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peterjcpeterjc
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Proof of principle deployment to biopython/docs
Created a pass-phrase less SSH key, uploaded the public key to biopython/docs settings as a deployment key (write permissions). For TravisCI must escape the spaces and newlines as '\ ' and '\\n' respectively when setting DOC_KEY as a secure environment variable. Can test this locally by setting the DOC_KEY environment variable. Idea here is to call this from TravisCI/Tox after running Sphinx to build our API documentation.
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‎.github/deploy_docs.sh

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#!/bin/bash
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# Assumes being called from the Biopython repository's root folder,
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# (i.e. a clone of https://github.com/biopython/biopython) as part
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# of our continuous integration testing to save the compiled docs
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# to https://github.com/biopython/docs
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#
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# In order to have write permissions, we put a private key into the
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# TravisCI settings as a secure environment variable, and put the
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# matching public key into the GitHub documentation repository's
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# settings as a deploy key with write permissions.
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#
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# Key creation,
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#
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# $ ssh-keygen -t rsa -b 4096 -C "biopython documentation deploy key" -f biopython_doc_key -N ""
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# Generating public/private rsa key pair.
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# Your identification has been saved in biopython_doc_key.
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# Your public key has been saved in biopython_doc_key.pub.
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# The key fingerprint is:
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# SHA256:nFfhbwryDLDz8eDEHa4sjdH0gOgwyXGGDUBGfDi5luQ biopython documentation deploy key
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# The key's randomart image is:
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# +---[RSA 4096]----+
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# |===+o . |
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# |.B.*.. . . . |
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# |o X . o o . o |
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# | E + B * o . |
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# |. . + S * o |
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# | X @ . o |
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# | o * + . |
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# | . |
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# | |
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# +----[SHA256]-----+
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#
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# Next, we add the public key to https://github.com/biopython/docs as
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# a deployment key with write permission,
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#
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# $ cat biopython_doc_key.pub
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# ssh-rsa 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 biopython documentation deploy key
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#
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# Finally, we add the private key to TravisCI by going to
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# https://travis-ci.org/biopython/biopython/settings or any authorised
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# fork like https://travis-ci.org/peterjc/biopython/settings and
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# setting DOC_KEY to the following (secret) value:
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#
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# $ python -c "print(open('biopython_doc_key').read().strip().replace(' ', r'\ ').replace('\n', r'\\\n'))"
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# ...
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#
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# TravisCI requires we escape spaces as '\ ' and newlines as '\\n', and
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# we explicitly strip the trailing new line so that we don't get an extra
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# one when rebuilding the key later.
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#
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# Make sure "DISPLAY VALUE IN BUILD LOG" is off (the default).
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#
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# For testing locally, set local environment $DOC_KEY to this value.
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# Thereafter, when ever this script gets run on TravisCI it should
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# be able to deplop the HTML documentation to our documentation
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# repository (which will dispaly on biopython.org via GitHub pages).
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set -e
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if [ -z "$DOC_KEY" ]; then
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echo "Missing (secret) environment variable DOC_KEY,"
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echo "which should hold the private SSH deployment key."
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false
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fi
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set -euo pipefail
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DEST_SLUG=biopython/docs
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# Could look at $TRAVIS_TAG, e.g. DEST_DIR=${TRAVIS_TAG:-dev}
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# However, tags lack the dots in the version number. Since
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# Biopython was installed to run Sphinx and build the docs,
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# can use this:
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DEST_DIR=`python -c "import Bio; v=Bio.__version__; print('dev' if 'dev' in v else v)"`
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SOURCE_DIR=${TRAVIS_BUILD_DIR:-$PWD}/Doc/api/_build/html
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WORKING_DIR=/tmp/deploy_biopython_docs
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if [ -z "$DEST_DIR" ]; then
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echo "ERROR: Failed to get Biopython version, is it not installed?"
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python -c "import Bio; print(Bio.__version__)"
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false
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fi
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DEST_DIR=$DEST_DIR/api
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echo "Aiming to deploy $SOURCE_DIR to $DEST_SLUG branch gh-pages as $DEST_DIR"
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# On TravisCI, must create the variable using '\ ' and '\n', so
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# here we must unescape the whitespace to recover the SSH deploy key:
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python -c "import os; print(os.environ['DOC_KEY'].strip().replace(r'\ ', ' ').replace(r'\n', '\n'))" > $HOME/.biopython_doc_deploy.key
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# Check we have a sane looking line structure:
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if [ `grep -c "^\-\-\-\-\-" $HOME/.biopython_doc_deploy.key` -ne 2 ]; then
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echo "ERROR: Failed to rebuild the SSH key,"
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wc -l $HOME/.biopython_doc_deploy.key
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md5sum $HOME/.biopython_doc_deploy.key
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false
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fi
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chmod 600 $HOME/.biopython_doc_deploy.key
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export GIT_SSH=${TRAVIS_BUILD_DIR:-$PWD}/.github/ssh_via_deploy_key.sh
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if ! [[ -f "$GIT_SSH" ]]; then
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echo "Error, set GIT_SSH="$GIT_SSH" but does not exist"
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false
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elif ! [[ -x "$GIT_SSH" ]]; then
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echo "Error, set GIT_SSH="$GIT_SSH" but not executable"
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false
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fi;
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echo "Setting up clone of $DEST_SLUG locally at $WORKING_DIR"
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# Clone the destination under /tmp (public URL, no key needed)
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rm -rf $WORKING_DIR
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git clone https://github.com/$DEST_SLUG.git $WORKING_DIR
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pushd $WORKING_DIR
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git checkout gh-pages
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# Switch the git protocol to SSH based so we can use our key
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git remote set-url origin --push [email protected]:$DEST_SLUG.git
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popd
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echo "Copying $SOURCE_DIR/* to $WORKING_DIR/$DEST_DIR/ next"
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if [ ! -d $SOURCE_DIR ]; then
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echo "ERROR: Directory $SOURCE_DIR/ does not exist."
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false
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fi
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# Remove any old files
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pushd $WORKING_DIR
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if [ -d $DEST_DIR ]; then
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echo "Removing old files"
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git rm -r $DEST_DIR/
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fi
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mkdir -p $DEST_DIR
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echo "Copying files"
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cp -R $SOURCE_DIR/* $DEST_DIR/
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echo "Staging files in git"
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git add $DEST_DIR/
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if [[ -z $(git status --porcelain) ]]; then
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echo "Nothing has changed, nothing needs pushing."
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else
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echo "Making commit of new files"
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git commit -m "Automated update ${TRAVIS_COMMIT:-}" --author "TravisCI <[email protected]>"
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echo "Finally, pushing to $DEST_SLUG gh-pages branch"
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git push origin gh-pages
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echo "Documentation deployed!"
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fi
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popd

‎.github/ssh_via_deploy_key.sh

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#!/bin/bash
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# Call ssh using our GitHub repository deploy key (set via -i)
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# using -F to make sure this ignores ~/.ssh/config
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ssh -i "$HOME/.biopython_doc_deploy.key" -F /dev/null -p 22 $*

‎.travis.yml

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apt:
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packages:
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before_install: echo "Going to build API docs"
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after_success: .github/deploy_docs.sh
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- stage: test
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python: 2.7
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env: TOXENV=py27-cover

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