MAINT: Changelog bot is broken

[sappelhoff]

The circleci changelog job is broken:

bids-specification/.circleci/config.yml

Lines 127 to 154 in 537e28a

	# Push built changelog to repo
	Changelog-bot:
	working_directory: ~/build
	docker:
	- image: circleci/openjdk:8-jdk
	steps:
	- setup_remote_docker:
	version: 17.11.0-ce
	- checkout
	- attach_workspace:
	at: ~/build
	- deploy:
	name: Changelog deployment
	working_directory: ~/build
	command: |
	if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
	mv ~/build/tmp/CHANGES.md ~/build/src/CHANGES.md
	merge_message=$(git log -1 | grep Merge | grep "pull")
	PR_number=$(echo $merge_message | cut -d ' ' -f 4)
	git config credential.helper 'cache --timeout=120'
	git config user.email "bids.maintenance@gmail.com"
	git config user.name "bids-maintenance"
	git add ~/build/src/CHANGES.md
	git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
	git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
	else
	echo "Commit or Release, do nothing"
	fi

see the report: https://app.circleci.com/pipelines/github/bids-standard/bids-specification/2590/workflows/88816545-a3b1-4338-9dc9-76b09d1ea83b/jobs/6836

I don't know what the problem is right now. Most likely I screwed something up in #745 and #755.

If a fresh pair of eyes can find the problem, I'd be very grateful.

[sappelhoff]

I started debugging this now on my fork: sappelhoff#14

[sappelhoff]

One issue is that our linkcheck docker image yarikoptic/linkchecker:9.4.0.anchorfix1-1 does not have git, and never had git apparently.

This was somehow swallowed all this time, see some examples:

• https://app.circleci.com/pipelines/github/bids-standard/bids-specification/2446/workflows/50d67464-d678-4e68-b3e4-6ede40496040/jobs/6469
• https://app.circleci.com/pipelines/github/bids-standard/bids-specification/2510/workflows/6e105416-6768-419b-8ea1-7504bb4d56ce/jobs/6609
• https://app.circleci.com/pipelines/github/bids-standard/bids-specification/2389/workflows/14134e39-f07f-4e78-a54c-9fcf5ff3e1ed/jobs/6261

search for /bin/bash: git: command not found ... that one is always there, irrespective of the job succeeding or failing.

Somehow that doesn't show up as an error when wrapped into bash if-else, as we do:

bids-specification/.circleci/config.yml

Line 29 in 537e28a

if (! git log -1 --pretty=%b | grep REL:) ; then

Is it possible to simply add git to the image? @yarikoptic posted the build file here:

bids-specification/tools/linkchecker-docker/neurodocker-build.sh

Lines 1 to 27 in 537e28a

	#!/bin/bash
	# A script to build docker image with desired patched linkchecker
	# using neurodocker
	# TODOs:
	# - minimize image (currently >500MB) using reprozip
	# see https://github.com/kaczmarj/neurodocker/#minimize-existing-docker-image
	# for instructions
	# tag for patched linkchecker -- will also serve our image version
	version="9.4.0.anchorfix1"
	# docker image build
	build=1
	neurodocker generate docker \
	--base neurodebian:nd100 \
	--pkg-manager apt \
	--install python-pip python-requests python-dnspython python-setuptools python-wheel \
	--run "sed -e 's,^deb ,deb-src ,g' /etc/apt/sources.list > /etc/apt/sources.list.d/deb-sources.list \
	&& apt-get update \
	&& apt-get build-dep -y linkchecker \
	&& pip install pyxdg https://github.com/yarikoptic/linkchecker/archive/$version.zip \
	&& mkdir ~/.linkchecker && echo '[AnchorCheck]' > ~/.linkchecker/linkcheckerrc \
	" \
	--entrypoint /usr/local/bin/linkchecker \
	| docker build -t yarikoptic/linkchecker:$version-$build -

[sappelhoff]

I also find several issues in the "build pdf" step regarding images and characters not being available in a font. Worth investigating later.

These warnings look legitimate, especially in reference to the image files:

[WARNING] Duplicate link reference '[deprecated]' at line 2394 column 1
[WARNING] Duplicate link reference '[string]' at line 2396 column 1
[WARNING] Duplicate link reference '[strings]' at line 2398 column 1
[WARNING] Duplicate link reference '[uri]' at line 2414 column 1
[WARNING] Duplicate link reference '[strings]' at line 4302 column 1
[WARNING] Duplicate link reference '[string]' at line 4461 column 1
[WARNING] Duplicate link reference '[derived-dataset-description]' at line 4552 column 1
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pcasl_sequence.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_flowchart.png': replacing image with description
[WARNING] Missing character: There is no └ (U+2514) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no └ (U+2514) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ├ (U+251C) in font [lmmono10-regular]:!