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ENH: enable Travis to run shellcheck #12

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Merged
yarikoptic merged 3 commits into from
Jun 24, 2019
Merged

ENH: enable Travis to run shellcheck #12

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f3da1c7
BF: address shellcheck concerns: "", :upper/lower for tr, -r for read
yarikoptic Jun 24, 2019
c884dbc
ENH: rudimentary .travis.yml looking in the future so installing bats…
yarikoptic Jun 24, 2019
1266eaa
ENH: use neurodebian repo
yarikoptic Jun 24, 2019
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13 changes: 13 additions & 0 deletions .travis.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
# ATM we are pure bash scripts but eventually might RF into Python
language: python


install:
# So we get all backports etc
- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
- travis_retry sudo apt-get update -qq
- travis_retry sudo apt-get install eatmydata # to speedup some installations
- travis_retry sudo eatmydata apt-get install singularity-container shellcheck bats

script:
- shellcheck scripts/create_singularities
12 changes: 6 additions & 6 deletions scripts/create_singularities
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Expand Up @@ -37,22 +37,22 @@ IMAGES_DIR="images"


function debug() {
: # echo -e "D: $@" >&2
: # echo -e "D:" "$@" >&2
}

function info() {
echo -e "I: $@" >&2
echo -e "I:" "$@" >&2
}

function error() {
echo -e "E: $@" >&2
echo -e "E:" "$@" >&2
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@yarikoptic yarikoptic Jun 24, 2019 •
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I was not 100% certain that separating this way wouldn't cause some values to be interpreted as options to echo, but seems to be not:

$> cat /tmp/checkecho
#!/bin/bash
echo -e "I1: $@"
echo -e "I2:" "$@"

$> /tmp/checkecho '-n' 1 "2 3" '&' '${var}'
I1: -n 1 2 3 & ${var}
I2: -n 1 2 3 & ${var}

so all good

}



function get_last_docker_version_tag() {
dh="$1"
j=$(curl -s -k https://registry.hub.docker.com/v1/repositories/$dh/tags)
j=$(curl -s -k "https://registry.hub.docker.com/v1/repositories/$dh/tags")
versions=$(echo "$j" | jq -c '.[]["name"]' | sed -e 's,",,g' | sort -Vr)
nversions=$(echo "$versions" | wc -l)
if [ "$nversions" -gt 1 ]; then
Expand Down Expand Up @@ -187,7 +187,7 @@ function add_singularity_versioned_image() {

function generate_singularity_for_docker_image() {
githubid="$1"
dockerhubid="$(echo "$githubid" | tr 'A-Z' 'a-z')"
dockerhubid="$(echo "$githubid" | tr '[:upper:]' '[:lower:]')"
family="$2"

info "$family <- docker $dockerhubid"
Expand Down Expand Up @@ -234,7 +234,7 @@ function add_singularity_image_from_collection() {
curl -s -k https://raw.githubusercontent.com/BIDS-Apps/bids-apps.github.io/master/_config.yml \
| awk '/^ *dh:/{print $2}' \
| sed -e "s,',,g" \
| while read dockerhubid; do
| while read -r dockerhubid; do
generate_singularity_for_docker_image "$dockerhubid" "bids"
done

Expand Down