release
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#!/usr/bin/env sos-runner #fileformat=SOS1.0 # This script releases SoS to different destinations, including # # 1. source distribution to pip # 2. docker images to docker hub # 3. website to github.io [patch: shared='version'] parameter: version = str sh: perl -pi.bak -e "s/^__version__ = .*/__version__ = '${version}'/" ../src/sos/_version.py [pip] parameter: version = str # check the version of the latest version cur_ver = get_output("pip show sos | grep Version | cut -d' ' -f2").strip() # do not upload if the version on pip is the current one stop_if(cur_ver == version) sh: workdir='..' python setup.py sdist && \ rm -rf /tmp/test_sos && \ mkdir /tmp/test_sos && \ cp dist/sos-${version}.tar.gz /tmp/test_sos && \ cd /tmp/test_sos && \ tar zxf sos-${version}.tar.gz && \ cd sos-${version} && \ python setup.py install sh: workdir='..' python setup.py sdist upload && \ pip install sos --upgrade [update-docker] # add documentation to Docker container depends: executable('docker') # copy doc over run: workdir='..' rm -rf development/docker-notebook/doc # copy only ipynb and .sos files to docker rsync -av --prune-empty-dirs --include "*/" --exclude ".ipynb_checkpoints" \ --include "*.ipynb" --include "*.jpg" --include "*.png" --exclude "*" \ docs/src/documentation docs/src/tutorials docs/src/examples docs/doc/media \ development/docker-notebook/doc # update docker and push run: docker build --no-cache -t mdabioinfo/sos docker-base docker push mdabioinfo/sos docker build --no-cache -t mdabioinfo/sos-notebook docker-notebook docker push mdabioinfo/sos-notebook # update docker on ec2 [update-ec2] parameter: pem=glob.glob('mda*.pem') run: ssh -i ${pem} ubuntu@ec2-34-192-184-206.compute-1.amazonaws.com 'bash -s '< update_ec2_docker.sh [getFileNames] run: python ../docs/js/findnames.py [convert-documentation] input: '../docs/src/documentation/*.ipynb', group_by=1 depends: '../docs/src/documentation/toc_doc.tpl' output: _input[0].replace('/src/', '/doc/').replace('.ipynb', '.html') run: cd ../docs/src/documentation sos convert ${_input!a} ${_output!a} --template toc_doc perl -0777 -pi -e 'BEGIN{undef $/;} s/<style type=\"text\/css\">(.+?)<\/style>//smg' ${_output!a} [convert-tutorials] input: '../docs/src/tutorials/*.ipynb', group_by=1 depends: '../docs/src/tutorials/toc_tut.tpl' output: _input[0].replace('/src/', '/doc/').replace('.ipynb', '.html') run: cd ../docs/src/tutorials sos convert ${_input!a} ${_output!a} --template toc_tut perl -0777 -pi -e 'BEGIN{undef $/;} s/<style type=\"text\/css\">(.+?)<\/style>//smg' ${_output!a} [convert-homepage] input: '../docs/src/homepage/*.ipynb', group_by=1 output: "../docs/${_input!bn}.html" run: cd ../docs/src/tutorials sos convert ${_input!a} ${_output!a} --template basic [convert-example-scripts] input: '../docs/src/examples/*.sos', 'release', group_by=1 output: "../docs/doc/examples/${_input!bn}.html" run: workdir='../docs/doc/examples' cp ${_input!a} . sos convert ${_input!b} ${_output!b} --raw ${_input!b} --lineno --style tango [convert-example-notebooks] input: '../docs/src/examples/*.ipynb', group_by=1 depends: '../src/sos/jupyter/sos-full.tpl' output: "../docs/doc/examples/${_input!bn}.html" run: workdir='../docs/doc/examples' cp ${_input!a} . sos convert ${_input!b} ${_output!b} --template sos-full [convert-example-report] input: '../docs/src/examples/Preview_and_Report_Generation.ipynb', '../docs/src/examples/RNASeqDE.ipynb', group_by=1 depends: '../src/sos/jupyter/sos-report.tpl' output: "../docs/doc/examples/${_input!bn}_report.html" run: workdir='../docs/doc/examples' cp ${_input!a} . sos convert ${_input!b} ${_output!b} --template sos-report [convert-large-examples] input: '../docs/src/examples/*/*.sos', group_by=1 output: "../docs/doc/examples/${_input!db}/${_input!bn}.html" run: workdir='../docs/doc/examples' [ -d ${_input!db} ] || mkdir ${_input!db} cp ${_input!a} ${_input!db} cp ${_input!da}/README.md ${_input!db} cd ${_input!db} sos convert ${_input!b} ${_output!b} --raw ${_input!b} [update-website] # convert ipynb to HTML sos_run('getFileNames') sos_run('convert-documentation') sos_run('convert-tutorials') sos_run('convert-homepage') sos_run('convert-example-scripts') sos_run('convert-example-notebooks') sos_run('convert-example-report') sos_run('convert-large-examples') # push changes to website parameter: msg = "Update website" run: workdir='..' git add --all docs/doc/documentation docs/doc/tutorials docs/doc/examples docs/doc/media docs/js/docs.js docs/*.html git commit docs/*.html docs/doc/* --no-verify -m '${msg}' || true git push --no-verify || true [check-doc] # check if examples in the documentation can be run successfully input: '../docs/src/documentation/*.ipynb', group_by=1 run: # convert ipynb to sos sos convert ${_input!a} ${_input!bn}.sos # then from sos to ipynb with execution sos convert ${_input!bn}.sos ${_input!b} --execute [check-link] # https://www.npmjs.com/package/broken-link-checker # use command # # npm install broken-link-checker -g # # to install depends: executable('blc') # check homepage run: blc http://vatlab.github.io/SoS input: '../docs/src/*/*.ipynb', group_by=1 if 'homepage' in _input[0]: run("blc http://vatlab.github.io/SoS/${_input!bn}.html") else: run("blc http://vatlab.github.io/SoS/doc/${_input!db}/${_input!bn}.html") [default] sos_run('patch + pip + update-docker + update-website')