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Merged
lilyminium merged 5 commits into from
Dec 6, 2020
Merged

Deploy docs via GitHub Actions CI #3053

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51370c4
deploy docs
lilyminium Dec 3, 2020
3f58a89
rm script
lilyminium Dec 3, 2020
fc3e987
to undo: change site to lilyminium's
lilyminium Dec 3, 2020
4b02525
Try not turning off non-blocking mode
lilyminium Dec 5, 2020
d43c177
Revert "to undo: change site to lilyminium's"
lilyminium Dec 5, 2020
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53 changes: 51 additions & 2 deletions .github/workflows/gh-ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ env:
MDA_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
MDA_PIP_EXTRA_DEPS: 'duecredit parmed'


jobs:
main_tests:
if: "github.repository == 'MDAnalysis/mdanalysis'"
Expand Down Expand Up @@ -211,9 +212,57 @@ jobs:

- name: deploy_docs
if: github.event_name != 'pull_request'
env:
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@lilyminium lilyminium Dec 3, 2020

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Moved deployment to within this file because it saved a lot of variable checking and possibly insecure token passing

GH_USER: github-actions
GH_EMAIL: "github-action@users.noreply.github.com"
GH_REPOSITORY: "github.com/${{ github.repository }}.git"
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
URL: https://docs.mdanalysis.org

run: |
# place the deploy call here
echo "Oh, maple syrup roast parsnips [Richard Gowers]"
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@orbeckst orbeckst Dec 4, 2020

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Almost a shame to loose this citation ;-)

# set up environment variables
# cannot execute bash to make variables in env section
# export URL for the Python script $UPDATE_JSON
export URL
export VERSION=$(cd package/MDAnalysis; python -c 'import version; print(version.__version__)')
UPDATE_JSON=$(pwd)/maintainer/update_json_stubs_sitemap.py
BRANCH="${GITHUB_REF#refs/heads/}"

# the below turns off non-blocking as it causes large writes to stdout to fail
# (see https://github.com/travis-ci/travis-ci/issues/4704)
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@orbeckst orbeckst Dec 4, 2020

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Thanks for the comment. Btw, I think what we're doing here we enabled blocking mode again, in case it was switched to non-blocking, at least that's how I read travis-ci/travis-ci#4704 (comment) and flags&~os.O_NONBLOCK.

Was this someone we only needed for Travis or is this a general problem, i.e., does gh-actions also have something weird running that switches to non-blocking mode?

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@orbeckst orbeckst Dec 4, 2020

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P.S.: Even if we don't strictly need it here anymore, I would only ever comment the line and not delete it, just in case we need it ever again.

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@lilyminium lilyminium Dec 5, 2020

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Thanks for pointing that out @orbeckst; you're right, gh-actions did not have this problem the 2 times I ran the deployment (where Travis was previously failing every time). I've commented it out and left a note.

# commented out as this is not a problem with gh-actions
# python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
cd package/doc/html/html

# move docs into version subfolder
mkdir ../${VERSION} && mv * ../${VERSION} && mv ../${VERSION} $VERSION

# set up git
REV=$(git rev-parse --short HEAD)
git init
git config user.name $GH_USER
git config user.email $GH_EMAIL
git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}"
git fetch --depth 50 upstream $BRANCH gh-pages
git reset upstream/gh-pages

# redirects and copies
mkdir latest
python $UPDATE_JSON
touch .
touch .nojekyll

git add -A ${VERSION}/
git add .nojekyll versions.json *.xml *.html index.html latest

for dirname in dev stable documentation_pages ; do
if [ -d $dirname ]; then git add $dirname; fi
done

# check for anything to commit
# https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes
git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs for version ${VERSION} from branch ${BRANCH} with sphinx at ${REV}"
git push -q upstream HEAD:gh-pages


pylint_check:
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82 changes: 0 additions & 82 deletions maintainer/deploy_docs_via_travis.sh
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