daoBase

basic tools for dao

📖 Documentation

The complete documentation for installation, usage, and API reference can be found here:

Read the Docs

---

Citation

If you use this software in your research or work, please cite it using the following DOI:

DOI: 10.5281/zenodo.17264152

BibTeX

@software{barr_2025_17264152,
  author       = {Barr, David and
                  Cetre, Sylvain and
                  Connolly, John and
                  Thomas Davies},
  title        = {Durham-Adaptive-Optics/daoBase: Initial Release},
  month        = oct,
  year         = 2025,
  publisher    = {Zenodo},
  version      = {v0.0.1},
  doi          = {10.5281/zenodo.17264152},
  url          = {https://doi.org/10.5281/zenodo.17264152},
  swhid        = {swh:1:dir:e28d715b004461ad5ac69d7ac13d5a4a0f8fc196
                   ;origin=https://doi.org/10.5281/zenodo.17264151;vi
                   sit=swh:1:snp:c39ecfb0c6dc79d3ad9523b5cdd88dc1a14f
                   43e2;anchor=swh:1:rel:b822be04b6dda609af461bb157fc
                   b1ec74853023;path=Durham-Adaptive-Optics-daoBase-
                   ccd63ee
                  },
}

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Build

(for build instructions on Windows, see windows-build.md)

Prerequiries

Linux package

Package for Redhat based distribution... to be adapted for other Linux distrib

yum install openssl-devel protobuf-devel gsl-devel numactl-devel glibc-devel ncurses-devel redis gtest-devel zeromq zeromq-devel

for ubuntu distribution:

sudo apt install -y libtool pkg-config build-essential autoconf automake python3 python-is-python3 libssl-dev libncurses5-dev libncursesw5-dev redis libgtest-dev libgsl-dev libzmq3-dev protobuf-compiler numactl libnuma-dev

MAC

You need homebrew for the packages.

brew install pkg-config zeromq protobuf gsl

if you use anaconda there could be a conflict between protobuf versions so uninstall using

conda uninstall libprotobuf

Linux arm64

We encoutered several issue with the protobuf, usually related to the librptobuf vs protox version mismatch. One simple solution was to rebuild from the source

git clone https://github.com/abseil/abseil-cpp.git
cd abseil-cpp
mkdir build && cd build
cmake .. -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_BUILD_TYPE=Release
make -j$(nproc)
sudo make install

then protobuf

wget https://github.com/protocolbuffers/protobuf/releases/download/v25.3/protobuf-25.3.tar.gz
tar zxvf protobuf-25.4.tar.gz
cd protobuf-25.3-full
mkdir -p cmake/build
cd cmake/build

cmake ../.. \
  -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
  -Dprotobuf_BUILD_TESTS=OFF \
  -Dprotobuf_ABSL_PROVIDER=package

make -j$(nproc)
sudo make install
sudo ldconfig

and

Waf

waf needs to be installed and in the path: see https://waf.io/book/.
Our typical install

mkdir ~/bin
cd ~/bin
wget https://waf.io/waf-2.0.26
ln -s waf-2.0.26 waf
chmod u+x *

and add $HOME/bin in your path

Python

a python install is needed. We usually used miniconda but any aother install will work. here is our typical install command. For Linux x86_64

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh

Linux arm64

mkdir -p ~/miniconda3
curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -o ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh

For MACOS arm64 install

mkdir -p ~/miniconda3
curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh

The following package should be installed

pip install posix_ipc zmq protobuf==3.20.0 astropy python-statemachine statemachine redis sphinx screeninfo

For MACOS, check the version of your protoc

protoc --version
libprotoc 29.3

Corresponding protobuf is

pip install protobuf==5.29.3

Environment

export DAOROOT=$HOME/DAOROOT
export DAODATA=$HOME/DAODATA
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$DAOROOT/lib:$DAOROOT/lib64
export PATH=$PATH:$HOME/bin:$HOME/DAOROOT/bin
export PYTHONPATH=$PYTHONPATH:$DAOROOT/python
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$DAOROOT/lib/pkgconfig

For MACOS, add the following variables in your environment

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/opt/homebrew/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/homebrew/lib
 
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/opt/homebrew/include
export C_INCLUDE_PATH=$C_INCLUDE_PATH:/opt/homebrew/include
export CPATH=$CPATH:/opt/homebrew/include
export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig

!! BE SURE THE DAOROOT exists. In the example

mkdir $HOME/DAOROOT

Build

waf configure --prefix=$DAOROOT
waf
waf install

Documentation

Documents are built using doxygen and sphinx. To build the documents use the following command

waf build_docs

To clean the document build.

waf clean_docs

Build Options

The following build options are available

Debug

Add debug flag to support debuging build and install with '-g' to support use of gdb

waf build --debug

Sanitiser

Mostly used for developers it is available to check address sanitisation

waf build --santizer

UNIT tests.

The build include unit tests under tests. These can be built and run by running with the following

waf --test

This will build and run the tests.