WIP: Github actions by arokem · Pull Request #52 · nipreps/dmriprep

@@           Coverage Diff           @@
##           master      #52   +/-   ##
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  Coverage   55.51%   55.51%           
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  Files          11       11           
  Lines         762      762           
  Branches      110      110           
=======================================
  Hits          423      423           
  Misses        338      338           
  Partials        1        1

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arokem · 2020-01-14T21:39:42Z

I think that this is ready to go. This now (hopefully) does: test-suite, documentation build and docker image building. I will do the pypi deploy stuff on a separate PR.

arokem · 2020-01-15T05:29:40Z

Please hold off on merging this for now. The recent 079a3b2 tries to use the canned action again. I might back off this in the end, but the developer of this action has made the additional effort of implementing this, so the least I can do is give it a whirl.

oesteban · 2020-01-15T04:18:07Z

.github/workflows/docbuild.yml

+        pip install .[all]
+    - name: Build docs
+      run: |
+        cd docs


please remove this line (and apply the next suggestion)

oesteban · 2020-01-15T04:19:04Z

.github/workflows/docbuild.yml

+    - name: Build docs
+      run: |
+        cd docs
+        make html


Suggested change

make html

make -C docs html

The rationale is that the makefile under docs/ inserts PWD in the pythonpath and you want it to be the root of the project :)

oesteban · 2020-01-15T04:24:54Z

.github/workflows/docbuild.yml

+      run: |
+        cd docs
+        make html
+    - name: Upload docs


We'll need to think a bit further about this:

If you just run make -C doc then the current version of the docs is built.

If you are to deploy, then the appropriate commandline is make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH} (replace $CIRCLE_TAG and $CIRCLE_BRANCH with appropriate values).

then, the versioned docs are deployed to gh-pages:

dmriprep/.circleci/config.yml

Lines 505 to 525 in b98c7e9

- run:

name: Generate Versioned Docs

command: |

set +e

force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[docs?[ _]?versions?\]' )"

set -e

if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then

echo "Not a tag or master branch - skipping versioned docs."

circleci step halt

else

make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}

fi

- save_cache:

key: docs-v1-{{ .Branch }}-{{ .Revision }}

paths:

- ./docs/_build/_html

- persist_to_workspace:

root: docs/_build

paths: html

- store_artifacts:

path: ./docs/_build/html

(the path that gets pushed is not the non-versioned docs)

Done (maybe?) in 313f5bf

oesteban · 2020-01-15T05:47:29Z

.github/workflows/test.yml

+        pip install .[all]
+    - name: Test
+      run: |
+        pytest -n 2 -vv --doctest-modules --cov dmriprep --cov-config .coveragerc --cov-report xml:cov.xml dmriprep


the options to pytest would be better set within the setup.cfg file.

Done in 0cc7787

Down the rabbit hole we go!

One of the following: - A tag - A branch called "docker/*" - A merge on master.

See: mr-smithers-excellent/docker-build-push#6

Hopefully addresses nipreps#52 (comment)

oesteban · 2020-12-10T17:25:39Z

I have added some github actions workflow to test package builds. Can we split this one and maybe add those workflows we want to keep?

oesteban · 2021-05-19T05:25:27Z

Closing for now.

arokem force-pushed the ga branch from 1999813 to 079a3b2 Compare January 15, 2020 05:27

oesteban reviewed Jan 15, 2020

View reviewed changes

arokem force-pushed the ga branch from 079a3b2 to 31be93d Compare January 15, 2020 06:05

arokem added 19 commits January 14, 2020 22:29

Adds an initial Github Actions config for test suite.

ee7f81a

This is actually a bit simpler.

d719d1c

Adds a documentation build GA workflow.

c8b6f1c

Try building this only once. Upload from correct path.

fd1bea3

Explicitly set to use Python 3.7

0e3e827

Adds a docker build/push workflow.

f6b17e1

Tweak tweak.

dff4a32

Rename this step to make sense.

ee52ea8

Use the bash script from the circleci config instead.

b472f5e

We might need Python 3.7 here.

f0eaef9

Install pyenv.

c725ad6

Down the rabbit hole we go!

Set up pyenv.

b185f11

Maybe we need to do this setup in the next step.

c3860ed

We don't need pyenv here.

5a5c229

Push to dockerhub based on a condition.

174948e

One of the following: - A tag - A branch called "docker/*" - A merge on master.

Be more specific about what this is.

ff1079a

Remove the cache-from argument.

d79f76c

Use the canned action again.

ba228be

See: mr-smithers-excellent/docker-build-push#6

Reinstate custom docker build.

edb50b5

arokem force-pushed the ga branch from f9c966e to edb50b5 Compare January 15, 2020 06:29

arokem added 3 commits January 14, 2020 23:10

Move pytest options to setup.cfg.

0cc7787

Fixes docbuild.

313f5bf

Hopefully addresses nipreps#52 (comment)

Correct directory name ("doc" => "docs")

bd82ae5

Need to also provide the make directive ("html")

d02f1d5

effigies mentioned this pull request Jan 16, 2020

MAINT: Add website builds for easier PR review bids-standard/bids-website#81

Closed

oesteban closed this May 19, 2021

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WIP: Github actions#52

WIP: Github actions#52
arokem wants to merge 23 commits intonipreps:masterfrom
arokem:ga

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	- run:
	name: Generate Versioned Docs
	command: \|
	set +e
	force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 \| grep -i -E '\[docs?[ _]?versions?\]' )"
	set -e
	if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then
	echo "Not a tag or master branch - skipping versioned docs."
	circleci step halt
	else
	make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
	fi
	- save_cache:
	key: docs-v1-{{ .Branch }}-{{ .Revision }}
	paths:
	- ./docs/_build/_html
	- persist_to_workspace:
	root: docs/_build
	paths: html
	- store_artifacts:
	path: ./docs/_build/html

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