3.0 REQUIRED)
# =============================================================================
# Include cmake modules. Filenames ensure we always pick up NMODL's versions.
# =============================================================================
include(cmake/ClangTidyHelper.cmake)
include(cmake/CompilerHelper.cmake)
include(cmake/FlexHelper.cmake)
include(cmake/GitRevision.cmake)
include(cmake/PythonLinkHelper.cmake)
include(cmake/RpathHelper.cmake)
include(cmake/ExternalProjectHelper.cmake)
# This should apply to all NMODL targets but should not leak out when NMODL is built as a submodule.
add_compile_options(${NMODL_COMPILER_WARNING_SUPPRESSIONS})
# =============================================================================
# Set the project version now using git
# =============================================================================
project(
NMODL
VERSION ${NMODL_GIT_LAST_TAG}
LANGUAGES CXX)
# =============================================================================
# HPC Coding Conventions
# =============================================================================
# initialize submodule of coding conventions under cmake
if(NOT EXISTS "${PROJECT_SOURCE_DIR}/cmake/hpc-coding-conventions/cpp/CMakeLists.txt")
initialize_submodule("${PROJECT_SOURCE_DIR}/cmake/hpc-coding-conventions")
endif()
set(CODING_CONV_PREFIX NMODL)
add_subdirectory(cmake/hpc-coding-conventions/cpp)
# =============================================================================
# Enable sanitizer support if the NMODL_SANITIZERS variable is set
# =============================================================================
include(cmake/hpc-coding-conventions/cpp/cmake/sanitizers.cmake)
list(APPEND NMODL_EXTRA_CXX_FLAGS ${NMODL_SANITIZER_COMPILER_FLAGS})
# =============================================================================
# Initialize external libraries as submodules
# =============================================================================
set(NMODL_3RDPARTY_DIR ext)
include(cmake/hpc-coding-conventions/cpp/cmake/3rdparty.cmake)
cpp_cc_git_submodule(catch2 BUILD PACKAGE Catch2 REQUIRED)
if(NMODL_3RDPARTY_USE_CATCH2)
# If we're using the submodule then make sure the Catch.cmake helper can be found. In newer
# versions of Catch2, and with hpc-coding-conventions#130, this should just work...
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/ext/catch2/contrib")
endif()
include(Catch)
# If we're being built as a submodule of CoreNEURON then CoreNEURON may have already found/loaded a
# CLI11 submodule.
if(NOT TARGET CLI11::CLI11)
cpp_cc_git_submodule(cli11 BUILD PACKAGE CLI11 REQUIRED)
endif()
# For the moment do not try and use an external Eigen.
cpp_cc_git_submodule(eigen)
cpp_cc_git_submodule(fmt BUILD PACKAGE fmt REQUIRED)
# If we're building from the submodule, make sure we pass -fPIC so that we can link the code into a
# shared library later.
if(NMODL_3RDPARTY_USE_FMT)
set_property(TARGET fmt PROPERTY POSITION_INDEPENDENT_CODE ON)
endif()
if(NOT NMODL_3RDPARTY_USE_FMT
AND ((NMODL_PGI_COMPILER AND CMAKE_CXX_COMPILER_VERSION LESS_EQUAL 22.3.0)
OR CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
message(
WARNING
"fmt might generate issues with NVHPC <=22.3 and Intel compiler when installed with C++11 or later standard enabled"
)
endif()
cpp_cc_git_submodule(json BUILD PACKAGE nlohmann_json REQUIRED)
cpp_cc_git_submodule(pybind11 BUILD PACKAGE pybind11 REQUIRED)
# Tell spdlog not to use its bundled fmt, it should either use the fmt submodule or a truly external
# installation for consistency. This line should be harmless if we use an external spdlog.
set(SPDLOG_FMT_EXTERNAL ON)
cpp_cc_git_submodule(spdlog BUILD PACKAGE spdlog REQUIRED)
if(NMODL_3RDPARTY_USE_SPDLOG)
# See above, same logic as fmt
set_property(TARGET spdlog PROPERTY POSITION_INDEPENDENT_CODE ON)
endif()
# =============================================================================
# Format & execute ipynb notebooks in place (pip install nbconvert clean-ipynb)
# =============================================================================
add_custom_target(
nb-format
jupyter
nbconvert
--to
notebook
--execute
--inplace
--ExecutePreprocessor.timeout=360
"${CMAKE_SOURCE_DIR}/docs/notebooks/*.ipynb"
&&
clean_ipynb
"${CMAKE_SOURCE_DIR}/docs/notebooks/*.ipynb")
# =============================================================================
# Adjust install prefix for wheel
# =============================================================================
if(NOT LINK_AGAINST_PYTHON)
set(NMODL_INSTALL_DIR_SUFFIX "nmodl/.data/")
endif()
# =============================================================================
# Find required python packages
# =============================================================================
message(STATUS "CHECKING FOR PYTHON")
find_package(PythonInterp 3.7 REQUIRED)
include(cmake/hpc-coding-conventions/cpp/cmake/bbp-find-python-module.cmake)
cpp_cc_find_python_module(jinja2 2.9.3 REQUIRED)
cpp_cc_find_python_module(pytest 3.3.0 REQUIRED)
cpp_cc_find_python_module(sympy 1.3 REQUIRED)
cpp_cc_find_python_module(textwrap 0.9 REQUIRED)
cpp_cc_find_python_module(yaml 3.12 REQUIRED)
# =============================================================================
# Compiler specific flags for external submodules
# =============================================================================
if(NMODL_PGI_COMPILER)
# PGI with llvm code generation doesn't have necessary assembly intrinsic headers
add_compile_definitions(EIGEN_DONT_VECTORIZE=1)
# nlohmann/json doesn't check for PGI compiler
add_compile_definitions(JSON_SKIP_UNSUPPORTED_COMPILER_CHECK=1)
endif()
include_directories(${NMODL_PROJECT_SOURCE_DIR} ${NMODL_PROJECT_SOURCE_DIR}/src
${PROJECT_BINARY_DIR}/src)
# generate file with version number from git and nrnunits.lib file path
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/src/config/config.cpp.in
${PROJECT_BINARY_DIR}/src/config/config.cpp @ONLY)
# generate Doxyfile with correct source paths
configure_file(${NMODL_PROJECT_SOURCE_DIR}/docs/Doxyfile.in
${NMODL_PROJECT_SOURCE_DIR}/docs/Doxyfile)
# =============================================================================
# Memory checker options and add tests
# =============================================================================
find_program(MEMORYCHECK_COMMAND valgrind)
set(MEMORYCHECK_COMMAND_OPTIONS
"--trace-children=yes \
--leak-check=full \
--track-origins=yes \
--show-possibly-lost=no")
# do not enable tests if nmodl is used as submodule
if(NOT NMODL_AS_SUBPROJECT)
include(CTest)
add_subdirectory(test/unit)
add_subdirectory(test/integration)
endif()
# =============================================================================
# list of autogenerated files
# =============================================================================
include(${PROJECT_SOURCE_DIR}/src/language/code_generator.cmake)
add_subdirectory(src)
# =============================================================================
# Prepare units database file from nrnunits.lib.in
# =============================================================================
if(NMODL_ENABLE_LEGACY_UNITS)
set(LegacyY "")
set(LegacyN "/")
else()
set(LegacyY "/")
set(LegacyN "")
endif()
configure_file(share/nrnunits.lib.in ${CMAKE_CURRENT_BINARY_DIR}/share/nmodl/nrnunits.lib @ONLY)
# =============================================================================
# Install unit database to share
# =============================================================================
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/share/nmodl/nrnunits.lib
DESTINATION ${NMODL_INSTALL_DIR_SUFFIX}share/nmodl)
# to print compiler flags in the build status
if(CMAKE_BUILD_TYPE)
string(TOUPPER ${CMAKE_BUILD_TYPE} BUILD_TYPE_UPPER)
set(COMPILER_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BUILD_TYPE_UPPER}}")
else()
set(COMPILER_FLAGS "${CMAKE_CXX_FLAGS}")
endif()
string(JOIN " " COMPILER_FLAGS "${COMPILER_FLAGS}" ${NMODL_EXTRA_CXX_FLAGS})
# =============================================================================
# Build status
# =============================================================================
message(STATUS "")
message(STATUS "Configured NMODL ${PROJECT_VERSION} (${NMODL_GIT_REVISION})")
message(STATUS "")
message(STATUS "You can now build NMODL using:")
message(STATUS " cmake --build . --parallel 8 [--target TARGET]")
message(STATUS "You might want to adjust the number of parallel build jobs for your system.")
message(STATUS "Some non-default targets you might want to build:")
message(STATUS "--------------------+--------------------------------------------------------")
message(STATUS " Target | Description")
message(STATUS "--------------------+--------------------------------------------------------")
message(STATUS "test | Run unit tests")
message(STATUS "install | Will install NMODL to: ${CMAKE_INSTALL_PREFIX}")
message(STATUS "--------------------+--------------------------------------------------------")
message(STATUS " Build option | Status")
message(STATUS "--------------------+--------------------------------------------------------")
message(STATUS "CXX COMPILER | ${CMAKE_CXX_COMPILER}")
message(STATUS "COMPILE FLAGS | ${COMPILER_FLAGS}")
message(STATUS "Build Type | ${CMAKE_BUILD_TYPE}")
message(STATUS "Legacy Units | ${NMODL_ENABLE_LEGACY_UNITS}")
message(STATUS "Python Bindings | ${NMODL_ENABLE_PYTHON_BINDINGS}")
message(STATUS "Flex | ${FLEX_EXECUTABLE}")
message(STATUS "Bison | ${BISON_EXECUTABLE}")
message(STATUS "Python | ${PYTHON_EXECUTABLE}")
message(STATUS "--------------+--------------------------------------------------------------")
message(STATUS " See documentation : https://github.com/BlueBrain/nmodl/")
message(STATUS "--------------+--------------------------------------------------------------")
message(STATUS "")
nmodl-0.6/CONTRIBUTING.md 0000664 0000000 0000000 00000014061 14420461415 0014724 0 ustar 00root root 0000000 0000000 # Contributing to the NMODL Framework
We would love for you to contribute to the NMODL Framework and help make it better than it is today. As a
contributor, here are the guidelines we would like you to follow:
- [Question or Problem?](#question)
- [Issues and Bugs](#issue)
- [Feature Requests](#feature)
- [Submission Guidelines](#submit)
- [Development Conventions](#devconv)
## Got a Question?
Please do not hesitate to raise an issue on [github project page][github].
## Found a Bug?
If you find a bug in the source code, you can help us by [submitting an issue](#submit-issue) to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#submit-pr) with a fix.
## Missing a Feature?
You can *request* a new feature by [submitting an issue](#submit-issue) to our GitHub Repository. If you would like to *implement* a new feature, please submit an issue with a proposal for your work first, to be sure that we can use it.
Please consider what kind of change it is:
* For a **Major Feature**, first open an issue and outline your proposal so that it can be
discussed. This will also allow us to better coordinate our efforts, prevent duplication of work,
and help you to craft the change so that it is successfully accepted into the project.
* **Small Features** can be crafted and directly [submitted as a Pull Request](#submit-pr).
## Submission Guidelines
### Submitting an Issue
Before you submit an issue, please search the issue tracker, maybe an issue for your problem already exists and the
discussion might inform you of workarounds readily available.
We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce and confirm it. In order to reproduce bugs we will need as much information as possible, and preferably a sample MOD file or Python example.
### Submitting a Pull Request (PR)
When you wish to contribute to the code base, please consider the following guidelines:
* Make a [fork](https://guides.github.com/activities/forking/) of this repository.
* Make your changes in your fork, in a new git branch:
```shell
git checkout -b my-fix-branch master
```
* Create your patch, **including appropriate test cases**.
* Enable `NMODL_TEST_FORMATTING` CMake variable
to ensure that your change follows the coding conventions of this project when running the tests.
The formatting utility can also be used directly:
* to format CMake and C++ files: `cmake/hpc-coding-conventions/bin/format`
* to format only the C++ files: `cmake/hpc-coding-conventions/bin/format --lang c++`
* to format a subset of files or directories: `cmake/hpc-coding-conventions/bin/format src/codegen/ src/main.cpp`
* to check the formatting of CMake files: `cmake/hpc-coding-conventions/bin/format --dry-run --lang cmake`
* Run the full test suite, and ensure that all tests pass.
* Commit your changes using a descriptive commit message.
```shell
git commit -a
```
* Push your branch to GitHub:
```shell
git push origin my-fix-branch
```
* In GitHub, send a Pull Request to the `master` branch of the upstream repository of the relevant component.
* If we suggest changes then:
* Make the required updates.
* Re-run the test suites to ensure tests are still passing.
* Rebase your branch and force push to your GitHub repository (this will update your Pull Request):
```shell
git rebase master -i
git push -f
```
That’s it! Thank you for your contribution!
#### After your pull request is merged
After your pull request is merged, you can safely delete your branch and pull the changes from the main (upstream)
repository:
* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:
```shell
git push origin --delete my-fix-branch
```
* Check out the master branch:
```shell
git checkout master -f
```
* Delete the local branch:
```shell
git branch -D my-fix-branch
```
* Update your master with the latest upstream version:
```shell
git pull --ff upstream master
```
[github]: https://github.com/BlueBrain/nmodl
## Development Conventions
If you are developing NMODL, make sure to enable both `NMODL_FORMATTING` and `NMODL_PRECOMMIT`
CMake variables to ensure that your contributions follow the coding conventions of this project:
```cmake
cmake -DNMODL_FORMATTING:BOOL=ON -DNMODL_PRECOMMIT:BOOL=ON
```
The first variable provides the following additional targets to format
C, C++, and CMake files:
```
make clang-format cmake-format
```
The second option activates Git hooks that will discard commits that
do not comply with coding conventions of this project. These 2 CMake variables require additional utilities:
* [ClangFormat 7](https://releases.llvm.org/7.0.0/tools/clang/docs/ClangFormat.html)
* [cmake-format](https://github.com/cheshirekow/cmake_format)
* [pre-commit](https://pre-commit.com/)
clang-format can be installed on Linux thanks
to [LLVM apt page](http://apt.llvm.org/). On MacOS, you can simply install llvm with brew:
`brew install llvm`.
_cmake-format_ and _pre-commit_ utilities can be installed with *pip*.
### Validate the Python package
You may run the Python test-suites if your contribution has an impact
on the Python API:
1. setup a sandbox environment with either _virtualenv_,
_pyenv_, or _pipenv_. For instance with _virtualenv_:
`python -m venv .venv && source .venv/bin/activate`
1. build the Python package with the command: `python setup.py build`
1. install _pytest_ Python package: `pip install pytest`
1. execute the unit-tests: `pytest`
### Memory Leaks and clang-tidy
If you want to test for memory leaks, do :
```
valgrind --leak-check=full --track-origins=yes ./bin/nmodl_lexer
```
Or using CTest as:
```
ctest -T memcheck
```
If you want to enable `clang-tidy` checks with CMake, make sure to have `CMake >= 3.15` and use following cmake option:
```
cmake .. -DENABLE_CLANG_TIDY=ON
```
nmodl-0.6/INSTALL.md 0000664 0000000 0000000 00000015466 14420461415 0014135 0 ustar 00root root 0000000 0000000 # Installing the NMODL Framework
## Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
## Cloning Source
The NMODL Framework is maintained on github. The best way to get the sources is to simply clone the repository.
**Note**: This project uses git submodules which must be cloned along with the repository itself:
```sh
git clone --recursive https://github.com/BlueBrain/nmodl.git
cd nmodl
```
## Prerequisites
To build the project from source, a modern C++ compiler with C++14 support is necessary. Make sure you have following packages available:
- flex (>=2.6)
- bison (>=3.0)
- CMake (>=3.15)
- Python (>=3.7)
- Python packages : jinja2 (>=2.10), pyyaml (>=3.13), pytest (>=4.0.0), sympy (>=1.3), textwrap
### On OS X
Typically the versions of bison and flex provided by the system are outdated and not compatible with our requirements.
To get recent version of all dependencies we recommend using [homebrew](https://brew.sh/):
```sh
brew install flex bison cmake python3
```
The necessary Python packages can then easily be added using the pip3 command.
```sh
pip3 install --user -r requirements.txt
```
Make sure to have latest flex/bison in $PATH :
```sh
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:/usr/local/bin/:$PATH
```
On Apple M1, corresponding brew paths are under `/opt/homebrew/opt/`:
```sh
export PATH=/opt/homebrew/opt/flex/bin:/opt/homebrew/opt/bison/bin:$PATH
```
### On Ubuntu
On Ubuntu (>=18.04) flex/bison versions are recent enough and are installed along with the system toolchain:
```sh
apt-get install flex bison gcc python3 python3-pip
```
The Python dependencies are installed using:
```sh
pip3 install --user -r requirements.txt
```
## Build Project
### Using CMake
Once all dependencies are in place, build project as:
```sh
mkdir -p nmodl/build
cd nmodl/build
cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/nmodl
make -j && make install
```
And set PYTHONPATH as:
```sh
export PYTHONPATH=$HOME/nmodl/lib:$PYTHONPATH
```
#### Flex / Bison Paths
If flex / bison are not in your default $PATH, you can provide the path to cmake as:
```sh
cmake .. -DFLEX_EXECUTABLE=/usr/local/opt/flex/bin/flex \
-DBISON_EXECUTABLE=/usr/local/opt/bison/bin/bison \
-DCMAKE_INSTALL_PREFIX=$HOME/nmodl
```
### Using Python setuptools
If you are mainly interested in the NMODL Framework parsing and analysis tools and wish to use them from Python, we
recommend building and installing using Python.
```sh
pip3 install --user .
```
This should build the NMODL framework and install it into your pip user `site-packages` folder such that it becomes
available as a Python module.
### When building without linking against libpython
NMODL uses an embedded python to symbolically evaluate differential equations. For this to work we would usually link
against libpython, which is automatically taken care of by pybind11. In some cases, for instance when building a
python wheel, we cannot link against libpython, because we cannot know where it will be at runtime. Instead, we load
the python library (along with a wrapper library that manages calls to embedded python) at runtime.
To disable linking against python and enabling dynamic loading of libpython at runtime we need to configure the build
with the cmake option `-DLINK_AGAINST_PYTHON=False`.
In order for NMODL binaries to know where to find libpython and our own libpywrapper two environment variables need to
be present:
* `NMODL_PYLIB`: This variable should point to the libpython shared-object (or dylib) file. On macos this could be
for example:
````sh
export NMODL_PYLIB=/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/Python
````
* 'NMODL_WRAPLIB': This variable should point to the `libpywrapper.so` built as part of NMODL, for example:
```sh
export NMODL_WRAPLIB=/opt/nmodl/lib/libpywrapper.so
```
**Note**: In order for all unit tests to function correctly when building without linking against libpython we must
set `NMODL_PYLIB` before running cmake!
## Testing the Installed Module
If you have installed the NMODL Framework using CMake, you can now run tests from the build directory as:
```bash
$ make test
Running tests...
Test project /Users/kumbhar/workarena/repos/bbp/incubator/nocmodl/cmake-build-debug
Start 1: testmodtoken/NMODL Lexer returning valid ModToken object
1/60 Test #1: testmodtoken/NMODL Lexer returning valid ModToken object ................................... Passed 0.01 sec
Start 2: testlexer/NMODL Lexer returning valid token types
2/60 Test #2: testlexer/NMODL Lexer returning valid token types .......................................... Passed 0.00 sec
Start 3: testparser/Scenario: NMODL can define macros using DEFINE keyword
3/60 Test #3: testparser/Scenario: NMODL can define macros using DEFINE keyword .......................... Passed 0.01 sec
Start 4: testparser/Scenario: Macros can be used anywhere in the mod file
4/60 Test #4: testparser/Scenario: Macros can be used anywhere in the mod file ........................... Passed 0.01 sec
Start 5: testparser/Scenario: NMODL parser accepts empty unit specification
5/60 Test #5: testparser/Scenario: NMODL parser accepts empty unit specification ......................... Passed 0.01 sec
Start 6: testparser/Scenario: NMODL parser running number of valid NMODL constructs
6/60 Test #6: testparser/Scenario: NMODL parser running number of valid NMODL constructs ................. Passed 0.04 sec
Start 7: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
7/60 Test #7: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ............... Passed 0.01 sec
Start 8: testparser/Scenario: Legacy differential equation solver from NEURON solve number of ODE
8/60 Test #8: testparser/Scenario: Legacy differential equation solver from NEURON solve number of ODE ... Passed 0.00 sec
...
```
To test the NMODL Framework python bindings, you can try a minimal example in your Python 3 interpeter as follows:
```python
>>> import nmodl.dsl as nmodl
>>> driver = nmodl.NmodlDriver()
>>> modast = driver.parse_string("NEURON { SUFFIX hh }")
>>> print ('%s' % modast)
{"Program":[{"NeuronBlock":[{"StatementBlock":[{"Suffix":[{"Name":[{"String":[{"name":"SUFFIX"}]}]},{"Name":[{"String":[{"name":"hh"}]}]}]}]}]}]}
>>> print (nmodl.to_nmodl(modast))
NEURON {
SUFFIX hh
}
```
NMODL is now setup correctly!
## Generating Documentation
In order to build the documentation you must have additionally `pandoc` installed. Use your
system's package manager to do this (e.g. `sudo apt-get install pandoc`).
You can build the entire documentation simply by using sphinx from `setup.py`:
```sh
python3 setup.py build_ext --inplace docs -G "Unix Makefiles"
```
nmodl-0.6/LGPL.txt 0000664 0000000 0000000 00000016743 14420461415 0014003 0 ustar 00root root 0000000 0000000 GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".
The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.
The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.
1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.
2. Conveying Modified Versions.
If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
version:
a) under this License, provided that you make a good faith effort to
ensure that, in the event an Application does not supply the
function or data, the facility still operates, and performs
whatever part of its purpose remains meaningful, or
b) under the GNU GPL, with none of the additional permissions of
this License applicable to that copy.
3. Object Code Incorporating Material from Library Header Files.
The object code form of an Application may incorporate material from
a header file that is part of the Library. You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
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(ten or fewer lines in length), you do both of the following:
a) Give prominent notice with each copy of the object code that the
Library is used in it and that the Library and its use are
covered by this License.
b) Accompany the object code with a copy of the GNU GPL and this license
document.
4. Combined Works.
You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
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the Library is used in it and that the Library and its use are
covered by this License.
b) Accompany the Combined Work with a copy of the GNU GPL and this license
document.
c) For a Combined Work that displays copyright notices during
execution, include the copyright notice for the Library among
these notices, as well as a reference directing the user to the
copies of the GNU GPL and this license document.
d) Do one of the following:
0) Convey the Minimal Corresponding Source under the terms of this
License, and the Corresponding Application Code in a form
suitable for, and under terms that permit, the user to
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the Linked Version to produce a modified Combined Work, in the
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1) Use a suitable shared library mechanism for linking with the
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e) Provide Installation Information, but only if you would otherwise
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License, and convey such a combined library under terms of your
choice, if you do both of the following:
a) Accompany the combined library with a copy of the same work based
on the Library, uncombined with any other library facilities,
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b) Give prominent notice with the combined library that part of it
is a work based on the Library, and explaining where to find the
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6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the
Library as you received it specifies that a certain numbered version
of the GNU Lesser General Public License "or any later version"
applies to it, you have the option of following the terms and
conditions either of that published version or of any later version
published by the Free Software Foundation. If the Library as you
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If the Library as you received it specifies that a proxy can decide
whether future versions of the GNU Lesser General Public License shall
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
Library.
nmodl-0.6/LICENSE 0000664 0000000 0000000 00000001711 14420461415 0013476 0 ustar 00root root 0000000 0000000 *********************************************************************************
* NMODL - NEURON Modeling Language Code Generation Framework
*
* Copyright (c) 2019-2022, Blue Brain Project, EPFL.
*
* NMODL is licensed under the LGPL, unless noted otherwise, e.g., for external
* dependencies. See file LGPL.txt for the full license. Examples and external
* dependencies are either LGPL or BSD-licensed.
*
* THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
*********************************************************************************/
nmodl-0.6/MANIFEST.in 0000664 0000000 0000000 00000000036 14420461415 0014226 0 ustar 00root root 0000000 0000000 recursive-include nmodl/ext *
nmodl-0.6/README.md 0000664 0000000 0000000 00000030464 14420461415 0013757 0 ustar 00root root 0000000 0000000 ## The NMODL Framework
[](https://travis-ci.org/BlueBrain/nmodl) [](https://dev.azure.com/pramodskumbhar/nmodl/_build/latest?definitionId=2&branchName=master) [](https://codecov.io/gh/BlueBrain/nmodl) [](https://bestpractices.coreinfrastructure.org/projects/4467)
The NMODL Framework is a code generation engine for **N**EURON **MOD**eling **L**anguage ([NMODL](https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechanisms/nmodl.html)). It is designed with modern compiler and code generation techniques to:
* Provide **modular tools** for parsing, analysing and transforming NMODL
* Provide **easy to use**, high level Python API
* Generate **optimised code** for modern compute architectures including CPUs, GPUs
* **Flexibility** to implement new simulator backends
* Support for **full** NMODL specification
### About NMODL
Simulators like [NEURON](https://www.neuron.yale.edu/neuron/) use NMODL as a domain specific language (DSL) to describe a wide range of membrane and intracellular submodels. Here is an example of exponential synapse specified in NMODL:
```python
NEURON {
POINT_PROCESS ExpSyn
RANGE tau, e, i
NONSPECIFIC_CURRENT i
}
UNITS {
(nA) = (nanoamp)
(mV) = (millivolt)
(uS) = (microsiemens)
}
PARAMETER {
tau = 0.1 (ms) <1e-9,1e9>
e = 0 (mV)
}
ASSIGNED {
v (mV)
i (nA)
}
STATE {
g (uS)
}
INITIAL {
g = 0
}
BREAKPOINT {
SOLVE state METHOD cnexp
i = g*(v - e)
}
DERIVATIVE state {
g' = -g/tau
}
NET_RECEIVE(weight (uS)) {
g = g + weight
}
```
### Installation
See [INSTALL.md](https://github.com/BlueBrain/nmodl/blob/master/INSTALL.md) for detailed instructions to build the NMODL from source.
### Try NMODL with Docker
To quickly test the NMODL Framework's analysis capabilities we provide a
[docker](https://www.docker.com) image, which includes the NMODL Framework python library and a
fully functional Jupyter notebook environment. After installing [docker](https://docs.docker.com/compose/install/) and [docker-compose](https://docs.docker.com/compose/install/) you can pull and run the NMODL image from your terminal.
To try Python interface directly from CLI, you can run docker image as:
```
docker run -it --entrypoint=/bin/sh bluebrain/nmodl
```
And try NMODL Python API discussed later in this README as:
```
$ python3
Python 3.6.8 (default, Apr 8 2019, 18:17:52)
>>> from nmodl import dsl
>>> import os
>>> examples = dsl.list_examples()
>>> nmodl_string = dsl.load_example(examples[-1])
...
```
To try Jupyter notebooks you can download docker compose file and run it as:
```sh
wget "https://raw.githubusercontent.com/BlueBrain/nmodl/master/docker/docker-compose.yml"
DUID=$(id -u) DGID=$(id -g) HOSTNAME=$(hostname) docker-compose up
```
If all goes well you should see at the end status messages similar to these:
```
[I 09:49:53.923 NotebookApp] The Jupyter Notebook is running at:
[I 09:49:53.923 NotebookApp] http://(4c8edabe52e1 or 127.0.0.1):8888/?token=a7902983bad430a11935
[I 09:49:53.923 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
To access the notebook, open this file in a browser:
file:///root/.local/share/jupyter/runtime/nbserver-1-open.html
Or copy and paste one of these URLs:
http://(4c8edabe52e1 or 127.0.0.1):8888/?token=a7902983bad430a11935
```
Based on the example above you should then open your browser and navigate to the URL `http://127.0.0.1:8888/?token=a7902983bad430a11935`.
You can open and run all example notebooks provided in the `examples` folder. You can also create
new notebooks in `my_notebooks`, which will be stored in a subfolder `notebooks` at your current
working directory.
### Using the Python API
Once the NMODL Framework is installed, you can use the Python parsing API to load NMOD file as:
```python
from nmodl import dsl
examples = dsl.list_examples()
nmodl_string = dsl.load_example(examples[-1])
driver = dsl.NmodlDriver()
modast = driver.parse_string(nmodl_string)
```
The `parse_file` API returns Abstract Syntax Tree ([AST](https://en.wikipedia.org/wiki/Abstract_syntax_tree)) representation of input NMODL file. One can look at the AST by converting to JSON form as:
```python
>>> print (dsl.to_json(modast))
{
"Program": [
{
"NeuronBlock": [
{
"StatementBlock": [
{
"Suffix": [
{
"Name": [
{
"String": [
{
"name": "POINT_PROCESS"
}
...
```
Every key in the JSON form represent a node in the AST. You can also use visualization API to look at the details of AST as:
```
from nmodl import ast
ast.view(modast)
```
which will open AST view in web browser:
The central *Program* node represents the whole MOD file and each of it's children represent the block in the input NMODL file. Note that this requires X-forwarding if you are using Docker image.
Once the AST is created, one can use exisiting visitors to perform various analysis/optimisations. One can also easily write his own custom visitor using Python Visitor API. See [Python API tutorial](docs/notebooks/nmodl-python-tutorial.ipynb) for details.
NMODL Frameowrk also allows to transform AST representation back to NMODL form as:
```python
>>> print (dsl.to_nmodl(modast))
NEURON {
POINT_PROCESS ExpSyn
RANGE tau, e, i
NONSPECIFIC_CURRENT i
}
UNITS {
(nA) = (nanoamp)
(mV) = (millivolt)
(uS) = (microsiemens)
}
PARAMETER {
tau = 0.1 (ms) <1e-09,1000000000>
e = 0 (mV)
}
...
```
### High Level Analysis and Code Generation
The NMODL Framework provides rich model introspection and analysis capabilities using [various visitors](https://bluebrain.github.io/nmodl/html/doxygen/group__visitor__classes.html). Here is an example of theoretical performance characterisation of channels and synapses from rat neocortical column microcircuit [published in 2015](https://www.cell.com/abstract/S0092-8674%2815%2901191-5):
To understand how you can write your own introspection and analysis tool, see [this tutorial](docs/notebooks/nmodl-python-tutorial.ipynb).
Once analysis and optimization passes are performed, the NMODL Framework can generate optimised code for modern compute architectures including CPUs (Intel, AMD, ARM) and GPUs (NVIDIA, AMD) platforms. For example, C++, OpenACC and OpenMP backends are implemented and one can choose these backends on command line as:
```
$ nmodl expsyn.mod sympy --analytic
```
To know more about code generation backends, [see here](https://bluebrain.github.io/nmodl/html/doxygen/group__codegen__backends.html). NMODL Framework provides number of options (for code generation, optimization passes and ODE solver) which can be listed as:
```
$ nmodl -H
NMODL : Source-to-Source Code Generation Framework [version]
Usage: /path/<>/nmodl [OPTIONS] file... [SUBCOMMAND]
Positionals:
file TEXT:FILE ... REQUIRED One or more MOD files to process
Options:
-h,--help Print this help message and exit
-H,--help-all Print this help message including all sub-commands
--verbose=info Verbose logger output (trace, debug, info, warning, error, critical, off)
-o,--output TEXT=. Directory for backend code output
--scratch TEXT=tmp Directory for intermediate code output
--units TEXT=/path/<>/nrnunits.lib
Directory of units lib file
Subcommands:
host
HOST/CPU code backends
Options:
--c C/C++ backend (true)
acc
Accelerator code backends
Options:
--oacc C/C++ backend with OpenACC (false)
sympy
SymPy based analysis and optimizations
Options:
--analytic Solve ODEs using SymPy analytic integration (false)
--pade Pade approximation in SymPy analytic integration (false)
--cse CSE (Common Subexpression Elimination) in SymPy analytic integration (false)
--conductance Add CONDUCTANCE keyword in BREAKPOINT (false)
passes
Analyse/Optimization passes
Options:
--inline Perform inlining at NMODL level (false)
--unroll Perform loop unroll at NMODL level (false)
--const-folding Perform constant folding at NMODL level (false)
--localize Convert RANGE variables to LOCAL (false)
--global-to-range Convert GLOBAL variables to RANGE (false)
--localize-verbatim Convert RANGE variables to LOCAL even if verbatim block exist (false)
--local-rename Rename LOCAL variable if variable of same name exist in global scope (false)
--verbatim-inline Inline even if verbatim block exist (false)
--verbatim-rename Rename variables in verbatim block (true)
--json-ast Write AST to JSON file (false)
--nmodl-ast Write AST to NMODL file (false)
--json-perf Write performance statistics to JSON file (false)
--show-symtab Write symbol table to stdout (false)
codegen
Code generation options
Options:
--layout TEXT:{aos,soa}=soa Memory layout for code generation
--datatype TEXT:{float,double}=soa Data type for floating point variables
--force Force code generation even if there is any incompatibility
--only-check-compatibility Check compatibility and return without generating code
--opt-ionvar-copy Optimize copies of ion variables (false)
```
### Documentation
We are working on user documentation, you can find current drafts of :
* [User Documentation](https://bluebrain.github.io/nmodl/)
* [Developer / API Documentation](https://bluebrain.github.io/nmodl/html/doxygen/index.html)
### Citation
If you would like to know more about the the NMODL Framework, see following paper:
* Pramod Kumbhar, Omar Awile, Liam Keegan, Jorge Alonso, James King, Michael Hines and Felix Schürmann. 2019. An optimizing multi-platform source-to-source compiler framework for the NEURON MODeling Language. In Eprint : [arXiv:1905.02241](https://arxiv.org/pdf/1905.02241.pdf)
### Support / Contribuition
If you see any issue, feel free to [raise a ticket](https://github.com/BlueBrain/nmodl/issues/new). If you would like to improve this framework, see [open issues](https://github.com/BlueBrain/nmodl/issues) and [contribution guidelines](CONTRIBUTING.md).
### Examples / Benchmarks
The benchmarks used to test the performance and parsing capabilities of NMODL Framework are currently being migrated to GitHub. These benchmarks will be published soon in following repositories:
* [NMODL Benchmark](https://github.com/BlueBrain/nmodlbench)
* [NMODL Database](https://github.com/BlueBrain/nmodldb)
## Funding & Acknowledgment
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology. In addition, the development was supported by funding from the National Institutes of Health (NIH) under the Grant Number R01NS11613 (Yale University) and the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
Copyright © 2017-2022 Blue Brain Project/EPFL
nmodl-0.6/azure-pipelines.yml 0000664 0000000 0000000 00000026730 14420461415 0016340 0 ustar 00root root 0000000 0000000 #=============================================================================
# Azure Pipeline NMODL settings
#=============================================================================
variables:
# defined in UI
#- ReleaseWheelBuild: False
#- UploadWheel: False
buildWheel: ${{ or(in(variables['Build.Reason'], 'Schedule'), in(variables['Build.Reason'], 'Manual')) }}
MACOSX_DEPLOYMENT_TARGET: 10.15
# Nightly build master for pypi upload
schedules:
- cron: "5 0 * * *"
branches:
include:
- master
always: True
# Auto cancel old PR builds
pr:
autoCancel: true
# Trigger build for certain branches only
trigger:
- master
- llvm
- releases/*
stages:
- stage: fetch_config
jobs:
- job: github
pool:
vmImage: ubuntu-latest
steps:
- checkout: none
- script: |
if [[ -z ${SYSTEM_PULLREQUEST_PULLREQUESTNUMBER+x} ]]; then
echo "Not running on a PR."
exit 0
fi
cat > parse_description.py << END_SCRIPT
import os
import re
import requests
pr_info = requests.get("https://api.github.com/repos/{}/pulls/{}".format(
os.environ['BUILD_REPOSITORY_NAME'],
os.environ['SYSTEM_PULLREQUEST_PULLREQUESTNUMBER']),
headers={'Accept': 'application/vnd.github.v3+json'})
pr_body = pr_info.json()["body"]
# match something like NEURON_BRANCH=foo/bar
pat = re.compile('^([A-Z0-9_]+)_([A-Z]+)=([A-Z0-9\-\_\/\+]+)$', re.IGNORECASE)
def parse_term(m):
ref_type = m.group(2).lower()
if ref_type not in {'branch', 'tag', 'ref'}: return
variable = m.group(1).upper() + '_' + ref_type.upper()
value = m.group(3)
print('{}={}'.format(variable, value))
print('#{}[task.setvariable variable={};isOutput=true]{}'.format('#vso', variable, value))
if pr_body is not None:
for pr_body_line in pr_body.splitlines():
if not pr_body_line.startswith('CI_BRANCHES:'): continue
for config_term in pr_body_line[12:].split(','):
pat.sub(parse_term, config_term)
END_SCRIPT
echo '----'
cat parse_description.py
echo '----'
python parse_description.py
name: prdesc
- stage: build
dependsOn: fetch_config
variables:
NEURON_BRANCH: $[stageDependencies.fetch_config.github.outputs['prdesc.NEURON_BRANCH']]
jobs:
- job: 'ubuntu2004'
pool:
vmImage: 'ubuntu-20.04'
displayName: 'Ubuntu (20.04), GCC 9.4'
steps:
- checkout: self
submodules: False
- script: |
sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
sudo apt-add-repository -y ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y g++-9 flex bison libfl-dev cython libx11-dev libxcomposite-dev libncurses-dev mpich
sudo apt-get install -y python3.8 python3.8-dev python3.8-venv ninja-build
python3.8 -m pip install --upgrade pip setuptools
python3.8 -m pip install --user -r $(Build.Repository.LocalPath)/requirements.txt
# we manually get version 3.15.0 to make sure that changes in the cmake
# files do not require unsupported versions of cmake in our package.
wget --quiet --output-document=- "https://github.com/Kitware/CMake/releases/download/$CMAKE_VER/$CMAKE_PKG.tar.gz" | tar xzpf -
env:
CMAKE_VER: 'v3.15.0'
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
displayName: 'Install Dependencies'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export CXX='g++-9'
mkdir -p $(Build.Repository.LocalPath)/build
cd $(Build.Repository.LocalPath)/build
cmake --version
cmake .. -DPYTHON_EXECUTABLE=$(which python3.8) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=Release
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
make install #this is needed for the integration tests
env CTEST_OUTPUT_ON_FAILURE=1 make test
env:
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
displayName: 'Build and Run Unit Tests'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export CC='gcc-9'
export CXX='g++-9'
git clone${NEURON_BRANCH:+ --branch }${NEURON_BRANCH} --single-branch https://github.com/neuronsimulator/nrn.git
mkdir nrn/build
cd nrn/build
cmake --version
cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -Dnmodl_PYTHONPATH=$HOME/nmodl/lib -DPYTHON_EXECUTABLE=$(which python3.8) -DCORENRN_NMODL_FLAGS="sympy --analytic"
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
./bin/nrnivmodl-core $(Build.Repository.LocalPath)/test/integration/mod
env:
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
SHELL: 'bash'
displayName: 'Build Neuron and Run Integration Tests'
- job: 'osx11'
pool:
vmImage: 'macOS-11'
displayName: 'MacOS (11), AppleClang 12.0'
steps:
- checkout: self
submodules: True
- script: |
brew install flex bison cmake python@3
python3 -m pip install --upgrade pip setuptools
python3 -m pip install --user -r $(Build.Repository.LocalPath)/requirements.txt
displayName: 'Install Dependencies'
- script: |
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
mkdir -p $(Build.Repository.LocalPath)/build
cd $(Build.Repository.LocalPath)/build
cmake .. -DPYTHON_EXECUTABLE=$(which python3) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=RelWithDebInfo -DNMODL_ENABLE_PYTHON_BINDINGS=OFF
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
make install
displayName: 'Build and Run Tests'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
export CC='gcc'
export CXX='g++'
git clone${NEURON_BRANCH:+ --branch }${NEURON_BRANCH} --single-branch https://github.com/neuronsimulator/nrn.git
mkdir nrn/build
cd nrn/build
cmake --version
cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_MPI=OFF -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -Dnmodl_PYTHONPATH=$HOME/nmodl/lib -DPYTHON_EXECUTABLE=$(which python3) -DCORENRN_NMODL_FLAGS="sympy --analytic"
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
./bin/nrnivmodl-core $(Build.Repository.LocalPath)/test/integration/mod
env:
SHELL: 'bash'
displayName: 'Build Neuron and Run Integration Tests'
- job: 'manylinux_wheels'
timeoutInMinutes: 45
pool:
vmImage: 'ubuntu-20.04'
strategy:
matrix:
${{ if eq(variables.buildWheel, True) }}:
Python37:
python.version: '3.7'
Python38:
python.version: '3.8'
Python39:
python.version: '3.9'
Python310:
python.version: '3.10'
Python311:
python.version: '3.11'
${{ if eq(variables.buildWheel, False) }}:
Python311:
python.version: '3.11'
steps:
- checkout: self
submodules: True
condition: succeeded()
- script: |
if [[ "$(RELEASEWHEELBUILD)" != "True" ]]; then
export TAG="-nightly"
else
export TAG=""
fi
docker run --rm \
-w /root/nmodl \
-v $PWD:/root/nmodl \
-e NMODL_NIGHTLY_TAG=$TAG \
'bluebrain/nmodl:wheel' \
packaging/build_wheels.bash linux $(python.version)
condition: succeeded()
displayName: 'Building ManyLinux Wheel'
- task: PublishBuildArtifacts@1
inputs:
pathToPublish: '$(Build.SourcesDirectory)/wheelhouse'
condition: succeeded()
displayName: 'Publish wheel as build artifact'
- script: |
sudo apt-add-repository -y ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y python$(python.version) python$(python.version)-dev python$(python.version)-venv
packaging/test_wheel.bash python$(python.version) wheelhouse/*.whl
condition: succeeded()
displayName: 'Test ManyLinux Wheel with Python $(python.version)'
- template: ci/upload-wheels.yml
- job: 'macos_wheels'
timeoutInMinutes: 45
pool:
vmImage: 'macOS-11'
strategy:
matrix:
${{ if eq(variables.buildWheel, True) }}:
Python37:
python.version: '3.7'
python.org.version: '3.7.9'
python.installer.name: 'macosx10.9.pkg'
Python38:
python.version: '3.8'
python.org.version: '3.8.10'
python.installer.name: 'macosx10.9.pkg'
Python39:
python.version: '3.9'
python.org.version: '3.9.13'
python.installer.name: 'macosx10.9.pkg'
Python310:
python.version: '3.10'
python.org.version: '3.10.5'
python.installer.name: 'macos11.pkg'
Python311:
python.version: '3.11'
python.org.version: '3.11.1'
python.installer.name: 'macos11.pkg'
${{ if eq(variables.buildWheel, False) }}:
Python311:
python.version: '3.11'
python.org.version: '3.11.1'
python.installer.name: 'macos11.pkg'
steps:
- checkout: self
submodules: True
condition: succeeded()
- script: |
brew install flex bison cmake ninja
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
condition: succeeded()
displayName: 'Install Dependencies'
- script: |
installer=python-$(python.org.version)-$(python.installer.name)
url=https://www.python.org/ftp/python/$(python.org.version)/$installer
curl $url -o $installer
sudo installer -pkg $installer -target /
condition: succeeded()
displayName: 'Install Python from python.org'
- script: |
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH
export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
if [[ "$(RELEASEWHEELBUILD)" != "True" ]]; then
export NMODL_NIGHTLY_TAG="-nightly"
else
export NMODL_NIGHTLY_TAG=""
fi
packaging/build_wheels.bash osx $(python.version)
condition: succeeded()
displayName: 'Build macos Wheel'
- task: PublishBuildArtifacts@1
inputs:
pathToPublish: '$(Build.SourcesDirectory)/wheelhouse'
condition: succeeded()
displayName: 'Publish wheel as build artifact'
- script: |
packaging/test_wheel.bash python$(python.version) wheelhouse/*.whl
condition: succeeded()
displayName: 'Test macos Wheel with Python $(python.version)'
- template: ci/upload-wheels.yml
nmodl-0.6/ci/ 0000775 0000000 0000000 00000000000 14420461415 0013064 5 ustar 00root root 0000000 0000000 nmodl-0.6/ci/upload-wheels.yml 0000664 0000000 0000000 00000002267 14420461415 0016367 0 ustar 00root root 0000000 0000000 steps:
- task: UsePythonVersion@0
inputs:
versionSpec: '$(python.version)'
- task: TwineAuthenticate@1
inputs:
pythonUploadServiceConnection: AzureNMODLPypiNightly
condition: and(succeeded(), eq(variables.buildWheel, true))
- script: |
python -m pip install twine
cat $(PYPIRC_PATH)
python -m twine upload --verbose --skip-existing -r NMODLPypiNightly --config-file $(PYPIRC_PATH) wheelhouse/*.whl
condition: and(succeeded(), eq(variables.buildWheel, true), ne(variables['UploadWheel'], false), ne(variables.ReleaseWheelBuild, true))
displayName: 'Upload nightly wheel to pypi.org'
- task: TwineAuthenticate@1
inputs:
pythonUploadServiceConnection: AzureNMODLPypi
condition: and(succeeded(), in(variables['Build.Reason'], 'Manual'), eq(variables.ReleaseWheelBuild, true))
- script: |
python -m pip install twine
python -m twine upload --verbose --skip-existing -r NMODLPypi --config-file $(PYPIRC_PATH) wheelhouse/*.whl
condition: and(succeeded(), in(variables['Build.Reason'], 'Manual'), eq(variables.ReleaseWheelBuild, true), ne(variables['UploadWheel'], false))
displayName: 'Upload release wheel to pypi.org'
nmodl-0.6/cmake/ 0000775 0000000 0000000 00000000000 14420461415 0013551 5 ustar 00root root 0000000 0000000 nmodl-0.6/cmake/ClangTidyHelper.cmake 0000664 0000000 0000000 00000001270 14420461415 0017571 0 ustar 00root root 0000000 0000000 set(ENABLE_CLANG_TIDY
OFF
CACHE BOOL "Add clang-tidy automatically to builds")
if(ENABLE_CLANG_TIDY)
find_program(CLANG_TIDY_EXE NAMES "clang-tidy")
if(CLANG_TIDY_EXE)
message(STATUS "clang-tidy found: ${CLANG_TIDY_EXE}")
set(CLANG_TIDY_CHECKS
"-*,modernize-*,readability-*,performance-*,cppcoreguidelines-*,clang-analyzer-core*,google-*"
)
set(CMAKE_CXX_CLANG_TIDY
"${CLANG_TIDY_EXE};-checks=${CLANG_TIDY_CHECKS};-fix;-header-filter='${CMAKE_SOURCE_DIR}/*'"
CACHE STRING "" FORCE)
else()
message(AUTHOR_WARNING "clang-tidy not found!")
set(CMAKE_CXX_CLANG_TIDY
""
CACHE STRING "" FORCE) # delete it
endif()
endif()
nmodl-0.6/cmake/CompilerHelper.cmake 0000664 0000000 0000000 00000005616 14420461415 0017475 0 ustar 00root root 0000000 0000000 if(CMAKE_CXX_COMPILER_ID MATCHES "PGI" OR CMAKE_CXX_COMPILER_ID MATCHES "NVHPC")
set(NMODL_PGI_COMPILER TRUE)
# CMake adds standard complaint PGI flag "-A" which breaks compilation of of spdlog and fmt
set(CMAKE_CXX14_STANDARD_COMPILE_OPTION --c++14)
# Avoid errors related to "excessive recursion at instantiation of function ...", Eigen-related
# (in accelerated regions), e.g., transposeInPlace()
list(APPEND NMODL_EXTRA_CXX_FLAGS "-Wc,--pending_instantiations=0")
# ~~~
# PGI enables number of diagnostic messages by default classes which results into thousands of
# messages specifically for AST. Disable these verbose warnings for now.
# TODO : fix these warnings from template modification (#272)
# ~~~
if(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 20.7)
set(NMODL_COMPILER_WARNING_SUPPRESSIONS --diag_suppress=1,82,111,115,177,186,611,997,1097,1625)
else()
# https://forums.developer.nvidia.com/t/many-all-diagnostic-numbers-increased-by-1-from-previous-values/146268/3
# changed the numbering scheme in newer versions. The following list is from a clean start 13
# August 2021. It would clearly be nicer to apply these suppressions only to relevant files.
# Examples of the suppressed warnings are given below.
# ~~~
# "ext/spdlog/include/spdlog/fmt/fmt.h", warning #1-D: last line of file ends without a newline
# "ext/fmt/include/fmt/format.h", warning #111-D: statement is unreachable
# "ext/fmt/include/fmt/format.h", warning #128-D: loop is not reachable
# "ext/spdlog/include/spdlog/fmt/bundled/format.h", warning #185-D: dynamic initialization in unreachable code
# "ext/json/json.hpp", warning #186-D: pointless comparison of unsigned integer with zero
# "src/ast/all.hpp", warning #998-D: function "..." is hidden by "..." -- virtual function override intended?
# "ext/spdlog/include/spdlog/fmt/bundled/format.h", warning #1098-D: unknown attribute "fallthrough"
# "ext/pybind11/include/pybind11/detail/common.h", warning #1626-D: routine is both "inline" and "noinline"
# "ext/spdlog/include/spdlog/fmt/bundled/core.h", warning #1676-D: unrecognized GCC pragma
# ~~~
# The following warnings do not seem to be suppressible with --diag_suppress:
# ~~~
# "src/codegen/codegen_cuda_visitor.cpp", NVC++-W-0277-Cannot inline function - data type mismatch
# "nvc++IkWUbMugiSgNH.s: Warning: stand-alone `data16' prefix
# ~~~
# The situation may be better once https://github.com/fmtlib/fmt/pull/2582 is included in a
# release.
set(NMODL_COMPILER_WARNING_SUPPRESSIONS --diag_suppress=1,111,128,185,186,998,1098,1626,1676)
# There are a few more warnings produced by the unit test infrastructure.
# ~~~
# "test/unit/visitor/constant_folder.cpp", warning #177-D: variable "..." was declared but never referenced
# ~~~
set(NMODL_TESTS_COMPILER_WARNING_SUPPRESSIONS --diag_suppress=177)
endif()
endif()
nmodl-0.6/cmake/ExternalProjectHelper.cmake 0000664 0000000 0000000 00000000731 14420461415 0021025 0 ustar 00root root 0000000 0000000 find_package(Git QUIET)
# initialize submodule with given path
function(initialize_submodule path)
if(NOT ${GIT_FOUND})
message(
FATAL_ERROR "git not found and ${path} sub-module not cloned (use git clone --recursive)")
endif()
message(STATUS "Sub-module : missing ${path}: running git submodule update --init")
execute_process(COMMAND git submodule update --init -- ${path}
WORKING_DIRECTORY ${NMODL_PROJECT_SOURCE_DIR})
endfunction()
nmodl-0.6/cmake/FlexHelper.cmake 0000664 0000000 0000000 00000001355 14420461415 0016615 0 ustar 00root root 0000000 0000000 # Often older version of flex is available in /usr. Even we set PATH for newer flex, CMake will set
# FLEX_INCLUDE_DIRS to /usr/include. This will result in compilation errors. Hence we check for flex
# include directory for the corresponding FLEX_EXECUTABLE. If found, we add that first and then we
# include include path from CMake.
get_filename_component(FLEX_BIN_DIR ${FLEX_EXECUTABLE} DIRECTORY)
if(NOT FLEX_BIN_DIR MATCHES "/usr/bin")
get_filename_component(FLEX_INCLUDE_PATH ${FLEX_BIN_DIR} PATH)
set(FLEX_INCLUDE_PATH ${FLEX_INCLUDE_PATH}/include/)
if(EXISTS "${FLEX_INCLUDE_PATH}/FlexLexer.h")
message(STATUS " Adding Flex include path as : ${FLEX_INCLUDE_PATH}")
include_directories(${FLEX_INCLUDE_PATH})
endif()
endif()
nmodl-0.6/cmake/GitRevision.cmake 0000664 0000000 0000000 00000003163 14420461415 0017020 0 ustar 00root root 0000000 0000000 # For now use simple approach to get version information as git is always avaialble on the machine
# where we are building
find_package(Git)
if(GIT_FOUND)
# get last commit sha1
execute_process(
COMMAND ${GIT_EXECUTABLE} log -1 --format=%h
WORKING_DIRECTORY ${NMODL_PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE NMODL_GIT_REVISION_SHA1
RESULT_VARIABLE NMODL_GIT_STATUS
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT NMODL_GIT_STATUS EQUAL 0)
set(NMODL_GIT_REVISION_SHA1 "git-error")
endif()
# get last commit date
execute_process(
COMMAND ${GIT_EXECUTABLE} show -s --format=%ci
WORKING_DIRECTORY ${NMODL_PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE NMODL_GIT_REVISION_DATE
RESULT_VARIABLE NMODL_GIT_STATUS
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT NMODL_GIT_STATUS EQUAL 0)
set(NMODL_GIT_REVISION_SHA1 "git-error")
endif()
# remove extra double quotes
string(REGEX REPLACE "\"" "" NMODL_GIT_REVISION_DATE "${NMODL_GIT_REVISION_DATE}")
set(NMODL_GIT_REVISION "${NMODL_GIT_REVISION_SHA1} ${NMODL_GIT_REVISION_DATE}")
# get the last version tag from git
execute_process(
COMMAND ${GIT_EXECUTABLE} describe --abbrev=0 --tags
WORKING_DIRECTORY ${NMODL_PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE NMODL_GIT_LAST_TAG
RESULT_VARIABLE NMODL_GIT_STATUS
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT NMODL_GIT_STATUS EQUAL 0)
# Must be a valid version from CMake's perspective.
set(NMODL_GIT_LAST_TAG "0.0")
endif()
else()
set(NMODL_GIT_REVISION "unknown")
# Must be a valid version from CMake's perspective.
set(NMODL_GIT_LAST_TAG "0.0")
endif()
nmodl-0.6/cmake/PythonLinkHelper.cmake 0000664 0000000 0000000 00000002120 14420461415 0020005 0 ustar 00root root 0000000 0000000 # =============================================================================
# Support for building NMODL without python library
# =============================================================================
# ~~~
# When NMODL is built under environment (e.g. manylinux) without python-dev
# package i.e. libpython.so, we have to build extension and binaries by
# ignoring undefned symbols. The python library will be loaded later on target
# system.
# ~~~
# use same variable name as NEURON as it won't be user option
set(LINK_AGAINST_PYTHON
TRUE
CACHE BOOL "Disable linking to python library")
mark_as_advanced(LINK_AGAINST_PYTHON)
# Flags for ignoring undefined symbols for wheel
if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
set(UNDEFINED_SYMBOLS_IGNORE_FLAG "-Wl,-undefined,dynamic_lookup")
else()
set(UNDEFINED_SYMBOLS_IGNORE_FLAG "-Wl,--unresolved-symbols=ignore-all")
endif()
if(NOT LINK_AGAINST_PYTHON)
string(APPEND CMAKE_EXE_LINKER_FLAGS " ${UNDEFINED_SYMBOLS_IGNORE_FLAG}")
set(NMODL_WRAPPER_LIBS pyembed dl)
else()
set(NMODL_WRAPPER_LIBS pyembed pywrapper dl)
endif()
nmodl-0.6/cmake/RpathHelper.cmake 0000664 0000000 0000000 00000002475 14420461415 0017001 0 ustar 00root root 0000000 0000000 # =============================================================================
# Copyright (C) 2018-2022 Blue Brain Project
#
# This file is part of NMODL distributed under the terms of the GNU Lesser General Public License.
# See top-level LICENSE file for details.
# =============================================================================
# =============================================================================
# Set full RPATHs in build-tree, also set RPATHs in install for non-system libs
# =============================================================================
# use, i.e. don't skip the full RPATH for the build tree
set(CMAKE_SKIP_BUILD_RPATH FALSE)
# when building, don't use the install RPATH already (but later on when installing)
set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
# add the automatically determined parts of the RPATH which point to directories outside the build
# tree to the install RPATH
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
# the RPATH to be used when installing, but only if it's not a system directory
list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
if("${isSystemDir}" STREQUAL "-1")
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
endif("${isSystemDir}" STREQUAL "-1")
nmodl-0.6/cmake/hpc-coding-conventions/ 0000775 0000000 0000000 00000000000 14420461415 0020127 5 ustar 00root root 0000000 0000000 nmodl-0.6/docs/ 0000775 0000000 0000000 00000000000 14420461415 0013421 5 ustar 00root root 0000000 0000000 nmodl-0.6/docs/Doxyfile.in 0000664 0000000 0000000 00000336353 14420461415 0015551 0 ustar 00root root 0000000 0000000 # Doxyfile 1.9.1
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the configuration
# file that follow. The default is UTF-8 which is also the encoding used for all
# text before the first occurrence of this tag. Doxygen uses libiconv (or the
# iconv built into libc) for the transcoding. See
# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "User Guide"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER =
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
# in the documentation. The maximum height of the logo should not exceed 55
# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
# the logo to the output directory.
PROJECT_LOGO = logo.png
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = sphinx_doxygen
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
# will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system.
# The default value is: NO.
CREATE_SUBDIRS = NO
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
# Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all generated output in the proper direction.
# Possible values are: None, LTR, RTL and Context.
# The default value is: None.
OUTPUT_TEXT_DIRECTION = None
# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF = "The $name class" \
"The $name widget" \
"The $name file" \
is \
provides \
specifies \
contains \
represents \
a \
an \
the
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = YES
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = YES
# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
# such as
# /***************
# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
# Javadoc-style will behave just like regular comments and it will not be
# interpreted by doxygen.
# The default value is: NO.
JAVADOC_BANNER = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# By default Python docstrings are displayed as preformatted text and doxygen's
# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
# doxygen's special commands can be used and the contents of the docstring
# documentation blocks is shown as doxygen documentation.
# The default value is: YES.
PYTHON_DOCSTRING = YES
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
# page for each member. If set to NO, the documentation of a member will be part
# of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 4
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:\n"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines (in the resulting output). You can put ^^ in the value part of an
# alias to insert a newline as if a physical newline was in the original file.
# When you need a literal { or } or , in the value part of an alias you have to
# escape them by means of a backslash (\), this can lead to conflicts with the
# commands \{ and \} for these it is advised to use the version @{ and @} or use
# a double escape (\\{ and \\})
ALIASES =
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
# sources only. Doxygen will then generate output that is more tailored for that
# language. For instance, namespaces will be presented as modules, types will be
# separated into more groups, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_SLICE = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
# tries to guess whether the code is fixed or free formatted code, this is the
# default for Fortran type files). For instance to make doxygen treat .inc files
# as Fortran files (default is PHP), and .f files as C (default is Fortran),
# use: inc=Fortran f=C.
#
# Note: For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen. When specifying no_extension you should add
# * to the FILE_PATTERNS.
#
# Note see also the list of default file extension mappings.
EXTENSION_MAPPING = .yaml=Python
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See https://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
# to that level are automatically included in the table of contents, even if
# they do not have an id attribute.
# Note: This feature currently applies only to Markdown headings.
# Minimum value: 0, maximum value: 99, default value: 5.
# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
TOC_INCLUDE_HEADINGS = 0
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by putting a % sign in front of the word or
# globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
# If one adds a struct or class to a group and this option is enabled, then also
# any nested class or struct is added to the same group. By default this option
# is disabled and one has to add nested compounds explicitly via \ingroup.
# The default value is: NO.
GROUP_NESTED_COMPOUNDS = NO
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use
# during processing. When set to 0 doxygen will based this on the number of
# cores available in the system. You can set it explicitly to a value larger
# than 0 to get more control over the balance between CPU load and processing
# speed. At this moment only the input processing can be done using multiple
# threads. Since this is still an experimental feature the default is set to 1,
# which efficively disables parallel processing. Please report any issues you
# encounter. Generating dot graphs in parallel is controlled by the
# DOT_NUM_THREADS setting.
# Minimum value: 0, maximum value: 32, default value: 1.
NUM_PROC_THREADS = 1
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = YES
# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
# methods of a class will be included in the documentation.
# The default value is: NO.
EXTRACT_PRIV_VIRTUAL = NO
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = YES
# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = YES
# This flag is only useful for Objective-C code. If set to YES, local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO, only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If this flag is set to YES, the name of an unnamed parameter in a declaration
# will be determined by the corresponding definition. By default unnamed
# parameters remain unnamed in the output.
# The default value is: YES.
RESOLVE_UNNAMED_PARAMS = YES
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO, these classes will be included in the various overviews. This option
# has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# declarations. If set to NO, these declarations will be included in the
# documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO, these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = NO
# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
# able to match the capabilities of the underlying filesystem. In case the
# filesystem is case sensitive (i.e. it supports files in the same directory
# whose names only differ in casing), the option must be set to YES to properly
# deal with such files in case they appear in the input. For filesystems that
# are not case sensitive the option should be be set to NO to properly deal with
# output files written for symbols that only differ in casing, such as for two
# classes, one named CLASS and the other named Class, and to also support
# references to files without having to specify the exact matching casing. On
# Windows (including Cygwin) and MacOS, users should typically set this option
# to NO, whereas on Linux or other Unix flavors it should typically be set to
# YES.
# The default value is: system dependent.
CASE_SENSE_NAMES = NO
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES, the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
# append additional text to a page's title, such as Class Reference. If set to
# YES the compound reference will be hidden.
# The default value is: NO.
HIDE_COMPOUND_REFERENCE= NO
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
# list. This list is created by putting \todo commands in the documentation.
# The default value is: YES.
GENERATE_TODOLIST = YES
# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
# list. This list is created by putting \test commands in the documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = YES
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= YES
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if ... \endif and \cond
# ... \endcond blocks.
ENABLED_SECTIONS =
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE = DoxygenLayout.xml
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as not documenting some parameters
# in a documented function, or documenting parameters that don't exist or using
# markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO, doxygen will only warn about wrong or incomplete
# parameter documentation, but not about the absence of documentation. If
# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
# at the end of the doxygen process doxygen will return with a non-zero status.
# Possible values are: NO, YES and FAIL_ON_WARNINGS.
# The default value is: NO.
WARN_AS_ERROR = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = @NMODL_PROJECT_SOURCE_DIR@/src \
@NMODL_PROJECT_SOURCE_DIR@/test \
@PROJECT_BINARY_DIR@/src/ast \
@PROJECT_BINARY_DIR@/src/visitors \
../README.md
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see:
# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# read by doxygen.
#
# Note the list of default checked file patterns might differ from the list of
# default file extension mappings.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
# *.ucf, *.qsf and *.ice.
FILE_PATTERNS = *.c \
*.cc \
*.cxx \
*.cpp \
*.c++ \
*.ipp \
*.h \
*.hh \
*.hxx \
*.hpp \
*.h++ \
*.markdown \
*.md \
*.mm \
*.dox \
*.yaml
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE = @NMODL_PROJECT_SOURCE_DIR@/src/pybind/pybind_utils.hpp
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = */src/language/*
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS = *
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = NO
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH =
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
#
#
# where is the value of the INPUT_FILTER tag, and is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
FILTER_PATTERNS =
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE = ../README.md
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = NO
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# entity all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = NO
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = NO
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see https://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
# can be used to specify a prefix (or a list of prefixes) that should be ignored
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = doxygen
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER = footer.html
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefore more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET = doxygen_nmodl.css
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES = background.png
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
# this color. Hue is specified as an angle on a colorwheel, see
# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 344
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use grayscales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = NO
# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
# are dynamically created via JavaScript. If disabled, the navigation index will
# consists of multiple levels of tabs that are statically embedded in every HTML
# page. Disable this option to support browsers that do not have JavaScript,
# like the Qt help browser.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_MENUS = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = NO
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see:
# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
# create a documentation set, doxygen will generate a Makefile in the HTML
# output directory. Running make will produce the docset in that directory and
# running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
# genXcode/_index.html for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# (see:
# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows.
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler (hhc.exe). If non-empty,
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated
# (YES) or that it should be included in the main .chm file (NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated
# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = NO
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = org.doxygen.Project
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = doc
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location (absolute path
# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
# run qhelpgenerator on the generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
# further fine-tune the look of the index. As an example, the default style
# sheet generated by doxygen has an example that shows how to put an image at
# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
# the same information as the tab index, you could consider setting
# DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
# the HTML output. These images will generally look nicer at scaled resolutions.
# Possible values are: png (the default) and svg (looks nicer but requires the
# pdf2svg or inkscape tool).
# The default value is: png.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FORMULA_FORMAT = png
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
# to create new LaTeX commands to be used in formulas as building blocks. See
# the section "Including formulas" for details.
FORMULA_MACROFILE =
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# https://www.mathjax.org) which uses client side JavaScript for the rendering
# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = YES
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. See the MathJax site (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details.
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility), NativeMML (i.e. MathML) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from https://www.mathjax.org before deployment.
# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use + S
# (what the is depends on the OS and browser, but it is typically
# , /