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dev.sh
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#!/bin/bash
# dev script version 1.0
HERE=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
NAME=metasmith
DEV_USER=hallamlab
_ver_file=$(find $HERE/src | grep version.txt)
# VER="$(cat $_ver_file).$(git branch --show-current)-$(git rev-parse --short HEAD)"
VER="$(cat $_ver_file)"
DOCKER_IMAGE=quay.io/$DEV_USER/$NAME
# CONDA=conda
CONDA=mamba # https://mamba.readthedocs.io/en/latest/mamba-installation.html#mamba-install
echo image: $DOCKER_IMAGE:$VER
echo ""
# this file contains a list of commands useful for dev,
# providing automation for some build tasks
#
# example workflow 1, pip:
# dev.sh --idev # create a local conda dev env
# # add pypi api token as file to ./secrets [https://pypi.org/help/#apitoken]
# # make some changes to source
# # bump up ./src/*/version.txt
# dev.sh -bp # build the pip package
# dev.sh -up # test upload to testpypi
# dev.sh -upload-pypi # release to pypi index for pip install
#
# example workflow 2, conda:
# dev.sh --idev # create a local conda dev env
# dev.sh -bp # build the pip package
# dev.sh -bc # build conda package from pip package
# dev.sh -uc # publish to conda index
#
# example workflow 3, containerization:
# dev.sh --idev # create a local conda dev env
# dev.sh -bd # build docker image
# dev.sh -ud # publish to quay.io
# dev.sh -bs # build apptainer image from local docker image
case $1 in
###################################################
# environments
--idev) # with dev tools for packaging
cd $HERE/envs
echo "creating new conda env: $NAME"
echo "WARNING: you will need to install docker and apptainer individually"
sleep 2
$CONDA env create --no-default-packages -n $NAME -f ./base.yml \
&& $CONDA env update -n $NAME -f ./dev.yml
;;
--ibase) # base only
cd $HERE/envs
echo "creating new conda env: $NAME"
sleep 2
$CONDA env create --no-default-packages -n $NAME -f ./base.yml
;;
###################################################
# build
-bp) # pip
# build pip package
[ -d ./build ] && rm -r build
[ -d ./dist ] && rm -r dist
python -m build
;;
-bpi) # pip - test install
pip install $HERE/dist/$NAME-$VER-py3-none-any.whl
;;
-bpx) # pip - remove package
pip uninstall -y $NAME
;;
-bc) # conda
# requires built pip package
rm -r $HERE/conda_build
python ./conda_recipe/compile_recipe.py
$HERE/conda_recipe/call_build.sh
;;
-bd) # docker
# pre-download requirements
mkdir -p $HERE/lib
cd $HERE/lib
TINI_VERSION=v0.19.0
! [ -f tini ] && wget https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini && chmod +x ./tini
if ! [ -d globusconnectpersonal-latest ]; then
wget -continue https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz
tar -xvf globusconnectpersonal-latest.tgz
rm globusconnectpersonal-latest.tgz
mv globusconnectpersonal-* globusconnectpersonal-latest
fi
NEXTFLOW_VERSION=$(cat ../envs/base.yml | grep nextflow | cut -c14- | xargs)
echo "nextflow version: $NEXTFLOW_VERSION"
! [ -f nextflow ] && wget https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}}/nextflow && chmod +x ./nextflow
cd $HERE
# build the docker container locally
export DOCKER_BUILDKIT=1
docker build \
--build-arg="CONDA_ENV=${NAME}_env" \
--build-arg="PACKAGE=${NAME}" \
--build-arg="VERSION=${VER}" \
-t $DOCKER_IMAGE:$VER .
;;
-bs) # apptainer image *from docker*
apptainer build $NAME.sif docker-daemon://$DOCKER_IMAGE:$VER
;;
###################################################
# upload
-up) # pip (testpypi)
PYPI=testpypi
TOKEN=$(cat secrets/${PYPI}) # https://pypi.org/help/#apitoken
python -m twine upload --repository $PYPI dist/*.whl -u __token__ -p $TOKEN
;;
-upload-pypi) # pip (pypi)
echo "not all dependencies are available on pypi, so this is not a good idea..."
# PYPI=pypi
# TOKEN=$(cat secrets/${PYPI}) # https://pypi.org/help/#apitoken
# python -m twine upload --repository $PYPI dist/*.whl -u __token__ -p $TOKEN
;;
-uc) # conda (personal channel)
# run `anaconda login` first
find ./conda_build -name *.tar.bz2 | xargs -I % anaconda upload -u $DEV_USER %
;;
-ud) # docker
# login and push image to quay.io
# sudo docker login quay.io
docker push $DOCKER_IMAGE:$VER
echo "!!!"
echo "remember to update the \"latest\" tag"
echo "https://$DOCKER_IMAGE?tab=tags"
;;
###################################################
# run
-r)
shift
export PYTHONPATH=$HERE/src:$PYTHONPATH
python -m $NAME $@
;;
-rd) # docker
# -e XDG_CACHE_HOME="/ws"\
shift
mkdir -p ./scratch/docker
cd ./scratch/docker
# mkdir -p cache/.globus cache/.globusonline
docker run -it --rm \
-u $(id -u):$(id -g) \
--mount type=bind,source="$HERE/scratch/docker",target="/ws"\
--mount type=bind,source="$HOME/.globus",target="/.globus"\
--mount type=bind,source="$HOME/.globusonline",target="/.globusonline"\
--workdir="/ws" \
$DOCKER_IMAGE:$VER /bin/bash
;;
-rs) # apptainer
# -e XDG_CACHE_HOME="/ws"\
shift
mkdir -p ./scratch/docker
cd ./scratch/docker
apptainer exec \
--bind ./:/ws \
--workdir /ws \
--no-home \
$HERE/$NAME.sif /bin/bash
# docker-daemon://$DOCKER_IMAGE:$VER /bin/bash
;;
###################################################
# test
-t)
shift
export PYTHONPATH=$HERE/src:$PYTHONPATH
python -m $NAME $@ deploy
;;
-t2)
cd ./main/relay_agent/scratch/cache/mock
# mkdir -p cache/.globus cache/.globusonline
docker run -it --rm \
-u $(id -u):$(id -g) \
--mount type=bind,source="./work",target="/ws"\
--mount type=bind,source="./home",target="/msm_home"\
--mount type=bind,source="$HOME/.globus",target="/.globus"\
--mount type=bind,source="$HOME/.globusonline",target="/.globusonline"\
--workdir="/ws" \
$DOCKER_IMAGE:$VER /bin/bash
;;
###################################################
*)
echo "bad option"
echo $1
;;
esac