Fix hail-ci incompatibility: /bin/sh is not bash (#4129)

* understand ci failure * Update makeDocs.sh * fix makeDocs.sh * add xsltproc and fix workdir * also install pandoc * make a zip and maybe fix tests directory * fix image
hail-is · Aug 10, 2018 · c91400d · c91400d
1 parent 71878c1
commit c91400d
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Showing 5 changed files with 10 additions and 6 deletions.
diff --git a/Dockerfile.pr-builder b/Dockerfile.pr-builder
@@ -56,3 +56,7 @@ ADD https://archive.apache.org/dist/spark/spark-2.2.0/spark-2.2.0-bin-hadoop2.7.
 RUN tar --strip-components=1 -xvzf spark-2.2.0-bin-hadoop2.7.tgz -C /spark && \
     rm -rf spark-2.2.2-bin-hadoop2.7.tgz
 ENV SPARK_HOME /spark/
+
+RUN apt-get -y install xsltproc pandoc
+
+WORKDIR /hail
diff --git a/build.gradle b/build.gradle
@@ -397,7 +397,7 @@ task generateDistLinks(type: Exec, dependsOn: ['cleanDocs']) {
 }
 
 task makeDocs(type: Exec, dependsOn: ['shadowJar', 'generateDistLinks']) {
-    commandLine 'sh', 'python/hail/docs/makeDocs.sh'
+    commandLine 'bash', 'python/hail/docs/makeDocs.sh'
     environment SPARK_HOME: sparkHome
     environment PYSPARK_SUBMIT_ARGS: '--conf spark.driver.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar --conf spark.executor.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar pyspark-shell'
     environment PYTHONPATH: '' + projectDir + '/python:' + sparkHome + '/python:' + sparkHome + '/python/lib/py4j-' + py4jVersion + '-src.zip'
@@ -406,7 +406,7 @@ task makeDocs(type: Exec, dependsOn: ['shadowJar', 'generateDistLinks']) {
 }
 
 task makeDocsNoTest(type: Exec, dependsOn: ['shadowJar', 'generateDistLinks']) {
-    commandLine 'sh', 'python/hail/docs/makeDocs.sh'
+    commandLine 'bash', 'python/hail/docs/makeDocs.sh'
     environment SPARK_HOME: sparkHome
     environment PYSPARK_SUBMIT_ARGS: '--conf spark.driver.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar --conf spark.executor.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar pyspark-shell'
     environment PYTHONPATH: '' + projectDir + '/python:' + sparkHome + '/python:' + sparkHome + '/python/lib/py4j-' + py4jVersion + '-src.zip'

diff --git a/hail-ci-build-image b/hail-ci-build-image
@@ -1 +1 @@
-gcr.io/broad-ctsa/hail-pr-builder:3c7ad9dfced59f4ee54f9137e550051ae3b92c94
+gcr.io/broad-ctsa/hail-pr-builder:45c84e01b80ad990ce053b22cb07ed2187954712
diff --git a/hail-ci-build.sh b/hail-ci-build.sh
@@ -1,13 +1,13 @@
 set -x
 source activate hail
-GRADLE_OPTS=-Xmx2048m ./gradlew testAll makeDocs --gradle-user-home /gradle-cache
+GRADLE_OPTS=-Xmx2048m ./gradlew testAll makeDocs archiveZip --gradle-user-home /gradle-cache
 EXIT_CODE=$?
 rm -rf artifacts
 mkdir -p artifacts
 cp build/libs/hail-all-spark.jar artifacts/hail-all-spark.jar
 cp build/distributions/hail-python.zip artifacts/hail-python.zip
 cp -R build/www artifacts/www
-cp -R build/reports/tests/test artifacts/test-report
+cp -R build/reports/tests artifacts/test-report
 cat <<EOF > artifacts/index.html
 <html>
 <body>

diff --git a/python/hail/docs/makeDocs.sh b/python/hail/docs/makeDocs.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 set -e